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Sample records for survivorship quantitative trait

  1. Quantitative genetics of disease traits.

    Science.gov (United States)

    Wray, N R; Visscher, P M

    2015-04-01

    John James authored two key papers on the theory of risk to relatives for binary disease traits and the relationship between parameters on the observed binary scale and an unobserved scale of liability (James Annals of Human Genetics, 1971; 35: 47; Reich, James and Morris Annals of Human Genetics, 1972; 36: 163). These two papers are John James' most cited papers (198 and 328 citations, November 2014). They have been influential in human genetics and have recently gained renewed popularity because of their relevance to the estimation of quantitative genetics parameters for disease traits using SNP data. In this review, we summarize the two early papers and put them into context. We show recent extensions of the theory for ascertained case-control data and review recent applications in human genetics. © 2015 Blackwell Verlag GmbH.

  2. Quantitative trait loci (QTL) mapping for inflorescence length traits in ...

    African Journals Online (AJOL)

    Lablab purpureus (L.) sweet is an ancient legume species whose immature pods serve as a vegetable in south and south-east Asia. The objective of this study is to identify quantitative trait loci (QTLs) associated with quantitative traits such as inflorescence length, peduncle length from branch to axil, peduncle length from ...

  3. Quantitative Trait Loci for Fertility Traits in Finnish Ayrshire Cattle

    DEFF Research Database (Denmark)

    Schulman, Nina F; Sahana, Goutam; Lund, Mogens S

    2008-01-01

    combinations, which were observed significant in the regression method. Twenty-two chromosome-wise significant QTL were detected. Several of the detected QTL areas were overlapping with milk production QTL previously identified in the same population. Multi-trait QTL analyses were carried out to test......A whole genome scan was carried out to detect quantitative trait loci (QTL) for fertility traits in Finnish Ayrshire cattle. The mapping population consisted of 12 bulls and 493 sons. Estimated breeding values for days open, fertility treatments, maternal calf mortality and paternal non-return rate...... were used as phenotypic data. In a granddaughter design, 171 markers were typed on all 29 bovine autosomes. Associations between markers and traits were analysed by multiple marker regression. Multi-trait analyses were carried out with a variance component based approach for the chromosomes and trait...

  4. Quantitative Trait Loci Affecting Calving Traits in Danish Holstein Cattle

    DEFF Research Database (Denmark)

    Thomasen, J R; Guldbrandtsen, B; Sørensen, P

    2008-01-01

    The objectives of this study were 1) to detect quantitative trait loci (QTL) affecting direct and maternal calving traits at first calving in the Danish Holstein population, 2) to distinguish between pleiotropic and linked QTL for chromosome regions affecting more than one trait, and 3) to detect...... QTL affecting stillbirth and calving difficulties but not calf size that could be used in selection to improve calving performance. Progeny-tested sons (2,297) were genotyped for 356 microsatellites in 34 grandsire families on all 29 autosomes. A total of 27 significant QTL on 17 chromosomes were...... detected using a between-families linear regression model. For the direct calving traits, 4 QTL significantly affected calving difficulty, 5 QTL affected stillbirth, and 7 QTL affected calf size subjectively assessed by the farmer as a categorical trait. When the maternal components of the same traits were...

  5. [An allelism test for quantitative trait genes].

    Science.gov (United States)

    Smiriaev, A V

    2011-04-01

    Analytical modeling has been used to test assumptions on the mode of inheritance of a quantitative trait in the course of diallel crossing between pure strains that are sufficient for adequacy of a simple regression model. This model frequently proved to be adequate in analysis of numerous data on diallel crossings of wheat and maize. An allelism test for quantitative trait genes has been suggested. Computer simulation has been used to estimate the effect of random experimental errors and deviations from the suggested model.

  6. Interval Mapping of Multiple Quantitative Trait Loci

    NARCIS (Netherlands)

    Jansen, Ritsert C.

    1993-01-01

    The interval mapping method is widely used for the mapping of quantitative trait loci (QTLs) in segregating generations derived from crosses between inbred lines. The efficiency of detecting and the accuracy of mapping multiple QTLs by using genetic markers are much increased by employing multiple

  7. Influence analysis in quantitative trait loci detection.

    Science.gov (United States)

    Dou, Xiaoling; Kuriki, Satoshi; Maeno, Akiteru; Takada, Toyoyuki; Shiroishi, Toshihiko

    2014-07-01

    This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods-the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation-based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics. © 2014 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Mapping quantitative trait loci for binary trait in the F2: 3 design

    Indian Academy of Sciences (India)

    In the analysis of inheritance of quantitative traits with low heritability, an F2:3 design that genotypes plants in F2 and phenotypes plants in F2:3 progeny is often used in plant genetics. Although statistical approaches for mapping quantitative trait loci (QTL) in the F2:3 design have been well developed, those for binary traits ...

  9. Genetic mapping of quantitative trait loci (QTLs) with effects on ...

    African Journals Online (AJOL)

    Genetic mapping of quantitative trait loci (QTLs) with effects on resistance to flower bud thrips ( Megalurothrips sjostedti ) identified in recombinant inbred lines of cowpea ( Vigna unguiculata (L.) Walp)

  10. Multiparent intercross populations in analysis of quantitative traits

    Indian Academy of Sciences (India)

    Most traits of interest to medical, agricultural and animal scientists show continuous variation and complex mode of inheritance. DNA-based markers are being deployed to analyse such complex traits, that are known as quantitative trait loci (QTL). In conventional QTL analysis, F2, backcross populations, recombinant inbred ...

  11. Quantitative traits in wheat ( Triticum aestivum L. cv. 'Novosadska ...

    African Journals Online (AJOL)

    The effect of the use of different lime rates on the pH values and subsequently on the quantitative traits in wheat (Triticum aestivum L. cv. 'Novosadska rana 5') was investigated on the pseudogley type of soil. Of the quantitative traits in wheat, spike length, number of spikes per m2, grain mass per spike, number of grains per ...

  12. Genetic mapping of quantitative trait loci in crops

    OpenAIRE

    Xu, Yang; Li, Pengcheng; Yang, Zefeng; Xu, Chenwu

    2017-01-01

    Dissecting the genetic architecture of complex traits is an ongoing challenge for geneticists. Two complementary approaches for genetic mapping, linkage mapping and association mapping have led to successful dissection of complex traits in many crop species. Both of these methods detect quantitative trait loci (QTL) by identifying marker–trait associations, and the only fundamental difference between them is that between mapping populations, which directly determine mapping resolution and pow...

  13. Quantitative trait loci analysis of swine meat quality traits

    DEFF Research Database (Denmark)

    Li, H D; Lund, M S; Christensen, O F

    2010-01-01

    loss, and the Minolta color measurements L*, a*, and b* representing meat lightness, redness, and yellowness, respectively. The families consist of 3,883 progenies of 12 Duroc boars that were evaluated to identify the QTL. The linkage map consists of 462 SNP markers on 18 porcine autosomes...... were estimated from a posterior distribution of the QTL position. In total, 31 QTL for the 6 meat quality traits were found to be significant at the 5% chromosome-wide level, among which 11 QTL were significant at the 5% genome-wide level and 5 of these were significant at the 0.1% genome-wide level...... will be helpful for fine mapping and identifying genes affecting meat quality traits, and tightly linked markers may be incorporated into marker-assisted selection programs...

  14. Identification of quantitative trait loci for leaf traits in rice

    Directory of Open Access Journals (Sweden)

    Jia Baoyan

    2016-01-01

    Full Text Available A recombinant inbred lines (RILs population of 90 lines were developed from a subspecies cross between an indica type cultivar, ‘Cheongcheong’, and a japonica rice cultivar, ‘Nagdong’ was evaluated for leaf traits in 2009. A genetic linkage map consisting of 154 simple sequence repeat (SSR markers was constructed, covering 1973.6 cM of 12 chromosomes with an average map distance of 13.9 cM between markers. By composite interval mapping method a total of 19 QTLs were identified for the leaf traits on 5 chromosomes (Chr.1, Chr.3, Chr.6, Chr.8 and Chr.11. The percentage of phenotypic variance explained by each QTL varied from 8.1% to 29.4%. Five pleiotropic effects loci were identified on chromosomes 1,6.

  15. Mapping of quantitative trait loci controlling Orobanche foetida Poir ...

    African Journals Online (AJOL)

    Mapping of quantitative trait loci controlling Orobanche foetida Poir. resistance in faba bean (Vicia faba L.) R Díaz-Ruiz, A Torres, MV Gutierrez, D Rubiales, JI Cubero, M Kharrat, Z Satovic, B Román ...

  16. Data-driven encoding for quantitative genetic trait prediction.

    Science.gov (United States)

    He, Dan; Wang, Zhanyong; Parida, Laxmi

    2015-01-01

    Given a set of biallelic molecular markers, such as SNPs, with genotype values on a collection of plant, animal or human samples, the goal of quantitative genetic trait prediction is to predict the quantitative trait values by simultaneously modeling all marker effects. Quantitative genetic trait prediction is usually represented as linear regression models which require quantitative encodings for the genotypes: the three distinct genotype values, corresponding to one heterozygous and two homozygous alleles, are usually coded as integers, and manipulated algebraically in the model. Further, epistasis between multiple markers is modeled as multiplication between the markers: it is unclear that the regression model continues to be effective under this. In this work we investigate the effects of encodings to the quantitative genetic trait prediction problem. We first showed that different encodings lead to different prediction accuracies, in many test cases. We then proposed a data-driven encoding strategy, where we encode the genotypes according to their distribution in the phenotypes and we allow each marker to have different encodings. We show in our experiments that this encoding strategy is able to improve the performance of the genetic trait prediction method and it is more helpful for the oligogenic traits, whose values rely on a relatively small set of markers. To the best of our knowledge, this is the first paper that discusses the effects of encodings to the genetic trait prediction problem.

  17. PEMETAAN QUANTITATIVE TRAIT LOCI UNTUK SIFAT BERSKALA KATEGORIK

    Directory of Open Access Journals (Sweden)

    Farit Mochamad Afendi

    2007-04-01

    Full Text Available Genes or regions on chromosome underlying a quantitative trait are called quantitative trait loci (QTL. Characterizing genes controlling quantitative trait on their position in chromosome and their effect on trait is through a process called QTL mapping. In estimating the QTL position and its effect, QTL mapping utilizes the association between QTL and DNA makers. However, many important traits are obtained in categorical scale, such as resistance from certain disease. From a theoritical point of view, QTL mapping method assuming continuous trait could not be applied to categorical trait. This research was facusing on the assessment of the performance of maximum likehood (ML and regression (REG approach employed in QTL mapping for binary trait by means of simulation study. The simulation study to evaluate the performance of ML and REG approach was conducted by taking into accounte several factors that may affecting the performance of both approaches. The factors are (1 maker density, (2 QTL effect, (3 sample size, and (4 shape of phenotypic distribution. Form simulation study, it was obtained that the two approaches showing comparable performance. Hence, QTL analysis could be performed using these two approaches due to their similar performance

  18. Statistical mechanics and the evolution of polygenic quantitative traits

    NARCIS (Netherlands)

    Barton, N.H.; De Vladar, H.P.

    The evolution of quantitative characters depends on the frequencies of the alleles involved, yet these frequencies cannot usually be measured. Previous groups have proposed an approximation to the dynamics of quantitative traits, based on an analogy with statistical mechanics. We present a modified

  19. Mapping quantitative trait loci for fruit traits and powdery mildew resistance in melon (Cucumis melo)

    National Research Council Canada - National Science Library

    Wang, Yu-Hua; Wu, Dong-Hong; Huang, Jin-Hsing; Tsao, Shing-Jy; Hwu, Kae-Kang; Lo, Hsiao-Feng

    2016-01-01

    ... and disease resistance is required.The F2 populations from the cross of TARI-08874 (Cucumis melo ssp. melo) and ‘Bai-li-gua’ (C. melo ssp. agrestis) were used to map the quantitative trait loci...

  20. Quantitative trait loci for rice yield-related traits using recombinant ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 90; Issue 2. Quantitative trait loci for rice yield-related traits using recombinant inbred lines derived from two diverse cultivars. Xu Feng Bai Li Jun Luo Wen Hao Yan Mallikarjuna Rao Kovi Yong Zhong Xing. Research Article Volume 90 Issue 2 August 2011 pp 209-215 ...

  1. An international collaborative family-based whole genome quantitative trait linkage scan for myopic refractive error

    DEFF Research Database (Denmark)

    Abbott, Diana; Li, Yi-Ju; Guggenheim, Jeremy A

    2012-01-01

    To investigate quantitative trait loci linked to refractive error, we performed a genome-wide quantitative trait linkage analysis using single nucleotide polymorphism markers and family data from five international sites.......To investigate quantitative trait loci linked to refractive error, we performed a genome-wide quantitative trait linkage analysis using single nucleotide polymorphism markers and family data from five international sites....

  2. Genome Scan Detects Quantitative Trait Loci Affecting Female Fertility Traits in Danish and Swedish Holstein Cattle

    DEFF Research Database (Denmark)

    Höglund, Johanna Karolina; Guldbrandtsen, B; Su, G

    2009-01-01

    microsatellite markers. Single trait breeding values were used for 12 traits relating to female fertility and female reproductive disorders. Data were analyzed by least squares regression analysis within and across families. Twenty-six QTL were detected on 17 different chromosomes. The best evidence was found......Data from the joint Nordic breeding value prediction for Danish and Swedish Holstein grandsire families were used to locate quantitative trait loci (QTL) for female fertility traits in Danish and Swedish Holstein cattle. Up to 36 Holstein grandsires with over 2,000 sons were genotyped for 416...

  3. Multivariate analysis of quantitative traits can effectively classify rapeseed germplasm

    Directory of Open Access Journals (Sweden)

    Jankulovska Mirjana

    2014-01-01

    Full Text Available In this study, the use of different multivariate approaches to classify rapeseed genotypes based on quantitative traits has been presented. Tree regression analysis, PCA analysis and two-way cluster analysis were applied in order todescribe and understand the extent of genetic variability in spring rapeseed genotype by trait data. The traits which highly influenced seed and oil yield in rapeseed were successfully identified by the tree regression analysis. Principal predictor for both response variables was number of pods per plant (NP. NP and 1000 seed weight could help in the selection of high yielding genotypes. High values for both traits and oil content could lead to high oil yielding genotypes. These traits may serve as indirect selection criteria and can lead to improvement of seed and oil yield in rapeseed. Quantitative traits that explained most of the variability in the studied germplasm were classified using principal component analysis. In this data set, five PCs were identified, out of which the first three PCs explained 63% of the total variance. It helped in facilitating the choice of variables based on which the genotypes’ clustering could be performed. The two-way cluster analysissimultaneously clustered genotypes and quantitative traits. The final number of clusters was determined using bootstrapping technique. This approach provided clear overview on the variability of the analyzed genotypes. The genotypes that have similar performance regarding the traits included in this study can be easily detected on the heatmap. Genotypes grouped in the clusters 1 and 8 had high values for seed and oil yield, and relatively short vegetative growth duration period and those in cluster 9, combined moderate to low values for vegetative growth duration and moderate to high seed and oil yield. These genotypes should be further exploited and implemented in the rapeseed breeding program. The combined application of these multivariate methods

  4. R/qtlcharts: interactive graphics for quantitative trait locus mapping.

    Science.gov (United States)

    Broman, Karl W

    2015-02-01

    Every data visualization can be improved with some level of interactivity. Interactive graphics hold particular promise for the exploration of high-dimensional data. R/qtlcharts is an R package to create interactive graphics for experiments to map quantitative trait loci (QTL) (genetic loci that influence quantitative traits). R/qtlcharts serves as a companion to the R/qtl package, providing interactive versions of R/qtl's static graphs, as well as additional interactive graphs for the exploration of high-dimensional genotype and phenotype data. Copyright © 2015 by the Genetics Society of America.

  5. Complex genetic interactions in a quantitative trait locus.

    Directory of Open Access Journals (Sweden)

    Himanshu Sinha

    2006-02-01

    Full Text Available Whether in natural populations or between two unrelated members of a species, most phenotypic variation is quantitative. To analyze such quantitative traits, one must first map the underlying quantitative trait loci. Next, and far more difficult, one must identify the quantitative trait genes (QTGs, characterize QTG interactions, and identify the phenotypically relevant polymorphisms to determine how QTGs contribute to phenotype. In this work, we analyzed three Saccharomyces cerevisiae high-temperature growth (Htg QTGs (MKT1, END3, and RHO2. We observed a high level of genetic interactions among QTGs and strain background. Interestingly, while the MKT1 and END3 coding polymorphisms contribute to phenotype, it is the RHO2 3'UTR polymorphisms that are phenotypically relevant. Reciprocal hemizygosity analysis of the Htg QTGs in hybrids between S288c and ten unrelated S. cerevisiae strains reveals that the contributions of the Htg QTGs are not conserved in nine other hybrids, which has implications for QTG identification by marker-trait association. Our findings demonstrate the variety and complexity of QTG contributions to phenotype, the impact of genetic background, and the value of quantitative genetic studies in S. cerevisiae.

  6. Evolution of quantitative traits in the wild: mind the ecology.

    Science.gov (United States)

    Pemberton, Josephine M

    2010-08-27

    Recent advances in the quantitative genetics of traits in wild animal populations have created new interest in whether natural selection, and genetic response to it, can be detected within long-term ecological studies. However, such studies have re-emphasized the fact that ecological heterogeneity can confound our ability to infer selection on genetic variation and detect a population's response to selection by conventional quantitative genetics approaches. Here, I highlight three manifestations of this issue: counter gradient variation, environmentally induced covariance between traits and the correlated effects of a fluctuating environment. These effects are symptomatic of the oversimplifications and strong assumptions of the breeder's equation when it is applied to natural populations. In addition, methods to assay genetic change in quantitative traits have overestimated the precision with which change can be measured. In the future, a more conservative approach to inferring quantitative genetic response to selection, or genomic approaches allowing the estimation of selection intensity and responses to selection at known quantitative trait loci, will provide a more precise view of evolution in ecological time.

  7. Genetic distances based on quantitative traits.

    Science.gov (United States)

    Camussi, A; Ottaviano, E; Calinski, T; Kaczmarek, Z

    1985-12-01

    Morphological data showing continuous distributions, polygenically controlled, may be particularly useful in intergroup classification below the species level; an appropriate distance analysis based on these traits is an important tool in evolutionary biology and in plant and animal breeding.--The interpretation of morphological distances in genetic terms is not easy because simple phenotypic data may lead to biased estimates of genetic distances. Convenient estimates can be obtained whenever it is possible to breed populations according to a suitable crossing design and to derive information from genetic parameters.--A general method for determining genetic distances is proposed. The procedure of multivariate analysis of variance is extended to estimate appropriate genetic parameters (genetic effects). Not only are optimal statistical estimates of parameters obtained but also the procedure allows the measurement of genetic distances between populations as linear functions of the estimated parameters, providing an appropriate distance matrix that can be defined in terms of these parameters. The use of the T2 statistic, defined in terms of the vector of contrasts specifying the distance, permits the testing of the significance of any distance between any pair of populations that may be of interest from a genetic point of view.--A numerical example from maize diallel data is reported in order to illustrate the procedure. In particular, heterosis effects are used as the basis for estimates of genetic divergence between populations.

  8. Longitudinal Association Analysis of Quantitative Traits

    Science.gov (United States)

    Fan, Ruzong; Zhang, Yiwei; Albert, Paul S.; Liu, Aiyi; Wang, Yuanjia; Xiong, Momiao

    2015-01-01

    Longitudinal genetic studies provide a valuable resource for exploring key genetic and environmental factors that affect complex traits over time. Genetic analysis of longitudinal data that incorporate temporal variations is important for understanding genetic architecture and biological variations of common complex diseases. Although they are important, there is a paucity of statistical methods to analyze longitudinal human genetic data. In this article, longitudinal methods are developed for temporal association mapping to analyze population longitudinal data. Both parametric and nonparametric models are proposed. The models can be applied to multiple diallelic genetic markers such as single-nucleotide polymorphisms and multiallelic markers such as microsatellites. By analytical formulae, we show that the models take both the linkage disequilibrium and temporal trends into account simultaneously. Variance-covariance structure is constructed to model the single measurement variation and multiple measurement correlations of an individual based on the theory of stochastic processes. Novel penalized spline models are used to estimate the time-dependent mean functions and regression coefficients. The methods were applied to analyze Framingham Heart Study data of Genetic Analysis Workshop (GAW) 13 and GAW 16. The temporal trends and genetic effects of the systolic blood pressure are successfully detected by the proposed approaches. Simulation studies were performed to find out that the nonparametric penalized linear model is the best choice in fitting real data. The research sheds light on the important area of longitudinal genetic analysis, and it provides a basis for future methodological investigations and practical applications. PMID:22965819

  9. Variability and Association of Quantitative Traits in Plectranthus ...

    African Journals Online (AJOL)

    Variability and Association of Quantitative Traits in Plectranthus edulis (Vatke) Agnew. W Garedew, A Tsegaye, B Tesfaye, H Mohammed. Abstract. Thirty six accessions of Plectranthus edulis were evaluated to estimate the nature and magnitude of variability and associations among tuber yield and related characteristics.

  10. Quantitative trait locus (QTL) mapping for 100-kernel weight of ...

    African Journals Online (AJOL)

    hope&shola

    2010-12-06

    Dec 6, 2010 ... Abbreviations: KW, 100-kernel weight; CIM, composite interval mapping; CV, coefficient of variation; HNR, high nitrogen regime; LNR, low nitrogen regime; LOD, log10 of odds ratio;. MAS, marker-assisted selection; QTL, quantitative trait locus;. R2, percentage of phenotypic variance explained by QTL; RIL,.

  11. Unraveling possible association between quantitative trait loci (QTL ...

    African Journals Online (AJOL)

    Many quantitative trait loci (QTLs) in different barley populations were discovered for resistance to Puccinia hordei and heterologous rust species. Partial resistance (host basal resistance) and nonhost resistance (nonhost basal resistance) in barley to leaf rusts are based on prehaustorial mechanism of resistance which is ...

  12. Correlation and path coefficient analysis of some quantitative traits ...

    African Journals Online (AJOL)

    Thirty-seven wheat genotypes and three check varieties were studied for correlation and path coefficient analysis of some quantitative traits in wheat at Kisan (P.G), College, Simbhaoli in India. Generally, the estimates of genotypic correlation coefficients were higher than the corresponding phenotypic correlation coefficients ...

  13. Variablity, heritability and genetic advance in quantitative traits of Tef ...

    African Journals Online (AJOL)

    Seventy nine tef populations collected from ten administrative regions and seven altitude classes were planted with two improved varieties in simple lattice design at Gute and Bako during 2007 and 2008 cropping season, respectively, to assess variability, and estimate heritability and genetic advance of quantitative traits.

  14. Quantitative trait loci mapping and genetic dissection for lint ...

    Indian Academy of Sciences (India)

    2014-08-01

    Aug 1, 2014 ... [Wang M., Li C. and Wang Q. 2014 Quantitative trait loci mapping and genetic dissection for lint percentage in upland cotton (Gossypium hirsutum). J. Genet. ... nents and has high heritability in upland cotton (G. hirsu- tum). Lint percentage ... quality, and disease and insect resistance (Wang 2004). TM-.

  15. Quantitative trait loci analysis of individual and total isoflavone ...

    Indian Academy of Sciences (India)

    Soybean isoflavones play diverse roles in human health, including cancers, osteoporosis, heart disease, menopausal symptoms and pabulums. The objective of this study was to identify the quantitative trait loci (QTL) associated with the isoflavones daidzein (DC), genistein (GeC), glycitein (GlC) and total isoflavone ...

  16. Quantitative trait loci for yield and morphological traits in maize under drought stress

    Directory of Open Access Journals (Sweden)

    Nikolić Ana

    2011-01-01

    Full Text Available Drought is one of the most important factors contributing to crop yield loss. In order to develop maize varieties with drought tolerance, it is necessary to explore the genetic basis. Mapping quantitative trait loci (QTL that control the yield and associate agronomic traits is one way of understanding drought genetics. QTLs associated with grain yield (GY, leaf width (LW3, LW4 plant height (PH, ear height (EH, leaf number (NL, tassel branch number (TBN and tassel length (TL were studied with composite interval mapping. A total of 43 QTLs were detected, distributed on all chromosomes, except chromosome 9. Phenotypic variability determined for the identified QTLs for all the traits was in the range from 20.99 to 87.24%. Mapping analysis identified genomic regions associated with two traits in a manner that was consistent with phenotypic correlation among traits, supporting either pleiotropy or tight linkage among QTLs.

  17. Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing.

    Science.gov (United States)

    Rodríguez-Leal, Daniel; Lemmon, Zachary H; Man, Jarrett; Bartlett, Madelaine E; Lippman, Zachary B

    2017-10-05

    Major advances in crop yields are needed in the coming decades. However, plant breeding is currently limited by incremental improvements in quantitative traits that often rely on laborious selection of rare naturally occurring mutations in gene-regulatory regions. Here, we demonstrate that CRISPR/Cas9 genome editing of promoters generates diverse cis-regulatory alleles that provide beneficial quantitative variation for breeding. We devised a simple genetic scheme, which exploits trans-generational heritability of Cas9 activity in heterozygous loss-of-function mutant backgrounds, to rapidly evaluate the phenotypic impact of numerous promoter variants for genes regulating three major productivity traits in tomato: fruit size, inflorescence branching, and plant architecture. Our approach allows immediate selection and fixation of novel alleles in transgene-free plants and fine manipulation of yield components. Beyond a platform to enhance variation for diverse agricultural traits, our findings provide a foundation for dissecting complex relationships between gene-regulatory changes and control of quantitative traits. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Functional mapping imprinted quantitative trait loci underlying developmental characteristics

    Directory of Open Access Journals (Sweden)

    Li Gengxin

    2008-03-01

    Full Text Available Abstract Background Genomic imprinting, a phenomenon referring to nonequivalent expression of alleles depending on their parental origins, has been widely observed in nature. It has been shown recently that the epigenetic modification of an imprinted gene can be detected through a genetic mapping approach. Such an approach is developed based on traditional quantitative trait loci (QTL mapping focusing on single trait analysis. Recent studies have shown that most imprinted genes in mammals play an important role in controlling embryonic growth and post-natal development. For a developmental character such as growth, current approach is less efficient in dissecting the dynamic genetic effect of imprinted genes during individual ontology. Results Functional mapping has been emerging as a powerful framework for mapping quantitative trait loci underlying complex traits showing developmental characteristics. To understand the genetic architecture of dynamic imprinted traits, we propose a mapping strategy by integrating the functional mapping approach with genomic imprinting. We demonstrate the approach through mapping imprinted QTL controlling growth trajectories in an inbred F2 population. The statistical behavior of the approach is shown through simulation studies, in which the parameters can be estimated with reasonable precision under different simulation scenarios. The utility of the approach is illustrated through real data analysis in an F2 family derived from LG/J and SM/J mouse stains. Three maternally imprinted QTLs are identified as regulating the growth trajectory of mouse body weight. Conclusion The functional iQTL mapping approach developed here provides a quantitative and testable framework for assessing the interplay between imprinted genes and a developmental process, and will have important implications for elucidating the genetic architecture of imprinted traits.

  19. Mapping quantitative trait loci for binary trait in the F2:3 design

    Indian Academy of Sciences (India)

    In the analysis of inheritance of quantitative traits with low heritability, an F2:3 design that genotypes plants in F2 and phe- notypes plants in F2:3 progeny is often ... to substantial cost saving. Acutally, one can arbitrarily in- ...... experiments show that the estimates for logistic analysis and the liability model are close to the ...

  20. Effects of normalization on quantitative traits in association test

    Directory of Open Access Journals (Sweden)

    Yap Von Bing

    2009-12-01

    Full Text Available Abstract Background Quantitative trait loci analysis assumes that the trait is normally distributed. In reality, this is often not observed and one strategy is to transform the trait. However, it is not clear how much normality is required and which transformation works best in association studies. Results We performed simulations on four types of common quantitative traits to evaluate the effects of normalization using the logarithm, Box-Cox, and rank-based transformations. The impact of sample size and genetic effects on normalization is also investigated. Our results show that rank-based transformation gives generally the best and consistent performance in identifying the causal polymorphism and ranking it highly in association tests, with a slight increase in false positive rate. Conclusion For small sample size or genetic effects, the improvement in sensitivity for rank transformation outweighs the slight increase in false positive rate. However, for large sample size and genetic effects, normalization may not be necessary since the increase in sensitivity is relatively modest.

  1. A note on permutation tests for genetic association analysis of quantitative traits when variances are heterogeneous

    NARCIS (Netherlands)

    Posthuma, D.; de Koning, D.J.; Dolan, C.V.; Goddard, M.E.; Visscher, P.M.

    2009-01-01

    The genetic dissection of quantitative traits, or endophenotypes, usually involves genetic linkage or association analysis in pedigrees and subsequent fine mapping association analysis in the population. The ascertainment procedure for quantitative traits often results in unequal variance of

  2. Replacing qualitative life-history traits by quantitative indices in parasitoid evolutionary ecology

    NARCIS (Netherlands)

    Boivin, G.; Ellers, J.

    2016-01-01

    Life-history traits, which describe the various aspects of the life cycle of a species, can be either quantitative or qualitative. Quantitative traits are likely to adapt to gradual changes in the environment of a species, whereas qualitative traits, which refer to traits that are discontinuous in

  3. Mapping Mendelian Factors Underlying Quantitative Traits Using RFLP Linkage Maps

    Science.gov (United States)

    Lander, E. S.; Botstein, D.

    1989-01-01

    The advent of complete genetic linkage maps consisting of codominant DNA markers [typically restriction fragment length polymorphisms (RFLPs)] has stimulated interest in the systematic genetic dissection of discrete Mendelian factors underlying quantitative traits in experimental organisms. We describe here a set of analytical methods that modify and extend the classical theory for mapping such quantitative trait loci (QTLs). These include: (i) a method of identifying promising crosses for QTL mapping by exploiting a classical formula of SEWALL WRIGHT; (ii) a method (interval mapping) for exploiting the full power of RFLP linkage maps by adapting the approach of LOD score analysis used in human genetics, to obtain accurate estimates of the genetic location and phenotypic effect of QTLs; and (iii) a method (selective genotyping) that allows a substantial reduction in the number of progeny that need to be scored with the DNA markers. In addition to the exposition of the methods, explicit graphs are provided that allow experimental geneticists to estimate, in any particular case, the number of progeny required to map QTLs underlying a quantitative trait. PMID:2563713

  4. Mapping quantitative trait loci for kernel composition in almond

    Directory of Open Access Journals (Sweden)

    i Forcada Carolina

    2012-06-01

    Full Text Available Abstract Background Almond breeding is increasingly taking into account kernel quality as a breeding objective. Information on the parameters to be considered in evaluating almond quality, such as protein and oil content, as well as oleic acid and tocopherol concentration, has been recently compiled. The genetic control of these traits has not yet been studied in almond, although this information would improve the efficiency of almond breeding programs. Results A map with 56 simple sequence repeat or microsatellite (SSR markers was constructed for an almond population showing a wide range of variability for the chemical components of the almond kernel. A total of 12 putative quantitative trait loci (QTL controlling these chemical traits have been detected in this analysis, corresponding to seven genomic regions of the eight almond linkage groups (LG. Some QTL were clustered in the same region or shared the same molecular markers, according to the correlations already found between the chemical traits. The logarithm of the odds (LOD values for any given trait ranged from 2.12 to 4.87, explaining from 11.0 to 33.1 % of the phenotypic variance of the trait. Conclusions The results produced in the study offer the opportunity to include the new genetic information in almond breeding programs. Increases in the positive traits of kernel quality may be looked for simultaneously whenever they are genetically independent, even if they are negatively correlated. We have provided the first genetic framework for the chemical components of the almond kernel, with twelve QTL in agreement with the large number of genes controlling their metabolism.

  5. Linkage Map Construction and Quantitative Trait Locus Analysis of Agronomic and Fiber Quality Traits in Cotton

    Directory of Open Access Journals (Sweden)

    Michael A. Gore

    2014-03-01

    Full Text Available The superior fiber properties of L. serve as a source of novel variation for improving fiber quality in Upland cotton ( L., but introgression from has been largely unsuccessful due to hybrid breakdown and a lack of genetic and genomic resources. In an effort to overcome these limitations, we constructed a linkage map and conducted a quantitative trait locus (QTL analysis of 10 agronomic and fiber quality traits in a recombinant inbred mapping population derived from a cross between TM-1, an Upland cotton line, and NM24016, an elite line with stabilized introgression from . The linkage map consisted of 429 simple-sequence repeat (SSR and 412 genotyping-by-sequencing (GBS-based single-nucleotide polymorphism (SNP marker loci that covered half of the tetraploid cotton genome. Notably, the 841 marker loci were unevenly distributed among the 26 chromosomes of tetraploid cotton. The 10 traits evaluated on the TM-1 × NM24016 population in a multienvironment trial were highly heritable, and most of the fiber traits showed considerable transgressive variation. Through the QTL analysis, we identified a total of 28 QTLs associated with the 10 traits. Our study provides a novel resource that can be used by breeders and geneticists for the genetic improvement of agronomic and fiber quality traits in Upland cotton.

  6. Genetic complexity and quantitative trait loci mapping of yeast morphological traits.

    Directory of Open Access Journals (Sweden)

    Satoru Nogami

    2007-02-01

    Full Text Available Functional genomics relies on two essential parameters: the sensitivity of phenotypic measures and the power to detect genomic perturbations that cause phenotypic variations. In model organisms, two types of perturbations are widely used. Artificial mutations can be introduced in virtually any gene and allow the systematic analysis of gene function via mutants fitness. Alternatively, natural genetic variations can be associated to particular phenotypes via genetic mapping. However, the access to genome manipulation and breeding provided by model organisms is sometimes counterbalanced by phenotyping limitations. Here we investigated the natural genetic diversity of Saccharomyces cerevisiae cellular morphology using a very sensitive high-throughput imaging platform. We quantified 501 morphological parameters in over 50,000 yeast cells from a cross between two wild-type divergent backgrounds. Extensive morphological differences were found between these backgrounds. The genetic architecture of the traits was complex, with evidence of both epistasis and transgressive segregation. We mapped quantitative trait loci (QTL for 67 traits and discovered 364 correlations between traits segregation and inheritance of gene expression levels. We validated one QTL by the replacement of a single base in the genome. This study illustrates the natural diversity and complexity of cellular traits among natural yeast strains and provides an ideal framework for a genetical genomics dissection of multiple traits. Our results did not overlap with results previously obtained from systematic deletion strains, showing that both approaches are necessary for the functional exploration of genomes.

  7. Quantitative trait loci for milk production and functional traits in two Danish Cattle breeds

    DEFF Research Database (Denmark)

    Mai, M D; Rychtarova, J; Zink, V

    2010-01-01

    ), protein percentage (PP), clinical mastitis (CM), somatic cell score (SCS), maternal stillbirth, maternal calf size (MCS) and maternal calving difficulty. For Red breed, nine grandsire families were genotyped for 166 markers on 18 BTAs. Six traits analysed were MY, FP, PP, CM, SCS and female fertility......Quantitative trait loci (QTL) in Danish Jersey and Danish Red cattle were independently mapped by least squares regression analysis. For Jersey breed, five grandsire families were genotyped for 186 markers on 16 chromosomes (BTAs). Eight traits analysed were milk yield (MY), fat percentage (FP....... Nine and five QTL were detected in Jersey and Red breed, respectively, in across family tests. In Jersey breed, the results indicate QTL for CM and MCS on BTA 3. Additionally, there is an indication of QTL for MCS and FP on BTA 1 and a tentative evidence for a QTL for MY on BTA 26. There is a high risk...

  8. Genetic mapping of quantitative trait loci in crops

    Directory of Open Access Journals (Sweden)

    Yang Xu

    2017-04-01

    Full Text Available Dissecting the genetic architecture of complex traits is an ongoing challenge for geneticists. Two complementary approaches for genetic mapping, linkage mapping and association mapping have led to successful dissection of complex traits in many crop species. Both of these methods detect quantitative trait loci (QTL by identifying marker–trait associations, and the only fundamental difference between them is that between mapping populations, which directly determine mapping resolution and power. Based on this difference, we first summarize in this review the advances and limitations of family-based mapping and natural population-based mapping instead of linkage mapping and association mapping. We then describe statistical methods used for improving detection power and computational speed and outline emerging areas such as large-scale meta-analysis for genetic mapping in crops. In the era of next-generation sequencing, there has arisen an urgent need for proper population design, advanced statistical strategies, and precision phenotyping to fully exploit high-throughput genotyping.

  9. Identification of quantitative trait loci (QTL) for fruit quality traits and number of weeks of flowering in the cultivated strawberry

    Science.gov (United States)

    Fruit quality traits and dayneutrality are two major foci of several strawberry breeding programs. The identification of quantitative trait loci (QTL) and molecular markers linked to these traits could improve breeding efficiency. In this work, an F1 population derived from the cross ‘Delmarvel’ × ...

  10. Quantitative trait loci (QTL mapping for growth traits on bovine chromosome 14

    Directory of Open Access Journals (Sweden)

    Marcelo Miyata

    2007-03-01

    Full Text Available Quantitative trait loci (QTL mapping in livestock allows the identification of genes that determine the genetic variation affecting traits of economic interest. We analyzed the birth weight and weight at 60 days QTL segregating on bovine chromosome BTA14 in a F2 resource population using genotypes produced from seven microsatellite markers. Phenotypes were derived from 346 F2 progeny produced from crossing Bos indicus Gyr x Holstein Bos taurus F1 parents. Interval analysis to detect QTL for birth weight revealed the presence of a QTL (p < 0.05 at 1 centimorgan (cM from the centromere with an additive effect of 1.210 ± 0.438 kg. Interval analysis for weight at 60 days revealed the presence of a QTL (p < 0.05 at 0 cM from the centromere with an additive effect of 2.122 ± 0.735 kg. The region to which the QTL were assigned is described in the literature as responsible for some growth traits, milk yield, milk composition, fat deposition and has also been related to reproductive traits such as daughter pregnancy rate and ovulation rate. The effects of the QTL described on other traits were not investigated.

  11. A strategy to apply quantitative epistasis analysis on developmental traits.

    Science.gov (United States)

    Labocha, Marta K; Yuan, Wang; Aleman-Meza, Boanerges; Zhong, Weiwei

    2017-05-15

    Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits. In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement. Using two different C. elegans developmental phenotypes, body length and sex ratio, as examples, we showed that this method could accommodate various metazoan phenotypes with performances comparable to those methods in single cell growth studies. Comparing with qualitative observations, this method of quantitative epistasis enabled detection of new interactions involving subtle phenotypes. For example, several sex-ratio genes were found to interact with brc-1 and brd-1, the orthologs of the human breast cancer genes BRCA1 and BARD1, respectively. We confirmed the brc-1 interactions with the following genes in DNA damage response: C34F6.1, him-3 (ortholog of HORMAD1, HORMAD2), sdc-1, and set-2 (ortholog of SETD1A, SETD1B, KMT2C, KMT2D), validating the effectiveness of our method in detecting genetic interactions. We developed a reliable, high-throughput method for quantitative epistasis analysis of developmental phenotypes.

  12. Bayesian B-spline mapping for dynamic quantitative traits.

    Science.gov (United States)

    Xing, Jun; Li, Jiahan; Yang, Runqing; Zhou, Xiaojing; Xu, Shizhong

    2012-04-01

    Owing to their ability and flexibility to describe individual gene expression at different time points, random regression (RR) analyses have become a popular procedure for the genetic analysis of dynamic traits whose phenotypes are collected over time. Specifically, when modelling the dynamic patterns of gene expressions in the RR framework, B-splines have been proved successful as an alternative to orthogonal polynomials. In the so-called Bayesian B-spline quantitative trait locus (QTL) mapping, B-splines are used to characterize the patterns of QTL effects and individual-specific time-dependent environmental errors over time, and the Bayesian shrinkage estimation method is employed to estimate model parameters. Extensive simulations demonstrate that (1) in terms of statistical power, Bayesian B-spline mapping outperforms the interval mapping based on the maximum likelihood; (2) for the simulated dataset with complicated growth curve simulated by B-splines, Legendre polynomial-based Bayesian mapping is not capable of identifying the designed QTLs accurately, even when higher-order Legendre polynomials are considered and (3) for the simulated dataset using Legendre polynomials, the Bayesian B-spline mapping can find the same QTLs as those identified by Legendre polynomial analysis. All simulation results support the necessity and flexibility of B-spline in Bayesian mapping of dynamic traits. The proposed method is also applied to a real dataset, where QTLs controlling the growth trajectory of stem diameters in Populus are located.

  13. Bayesian analysis of multilocus association in quantitative and qualitative traits.

    Science.gov (United States)

    Kilpikari, Riika; Sillanpää, Mikko J

    2003-09-01

    A Bayesian model-based method for multilocus association analysis of quantitative and qualitative (binary) traits is presented. The method selects a trait-associated subset of markers among candidates, and is equally applicable for analyzing wide chromosomal segments (genome scans) and small candidate regions. The method can be applied in situations involving missing genotype data. The number of trait loci, their marker positions, and the magnitudes of their gene effects (strengths of association) are all estimated simultaneously. The inference of parameters is based on their posterior distributions, which are obtained through Markov chain Monte Carlo simulations. The strengths of the approach are: 1) flexible use of oligogenic models with unknown number of loci, 2) performing the estimation of association jointly with model selection, and 3) avoidance of the multiple testing problem, which typically complicates the approaches based on association testing. The performance of the method was tested and compared to the multilocus conditional search procedure by analyzing two simulated data sets. We also applied the method to cystic fibrosis haplotype data (two-locus haplotypes), where gene position has already been identified. The method is implemented as a software package, which is freely available for research purposes under the name BAMA. Copyright 2003 Wiley-Liss, Inc.

  14. Quantitative Trait Loci Mapping for Tillering-Related Traits in Two Switchgrass Populations

    Directory of Open Access Journals (Sweden)

    Dan Chang

    2016-07-01

    Full Text Available Plant tillering and related traits are morphologically important components contributing to switchgrass ( L. biomass yield. The objectives of this study were to estimate broad-sense heritabilities for tillering-related traits, to analyze correlations between biomass yield and the traits, and to identify quantitative trait loci (QTL for them. A first-generation selfed population of NL94 plant and a hybrid population between NL94 and SL93 plants were field established in a randomized complete block design with three replications in Stillwater and Perkins, OK. Phenotypic data were collected in 2 yr and genotypic data were obtained by genotyping simple-sequence repeat (SSR markers in the two populations on the basis of two preexisting genetic maps. Plant base size (PBS, plant girth (PG, tillering ability (TA, tiller diameter (TD, and tiller dry weight (TDW were positively correlated with biomass yield in both populations. Consistently, PBS had the largest correlation coefficients for biomass yield, suggesting its value as an indirect selection criterion for biomass yield. Twenty and 26 QTL for six tillering-related traits were detected in the hybrid and selfed population, respectively. Among the QTL, one on linkage group (LG 5a between sww-2387/PVCAG-2197/2198 and PVGA-1649/1650 for PBS, PG, and TA and another on LG 2a between sww-2640/sww-2545 and PVCA-765/766 for TD and TDW were stably detected in multiple environments in the two populations. The findings add to the knowledge base regarding the genetics of tillering-related traits that could be used in accelerating the development of high-yielding cultivars through marker-assisted selection.

  15. Mapping of quantitative trait loci (QTL) for production, resistance and tolerance traits in Salix. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Roennberg-Waestljung, Ann Christin; Bertholdsson, Nils-Ove; Glynn, Carolyn; Weih, Martin; Aahman, Inger [SLU, Uppsala (Sweden). Dept. of Plant Biology and Forest Genetics

    2004-05-01

    Quantitative trait loci (QTL) for growth traits, water use efficiency and tolerance/resistance against metals and herbivores have been identified. A hybrid F2 population originating from a cross between a Salix dasyclados-clone (SW901290) and a S. viminalis-clone ('Jorunn') was used for the different studies in this project. The growth response was analyzed in a greenhouse experiment with two water treatments, normal and drought. In addition, three field experiments with contrasting soils and climates were established. QTL specific for each treatment or field environment but also QTL stable over the treatments or field environments were detected. Each QTL explained from 8 to 29 % of the phenotypic variation depending on trait, treatment or field environment. Clusters of QTL for different traits were mapped indicating a common genetic base or tightly-linked QTL. Stable QTL identified for dryweight can be useful tools for early selection in Salix. In a separate greenhouse experiment, with a subset of ten genotypes from the F2 population, we show that genotype is more important than irrigation treatment for production of phenolic substances as well as for resistance to herbivory by P vulgatissima.

  16. Quantitative Trait Loci Analysis of Allelopathy in Rice

    DEFF Research Database (Denmark)

    Jensen, L B; Courtois, B; Olofsdotter, M

    2008-01-01

    The allelopathic potential of rice (Oryza sativa L.) against Echinochloa crus-galli (L.) Beauv. was investigated under both laboratory and greenhouse conditions. A population of 150 recombinant inbred lines (RILs) was derived through single-seed descent from a cross between the indica cultivar AC...... the population phenotype was normally distributed. Two quantitative trait loci (QTLs) were located on chromosomes 4 and 7, explaining 20% of the phenotypic variation. A second relay seeding experiment was set up, this time including charcoal in the perlite. This screening showed that the allelopathic rice......1423, known to have a strong allelopathic potential, and the aus cultivar Aus196, with low allelopathic potential. The RILs together with the parents were first phenotyped using the laboratory assay known as the relay seeding technique. The screening showed that with regards to allelopathic potential...

  17. Dynamic Quantitative Trait Locus Analysis of Plant Phenomic Data.

    Science.gov (United States)

    Li, Zitong; Sillanpää, Mikko J

    2015-12-01

    Advanced platforms have recently become available for automatic and systematic quantification of plant growth and development. These new techniques can efficiently produce multiple measurements of phenotypes over time, and introduce time as an extra dimension to quantitative trait locus (QTL) studies. Functional mapping utilizes a class of statistical models for identifying QTLs associated with the growth characteristics of interest. A major benefit of functional mapping is that it integrates information over multiple timepoints, and therefore could increase the statistical power for QTL detection. We review the current development of computationally efficient functional mapping methods which provide invaluable tools for analyzing large-scale timecourse data that are readily available in our post-genome era. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Genetic architecture of quantitative traits and complex diseases.

    Science.gov (United States)

    Fu, Wenqing; O'Connor, Timothy D; Akey, Joshua M

    2013-12-01

    More than 150 years after Mendel discovered the laws of heredity, the genetic architecture of phenotypic variation remains elusive. Here, we discuss recent progress in deciphering how genotypes map onto phenotypes, sources of genetic complexity, and how model organisms are illuminating general principles about the relationship between genetic and phenotypic variation. Moreover, we highlight insights gleaned from large-scale sequencing studies in humans, and how this knowledge informs outstanding questions about the genetic architecture of quantitative traits and complex diseases. Finally, we articulate how the confluence of technologies enabling whole-genome sequencing, comprehensive phenotyping, and high-throughput functional assays of polymorphisms will facilitate a more principled and mechanistic understanding of the genetic architecture of phenotypic variation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Quantitative Trait Loci (QTL)-Guided Metabolic Engineering of a Complex Trait.

    Science.gov (United States)

    Maurer, Matthew J; Sutardja, Lawrence; Pinel, Dominic; Bauer, Stefan; Muehlbauer, Amanda L; Ames, Tyler D; Skerker, Jeffrey M; Arkin, Adam P

    2017-03-17

    Engineering complex phenotypes for industrial and synthetic biology applications is difficult and often confounds rational design. Bioethanol production from lignocellulosic feedstocks is a complex trait that requires multiple host systems to utilize, detoxify, and metabolize a mixture of sugars and inhibitors present in plant hydrolysates. Here, we demonstrate an integrated approach to discovering and optimizing host factors that impact fitness of Saccharomyces cerevisiae during fermentation of a Miscanthus x giganteus plant hydrolysate. We first used high-resolution Quantitative Trait Loci (QTL) mapping and systematic bulk Reciprocal Hemizygosity Analysis (bRHA) to discover 17 loci that differentiate hydrolysate tolerance between an industrially related (JAY291) and a laboratory (S288C) strain. We then used this data to identify a subset of favorable allelic loci that were most amenable for strain engineering. Guided by this "genetic blueprint", and using a dual-guide Cas9-based method to efficiently perform multikilobase locus replacements, we engineered an S288C-derived strain with superior hydrolysate tolerance than JAY291. Our methods should be generalizable to engineering any complex trait in S. cerevisiae, as well as other organisms.

  20. Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping.

    Science.gov (United States)

    Cai, Xiaodong; Huang, Anhui; Xu, Shizhong

    2011-05-26

    The Bayesian shrinkage technique has been applied to multiple quantitative trait loci (QTLs) mapping to estimate the genetic effects of QTLs on quantitative traits from a very large set of possible effects including the main and epistatic effects of QTLs. Although the recently developed empirical Bayes (EB) method significantly reduced computation comparing with the fully Bayesian approach, its speed and accuracy are limited by the fact that numerical optimization is required to estimate the variance components in the QTL model. We developed a fast empirical Bayesian LASSO (EBLASSO) method for multiple QTL mapping. The fact that the EBLASSO can estimate the variance components in a closed form along with other algorithmic techniques render the EBLASSO method more efficient and accurate. Comparing with the EB method, our simulation study demonstrated that the EBLASSO method could substantially improve the computational speed and detect more QTL effects without increasing the false positive rate. Particularly, the EBLASSO algorithm running on a personal computer could easily handle a linear QTL model with more than 100,000 variables in our simulation study. Real data analysis also demonstrated that the EBLASSO method detected more reasonable effects than the EB method. Comparing with the LASSO, our simulation showed that the current version of the EBLASSO implemented in Matlab had similar speed as the LASSO implemented in Fortran, and that the EBLASSO detected the same number of true effects as the LASSO but a much smaller number of false positive effects. The EBLASSO method can handle a large number of effects possibly including both the main and epistatic QTL effects, environmental effects and the effects of gene-environment interactions. It will be a very useful tool for multiple QTL mapping.

  1. Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping

    Directory of Open Access Journals (Sweden)

    Xu Shizhong

    2011-05-01

    Full Text Available Abstract Background The Bayesian shrinkage technique has been applied to multiple quantitative trait loci (QTLs mapping to estimate the genetic effects of QTLs on quantitative traits from a very large set of possible effects including the main and epistatic effects of QTLs. Although the recently developed empirical Bayes (EB method significantly reduced computation comparing with the fully Bayesian approach, its speed and accuracy are limited by the fact that numerical optimization is required to estimate the variance components in the QTL model. Results We developed a fast empirical Bayesian LASSO (EBLASSO method for multiple QTL mapping. The fact that the EBLASSO can estimate the variance components in a closed form along with other algorithmic techniques render the EBLASSO method more efficient and accurate. Comparing with the EB method, our simulation study demonstrated that the EBLASSO method could substantially improve the computational speed and detect more QTL effects without increasing the false positive rate. Particularly, the EBLASSO algorithm running on a personal computer could easily handle a linear QTL model with more than 100,000 variables in our simulation study. Real data analysis also demonstrated that the EBLASSO method detected more reasonable effects than the EB method. Comparing with the LASSO, our simulation showed that the current version of the EBLASSO implemented in Matlab had similar speed as the LASSO implemented in Fortran, and that the EBLASSO detected the same number of true effects as the LASSO but a much smaller number of false positive effects. Conclusions The EBLASSO method can handle a large number of effects possibly including both the main and epistatic QTL effects, environmental effects and the effects of gene-environment interactions. It will be a very useful tool for multiple QTL mapping.

  2. Identification of quantitative trait loci for wool traits in Iranian Baluchi sheep. Indian Journal of Animal Sciences

    DEFF Research Database (Denmark)

    Dashab, G R; Aslaminejad, A; Nassiri, M R

    2012-01-01

    Regions on 3 ovine chromosomes (OAR1, 5 and 25) were selected to study quantitative trait loci (QTL) segregating for wool traits in Baluchi sheep, an indigenous sheep breed in Iran. Progenies (503) from 13 half-sib families were genotyped for 15 microsatellite markers. The average number of proge...

  3. Incorporating pleiotropic quantitative trait loci in dissection of complex traits: seed yield in rapeseed as an example.

    Science.gov (United States)

    Luo, Ziliang; Wang, Meng; Long, Yan; Huang, Yongju; Shi, Lei; Zhang, Chunyu; Liu, Xiang; Fitt, Bruce D L; Xiang, Jinxia; Mason, Annaliese S; Snowdon, Rod J; Liu, Peifa; Meng, Jinling; Zou, Jun

    2017-08-01

    A comprehensive linkage atlas for seed yield in rapeseed. Most agronomic traits of interest for crop improvement (including seed yield) are highly complex quantitative traits controlled by numerous genetic loci, which brings challenges for comprehensively capturing associated markers/genes. We propose that multiple trait interactions underlie complex traits such as seed yield, and that considering these component traits and their interactions can dissect individual quantitative trait loci (QTL) effects more effectively and improve yield predictions. Using a segregating rapeseed (Brassica napus) population, we analyzed a large set of trait data generated in 19 independent experiments to investigate correlations between seed yield and other complex traits, and further identified QTL in this population with a SNP-based genetic bin map. A total of 1904 consensus QTL accounting for 22 traits, including 80 QTL directly affecting seed yield, were anchored to the B. napus reference sequence. Through trait association analysis and QTL meta-analysis, we identified a total of 525 indivisible QTL that either directly or indirectly contributed to seed yield, of which 295 QTL were detected across multiple environments. A majority (81.5%) of the 525 QTL were pleiotropic. By considering associations between traits, we identified 25 yield-related QTL previously ignored due to contrasting genetic effects, as well as 31 QTL with minor complementary effects. Implementation of the 525 QTL in genomic prediction models improved seed yield prediction accuracy. Dissecting the genetic and phenotypic interrelationships underlying complex quantitative traits using this method will provide valuable insights for genomics-based crop improvement.

  4. Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp. sativa) berry: a quantitative trait locus to quantitative trait nucleotide integrated study.

    Science.gov (United States)

    Fournier-Level, Alexandre; Le Cunff, Loïc; Gomez, Camila; Doligez, Agnès; Ageorges, Agnès; Roux, Catherine; Bertrand, Yves; Souquet, Jean-Marc; Cheynier, Véronique; This, Patrice

    2009-11-01

    The combination of QTL mapping studies of synthetic lines and association mapping studies of natural diversity represents an opportunity to throw light on the genetically based variation of quantitative traits. With the positional information provided through quantitative trait locus (QTL) mapping, which often leads to wide intervals encompassing numerous genes, it is now feasible to directly target candidate genes that are likely to be responsible for the observed variation in completely sequenced genomes and to test their effects through association genetics. This approach was performed in grape, a newly sequenced genome, to decipher the genetic architecture of anthocyanin content. Grapes may be either white or colored, ranging from the lightest pink to the darkest purple tones according to the amount of anthocyanin accumulated in the berry skin, which is a crucial trait for both wine quality and human nutrition. Although the determinism of the white phenotype has been fully identified, the genetic bases of the quantitative variation of anthocyanin content in berry skin remain unclear. A single QTL responsible for up to 62% of the variation in the anthocyanin content was mapped on a Syrah x Grenache F(1) pseudo-testcross. Among the 68 unigenes identified in the grape genome within the QTL interval, a cluster of four Myb-type genes was selected on the basis of physiological evidence (VvMybA1, VvMybA2, VvMybA3, and VvMybA4). From a core collection of natural resources (141 individuals), 32 polymorphisms revealed significant association, and extended linkage disequilibrium was observed. Using a multivariate regression method, we demonstrated that five polymorphisms in VvMybA genes except VvMybA4 (one retrotransposon, three single nucleotide polymorphisms and one 2-bp insertion/deletion) accounted for 84% of the observed variation. All these polymorphisms led to either structural changes in the MYB proteins or differences in the VvMybAs promoters. We concluded that

  5. Genome-wide identification of quantitative trait loci in a cross between Hampshire and Landrace II

    DEFF Research Database (Denmark)

    Markljung, Ellen; Braunschweig, Martin H.; Karlskov-Mortensen, Peter

    2008-01-01

    Background: Meat quality traits are important in pig breeding programs, but they are difficult to include in a traditional selection program. Marker assisted selection (MAS) of meat quality traits is therefore of interest in breeding programs and a Quantitative Trait Locus (QTL) analysis is the k...

  6. Identification of quantitative trait locus (QTLs) for γ-aminobutyric acid ...

    African Journals Online (AJOL)

    Identification of quantitative trait locus (QTLs) for γ-aminobutyric acid content in grain of barley. ... These results are beneficial for understanding the genetic basis of GABA and developing the markers linked with GABA for marker-assisted selection breeding in barley. Key words: γ-Aminobutyric acid (GABA), quantitative trait ...

  7. A general mixture model for mapping quantitative trait loci by using molecular markers

    NARCIS (Netherlands)

    Jansen, R.C.

    1992-01-01

    In a segregating population a quantitative trait may be considered to follow a mixture of (normal) distributions, the mixing proportions being based on Mendelian segregation rules. A general and flexible mixture model is proposed for mapping quantitative trait loci (QTLs) by using molecular markers.

  8. A quantitative trait locus for the number of days from sowing to ...

    African Journals Online (AJOL)

    Quantitative trait locus (QTL) mapping provides useful information for breeding programs since it allows the estimation of genomic locations and genetic effects of chromosomal regions related to the expression of quantitative traits. The number of days from sowing to seedling emergence (NDSSE) is an important agronomic ...

  9. An improved procedure of mapping a quantitative trait locus via the ...

    Indian Academy of Sciences (India)

    Data on the quantitative trait under consideration and several codominant genetic markers with known genomic locations are collected from members of families and statistically analysed to estimate the recombination fraction, , between the putative quantitative trait locus and a genetic marker. One of the major ...

  10. Quantitative trait loci influencing honeybee alarm pheromone levels.

    Science.gov (United States)

    Hunt, G J; Collins, A M; Rivera, R; Page, R E; Guzmán-Novoa, E

    1999-01-01

    Quantitative trait loci (QTL) mapping procedures were used to identify loci that influence the levels of alarm pheromones found in the stinging apparatus of worker honeybees. An F1 queen was produced from a cross between a queen of European origin and a drone descended from an African subspecies. Haploid drones from the hybrid queen were individually backcrossed to European queens to produce 172 colonies. Samples of stings were taken from backcross workers of these colonies. Alarm pheromone levels were determined by gas chromatography. RAPD markers were scored from the haploid drone fathers of these colonies. The multiple-QTL model (MQM) of MapQTL was used to identify QTLs that influence the levels of four alarm pheromone components. Seven independent, potential QTLs were identified with LOD scores greater than two, and one at LOD 1.88. We identified one QTL for n-decyl acetate, three for n-octanol, four for isopentyl acetate, and one for hexyl acetate. One region of linkage group XI shows a strong influence on body size and the levels of three alarm pheromone components. This locus explained 40% of the variance for the amount of n-decyl acetate (LOD 6.57). In general, the QTLs influencing alarm pheromone levels were independent of previously identified loci that influenced the stinging behavior of these colonies. The only exception was a potential locus influencing levels of n-octanol, which was inversely correlated with stinging behavior.

  11. Quantitative Trait Loci for Mercury Tolerance in Rice Seedlings

    Directory of Open Access Journals (Sweden)

    Chong-qing WANG

    2013-05-01

    Full Text Available Mercury (Hg is one of the most toxic heavy metals to living organisms and its conspicuous effect is the inhibition of root growth. However, little is known about the molecular genetic basis for root growth under excess Hg2+ stress. To map quantitative trait loci (QTLs in rice for Hg2+ tolerance, a population of 120 recombinant inbred lines derived from a cross between two japonica cultivars Yuefu and IRAT109 was grown in 0.5 mmol/L CaCl2 solution. Relative root length (RRL, percentage of the seminal root length in +HgCl2 to –HgCl2, was used for assessing Hg2+ tolerance. In a dose-response experiment, Yuefu had a higher RRL than IRAT109 and showed the most significant difference at the Hg2+ concentration of 1.5 μmol/L. Three putative QTLs for RRL were detected on chromosomes 1, 2 and 5, and totally explained about 35.7% of the phenotypic variance in Hg2+ tolerance. The identified QTLs for RRL might be useful for improving Hg2+ tolerance of rice by molecular marker-assisted selection.

  12. Quantitative trait loci for energy balance traits in an advanced intercross line derived from mice divergently selected for heat loss

    Directory of Open Access Journals (Sweden)

    Larry J. Leamy

    2014-05-01

    Full Text Available Obesity in human populations, currently a serious health concern, is considered to be the consequence of an energy imbalance in which more energy in calories is consumed than is expended. We used interval mapping techniques to investigate the genetic basis of a number of energy balance traits in an F11 advanced intercross population of mice created from an original intercross of lines selected for increased and decreased heat loss. We uncovered a total of 137 quantitative trait loci (QTLs for these traits at 41 unique sites on 18 of the 20 chromosomes in the mouse genome, with X-linked QTLs being most prevalent. Two QTLs were found for the selection target of heat loss, one on distal chromosome 1 and another on proximal chromosome 2. The number of QTLs affecting the various traits generally was consistent with previous estimates of heritabilities in the same population, with the most found for two bone mineral traits and the least for feed intake and several body composition traits. QTLs were generally additive in their effects, and some, especially those affecting the body weight traits, were sex-specific. Pleiotropy was extensive within trait groups (body weights, adiposity and organ weight traits, bone traits and especially between body composition traits adjusted and not adjusted for body weight at sacrifice. Nine QTLs were found for one or more of the adiposity traits, five of which appeared to be unique. The confidence intervals among all QTLs averaged 13.3 Mb, much smaller than usually observed in an F2 cross, and in some cases this allowed us to make reasonable inferences about candidate genes underlying these QTLs. This study combined QTL mapping with genetic parameter analysis in a large segregating population, and has advanced our understanding of the genetic architecture of complex traits related to obesity.

  13. Quantitative trait loci for energy balance traits in an advanced intercross line derived from mice divergently selected for heat loss.

    Science.gov (United States)

    Leamy, Larry J; Elo, Kari; Nielsen, Merlyn K; Thorn, Stephanie R; Valdar, William; Pomp, Daniel

    2014-01-01

    Obesity in human populations, currently a serious health concern, is considered to be the consequence of an energy imbalance in which more energy in calories is consumed than is expended. We used interval mapping techniques to investigate the genetic basis of a number of energy balance traits in an F11 advanced intercross population of mice created from an original intercross of lines selected for increased and decreased heat loss. We uncovered a total of 137 quantitative trait loci (QTLs) for these traits at 41 unique sites on 18 of the 20 chromosomes in the mouse genome, with X-linked QTLs being most prevalent. Two QTLs were found for the selection target of heat loss, one on distal chromosome 1 and another on proximal chromosome 2. The number of QTLs affecting the various traits generally was consistent with previous estimates of heritabilities in the same population, with the most found for two bone mineral traits and the least for feed intake and several body composition traits. QTLs were generally additive in their effects, and some, especially those affecting the body weight traits, were sex-specific. Pleiotropy was extensive within trait groups (body weights, adiposity and organ weight traits, bone traits) and especially between body composition traits adjusted and not adjusted for body weight at sacrifice. Nine QTLs were found for one or more of the adiposity traits, five of which appeared to be unique. The confidence intervals among all QTLs averaged 13.3 Mb, much smaller than usually observed in an F2 cross, and in some cases this allowed us to make reasonable inferences about candidate genes underlying these QTLs. This study combined QTL mapping with genetic parameter analysis in a large segregating population, and has advanced our understanding of the genetic architecture of complex traits related to obesity.

  14. Identification of quantitative trait loci for cadmium tolerance and accumulation in wheat

    DEFF Research Database (Denmark)

    Ci, Dunwei; Jiang, Dong; Li, Sishen

    2012-01-01

    Quantitative trait loci (QTL) for Cadmium (Cd) tolerance and accumulation in wheat (Triticum aestivum L.) were identified, using 103 recombinant inbred lines (RILs) derived from a cross of Ch×Sh at germination and seedling stages. The traits of germination, growth and physiology were measured. Cd....... Therefore, in this study, the properties of Cd tolerance and accumulation showed to be independent traits in wheat.......Quantitative trait loci (QTL) for Cadmium (Cd) tolerance and accumulation in wheat (Triticum aestivum L.) were identified, using 103 recombinant inbred lines (RILs) derived from a cross of Ch×Sh at germination and seedling stages. The traits of germination, growth and physiology were measured. Cd...... effects coming from Ch) while the remaining 12 QTLs were negative (with the additive effects contributed by Sh). No QTL were detected in the same region on the chromosomes of wheat. The results indicated that genetic mechanisms controlling the traits of Cd tolerance were independent from each other...

  15. Understanding rice adaptation to varying agro-ecosystems: trait interactions and quantitative trait loci.

    Science.gov (United States)

    Dixit, Shalabh; Grondin, Alexandre; Lee, Cheng-Ruei; Henry, Amelia; Olds, Thomas-Mitchell; Kumar, Arvind

    2015-08-05

    Interaction and genetic control for traits influencing the adaptation of the rice crop to varying environments was studied in a mapping population derived from parents (Moroberekan and Swarna) contrasting for drought tolerance, yield potential, lodging resistance, and adaptation to dry direct seeding. A BC2F3-derived mapping population for traits related to these four trait groups was phenotyped to understand the interactions among traits and to map and align QTLs using composite interval mapping (CIM). The study also aimed to identify QTLs for the four trait groups as composite traits using multivariate least square interval mapping (MLSIM) to further understand the genetic control of these traits. Significant correlations between drought- and yield-related traits at seedling and reproductive stages respectively with traits for adaptation to dry direct-seeded conditions were observed. CIM and MLSIM methods were applied to identify QTLs for univariate and composite traits. QTL clusters showing alignment of QTLs for several traits within and across trait groups were detected at chromosomes 3, 4, and 7 through CIM. The largest number of QTLs related to traits belonging to all four trait groups were identified on chromosome 3 close to the qDTY 3.2 locus. These included QTLs for traits such as bleeding rate, shoot biomass, stem strength, and spikelet fertility. Multivariate QTLs were identified at loci supported by univariate QTLs such as on chromosomes 3 and 4 as well as at distinctly different loci on chromosome 8 which were undetected through CIM. Rice requires better adaptation across a wide range of environments and cultivation practices to adjust to climate change. Understanding the genetics and trade-offs related to each of these environments and cultivation practices thus becomes highly important to develop varieties with stability of yield across them. This study provides a wider picture of the genetics and physiology of adaptation of rice to wide range of

  16. Population differences in transcript-regulator expression quantitative trait loci.

    Directory of Open Access Journals (Sweden)

    Pierre R Bushel

    Full Text Available Gene expression quantitative trait loci (eQTL are useful for identifying single nucleotide polymorphisms (SNPs associated with diseases. At times, a genetic variant may be associated with a master regulator involved in the manifestation of a disease. The downstream target genes of the master regulator are typically co-expressed and share biological function. Therefore, it is practical to screen for eQTLs by identifying SNPs associated with the targets of a transcript-regulator (TR. We used a multivariate regression with the gene expression of known targets of TRs and SNPs to identify TReQTLs in European (CEU and African (YRI HapMap populations. A nominal p-value of <1×10(-6 revealed 234 SNPs in CEU and 154 in YRI as TReQTLs. These represent 36 independent (tag SNPs in CEU and 39 in YRI affecting the downstream targets of 25 and 36 TRs respectively. At a false discovery rate (FDR = 45%, one cis-acting tag SNP (within 1 kb of a gene in each population was identified as a TReQTL. In CEU, the SNP (rs16858621 in Pcnxl2 was found to be associated with the genes regulated by CREM whereas in YRI, the SNP (rs16909324 was linked to the targets of miRNA hsa-miR-125a. To infer the pathways that regulate expression, we ranked TReQTLs by connectivity within the structure of biological process subtrees. One TReQTL SNP (rs3790904 in CEU maps to Lphn2 and is associated (nominal p-value = 8.1×10(-7 with the targets of the X-linked breast cancer suppressor Foxp3. The structure of the biological process subtree and a gene interaction network of the TReQTL revealed that tumor necrosis factor, NF-kappaB and variants in G-protein coupled receptors signaling may play a central role as communicators in Foxp3 functional regulation. The potential pleiotropic effect of the Foxp3 TReQTLs was gleaned from integrating mRNA-Seq data and SNP-set enrichment into the analysis.

  17. Pleiotropy Analysis of Quantitative Traits at Gene Level by Multivariate Functional Linear Models

    OpenAIRE

    Wang, Yifan; Liu, Aiyi; Mills, James L.; Boehnke, Michael; Wilson, Alexander F.; Bailey-Wilson, Joan E.; Xiong, Momiao; Wu, Colin O.; Fan, Ruzong

    2015-01-01

    In genetics, pleiotropy describes the genetic effect of a single gene on multiple phenotypic traits. A common approach is to analyze the phenotypic traits separately using univariate analyses and combine the test results through multiple comparisons. This approach may lead to low power. Multivariate functional linear models are developed to connect genetic variant data to multiple quantitative traits adjusting for covariates for a unified analysis. Three types of approximate F-distribution te...

  18. A study on the qualitative and quantitative traits of barley ( Hordeum ...

    African Journals Online (AJOL)

    A study on the qualitative and quantitative traits of barley ( Hordeum vulgare L.) and narbon vetch ( Vicia narbonensis L.) in intercropping and sole cropping system under the interference and control of weeds in dry land farming...

  19. Mapping the quantitative trait loci (QTL) controlling seed morphology in sunflower (Helianthus annuus L.)

    Science.gov (United States)

    This paper reports the results of analyzing the quantitative trait loci (QTL) underlying sunflower seed morphological traits in a segregating population derived from an oilseed by confection cross. A linkage map containing 165 target region amplification polymorphism (TRAP) and 44 simple sequence re...

  20. Mapping of quantitative trait loci for oil content in cottonseed kernel

    Indian Academy of Sciences (India)

    Abstract. Oil content in cottonseed is a major quality trait which when improved through breeding could enhance the competitiveness of cottonseed oil among other vegetable oils. Cottonseed oil content is a quantitative trait controlled by genes in the tetraploid embryo and tetraploid maternal plant genomes, and the ...

  1. Evaluation of Quantitative and Qualitative Traits of 18 Potato Clones

    Directory of Open Access Journals (Sweden)

    A. R Bolandi

    2016-10-01

    to those of check. Based on results of this experiment, the clones 397003-7, 396151-27 and 397045-100 could be selected for Ardebil region. The objective of this research was to evaluate the quantitative and qualitative traits of cultivars and advanced potato clones in spring cultivation (Jolge-e-Rokh region. Materials and Methods In this research, 18 potato clones for the quantitative and qualitative traits were compared with three check cultivars including: Agria (suitable for French-fries, Marfona (suitable for boiled eating and Lady Rosetta (suitable for chips in Jolge-Rokh Agriculture Research Station, the location 35'¸ 50° north latitude and 59° east longitude and 1721 m above sea level, in crop year 2011. Experimental design was Randomized Complete Block Design (RCBD with three replications. Treatment consisted of 18 advanced potato clones: 396151-8, 397045-4, 397045-10, TP12-13, TP21-29, TP12-8, 397007-16, 397007-17, 396140-6, 397009-8, 397015-14, 397003-7, 396151-27, 397045-100, 397097-9, 396151-20, 397045-7 and 69 indigenous with three control cultivars (Agria, Marfona and Lady Rosetta. Tubers were planted on two rows with 6 meters length. Distance between row and plants on the row were 75 and 25 cm, respectively. Area of each plot was 9 square meter. The evaluated characters were total yield, marketable yield, eye number, dry matter percentage, tuber number per plant, tuber weight per plant and mean of tuber weight. In order to measure total yield, after maturity, and remove the aerial organs, all of the tubers were harvested and the fresh weight was obtained. After removal of the tumor in bad shape, with soft rot and smaller than 30 mm that cannot be sold as part of the marketable yield, rest of them were used to measure marketable yield. Tuber dry matter percentage (TDM% was determined from the relationship between fresh and dry weights of sub-sample of 8-10 thinly sliced tubers dried for 48 h at 80° C. Data were analyzed using SAS 9.1 software. The

  2. Quantitative genetic methods depending on the nature of the phenotypic trait.

    Science.gov (United States)

    de Villemereuil, Pierre

    2018-01-24

    A consequence of the assumptions of the infinitesimal model, one of the most important theoretical foundations of quantitative genetics, is that phenotypic traits are predicted to be most often normally distributed (so-called Gaussian traits). But phenotypic traits, especially those interesting for evolutionary biology, might be shaped according to very diverse distributions. Here, I show how quantitative genetics tools have been extended to account for a wider diversity of phenotypic traits using first the threshold model and then more recently using generalized linear mixed models. I explore the assumptions behind these models and how they can be used to study the genetics of non-Gaussian complex traits. I also comment on three recent methodological advances in quantitative genetics that widen our ability to study new kinds of traits: the use of "modular" hierarchical modeling (e.g., to study survival in the context of capture-recapture approaches for wild populations); the use of aster models to study a set of traits with conditional relationships (e.g., life-history traits); and, finally, the study of high-dimensional traits, such as gene expression. © 2018 New York Academy of Sciences.

  3. Joint analysis of binary and quantitative traits with data sharing and outcome-dependent sampling.

    Science.gov (United States)

    Zheng, Gang; Wu, Colin O; Kwak, Minjung; Jiang, Wenhua; Joo, Jungnam; Lima, Joao A C

    2012-04-01

    We study the analysis of a joint association between a genetic marker with both binary (case-control) and quantitative (continuous) traits, where the quantitative trait values are only available for the cases due to data sharing and outcome-dependent sampling. Data sharing becomes common in genetic association studies, and the outcome-dependent sampling is the consequence of data sharing, under which a phenotype of interest is not measured for some subgroup. The trend test (or Pearson's test) and F-test are often, respectively, used to analyze the binary and quantitative traits. Because of the outcome-dependent sampling, the usual F-test can be applied using the subgroup with the observed quantitative traits. We propose a modified F-test by also incorporating the genotype frequencies of the subgroup whose traits are not observed. Further, a combination of this modified F-test and Pearson's test is proposed by Fisher's combination of their P-values as a joint analysis. Because of the correlation of the two analyses, we propose to use a Gamma (scaled chi-squared) distribution to fit the asymptotic null distribution for the joint analysis. The proposed modified F-test and the joint analysis can also be applied to test single trait association (either binary or quantitative trait). Through simulations, we identify the situations under which the proposed tests are more powerful than the existing ones. Application to a real dataset of rheumatoid arthritis is presented. © 2012 Wiley Periodicals, Inc.

  4. Accounting for genetic interactions improves modeling of individual quantitative trait phenotypes in yeast

    OpenAIRE

    Forsberg, Simon K. G.; Bloom, Joshua S.; Sadhu, Meru J.; Kruglyak, Leonid; Carlborg, ?rjan

    2017-01-01

    Experiments in model organisms report abundant genetic interactions underlying biologically important traits, whereas quantitative genetics theory predicts, and data support, that most genetic variance in populations is additive. Here we describe networks of capacitating genetic interactions that contribute to quantitative trait variation in a large yeast intercross population. The additive variance explained by individual loci in a network is highly dependent on the allele frequencies of the...

  5. Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria × ananassa).

    Science.gov (United States)

    Zorrilla-Fontanesi, Yasmín; Cabeza, Amalia; Domínguez, Pedro; Medina, Juan Jesús; Valpuesta, Victoriano; Denoyes-Rothan, Beatrice; Sánchez-Sevilla, José F; Amaya, Iraida

    2011-09-01

    Breeding for fruit quality traits in strawberry (Fragaria × ananassa, 2n = 8x = 56) is complex due to the polygenic nature of these traits and the octoploid constitution of this species. In order to improve the efficiency of genotype selection, the identification of quantitative trait loci (QTL) and associated molecular markers will constitute a valuable tool for breeding programs. However, the implementation of these markers in breeding programs depends upon the complexity and stability of QTLs across different environments. In this work, the genetic control of 17 agronomical and fruit quality traits was investigated in strawberry using a F(1) population derived from an intraspecific cross between two contrasting selection lines, '232' and '1392'. QTL analyses were performed over three successive years based on the separate parental linkage maps and a pseudo-testcross strategy. The integrated strawberry genetic map consists of 338 molecular markers covering 37 linkage groups, thus exceeding the 28 chromosomes. 33 QTLs were identified for 14 of the 17 studied traits and approximately 37% of them were stable over time. For each trait, 1-5 QTLs were identified with individual effects ranging between 9.2 and 30.5% of the phenotypic variation, indicating that all analysed traits are complex and quantitatively inherited. Many QTLs controlling correlated traits were co-located in homoeology group V, indicating linkage or pleiotropic effects of loci. Candidate genes for several QTLs controlling yield, anthocyanins, firmness and L-ascorbic acid are proposed based on both their co-localization and predicted function. We also report conserved QTLs among strawberry and other Rosaceae based on their syntenic location.

  6. Quantitative trait loci for body weight in layers differ from quantitative trait loci specific for antibody responses to sheep red blood cells

    NARCIS (Netherlands)

    Siwek, M.Z.; Cornelissen, S.J.B.; Buitenhuis, A.J.; Nieuwland, M.G.B.; Bovenhuis, H.; Crooijmans, R.P.M.A.; Groenen, M.A.M.; Parmentier, H.K.; Poel, van der J.J.

    2004-01-01

    Quantitative trait loci for BW at 4, 6, 8, 12, and 18 wk of age were detected in an experimental F2 cross of layers divergently selected for primary antibody response to SRBC. A negative phenotypic correlation between levels of antibody titers and BW, was reported earlier within founder lines. The

  7. Quantitative trait locus (QTL) analysis of pod related traits in different ...

    African Journals Online (AJOL)

    Three agronomic traits showing clear phenotypic variations between parents were investigated and relevant QTLs were analyzed with software WindowsQTL Cartographer V2.5. The pod related traits are podwall thickness, weight of podwall, and ratio of podwall to pod (weight to weight). A total of 67 QTLs were mapped for ...

  8. Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits.

    Science.gov (United States)

    Kessner, Darren; Novembre, John

    2015-04-01

    Evolve and resequence studies combine artificial selection experiments with massively parallel sequencing technology to study the genetic basis for complex traits. In these experiments, individuals are selected for extreme values of a trait, causing alleles at quantitative trait loci (QTL) to increase or decrease in frequency in the experimental population. We present a new analysis of the power of artificial selection experiments to detect and localize quantitative trait loci. This analysis uses a simulation framework that explicitly models whole genomes of individuals, quantitative traits, and selection based on individual trait values. We find that explicitly modeling QTL provides qualitatively different insights than considering independent loci with constant selection coefficients. Specifically, we observe how interference between QTL under selection affects the trajectories and lengthens the fixation times of selected alleles. We also show that a substantial portion of the genetic variance of the trait (50-100%) can be explained by detected QTL in as little as 20 generations of selection, depending on the trait architecture and experimental design. Furthermore, we show that power depends crucially on the opportunity for recombination during the experiment. Finally, we show that an increase in power is obtained by leveraging founder haplotype information to obtain allele frequency estimates. Copyright © 2015 by the Genetics Society of America.

  9. Evidences of local adaptation in quantitative traits in Prosopis alba (Leguminosae).

    Science.gov (United States)

    Bessega, C; Pometti, C; Ewens, M; Saidman, B O; Vilardi, J C

    2015-02-01

    Signals of selection on quantitative traits can be detected by the comparison between the genetic differentiation of molecular (neutral) markers and quantitative traits, by multivariate extensions of the same model and by the observation of the additive covariance among relatives. We studied, by three different tests, signals of occurrence of selection in Prosopis alba populations over 15 quantitative traits: three economically important life history traits: height, basal diameter and biomass, 11 leaf morphology traits that may be related with heat-tolerance and physiological responses and spine length that is very important from silvicultural purposes. We analyzed 172 G1-generation trees growing in a common garden belonging to 32 open pollinated families from eight sampling sites in Argentina. The multivariate phenotypes differ significantly among origins, and the highest differentiation corresponded to foliar traits. Molecular genetic markers (SSR) exhibited significant differentiation and allowed us to provide convincing evidence that natural selection is responsible for the patterns of morphological differentiation. The heterogeneous selection over phenotypic traits observed suggested different optima in each population and has important implications for gene resource management. The results suggest that the adaptive significance of traits should be considered together with population provenance in breeding program as a crucial point prior to any selecting program, especially in Prosopis where the first steps are under development.

  10. Sensitivity of quantitative traits to mutational effects and number of loci.

    Science.gov (United States)

    Schraiber, Joshua G; Landis, Michael J

    2015-06-01

    When models of quantitative genetic variation are built from population genetic first principles, several assumptions are often made. One of the most important assumptions is that traits are controlled by many genes of small effect. This leads to a prediction of a Gaussian trait distribution in the population, via the Central Limit Theorem. Since these biological assumptions are often unknown or untrue, we characterized how finite numbers of loci or large mutational effects can impact the sampling distribution of a quantitative trait. To do so, we developed a neutral coalescent-based framework, allowing us to gain a detailed understanding of how number of loci and the underlying mutational model impacts the distribution of a quantitative trait. Through both analytical theory and simulation we found the normality assumption was highly sensitive to the details of the mutational process, with the greatest discrepancies arising when the number of loci was small or the mutational kernel was heavy-tailed. In particular, skewed mutational effects will produce skewed trait distributions and fat-tailed mutational kernels result in multimodal sampling distributions, even for traits controlled by a large number of loci. Since selection models and robust neutral models may produce qualitatively similar sampling distributions, we advise extra caution should be taken when interpreting model-based results for poorly understood systems of quantitative traits. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Mapping quantitative trait loci associated with yield and yield ...

    Indian Academy of Sciences (India)

    identify reproductive stage specific QTLs for salinity tolerance. Genetic linkage map was constructed using 123 microsatellite markers on 232 F2 progenies. Totally 35 QTLs for 11 traits under salinity stress were detected with LOD > 3, out of which. 28 QTLs that explained from 5.9 to 30.0% phenotypic variation were found to ...

  12. Multiparent intercross populations in analysis of quantitative traits

    Indian Academy of Sciences (India)

    2012-04-17

    Apr 17, 2012 ... 1Directorate of Sorghum Research, Rajendranagar, Hyderabad 500 030, India. 2Central Research Institute for Dryland Agriculture, Santoshnagar, Hyderabad 500 059, India. Abstract. Most traits of interest to .... making such populations, a cen- tral parent is crossed with other diverse parents in star design.

  13. Berry and phenology-related traits in grapevine (Vitis vinifera L.: From Quantitative Trait Loci to underlying genes

    Directory of Open Access Journals (Sweden)

    Fanizza Girolamo

    2008-04-01

    Full Text Available Abstract Background The timing of grape ripening initiation, length of maturation period, berry size and seed content are target traits in viticulture. The availability of early and late ripening varieties is desirable for staggering harvest along growing season, expanding production towards periods when the fruit gets a higher value in the market and ensuring an optimal plant adaptation to climatic and geographic conditions. Berry size determines grape productivity; seedlessness is especially demanded in the table grape market and is negatively correlated to fruit size. These traits result from complex developmental processes modified by genetic, physiological and environmental factors. In order to elucidate their genetic determinism we carried out a quantitative analysis in a 163 individuals-F1 segregating progeny obtained by crossing two table grape cultivars. Results Molecular linkage maps covering most of the genome (2n = 38 for Vitis vinifera were generated for each parent. Eighteen pairs of homologous groups were integrated into a consensus map spanning over 1426 cM with 341 markers (mainly microsatellite, AFLP and EST-derived markers and an average map distance between loci of 4.2 cM. Segregating traits were evaluated in three growing seasons by recording flowering, veraison and ripening dates and by measuring berry size, seed number and weight. QTL (Quantitative Trait Loci analysis was carried out based on single marker and interval mapping methods. QTLs were identified for all but one of the studied traits, a number of them steadily over more than one year. Clusters of QTLs for different characters were detected, suggesting linkage or pleiotropic effects of loci, as well as regions affecting specific traits. The most interesting QTLs were investigated at the gene level through a bioinformatic analysis of the underlying Pinot noir genomic sequence. Conclusion Our results revealed novel insights into the genetic control of relevant

  14. Your cancer survivorship care plan

    Science.gov (United States)

    ... use to create one: American Society of Clinical Oncology -- www.cancer.net/survivorship/follow-care-after-cancer-treatment/asco- ... your doctor visits. References American Society of Clinical Oncology. Survivorship. Cancer.net. Updated July 2016. www.cancer.net/survivorship . ...

  15. The Quantitative LOD Score: Test Statistic and Sample Size for Exclusion and Linkage of Quantitative Traits in Human Sibships

    OpenAIRE

    Page, Grier P.; Amos, Christopher I.; Boerwinkle, Eric

    1998-01-01

    We present a test statistic, the quantitative LOD (QLOD) score, for the testing of both linkage and exclusion of quantitative-trait loci in randomly selected human sibships. As with the traditional LOD score, the boundary values of 3, for linkage, and -2, for exclusion, can be used for the QLOD score. We investigated the sample sizes required for inferring exclusion and linkage, for various combinations of linked genetic variance, total heritability, recombination distance, and sibship size, ...

  16. Statistical estimation of correlated genome associations to a quantitative trait network.

    Directory of Open Access Journals (Sweden)

    Seyoung Kim

    2009-08-01

    Full Text Available Many complex disease syndromes, such as asthma, consist of a large number of highly related, rather than independent, clinical or molecular phenotypes. This raises a new technical challenge in identifying genetic variations associated simultaneously with correlated traits. In this study, we propose a new statistical framework called graph-guided fused lasso (GFlasso to directly and effectively incorporate the correlation structure of multiple quantitative traits such as clinical metrics and gene expressions in association analysis. Our approach represents correlation information explicitly among the quantitative traits as a quantitative trait network (QTN and then leverages this network to encode structured regularization functions in a multivariate regression model over the genotypes and traits. The result is that the genetic markers that jointly influence subgroups of highly correlated traits can be detected jointly with high sensitivity and specificity. While most of the traditional methods examined each phenotype independently and combined the results afterwards, our approach analyzes all of the traits jointly in a single statistical framework. This allows our method to borrow information across correlated phenotypes to discover the genetic markers that perturb a subset of the correlated traits synergistically. Using simulated datasets based on the HapMap consortium and an asthma dataset, we compared the performance of our method with other methods based on single-marker analysis and regression-based methods that do not use any of the relational information in the traits. We found that our method showed an increased power in detecting causal variants affecting correlated traits. Our results showed that, when correlation patterns among traits in a QTN are considered explicitly and directly during a structured multivariate genome association analysis using our proposed methods, the power of detecting true causal SNPs with possibly pleiotropic

  17. Genotype-by-environment interaction in genetic mapping of multiple quantitative trait loci

    NARCIS (Netherlands)

    Jansen, R.C.; Ooijen, J.W. van; Stam, P.; Lister, C.; Dean, C.

    1995-01-01

    The interval mapping method is widely used for the genetic mapping of quantitative trait loci (QTLs), though true resolution of quantitative variation into QTLs is hampered with this method. Separation of QTLs is troublesome, because single-QTL is models are fitted. Further, genotype-by-environment

  18. High resolution of quantitative traits into multiple loci via interval mapping.

    NARCIS (Netherlands)

    Jansen, R.C.; Stam, P.

    1994-01-01

    A very general method is described for multiple linear regression of a quantitative phenotype on genotype [putative quantitative trait loci (QTLs) and markers] in segregating generations obtained from line crosses. The method exploits two features, (a) the use of additional parental and F1 data,

  19. High Resolution of Quantitative Traits Into Multiple Loci via Interval Mapping

    NARCIS (Netherlands)

    Jansen, Ritsert C.; Stam, Piet

    1994-01-01

    A very general method is described for multiple linear regression of a quantitative phenotype on genotype [putative quantitative trait loci (QTLs) and markers] in segregating generations obtained from line crosses. The method exploits two features, (a) the use of additional parental and F1 data,

  20. Mapping of quantitative trait loci by using genetic markers : an overview of biometrical models used

    NARCIS (Netherlands)

    Jansen, Ritsert C.

    1994-01-01

    In crop plants quantitative variation is a feature of many important traits, such as yield, quality or disease resistance. Means of analyzing quantitative variation and especially of uncovering its potential genetic basis are therefore of prime importance for breeding purposes. It has been

  1. Population-specific quantitative trait loci mapping for functional stay-green trait in rice (Oryza sativa L.).

    Science.gov (United States)

    Fu, Jin-Dong; Yan, Yong-Feng; Kim, Moon Young; Lee, Suk-Ha; Lee, Byun-Woo

    2011-03-01

    The functional stay-green trait gives leaves a longer duration of greenness and photosynthetic capacity during the grain-filling period. We developed two independent recombinant inbred line populations from the intra- and intersubspecific crosses of Oryza sativa L. subsp. japonica 'Suweon490' (japonica) × O. sativa subsp. japonica 'SNU-SG1' (japonica) and O. sativa subsp. indica 'Andabyeo' (indica) × O. sativa subsp. japonica 'SNU-SG1' (japonica), respectively. The common parental line 'SNU-SG1' was the functional source for the stay-green trait. Quantitative trait locus (QTL) mapping based on simple sequence repeat markers identified a total of six QTLs associated with two stay-green traits across two populations. The two traits were cumulative chlorophyll content (SPAD value) of flag leaf (CSFL) and total cumulative SPAD value of the four upper leaves (TCS). Four QTLs, tcs4, csfl6, csfl9 (or tcs9), and csfl12, located on chromosomes 4, 6, 9, and 12, respectively, were detected simultaneously in both populations. The remaining two QTLs, csfl2 (or tcs2) and tcs5, on chromosomes 2 and 5, respectively, were found to be population specific. Moreover, the functional stay-green trait of 'SNU-SG1' positively correlated with grain yield performance. Two yield QTLs, yld6 and yld9, on chromosomes 6 and 9 found in both populations were positioned at the same locations with the csfl6 and tcs9 QTLs for stay-green traits. Thus, the identified chromosomal regions can be promising targets of marker-assisted introgression of the functional stay-green trait into breeding materials for improvement of rice yield.

  2. Quantitative trait loci analysis and genome-wide comparison for silique related traits in Brassica napus.

    Science.gov (United States)

    Wang, Xiaodong; Chen, Li; Wang, Aina; Wang, Hao; Tian, Jianhua; Zhao, Xiaoping; Chao, Hongbo; Zhao, Yajun; Zhao, Weiguo; Xiang, Jun; Gan, Jianping; Li, Maoteng

    2016-03-22

    Yield of rapeseed is determined by three components: silique number, seed number per silique and thousand seed weight. Seed number per silique and thousand seed weight are influenced by silique length, seed density, silique breadth, silique thickness and silique volume. Some QTLs for silique traits have been reported in B. napus, however, no studies have focused on the six agronomic traits (seed number per silique, silique length, silique breadth, silique thickness, seed density and silique volume) simultaneously, and the genetic determinism of such complex traits have not been fully elucidated. In this study, the six silique traits were evaluated using 348 lines of a doubled haploid population, the KN population. The results showed that 2, 4, 1, 1 and 2 QTLs explaining > 10 % of phenotypic variation were obtained for silique length, silique breadth, silique thickness, seed number per silique and silique volume, respectively. Notably, three major effect QTLs (cqSB-C6-1, cqSB-C6-2 and cqSV-C6-3) were identified in at least three environments, and 17 unique QTLs controlling at least two traits were obtained. A high-density consensus map containing 1225 markers was constructed for QTL comparison by combining the KN map with other five published maps. The comparative results revealed that 14, 13 and 11 QTLs for silique breadth, silique thickness and silique volume might be the potential new QTLs because few QTLs for these traits were reported in B. napus. In addition, potential new QTLs for silique length (11), seed number per silique (6) and seed density (5) were also identified. Twenty-five candidate genes underlying 27 QTLs for silique related traits were obtained. This study constructed QTL analysis in B. napus, and obtained 60 consensus QTLs for six silique related traits. The potential new QTLs will enhance our understanding of the genetic control of silique traits, and the stable QTLs provided the targets for improving seed yield in future. These findings

  3. Uncovering the genetic signature of quantitative trait evolution with replicated time series data.

    Science.gov (United States)

    Franssen, S U; Kofler, R; Schlötterer, C

    2017-01-01

    The genetic architecture of adaptation in natural populations has not yet been resolved: it is not clear to what extent the spread of beneficial mutations (selective sweeps) or the response of many quantitative trait loci drive adaptation to environmental changes. Although much attention has been given to the genomic footprint of selective sweeps, the importance of selection on quantitative traits is still not well studied, as the associated genomic signature is extremely difficult to detect. We propose 'Evolve and Resequence' as a promising tool, to study polygenic adaptation of quantitative traits in evolving populations. Simulating replicated time series data we show that adaptation to a new intermediate trait optimum has three characteristic phases that are reflected on the genomic level: (1) directional frequency changes towards the new trait optimum, (2) plateauing of allele frequencies when the new trait optimum has been reached and (3) subsequent divergence between replicated trajectories ultimately leading to the loss or fixation of alleles while the trait value does not change. We explore these 3 phase characteristics for relevant population genetic parameters to provide expectations for various experimental evolution designs. Remarkably, over a broad range of parameters the trajectories of selected alleles display a pattern across replicates, which differs both from neutrality and directional selection. We conclude that replicated time series data from experimental evolution studies provide a promising framework to study polygenic adaptation from whole-genome population genetics data.

  4. A search for quantitative trait loci controlling within-individual variation of physical activity traits in mice

    Directory of Open Access Journals (Sweden)

    Pomp Daniel

    2010-09-01

    Full Text Available Abstract Background In recent years it has become increasingly apparent that physical inactivity can predispose individuals to a host of health problems. While many studies have analyzed the effect of various environmental factors on activity, we know much less about the genetic control of physical activity. Some studies in mice have discovered quantitative trait loci (QTL influencing various physical activity traits, but mostly have analyzed inter-individual variation rather than variation in activity within individuals over time. We conducted a genome scan to identify QTLs controlling the distance, duration, and time run by mice over seven consecutive three-day intervals in an F2 population created by crossing two inbred strains (C57L/J and C3H/HeJ that differed widely (average of nearly 300% in their activity levels. Our objectives were (a to see if we would find QTLs not originally discovered in a previous investigation that assessed these traits over the entire 21-day period and (b to see if some of these QTLs discovered might affect the activity traits only in the early or in the late time intervals. Results This analysis uncovered 39 different QTLs, over half of which were new. Some QTLs affected the activity traits only in the early time intervals and typically exhibited significant dominance effects whereas others affected activity only in the later age intervals and exhibited less dominance. We also analyzed the regression slopes of the activity traits over the intervals, and found several QTLs affecting these traits that generally mapped to unique genomic locations. Conclusions It was concluded that the genetic architecture of physical activity in mice is much more complicated than has previously been recognized, and may change considerably depending on the age at which various activity measures are assessed.

  5. INHERITANCE OF QUANTITATIVE TRAITS IN DRY PEA (Pisum sativum L.

    Directory of Open Access Journals (Sweden)

    Ranko Gantner

    2012-12-01

    Full Text Available The research was conducted with six parental genotypes: varieties Anno, Gold, Joel, Junior, PF-G1 and Shawnee with aim to improve the dry pea breeding for higher grain yield. Objectives of the research were to investigate: a the inheritance of grain yield per plant and its components; b to determination of the combining ability of parents and their cross-combinations; c the interrelationships among grain yield, its components and morphological traits; d choosing the primary selection criteria; e choosing the best cross-combinations in order to achieve the highest selection response of grain yield; f simple and digenic epistatic gene-effects in the chosen cross-combinations which determ the trait chosen as a primary selection criterion; g the genetic components of variation in the chosen cross-combinations of the trait chosen as a primary selection criterion; h the anticipation of genetic gain of grain yield per plant of the chosen cross-combinations. The research was conducted on experimental fields and laboratories of the Agricultural Institute Osijek. Parental lines were chosen in 2006, the first series of crossings in a diallel fashion were performed in 2007, and the second series in 2008, in a diallel fashion plus back-crossing. The obtained generation material (P1, P2, F1, F2, BC1 i BC2 of 15 biparental combinations was seeded in the field trial in 2009. Measurement of the yield, its components and morfological traits was done at the end of vegetation. The inheritance of investigated traits was estimated using Hayman’s approach to diallel analysis, combining abilities were determined using Griffing’s approach to diallel analysis, interrelationships among investigated traits were determined using correlation analysis, the primary selection criterion was chosen according to the inheritance of the investigated traits and their interrelationships, best cross-combinations were chosen upon Griffing’s analysis results and two principles: a

  6. Genetic mapping of quantitative trait loci (QTLs) with effects on ...

    African Journals Online (AJOL)

    SERVER

    2008-02-05

    Feb 5, 2008 ... The first major insect pest of cowpea at reproductive stage is the flower bud thrips (FTh), which, if not controlled, is capable of causing significant grain yield reduction. Breeding for resistance to FTh in cowpea has been hindered by the quantitative nature of the resistance, and the breakdown of resistance ...

  7. Genetic mapping of quantitative trait loci (QTLs) with effects on ...

    African Journals Online (AJOL)

    SERVER

    2008-02-05

    Feb 5, 2008 ... Key words: Vigna unguiculata, Megalurothrips sjostedti, quantitative resistance, molecular markers, gene mapping. INTRODUCTION. Cowpea ..... importance is increasing as insecticides lose efficacy due to pest adaptation or are removed from .... highly self-pollinating crop. In addition, both belong to the.

  8. Effects of marked chromosome sections on quantitative traits in the mouse.

    Science.gov (United States)

    Kluge, R; Geldermann, H

    1982-03-01

    An investigation of the influences of marked chromosome sections on quantitative traits in a backcross-generation with 2321 mice (C57BL/6JHan × (AKR/NHan×C57BL/6JHan)) is described. In the animals the chromosomes 1, 4, 7, and 8 were marked by the gene loci Idh-1, Gpd-1, Gpi-1s, Es-1, resp. Within the backcross-generation, for Idh-1 and Es-1, more heterozygous genotypes were found than expected under random conditions. By comparing animal-groups with different homologous sections of the marked chromosomes, effects were observed on quantitative traits (body length and weight, dry weight and matter, fat weight and content). The results indicate that a few chromosome sections influence to a major extent the genetic variation of some quantitative traits.

  9. Principal Component Analysis of Some Quantitative and Qualitative Traits in Iranian Spinach Landraces

    Directory of Open Access Journals (Sweden)

    Mohebodini Mehdi

    2017-08-01

    Full Text Available Landraces of spinach in Iran have not been sufficiently characterised for their morpho-agronomic traits. Such characterisation would be helpful in the development of new genetically improved cultivars. In this study 54 spinach accessions collected from the major spinach growing areas of Iran were evaluated to determine their phenotypic diversity profile of spinach genotypes on the basis of 10 quantitative and 9 qualitative morpho-agronomic traits. High coefficients of variation were recorded in some quantitative traits (dry yield and leaf area and all of the qualitative traits. Using principal component analysis, the first four principal components with eigen-values more than 1 contributed 87% of the variability among accessions for quantitative traits, whereas the first four principal components with eigen-values more than 0.8 contributed 79% of the variability among accessions for qualitative traits. The most important relations observed on the first two principal components were a strong positive association between leaf width and petiole length; between leaf length and leaf numbers in flowering; and among fresh yield, dry yield and petiole diameter; a near zero correlation between days to flowering with leaf width and petiole length. Prickly seeds, high percentage of female plants, smooth leaf texture, high numbers of leaves at flowering, greygreen leaves, erect petiole attitude and long petiole length are important characters for spinach breeding programmes.

  10. Estimation of genetic parameters and detection of quantitative trait loci for metabolites in Danish Holstein milk

    DEFF Research Database (Denmark)

    Buitenhuis, Albert Johannes; Sundekilde, Ulrik; Poulsen, Nina Aagaard

    2013-01-01

    Small components and metabolites in milk are significant for the utilization of milk, not only in dairy food production but also as disease predictors in dairy cattle. This study focused on estimation of genetic parameters and detection of quantitative trait loci for metabolites in bovine milk. F...... for lactic acid to >0.8 for orotic acid and β-hydroxybutyrate. A single SNP association analysis revealed 7 genome-wide significant quantitative trait loci [malonate: Bos taurus autosome (BTA)2 and BTA7; galactose-1-phosphate: BTA2; cis-aconitate: BTA11; urea: BTA12; carnitine: BTA25...

  11. A generalized estimating equations approach to quantitative trait locus detection of non-normal traits

    Directory of Open Access Journals (Sweden)

    Thomson Peter C

    2003-05-01

    Full Text Available Abstract To date, most statistical developments in QTL detection methodology have been directed at continuous traits with an underlying normal distribution. This paper presents a method for QTL analysis of non-normal traits using a generalized linear mixed model approach. Development of this method has been motivated by a backcross experiment involving two inbred lines of mice that was conducted in order to locate a QTL for litter size. A Poisson regression form is used to model litter size, with allowances made for under- as well as over-dispersion, as suggested by the experimental data. In addition to fixed parity effects, random animal effects have also been included in the model. However, the method is not fully parametric as the model is specified only in terms of means, variances and covariances, and not as a full probability model. Consequently, a generalized estimating equations (GEE approach is used to fit the model. For statistical inferences, permutation tests and bootstrap procedures are used. This method is illustrated with simulated as well as experimental mouse data. Overall, the method is found to be quite reliable, and with modification, can be used for QTL detection for a range of other non-normally distributed traits.

  12. Mapping quantitative trait loci (QTL in sheep. IV. Analysis of lactation persistency and extended lactation traits in sheep

    Directory of Open Access Journals (Sweden)

    Lam Mary K

    2011-06-01

    Full Text Available Abstract Background In sheep dairy production, total lactation performance, and length of lactation of lactation are of economic significance. A more persistent lactation has been associated with improved udder health. An extended lactation is defined by a longer period of milkability. This study is the first investigation to examine the presence of quantitative trait loci (QTL for extended lactation and lactation persistency in sheep. Methods An (Awassi × Merino × Merino single-sire backcross family with 172 ewes was used to map QTL for lactation persistency and extended lactation traits on a framework map of 189 loci across all autosomes. The Wood model was fitted to data from multiple lactations to estimate parameters of ovine lactation curves, and these estimates were used to derive measures of lactation persistency and extended lactation traits of milk, protein, fat, lactose, useful yield, and somatic cell score. These derived traits were subjected to QTL analyses using maximum likelihood estimation and regression analysis. Results Overall, one highly significant (LOD > 3.0, four significant (2.0 Conclusion This study identified ten novel QTL for lactation persistency and extended lactation in sheep, but results suggest that lactation persistency and extended lactation do not have a major gene in common. These results provide a basis for further validation in extended families and other breeds as well as targeting regions for genome-wide association mapping using high-density SNP arrays.

  13. Genetic architecture of growth traits in Populus revealed by integrated quantitative trait locus (QTL) analysis and association studies.

    Science.gov (United States)

    Du, Qingzhang; Gong, Chenrui; Wang, Qingshi; Zhou, Daling; Yang, Haijiao; Pan, Wei; Li, Bailian; Zhang, Deqiang

    2016-02-01

    Deciphering the genetic architecture underlying polygenic traits in perennial species can inform molecular marker-assisted breeding. Recent advances in high-throughput sequencing have enabled strategies that integrate linkage-linkage disequilibrium (LD) mapping in Populus. We used an integrated method of quantitative trait locus (QTL) dissection with a high-resolution linkage map and multi-gene association mapping to decipher the nature of genetic architecture (additive, dominant, and epistatic effects) of potential QTLs for growth traits in a Populus linkage population (1200 progeny) and a natural population (435 individuals). Seventeen QTLs for tree height, diameter at breast height, and stem volume mapped to 11 linkage groups (logarithm of odds (LOD) ≥ 2.5), and explained 2.7-18.5% of the phenotypic variance. After comparative mapping and transcriptome analysis, 187 expressed genes (10 046 common single nucleotide polymorphisms (SNPs)) were selected from the segmental homology regions (SHRs) of 13 QTLs. Using multi-gene association models, we observed 202 significant SNPs in 63 promising genes from 10 QTLs (P ≤ 0.0001; FDR ≤ 0.10) that exhibited reproducible associations with additive/dominant effects, and further determined 11 top-ranked genes tightly linked to the QTLs. Epistasis analysis uncovered a uniquely interconnected gene-gene network for each trait. This study opens up opportunities to uncover the causal networks of interacting genes in plants using an integrated linkage-LD mapping approach. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  14. Quantitative trait locus mapping and candidate gene analysis for plant architecture traits using whole genome re-sequencing in rice.

    Science.gov (United States)

    Lim, Jung-Hyun; Yang, Hyun-Jung; Jung, Ki-Hong; Yoo, Soo-Cheul; Paek, Nam-Chon

    2014-02-01

    Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 F7 recombinant in-bred lines (RILs) from a cross of japonica rice line 'SNUSG1' and indica rice line 'Milyang23'. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.

  15. Quantitative trait locus linkage analysis in a large Amish pedigree identifies novel candidate loci for erythrocyte traits.

    Science.gov (United States)

    Hinckley, Jesse D; Abbott, Diana; Burns, Trudy L; Heiman, Meadow; Shapiro, Amy D; Wang, Kai; Di Paola, Jorge

    2013-09-01

    We characterized a large Amish pedigree and, in 384 pedigree members, analyzed the genetic variance components with covariate screen as well as genome-wide quantitative trait locus (QTL) linkage analysis of red blood cell count (RBC), hemoglobin (HB), hematocrit (HCT), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), red cell distribution width (RDW), platelet count (PLT), and white blood cell count (WBC) using SOLAR. Age and gender were found to be significant covariates in many CBC traits. We obtained significant heritability estimates for RBC, MCV, MCH, MCHC, RDW, PLT, and WBC. We report four candidate loci with LOD scores above 2.0: 6q25 (MCH), 9q33 (WBC), 10p12 (RDW), and 20q13 (MCV). We also report eleven candidate loci with LOD scores between 1.5 and focus the search for rare variants amidst the noise encountered in the large amounts of data generated by whole genome sequencing.

  16. Quantitative trait loci influencing forking defects in an outbred pedigree of loblolly pine.

    Science.gov (United States)

    Xiong, Jin S; McKeand, Steven E; Isik, Fikret; Wegrzyn, Jill; Neale, David B; Zeng, Zhao-Bang; da Costa E Silva, Luciano; Whetten, Ross W

    2016-10-18

    The use of wood as an industrial raw material has led to development of plantation forestry, in which trees are planted, managed, and harvested as crops. The productivity of such plantations often exceeds that of less-intensively-managed forests, and land managers have the option of choosing specific planting stock to produce specific types of wood for industrial use. Stem forking, or division of the stem into two or more stems of roughly equal size, is a character trait important in determining the quality of the stem for production of solid wood products. This trait typically has very low individual-tree heritability, but can be more accurately assessed in clonally-replicated plantings where each genotype is represented by several individual trees. We report results from a quantitative trait mapping experiment in a clonally-replicated full-sibling family of loblolly pine (Pinus taeda L.). Quantitative trait loci influencing forking defects were identified in an outbred full-sibling family of loblolly pine, using single-nucleotide polymorphism markers. Genetic markers in this family segregated either in 1:2:1 (F2 intercross-like segregation) or 1:1 ratio (backcross-like segregation). An integrated linkage map combining markers with different segregation ratios was assembled for this full-sib family, and a total of 409 SNP markers were mapped on 12 linkage groups, covering 1622 cM. Two and three trait loci were identified for forking and ramicorn branch traits, respectively, using the interval mapping method. Three trait loci were detected for both traits using multiple-trait analysis. The detection of three loci for forking and ramicorn branching in a multiple-trait analysis could mean that there are genes with pleiotropic effects on both traits, or that separate genes affecting different traits are clustered together. The detection of genetic loci associated with variation in stem quality traits in this study supports the hypothesis that marker

  17. The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci.

    Science.gov (United States)

    Polineni, Pavana; Aragonda, Prathyusha; Xavier, Suresh R; Furuta, Richard; Adelson, David L

    2006-06-05

    Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling) in cattle are quantitative traits. Most of the information on these traits has not previously been integrated into a genomic context. Without such integration application of these data to agricultural enterprises will remain slow and inefficient. Our goal was to populate a genomic database with data mined from the bovine quantitative trait literature and to make these data available in a genomic context to researchers via a user friendly query interface. The QTL (Quantitative Trait Locus) data and related information for bovine QTL are gathered from published work and from existing databases. An integrated database schema was designed and the database (MySQL) populated with the gathered data. The bovine QTL Viewer was developed for the integration of QTL data available for cattle. The tool consists of an integrated database of bovine QTL and the QTL viewer to display QTL and their chromosomal position. We present a web accessible, integrated database of bovine (dairy and beef cattle) QTL for use by animal geneticists. The viewer and database are of general applicability to any livestock species for which there are public QTL data. The viewer can be accessed at http://bovineqtl.tamu.edu.

  18. The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci

    Directory of Open Access Journals (Sweden)

    Xavier Suresh R

    2006-06-01

    Full Text Available Abstract Background Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling in cattle are quantitative traits. Most of the information on these traits has not previously been integrated into a genomic context. Without such integration application of these data to agricultural enterprises will remain slow and inefficient. Our goal was to populate a genomic database with data mined from the bovine quantitative trait literature and to make these data available in a genomic context to researchers via a user friendly query interface. Description The QTL (Quantitative Trait Locus data and related information for bovine QTL are gathered from published work and from existing databases. An integrated database schema was designed and the database (MySQL populated with the gathered data. The bovine QTL Viewer was developed for the integration of QTL data available for cattle. The tool consists of an integrated database of bovine QTL and the QTL viewer to display QTL and their chromosomal position. Conclusion We present a web accessible, integrated database of bovine (dairy and beef cattle QTL for use by animal geneticists. The viewer and database are of general applicability to any livestock species for which there are public QTL data. The viewer can be accessed at http://bovineqtl.tamu.edu.

  19. Detecting Genetic Interactions for Quantitative Traits Using m-Spacing Entropy Measure

    Directory of Open Access Journals (Sweden)

    Jaeyong Yee

    2015-01-01

    Full Text Available A number of statistical methods for detecting gene-gene interactions have been developed in genetic association studies with binary traits. However, many phenotype measures are intrinsically quantitative and categorizing continuous traits may not always be straightforward and meaningful. Association of gene-gene interactions with an observed distribution of such phenotypes needs to be investigated directly without categorization. Information gain based on entropy measure has previously been successful in identifying genetic associations with binary traits. We extend the usefulness of this information gain by proposing a nonparametric evaluation method of conditional entropy of a quantitative phenotype associated with a given genotype. Hence, the information gain can be obtained for any phenotype distribution. Because any functional form, such as Gaussian, is not assumed for the entire distribution of a trait or a given genotype, this method is expected to be robust enough to be applied to any phenotypic association data. Here, we show its use to successfully identify the main effect, as well as the genetic interactions, associated with a quantitative trait.

  20. Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants.

    Science.gov (United States)

    Kujur, Alice; Saxena, Maneesha S; Bajaj, Deepak; Laxmi; Parida, Swarup K

    2013-12-01

    The enormous population growth, climate change and global warming are now considered major threats to agriculture and world's food security. To improve the productivity and sustainability of agriculture, the development of highyielding and durable abiotic and biotic stress-tolerant cultivars and/climate resilient crops is essential. Henceforth, understanding the molecular mechanism and dissection of complex quantitative yield and stress tolerance traits is the prime objective in current agricultural biotechnology research. In recent years, tremendous progress has been made in plant genomics and molecular breeding research pertaining to conventional and next-generation whole genome, transcriptome and epigenome sequencing efforts, generation of huge genomic, transcriptomic and epigenomic resources and development of modern genomics-assisted breeding approaches in diverse crop genotypes with contrasting yield and abiotic stress tolerance traits. Unfortunately, the detailed molecular mechanism and gene regulatory networks controlling such complex quantitative traits is not yet well understood in crop plants. Therefore, we propose an integrated strategies involving available enormous and diverse traditional and modern -omics (structural, functional, comparative and epigenomics) approaches/resources and genomics-assisted breeding methods which agricultural biotechnologist can adopt/utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in crop plants. This would provide clues and much needed inputs for rapid selection of novel functionally relevant molecular tags regulating such complex traits to expedite traditional and modern marker-assisted genetic enhancement studies in target crop species for developing high-yielding stress-tolerant varieties.

  1. A method to prioritize quantitative traits and individuals for sequencing in family-based studies.

    Directory of Open Access Journals (Sweden)

    Kaanan P Shah

    Full Text Available Owing to recent advances in DNA sequencing, it is now technically feasible to evaluate the contribution of rare variation to complex traits and diseases. However, it is still cost prohibitive to sequence the whole genome (or exome of all individuals in each study. For quantitative traits, one strategy to reduce cost is to sequence individuals in the tails of the trait distribution. However, the next challenge becomes how to prioritize traits and individuals for sequencing since individuals are often characterized for dozens of medically relevant traits. In this article, we describe a new method, the Rare Variant Kinship Test (RVKT, which leverages relationship information in family-based studies to identify quantitative traits that are likely influenced by rare variants. Conditional on nuclear families and extended pedigrees, we evaluate the power of the RVKT via simulation. Not unexpectedly, the power of our method depends strongly on effect size, and to a lesser extent, on the frequency of the rare variant and the number and type of relationships in the sample. As an illustration, we also apply our method to data from two genetic studies in the Old Order Amish, a founder population with extensive genealogical records. Remarkably, we implicate the presence of a rare variant that lowers fasting triglyceride levels in the Heredity and Phenotype Intervention (HAPI Heart study (p = 0.044, consistent with the presence of a previously identified null mutation in the APOC3 gene that lowers fasting triglyceride levels in HAPI Heart study participants.

  2. Exercise and diet affect quantitative trait loci for body weight and composition traits in an advanced intercross population of mice.

    Science.gov (United States)

    Leamy, Larry J; Kelly, Scott A; Hua, Kunjie; Pomp, Daniel

    2012-12-01

    Driven by the recent obesity epidemic, interest in understanding the complex genetic and environmental basis of body weight and composition is great. We investigated this by searching for quantitative trait loci (QTLs) affecting a number of weight and adiposity traits in a G(10) advanced intercross population produced from crosses of mice in inbred strain C57BL/6J with those in a strain selected for high voluntary wheel running. The mice in this population were fed either a high-fat or a control diet throughout the study and also measured for four exercise traits prior to death, allowing us to test for pre- and postexercise QTLs as well as QTL-by-diet and QTL-by-exercise interactions. Our genome scan uncovered a number of QTLs, of which 40% replicated QTLs previously found for similar traits in an earlier (G(4)) generation. For those replicated QTLs, the confidence intervals were reduced from an average of 19 Mb in the G(4) to 8 Mb in the G(10). Four QTLs on chromosomes 3, 8, 13, and 18 were especially prominent in affecting the percentage of fat in the mice. About of all QTLs showed interactions with diet, exercise, or both, their genotypic effects on the traits showing a variety of patterns depending on the diet or level of exercise. It was concluded that the indirect effects of these QTLs provide an underlying genetic basis for the considerable variability in weight or fat loss typically found among individuals on the same diet and/or exercise regimen.

  3. Exercise and diet affect quantitative trait loci for body weight and composition traits in an advanced intercross population of mice

    Science.gov (United States)

    Kelly, Scott A.; Hua, Kunjie; Pomp, Daniel

    2012-01-01

    Driven by the recent obesity epidemic, interest in understanding the complex genetic and environmental basis of body weight and composition is great. We investigated this by searching for quantitative trait loci (QTLs) affecting a number of weight and adiposity traits in a G10 advanced intercross population produced from crosses of mice in inbred strain C57BL/6J with those in a strain selected for high voluntary wheel running. The mice in this population were fed either a high-fat or a control diet throughout the study and also measured for four exercise traits prior to death, allowing us to test for pre- and postexercise QTLs as well as QTL-by-diet and QTL-by-exercise interactions. Our genome scan uncovered a number of QTLs, of which 40% replicated QTLs previously found for similar traits in an earlier (G4) generation. For those replicated QTLs, the confidence intervals were reduced from an average of 19 Mb in the G4 to 8 Mb in the G10. Four QTLs on chromosomes 3, 8, 13, and 18 were especially prominent in affecting the percentage of fat in the mice. About of all QTLs showed interactions with diet, exercise, or both, their genotypic effects on the traits showing a variety of patterns depending on the diet or level of exercise. It was concluded that the indirect effects of these QTLs provide an underlying genetic basis for the considerable variability in weight or fat loss typically found among individuals on the same diet and/or exercise regimen. PMID:23048196

  4. Mapping quantitative trait loci (QTL) in sheep. IV. Analysis of lactation persistency and extended lactation traits in sheep

    Science.gov (United States)

    2011-01-01

    Background In sheep dairy production, total lactation performance, and length of lactation of lactation are of economic significance. A more persistent lactation has been associated with improved udder health. An extended lactation is defined by a longer period of milkability. This study is the first investigation to examine the presence of quantitative trait loci (QTL) for extended lactation and lactation persistency in sheep. Methods An (Awassi × Merino) × Merino single-sire backcross family with 172 ewes was used to map QTL for lactation persistency and extended lactation traits on a framework map of 189 loci across all autosomes. The Wood model was fitted to data from multiple lactations to estimate parameters of ovine lactation curves, and these estimates were used to derive measures of lactation persistency and extended lactation traits of milk, protein, fat, lactose, useful yield, and somatic cell score. These derived traits were subjected to QTL analyses using maximum likelihood estimation and regression analysis. Results Overall, one highly significant (LOD > 3.0), four significant (2.0 lactation persistency and extended lactation did not coincide. This suggests that persistency and extended lactation for the same as well as different milk yield and component traits are not controlled by the same genes. Conclusion This study identified ten novel QTL for lactation persistency and extended lactation in sheep, but results suggest that lactation persistency and extended lactation do not have a major gene in common. These results provide a basis for further validation in extended families and other breeds as well as targeting regions for genome-wide association mapping using high-density SNP arrays. PMID:21693024

  5. Influence of obesity gene in quantitative traits of swine

    Directory of Open Access Journals (Sweden)

    Graciele Segantini do Nascimento Borges

    2002-01-01

    -grandparental generation, when the male grandparent is replaced by the great-grandparental generation. The obesity gene did not influence any of the carcass evaluation data from crossbred animals. In pure swine, where the only genotypes were TT and TC, it greatly influenced shoulder weight and meat texture, with the highest average in heterozygotes (shoulder: 4.07 vs. 3.93; texture: 2.62 vs. 1.82, suggesting better carcass quality and worse meat quality than in homozygotes. The obesity gene did not influence any trait in the expected progeny difference (EPD study.

  6. Identification of major quantitative trait loci underlying floral pollination syndrome divergence in Penstemon.

    Science.gov (United States)

    Wessinger, Carolyn A; Hileman, Lena C; Rausher, Mark D

    2014-08-05

    Distinct floral pollination syndromes have emerged multiple times during the diversification of flowering plants. For example, in western North America, a hummingbird pollination syndrome has evolved more than 100 times, generally from within insect-pollinated lineages. The hummingbird syndrome is characterized by a suite of floral traits that attracts and facilitates pollen movement by hummingbirds, while at the same time discourages bee visitation. These floral traits generally include large nectar volume, red flower colour, elongated and narrow corolla tubes and reproductive organs that are exerted from the corolla. A handful of studies have examined the genetic architecture of hummingbird pollination syndrome evolution. These studies find that mutations of relatively large effect often explain increased nectar volume and transition to red flower colour. In addition, they suggest that adaptive suites of floral traits may often exhibit a high degree of genetic linkage, which could facilitate their fixation during pollination syndrome evolution. Here, we explore these emerging generalities by investigating the genetic basis of floral pollination syndrome divergence between two related Penstemon species with different pollination syndromes--bee-pollinated P. neomexicanus and closely related hummingbird-pollinated P. barbatus. In an F2 mapping population derived from a cross between these two species, we characterized the effect size of genetic loci underlying floral trait divergence associated with the transition to bird pollination, as well as correlation structure of floral trait variation. We find the effect sizes of quantitative trait loci for adaptive floral traits are in line with patterns observed in previous studies, and find strong evidence that suites of floral traits are genetically linked. This linkage may be due to genetic proximity or pleiotropic effects of single causative loci. Interestingly, our data suggest that the evolution of floral traits

  7. Quantitative trait loci for resistance to maize streak virus disease in ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-07-18

    Jul 18, 2008 ... characterized quantitative trait loci affecting resistance to maize streak virus in maize populations of S4 families from the cross of one resistant MAL13 and one susceptible MAL9 recombinant inbred lines. Resistance was evaluated in replicated field trials under artificial inoculation while selecting using.

  8. An improved procedure of mapping a quantitative trait locus via the ...

    Indian Academy of Sciences (India)

    Mapping a locus controlling a quantitative genetic trait (e.g. blood pressure) to a specific genomic region is of considerable contemporary interest. Data on the ... data of a sample of unrelated individuals and a Bayes's rule is used to classify each parent into a QTL genotypic class. In the second stage, we have proposed an ...

  9. Variation in seed dormancy quantitative trait loci in Arabidopsis thaliana originating from one site

    NARCIS (Netherlands)

    Silady, R.A.; Effgen, S.; Koornneef, M.; Reymond, M.

    2011-01-01

    A Quantitative Trait Locus (QTL) analysis was performed using two novel Recombinant Inbred Line (RIL) populations, derived from the progeny between two Arabidopsis thaliana genotypes collected at the same site in Kyoto (Japan) crossed with the reference laboratory strain Landsberg erecta (Ler). We

  10. Quantitative trait loci for resistance to maize streak virus disease in ...

    African Journals Online (AJOL)

    Maize streak virus disease is an important disease of maize in Kenya. In this study, we mapped and characterized quantitative trait loci affecting resistance to maize streak virus in maize populations of S4 families from the cross of one resistant MAL13 and one susceptible MAL9 recombinant inbred lines. Resistance was ...

  11. Quantitative trait loci (QTL) analysis of flag leaf senescence in wheat ...

    African Journals Online (AJOL)

    The objective of this study was to detect quantitative trait loci (QTL) associated with drought tolerance in wheat genotypes by simple sequence repeat (SSR) markers and to provide valuable information for marker assisted selection. SSR markers linked to flag leaf senescence (FLS) was identified in two DNA pools, which ...

  12. AFLP mapping of quantitative trait loci for yield-determining physiological characters in spring barley

    NARCIS (Netherlands)

    Yin, X.; Stam, P.; Dourleijn, J.C.; Kropff, M.J.

    1999-01-01

    An amplified fragment length polymorphism (AFLP) map covering 965 cM was constructed using 94 recombinant inbred lines of a cross between the spring barley varieties Prisma and Apex. This map was employed to identify quantitative trait loci (QTLs) controlling plant height, yield and

  13. Quantitative trait locus analysis of nitrogen use efficiency in barley (Hordeum vulgare L.)

    NARCIS (Netherlands)

    Kindu, G.A.; Tang, J.; Yin, X.; Struik, P.C.

    2014-01-01

    Quantitative trait locus (QTL) analysis of nitrogen use efficiency (NUE) of barley (Hordeum vulgare L.) was conducted on data generated from two pot experiments carried out in 2005 (using four nitrogen rates) and 2008 (with three rates) with AFLP markers and 94 recombinant inbred lines (RILs) of the

  14. Detection of a quantitative trait locus associated with resistance to Ascaris suum infection in pigs.

    Science.gov (United States)

    Skallerup, Per; Nejsum, Peter; Jørgensen, Claus B; Göring, Harald H H; Karlskov-Mortensen, Peter; Archibald, Alan L; Fredholm, Merete; Thamsborg, Stig M

    2012-04-01

    Helminths almost invariably have an over-dispersed distribution in the host population. Human and animal studies have provided evidence suggesting that a large part of this variation is due to host genetic factors. Recently, the heritability for roundworm (Ascaris suum) infection levels in pigs was estimated to be 0.45. We used single nucleotide polymorphism markers to perform a whole-genome scan on 195 pigs experimentally infected with A. suum. A putative quantitative trait locus for worm burden on chromosome 4 covering 2.5 Mbp was identified by measured genotype analysis, although none of the SNPs reached genome-wide significance. To validate the putative quantitative trait locus, we genotyped two of the SNPs within the region in unrelated, informative animals exposed to experimental or natural infections and from which we had worm counts and/or faecal egg counts; the validation studies showed that one of the SNPs (TXNIP) was associated with total worm burden (P < 0.001) and adult worm burden(P < 0.0001), whereas the other SNP (ARNT) was associated with adult worm burden (P < 0.025) in these populations. We were thus able to confirm the existence of the quantitative trait locus on chromosome 4.This is to our knowledge the first report of a quantitative trait locus associated with helminth burden in pigs.

  15. A General Monte Carlo Method for Mapping Multiple Quantitative Trait Loci

    NARCIS (Netherlands)

    Jansen, Ritsert C.

    1996-01-01

    In this paper we address the mapping of multiple quantitative trait loci (QTLs) in line crosses for which the genetic data are highly incomplete. Such complicated situations occur, for instance, when dominant markers are used or when unequally informative markers are used in experiments with outbred

  16. Quantitative trait loci for seed dormancy in wild barley (Hordeum spontaneum C. Koch)

    NARCIS (Netherlands)

    Vanhala, T.; Stam, P.

    2006-01-01

    A quantitative trait locus analysis was carried out to unravel the genetic basis of dormancy in wild barley (Hordeum spontaneum) from Israel. Two accessions, Ashkelon and Mehola, from divergent environments were crossed to produce a mapping population. A linkage map was produced from the F2

  17. Meta-Analysis of Results from Quantitative Trait Loci Mapping Studies on Pig Chromosome 4

    NARCIS (Netherlands)

    Moraes Silva, De K.M.; Bastiaansen, J.W.M.; Knol, E.F.; Merks, J.W.M.; Lopes, P.S.; Guimaraes, R.M.; Arendonk, van J.A.M.

    2011-01-01

    Meta-analysis of results from multiple studies could lead to more precise quantitative trait loci (QTL) position estimates compared to the individual experiments. As the raw data from many different studies are not readily available, the use of results from published articles may be helpful. In this

  18. Comparison of quantitative trait loci for rice yield, panicle length and ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 90; Issue 2. Comparison of quantitative trait loci for rice yield, panicle length and spikelet density across three connected populations. Touming Liu Lianzhi Li Yushan Zhang Caiguo Xu Xianghua Li Yongzhong Xing. Research Note Volume 90 Issue 2 August 2011 pp 377-382 ...

  19. Quantitative trait loci controlling Cu, Ca, Zn, Mn and Fe content in ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 87; Issue 3. Quantitative trait loci controlling Cu, Ca, Zn, Mn and Fe content in rice grains. Kaiyang Lu Lanzhi Li Xingfei Zheng Zhihong Zhang Tongmin Mou Zhongli Hu. Research Note Volume 87 Issue 3 December 2008 pp 305-310 ...

  20. Mapping quantitative trait loci in a selectively genotyped outbred population using a mixture model approach

    NARCIS (Netherlands)

    Johnson, David L.; Jansen, Ritsert C.; Arendonk, Johan A.M. van

    1999-01-01

    A mixture model approach is employed for the mapping of quantitative trait loci (QTL) for the situation where individuals, in an outbred population, are selectively genotyped. Maximum likelihood estimation of model parameters is obtained from an Expectation-Maximization (EM) algorithm facilitated by

  1. CBCL Pediatric Bipolar Disorder Profile and ADHD: Comorbidity and Quantitative Trait Loci Analysis

    Science.gov (United States)

    McGough, James J.; Loo, Sandra K.; McCracken, James T.; Dang, Jeffery; Clark, Shaunna; Nelson, Stanley F.; Smalley, Susan L.

    2008-01-01

    The pediatric bipolar disorder profile of the Child Behavior checklist is used to differentiate patterns of comorbidity and to search for quantitative trait loci in multiple affected ADHD sibling pairs. The CBCL-PBD profiling identified 8 percent of individuals with severe psychopathology and increased rates of oppositional defiant, conduct and…

  2. Protein quantitative trait locus study in obesity during weight-loss identifies a leptin regulator

    DEFF Research Database (Denmark)

    Carayol, Jérôme; Chabert, Christian; Di Cara, Alessandro

    2017-01-01

    Thousands of genetic variants have been associated with complex traits through genomewide association studies. However, the functional variants or mechanistic consequences remain elusive. Intermediate traits such as gene expression or protein levels are good proxies of the metabolic state...... of an organism. Proteome analysis especially can provide new insights into the molecular mechanisms of complex traits like obesity. The role of genetic variation in determining protein level variation has not been assessed in obesity. To address this, we design a large-scale protein quantitative trait locus (p......QTL) analysis based on a set of 1129 proteins from 494 obese subjects before and after a weight loss intervention. This reveals 55 BMI-associated cis-pQTLs and trans-pQTLs at baseline and 3 trans-pQTLs after the intervention. We provide evidence for distinct genetic mechanisms regulating BMI-associated proteins...

  3. Investigation of the Genetic Diversity and Quantitative Trait Loci Accounting for Important Agronomic and Seed Quality Traits in Brassica carinata

    Directory of Open Access Journals (Sweden)

    Harsh Raman

    2017-04-01

    Full Text Available Brassica carinata (BBCC is an allotetraploid in Brassicas with unique alleles for agronomic traits and has huge potential as source for biodiesel production. To investigate the genome-wide molecular diversity, population structure and linkage disequilibrium (LD pattern in this species, we genotyped a panel of 81 accessions of B. carinata with genotyping by sequencing approach DArTseq, generating a total of 54,510 polymorphic markers. Two subpopulations were exhibited in the B. carinata accessions. The average distance of LD decay (r2 = 0.1 in B subgenome (0.25 Mb was shorter than that of C subgenome (0.40 Mb. Genome-wide association analysis (GWAS identified a total of seven markers significantly associated with five seed quality traits in two experiments. To further identify the quantitative trait loci (QTL for important agronomic and seed quality traits, we phenotyped a doubled haploid (DH mapping population derived from the “YW” cross between two parents (Y-BcDH64 and W-BcDH76 representing from the two subpopulations. The YW DH population and its parents were grown in three contrasting environments; spring (Hezheng and Xining, China, semi-winter (Wuhan, China, and spring (Wagga Wagga, Australia across 5 years for QTL mapping. Genetic bases of phenotypic variation in seed yield and its seven related traits, and six seed quality traits were determined. A total of 282 consensus QTL accounting for these traits were identified including nine major QTL for flowering time, oleic acid, linolenic acid, pod number of main inflorescence, and seed weight. Of these, 109 and 134 QTL were specific to spring and semi-winter environment, respectively, while 39 consensus QTL were identified in both contrasting environments. Two QTL identified for linolenic acid (B3 and erucic acid (C7 were validated in the diverse lines used for GWAS. A total of 25 QTL accounting for flowering time, erucic acid, and oleic acid were aligned to the homologous QTL or

  4. Investigation of the Genetic Diversity and Quantitative Trait Loci Accounting for Important Agronomic and Seed Quality Traits in Brassica carinata.

    Science.gov (United States)

    Zhang, Wenshan; Hu, Dandan; Raman, Rosy; Guo, Shaomin; Wei, Zili; Shen, Xueqi; Meng, Jinling; Raman, Harsh; Zou, Jun

    2017-01-01

    Brassica carinata (BBCC) is an allotetraploid in Brassicas with unique alleles for agronomic traits and has huge potential as source for biodiesel production. To investigate the genome-wide molecular diversity, population structure and linkage disequilibrium (LD) pattern in this species, we genotyped a panel of 81 accessions of B. carinata with genotyping by sequencing approach DArTseq, generating a total of 54,510 polymorphic markers. Two subpopulations were exhibited in the B. carinata accessions. The average distance of LD decay (r2 = 0.1) in B subgenome (0.25 Mb) was shorter than that of C subgenome (0.40 Mb). Genome-wide association analysis (GWAS) identified a total of seven markers significantly associated with five seed quality traits in two experiments. To further identify the quantitative trait loci (QTL) for important agronomic and seed quality traits, we phenotyped a doubled haploid (DH) mapping population derived from the "YW" cross between two parents (Y-BcDH64 and W-BcDH76) representing from the two subpopulations. The YW DH population and its parents were grown in three contrasting environments; spring (Hezheng and Xining, China), semi-winter (Wuhan, China), and spring (Wagga Wagga, Australia) across 5 years for QTL mapping. Genetic bases of phenotypic variation in seed yield and its seven related traits, and six seed quality traits were determined. A total of 282 consensus QTL accounting for these traits were identified including nine major QTL for flowering time, oleic acid, linolenic acid, pod number of main inflorescence, and seed weight. Of these, 109 and 134 QTL were specific to spring and semi-winter environment, respectively, while 39 consensus QTL were identified in both contrasting environments. Two QTL identified for linolenic acid (B3) and erucic acid (C7) were validated in the diverse lines used for GWAS. A total of 25 QTL accounting for flowering time, erucic acid, and oleic acid were aligned to the homologous QTL or candidate gene

  5. Mapping the quantitative trait loci (QTL) controlling seed morphology and disk diameter in sunflower (Helianthus annuus L.)

    Science.gov (United States)

    Several seed morphological traits, along with disk diameter, differ greatly between oilseed and confection sunflower types, which are bred for different end-use purposes. This paper reports the results of analyzing the quantitative trait loci (QTL) underlying seed morphological traits and disk diam...

  6. Advancing genetic theory and application by metabolic quantitative trait loci analysis.

    Science.gov (United States)

    Kliebenstein, Danielj

    2009-06-01

    This review describes recent advances in the analysis of metabolism using quantitative genetics. It focuses on how recent metabolic quantitative trait loci (QTL) studies enhance our understanding of the genetic architecture underlying naturally variable phenotypes and the impact of this fundamental research on agriculture, specifically crop breeding. In particular, the role of whole-genome duplications in generating quantitative genetic variation within a species is highlighted and the potential uses of this phenomenon presented. Additionally, the review describes how new observations from metabolic QTL mapping analyses are helping to shape and expand the concepts of genetic epistasis.

  7. Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot

    Directory of Open Access Journals (Sweden)

    Diego Robledo

    2016-02-01

    Full Text Available Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs. Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species.

  8. Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot

    Science.gov (United States)

    Robledo, Diego; Fernández, Carlos; Hermida, Miguel; Sciara, Andrés; Álvarez-Dios, José Antonio; Cabaleiro, Santiago; Caamaño, Rubén; Martínez, Paulino; Bouza, Carmen

    2016-01-01

    Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs). Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species. PMID:26901189

  9. A Molecular Genetic Linkage Map of Eucommia ulmoides and Quantitative Trait Loci (QTL Analysis for Growth Traits

    Directory of Open Access Journals (Sweden)

    Yu Li

    2014-01-01

    Full Text Available Eucommia ulmoides is an economically important tree species for both herbal medicine and organic chemical industry. Effort to breed varieties with improved yield and quality is limited by the lack of knowledge on the genetic basis of the traits. A genetic linkage map of E. ulmoides was constructed from a full-sib family using sequence-related amplified polymorphism, amplified fragment length polymorphism, inter-simple sequence repeat and simple sequence repeat markers. In total, 706 markers were mapped in 25 linkage groups covering 2133 cM. The genetic linkage map covered approximately 89% of the estimated E. ulmoides genome with an average of 3.1 cM between adjacent markers. The present genetic linkage map was used to identify quantitative trait loci (QTL affecting growth-related traits. Eighteen QTLs were found to explain 12.4%–33.3% of the phenotypic variance. This genetic linkage map provides a tool for marker-assisted selection and for studies of genome in E. ulmoides.

  10. The influence of genetic drift and selection on quantitative traits in a plant pathogenic fungus.

    Science.gov (United States)

    Stefansson, Tryggvi S; McDonald, Bruce A; Willi, Yvonne

    2014-01-01

    Genetic drift and selection are ubiquitous evolutionary forces acting to shape genetic variation in populations. While their relative importance has been well studied in plants and animals, less is known about their relative importance in fungal pathogens. Because agro-ecosystems are more homogeneous environments than natural ecosystems, stabilizing selection may play a stronger role than genetic drift or diversifying selection in shaping genetic variation among populations of fungal pathogens in agro-ecosystems. We tested this hypothesis by conducting a QST/FST analysis using agricultural populations of the barley pathogen Rhynchosporium commune. Population divergence for eight quantitative traits (QST) was compared with divergence at eight neutral microsatellite loci (FST) for 126 pathogen strains originating from nine globally distributed field populations to infer the effects of genetic drift and types of selection acting on each trait. Our analyses indicated that five of the eight traits had QST values significantly lower than FST, consistent with stabilizing selection, whereas one trait, growth under heat stress (22°C), showed evidence of diversifying selection and local adaptation (QST>FST). Estimates of heritability were high for all traits (means ranging between 0.55-0.84), and average heritability across traits was negatively correlated with microsatellite gene diversity. Some trait pairs were genetically correlated and there was significant evidence for a trade-off between spore size and spore number, and between melanization and growth under benign temperature. Our findings indicate that many ecologically and agriculturally important traits are under stabilizing selection in R. commune and that high within-population genetic variation is maintained for these traits.

  11. Fine mapping and candidate gene prediction of a pleiotropic quantitative trait locus for yield-related trait in Zea mays.

    Directory of Open Access Journals (Sweden)

    Ruixiang Liu

    Full Text Available The yield of maize grain is a highly complex quantitative trait that is controlled by multiple quantitative trait loci (QTLs with small effects, and is frequently influenced by multiple genetic and environmental factors. Thus, it is challenging to clone a QTL for grain yield in the maize genome. Previously, we identified a major QTL, qKNPR6, for kernel number per row (KNPR across multiple environments, and developed two nearly isogenic lines, SL57-6 and Ye478, which differ only in the allelic constitution at the short segment harboring the QTL. Recently, qKNPR6 was re-evaluated in segregating populations derived from SL57-6×Ye478, and was narrowed down to a 2.8 cM interval, which explained 56.3% of the phenotypic variance of KNPR in 201 F(2∶3 families. The QTL simultaneously affected ear length, kernel weight and grain yield. Furthermore, a large F(2 population with more than 12,800 plants, 191 recombinant chromosomes and 10 overlapping recombinant lines placed qKNPR6 into a 0.91 cM interval corresponding to 198Kb of the B73 reference genome. In this region, six genes with expressed sequence tag (EST evidence were annotated. The expression pattern and DNA diversity of the six genes were assayed in Ye478 and SL57-6. The possible candidate gene and the pathway involved in inflorescence development were discussed.

  12. Admixture mapping of quantitative traits in Populus hybrid zones: power and limitations

    Science.gov (United States)

    Lindtke, D; González-Martínez, S C; Macaya-Sanz, D; Lexer, C

    2013-01-01

    Uncovering the genetic architecture of species differences is of central importance for understanding the origin and maintenance of biological diversity. Admixture mapping can be used to identify the number and effect sizes of genes that contribute to the divergence of ecologically important traits, even in taxa that are not amenable to laboratory crosses because of their long generation time or other limitations. Here, we apply admixture mapping to naturally occurring hybrids between two ecologically divergent Populus species. We map quantitative trait loci for eight leaf morphological traits using 77 mapped microsatellite markers from all 19 chromosomes of Populus. We apply multivariate linear regression analysis allowing the modeling of additive and non-additive gene action and identify several candidate genomic regions associated with leaf morphology using an information-theoretic approach. We perform simulation studies to assess the power and limitations of admixture mapping of quantitative traits in natural hybrid populations for a variety of genetic architectures and modes of gene action. Our results indicate that (1) admixture mapping has considerable power to identify the genetic architecture of species differences if sample sizes and marker densities are sufficiently high, (2) modeling of non-additive gene action can help to elucidate the discrepancy between genotype and phenotype sometimes seen in interspecific hybrids, and (3) the genetic architecture of leaf morphological traits in the studied Populus species involves complementary and overdominant gene action, providing the basis for rapid adaptation of these ecologically important forest trees. PMID:23860234

  13. Genome-wide Association Study to Identify Quantitative Trait Loci for Meat and Carcass Quality Traits in Berkshire

    Directory of Open Access Journals (Sweden)

    Asif Iqbal

    2015-11-01

    Full Text Available Meat and carcass quality attributes are of crucial importance influencing consumer preference and profitability in the pork industry. A set of 400 Berkshire pigs were collected from Dasan breeding farm, Namwon, Chonbuk province, Korea that were born between 2012 and 2013. To perform genome wide association studies (GWAS, eleven meat and carcass quality traits were considered, including carcass weight, backfat thickness, pH value after 24 hours (pH24, Commission Internationale de l’Eclairage lightness in meat color (CIE L, redness in meat color (CIE a, yellowness in meat color (CIE b, filtering, drip loss, heat loss, shear force and marbling score. All of the 400 animals were genotyped with the Porcine 62K SNP BeadChips (Illumina Inc., USA. A SAS general linear model procedure (SAS version 9.2 was used to pre-adjust the animal phenotypes before GWAS with sire and sex effects as fixed effects and slaughter age as a covariate. After fitting the fixed and covariate factors in the model, the residuals of the phenotype regressed on additive effects of each single nucleotide polymorphism (SNP under a linear regression model (PLINK version 1.07. The significant SNPs after permutation testing at a chromosome-wise level were subjected to stepwise regression analysis to determine the best set of SNP markers. A total of 55 significant (p<0.05 SNPs or quantitative trait loci (QTL were detected on various chromosomes. The QTLs explained from 5.06% to 8.28% of the total phenotypic variation of the traits. Some QTLs with pleiotropic effect were also identified. A pair of significant QTL for pH24 was also found to affect both CIE L and drip loss percentage. The significant QTL after characterization of the functional candidate genes on the QTL or around the QTL region may be effectively and efficiently used in marker assisted selection to achieve enhanced genetic improvement of the trait considered.

  14. A Strategy for Identifying Quantitative Trait Genes Using Gene Expression Analysis and Causal Analysis.

    Science.gov (United States)

    Ishikawa, Akira

    2017-11-27

    Large numbers of quantitative trait loci (QTL) affecting complex diseases and other quantitative traits have been reported in humans and model animals. However, the genetic architecture of these traits remains elusive due to the difficulty in identifying causal quantitative trait genes (QTGs) for common QTL with relatively small phenotypic effects. A traditional strategy based on techniques such as positional cloning does not always enable identification of a single candidate gene for a QTL of interest because it is difficult to narrow down a target genomic interval of the QTL to a very small interval harboring only one gene. A combination of gene expression analysis and statistical causal analysis can greatly reduce the number of candidate genes. This integrated approach provides causal evidence that one of the candidate genes is a putative QTG for the QTL. Using this approach, I have recently succeeded in identifying a single putative QTG for resistance to obesity in mice. Here, I outline the integration approach and discuss its usefulness using my studies as an example.

  15. Detection of parent-of-origin effects for quantitative traits using general pedigree data.

    Science.gov (United States)

    He, Hai-Qiang; Mao, Wei-Gao; Pan, Dongdong; Zhou, Ji-Yuan; Chen, Ping-Yan; Fung, Wing Kam

    2014-08-01

    Genomic imprinting is a genetic phenomenon in which certain alleles are differentially expressed in a parent-of-origin-specific manner, and plays an important role in the study of complex traits. For a diallelic marker locus in human, the parentalasymmetry tests Q-PAT(c) with any constant c were developed to detect parent-of-origin effects for quantitative traits. However, these methods can only be applied to deal with nuclear families and thus are not suitable for extended pedigrees. In this study, by making no assumption about the distribution of the quantitative trait, we first propose the pedigree parentalasymmetry tests Q-PPAT(c) with any constant c for quantitative traits to test for parent-of-origin effects based on nuclear families with complete information from general pedigree data, in the presence of association between marker alleles under study and quantitative traits. When there are any genotypes missing in pedigrees, we utilize Monte Carlo (MC) sampling and estimation and develop the Q-MCPPAT(c) statistics to test for parent-of-origin effects. Various simulation studies are conducted to assess the performance of the proposed methods, for different sample sizes, genotype missing rates, degrees of imprinting effects and population models. Simulation results show that the proposed methods control the size well under the null hypothesis of no parent-of-origin effects and Q-PPAT(c) are robust to population stratification. In addition, the power comparison demonstrates that Q-PPAT(c) and Q-MCPPAT(c) for pedigree data are much more powerful than Q-PAT(c) only using two-generation nuclear families selected from extended pedigrees.

  16. Quantitative autistic trait measurements index background genetic risk for ASD in Hispanic families.

    Science.gov (United States)

    Page, Joshua; Constantino, John Nicholas; Zambrana, Katherine; Martin, Eden; Tunc, Ilker; Zhang, Yi; Abbacchi, Anna; Messinger, Daniel

    2016-01-01

    Recent studies have indicated that quantitative autistic traits (QATs) of parents reflect inherited liabilities that may index background genetic risk for clinical autism spectrum disorder (ASD) in their offspring. Moreover, preferential mating for QATs has been observed as a potential factor in concentrating autistic liabilities in some families across generations. Heretofore, intergenerational studies of QATs have focused almost exclusively on Caucasian populations-the present study explored these phenomena in a well-characterized Hispanic population. The present study examined QAT scores in siblings and parents of 83 Hispanic probands meeting research diagnostic criteria for ASD, and 64 non-ASD controls, using the Social Responsiveness Scale-2 (SRS-2). Ancestry of the probands was characterized by genotype, using information from 541,929 single nucleotide polymorphic markers. In families of Hispanic children with an ASD diagnosis, the pattern of quantitative trait correlations observed between ASD-affected children and their first-degree relatives (ICCs on the order of 0.20), between unaffected first-degree relatives in ASD-affected families (sibling/mother ICC = 0.36; sibling/father ICC = 0.53), and between spouses (mother/father ICC = 0.48) were in keeping with the influence of transmitted background genetic risk and strong preferential mating for variation in quantitative autistic trait burden. Results from analysis of ancestry-informative genetic markers among probands in this sample were consistent with that from other Hispanic populations. Quantitative autistic traits represent measurable indices of inherited liability to ASD in Hispanic families. The accumulation of autistic traits occurs within generations, between spouses, and across generations, among Hispanic families affected by ASD. The occurrence of preferential mating for QATs-the magnitude of which may vary across cultures-constitutes a mechanism by which background genetic liability

  17. Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape.

    Science.gov (United States)

    Baker, Robert L; Leong, Wen Fung; Brock, Marcus T; Markelz, R J Cody; Covington, Michael F; Devisetty, Upendra K; Edwards, Christine E; Maloof, Julin; Welch, Stephen; Weinig, Cynthia

    2015-10-01

    Improved predictions of fitness and yield may be obtained by characterizing the genetic controls and environmental dependencies of organismal ontogeny. Elucidating the shape of growth curves may reveal novel genetic controls that single-time-point (STP) analyses do not because, in theory, infinite numbers of growth curves can result in the same final measurement. We measured leaf lengths and widths in Brassica rapa recombinant inbred lines (RILs) throughout ontogeny. We modeled leaf growth and allometry as function valued traits (FVT), and examined genetic correlations between these traits and aspects of phenology, physiology, circadian rhythms and fitness. We used RNA-seq to construct a SNP linkage map and mapped trait quantitative trait loci (QTL). We found genetic trade-offs between leaf size and growth rate FVT and uncovered differences in genotypic and QTL correlations involving FVT vs STPs. We identified leaf shape (allometry) as a genetic module independent of length and width and identified selection on FVT parameters of development. Leaf shape is associated with venation features that affect desiccation resistance. The genetic independence of leaf shape from other leaf traits may therefore enable crop optimization in leaf shape without negative effects on traits such as size, growth rate, duration or gas exchange. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  18. GWAPower: a statistical power calculation software for genome-wide association studies with quantitative traits

    Directory of Open Access Journals (Sweden)

    Chen Chia-Cheng

    2011-01-01

    Full Text Available Abstract Background In designing genome-wide association (GWA studies it is important to calculate statistical power. General statistical power calculation procedures for quantitative measures often require information concerning summary statistics of distributions such as mean and variance. However, with genetic studies, the effect size of quantitative traits is traditionally expressed as heritability, a quantity defined as the amount of phenotypic variation in the population that can be ascribed to the genetic variants among individuals. Heritability is hard to transform into summary statistics. Therefore, general power calculation procedures cannot be used directly in GWA studies. The development of appropriate statistical methods and a user-friendly software package to address this problem would be welcomed. Results This paper presents GWAPower, a statistical software package of power calculation designed for GWA studies with quantitative traits, where genetic effect is defined as heritability. Based on several popular one-degree-of-freedom genetic models, this method avoids the need to specify the non-centrality parameter of the F-distribution under the alternative hypothesis. Therefore, it can use heritability information directly without approximation. In GWAPower, the power calculation can be easily adjusted for adding covariates and linkage disequilibrium information. An example is provided to illustrate GWAPower, followed by discussions. Conclusions GWAPower is a user-friendly free software package for calculating statistical power based on heritability in GWA studies with quantitative traits. The software is freely available at: http://dl.dropbox.com/u/10502931/GWAPower.zip

  19. Smaller, scale-free gene networks increase quantitative trait heritability and result in faster population recovery.

    Directory of Open Access Journals (Sweden)

    Jacob W Malcom

    Full Text Available One of the goals of biology is to bridge levels of organization. Recent technological advances are enabling us to span from genetic sequence to traits, and then from traits to ecological dynamics. The quantitative genetics parameter heritability describes how quickly a trait can evolve, and in turn describes how quickly a population can recover from an environmental change. Here I propose that we can link the details of the genetic architecture of a quantitative trait--i.e., the number of underlying genes and their relationships in a network--to population recovery rates by way of heritability. I test this hypothesis using a set of agent-based models in which individuals possess one of two network topologies or a linear genotype-phenotype map, 16-256 genes underlying the trait, and a variety of mutation and recombination rates and degrees of environmental change. I find that the network architectures introduce extensive directional epistasis that systematically hides and reveals additive genetic variance and affects heritability: network size, topology, and recombination explain 81% of the variance in average heritability in a stable environment. Network size and topology, the width of the fitness function, pre-change additive variance, and certain interactions account for ∼75% of the variance in population recovery times after a sudden environmental change. These results suggest that not only the amount of additive variance, but importantly the number of loci across which it is distributed, is important in regulating the rate at which a trait can evolve and populations can recover. Taken in conjunction with previous research focused on differences in degree of network connectivity, these results provide a set of theoretical expectations and testable hypotheses for biologists working to span levels of organization from the genotype to the phenotype, and from the phenotype to the environment.

  20. Accounting for genetic interactions improves modeling of individual quantitative trait phenotypes in yeast.

    Science.gov (United States)

    Forsberg, Simon K G; Bloom, Joshua S; Sadhu, Meru J; Kruglyak, Leonid; Carlborg, Örjan

    2017-04-01

    Experiments in model organisms report abundant genetic interactions underlying biologically important traits, whereas quantitative genetics theory predicts, and data support, the notion that most genetic variance in populations is additive. Here we describe networks of capacitating genetic interactions that contribute to quantitative trait variation in a large yeast intercross population. The additive variance explained by individual loci in a network is highly dependent on the allele frequencies of the interacting loci. Modeling of phenotypes for multilocus genotype classes in the epistatic networks is often improved by accounting for the interactions. We discuss the implications of these results for attempts to dissect genetic architectures and to predict individual phenotypes and long-term responses to selection.

  1. Quantitative resistance can lead to evolutionary changes in traits not targeted by the resistance QTLs

    Science.gov (United States)

    Van den Berg, Femke; Lannou, Christian; Gilligan, Christopher A; van de Bosch, Frank

    2014-01-01

    This paper addresses the general concern in plant pathology that the introduction of quantitative resistance in the landscape can lead to increased pathogenicity. Hereto, we study the hypothetical case of a quantitative trait loci (QTL) acting on pathogen spore production per unit lesion area. To regain its original fitness, the pathogen can break the QTL, restoring its spore production capacity leading to an increased spore production per lesion. Or alternatively, it can increase its lesion size, also leading to an increased spore production per lesion. A data analysis shows that spore production per lesion (affected by the resistance QTL) and lesion size (not targeted by the QTL) are positively correlated traits, suggesting that a change in magnitude of a trait not targeted by the QTL (lesion size) might indirectly affect the targeted trait (spore production per lesion). Secondly, we model the effect of pathogen adaptation towards increased lesion size and analyse its consequences for spore production per lesion. The model calculations show that when the pathogen is unable to overcome the resistance associated QTL, it may compensate for its reduced fitness by indirect selection for increased pathogenicity on both the resistant and susceptible cultivar, but whereby the QTLs remain effective. PMID:24665339

  2. Genetic and Molecular Mechanisms of Quantitative Trait Loci Controlling Maize Inflorescence Architecture.

    Science.gov (United States)

    Li, Manfei; Zhong, Wanshun; Yang, Fang; Zhang, Zuxin

    2018-02-06

    The establishment of inflorescence architecture is critical for the reproduction of flowering plant species. The maize plant generates two types of inflorescences, the tassel and the ear, and their architectures have a large effect on grain yield and yield-related traits that are genetically controlled by quantitative trait loci (QTLs). Since ear and tassel architecture are deeply affected by the activity of inflorescence meristems, key QTLs and genes regulating meristematic activity have important impacts on inflorescence development and show great potential for optimizing grain yield. Isolation of yield trait-related QTLs is challenging but these QTLs have direct application in maize breeding. Additionally, characterization and functional dissection of QTLs can provide genetic and molecular knowledge of quantitative variation in inflorescence architecture. In this review, we summarize currently identified QTLs responsible for the establishment of ear and tassel architecture and discuss the potential genetic control of four ear-related and four tassel-related traits. In recent years, several inflorescence architecture-related QTLs have been characterized at the gene level. We review the mechanisms of these characterized QTLs. © The Author 2018. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Quantitative trait loci analysis for leg weakness-related traits in a Duroc × Pietrain crossbred population

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    Phatsara Chirawath

    2011-03-01

    Full Text Available Abstract Background Leg weakness issues are a great concern for the pig breeding industry, especially with regard to animal welfare. Traits associated with leg weakness are partly influenced by the genetic background of the animals but the genetic basis of these traits is not yet fully understood. The aim of this study was to identify quantitative trait loci (QTL affecting leg weakness in pigs. Methods Three hundred and ten F2 pigs from a Duroc × Pietrain resource population were genotyped using 82 genetic markers. Front and rear legs and feet scores were based on the standard scoring system. Osteochondrosis lesions were examined histologically at the head and the condylus medialis of the left femur and humerus. Bone mineral density, bone mineral content and bone mineral area were measured in the whole ulna and radius bones using dual energy X-ray absorptiometry. A line-cross model was applied to determine QTL regions associated with leg weakness using the QTL Express software. Results Eleven QTL affecting leg weakness were identified on eight autosomes. All QTL reached the 5% chromosome-wide significance level. Three QTL were associated with osteochondrosis on the humerus end, two with the fore feet score and two with the rear leg score. QTL on SSC2 and SSC3 influencing bone mineral content and bone mineral density, respectively, reached the 5% genome-wide significance level. Conclusions Our results confirm previous studies and provide information on new QTL associated with leg weakness in pigs. These results contribute towards a better understanding of the genetic background of leg weakness in pigs.

  4. Quantitative trait locus and haplotype analyses of wild and crop-mimic traits in U.S. weedy rice.

    Science.gov (United States)

    Mispan, Muhamad S; Zhang, Lihua; Feng, Jiuhuan; Gu, Xing-You

    2013-06-21

    Conspecific weeds retained characteristics from wild ancestors and also developed crop mimicries for adaptation and competitiveness. This research was conducted to identify quantitative trait loci (QTL) associated with the wild and crop-mimic traits and to determine haplotype variants for QTL-rich regions in U.S. weedy rice. An F2 population from the cross between a cultivated (EM93-1) and a U.S. weedy (US1) rice line was evaluated for six wild and eight crop-mimic traits in a greenhouse to identify the QTL. A core collection of 27 U.S. weedy red rice lines and 14 AA-genome wild rice lines were determined for the haplotype variants. A total of 49 QTL were identified, with 45 collocated as clusters on 14 genomic segments. The number of haplotypes across the 14 segments was lower in the weedy (6.1 ± 2.4) than in the wild (7.5 ± 1.8) rice sample. Both samples shared ~50% haplotypes (wild-like). The EM93-1-like haplotypes accounted for a greater proportion (30 ± 26%) of the haplotypes in the weedy than in the wild (7 ± 10%) rice. Based on haplotype patterns for the 14 QTL cluster regions, 26 of the 28 red rice lines were clustered into two groups corresponding to the black-hull awned and straw-hull awnless morphological types, respectively. The QTL analysis demonstrated that conspecific weed-crop differentiation involved many genomic segments with multiple loci regulating natural variation for adaptation and competitiveness. The haplotype analysis revealed that U.S. weedy rice retained large blocks of linkage disequilibrium for the multiple loci from the wild relatives and also incorporated haplotypes from cultivars.

  5. Determination of quantitative trait variants by concordance via application of the a posteriori granddaughter design to the U.S. Holstein population

    Science.gov (United States)

    Experimental designs that exploit family information can provide substantial predictive power in quantitative trait variant discovery projects. Concordance between quantitative trait locus genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 29 trai...

  6. Mapping quantitative trait loci and identification of genes that control fatness in poultry

    OpenAIRE

    Burt, David W.; Hocking, Paul M.

    2002-01-01

    Chicken genomics has benefited from the rapid technological advances in the genomics of model organisms and man. A number of resources and approaches are now well established, in the chicken, including genetic markers and maps (both genetic and physical), quantitative trait loci mapping, comparative mapping, expressed sequence tag and bacterial artificial chromosome resources, and physical mapping. In addition, the next phase of gene discovery, functional genomics, is underway. Progress in ma...

  7. Mapping quantitative trait loci with extreme discordant sib pairs: sampling considerations.

    OpenAIRE

    Risch, N. J.; Zhang, H.

    1996-01-01

    Elsewhere we have proposed the use of extreme discordant sib pairs (EDSPs) for mapping quantitative trait loci in humans. Here we present sample sizes necessary to achieve a given level of power with this study design, as well as the number of sibs that need to be screened to obtain the required sample. Further, we present simple formulas for adjusting sample sizes to account for variable significance levels and power, as well as the density and informativeness of linkage markers in a multipo...

  8. Replication and Narrowing of Gene Expression Quantitative Trait Loci using Inbred Mice

    OpenAIRE

    Gatti, Daniel M.; Harrill, Alison H.; Wright, Fred A.; Threadgill, David W.; Rusyn, Ivan

    2009-01-01

    Gene expression quantitative trait locus (eQTL) mapping has become a powerful tool in systems biology. While many authors have made important discoveries using this approach, one persistent challenge in eQTL studies is the selection of loci and genes that should receive further biological investigation. In this study, we compared eQTL generated from gene expression profiling in the livers of two panels of mouse strains, 41 BXD recombinant inbred and 36 mouse diversity panel (MDP) strains. Cis...

  9. A Major Locus for Quantitatively Measured Shank Skin Color Traits in Korean Native Chicken

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    S. Jin

    2016-11-01

    Full Text Available Shank skin color of Korean native chicken (KNC shows large color variations. It varies from white, yellow, green, bluish or grey to black, whilst in the majority of European breeds the shanks are typically yellow-colored. Three shank skin color-related traits (i.e., lightness [L*], redness [a*], and yellowness [b*] were measured by a spectrophotometer in 585 progeny from 68 nuclear families in the KNC resource population. We performed genome scan linkage analysis to identify loci that affect quantitatively measured shank skin color traits in KNC. All these birds were genotyped with 167 DNA markers located throughout the 26 autosomes. The SOLAR program was used to conduct multipoint variance-component quantitative trait locus (QTL analyses. We detected a major QTL that affects b* value (logarithm of odds [LOD] = 47.5, p = 1.60×10−49 on GGA24 (GGA for Gallus gallus. At the same location, we also detected a QTL that influences a* value (LOD = 14.2, p = 6.14×10−16. Additionally, beta-carotene dioxygenase 2 (BCDO2, the obvious positional candidate gene under the linkage peaks on GGA24, was investigated by the two association tests: i.e., measured genotype association (MGA and quantitative transmission disequilibrium test (QTDT. Significant associations were detected between BCDO2 g.9367 A>C and a* (PMGA = 1.69×10−28; PQTDT = 2.40×10−25. The strongest associations were between BCDO2 g.9367 A>C and b* (PMGA = 3.56×10−66; PQTDT = 1.68×10−65. However, linkage analyses conditional on the single nucleotide polymorphism indicated that other functional variants should exist. Taken together, we demonstrate for the first time the linkage and association between the BCDO2 locus on GGA24 and quantitatively measured shank skin color traits in KNC.

  10. Genetic basis for systems of skeletal quantitative traits: Principal component analysis of the canid skeleton

    OpenAIRE

    Chase, Kevin; Carrier, David R.; Frederick R. Adler; Jarvik, Tyler; Ostrander, Elaine A.; Lorentzen, Travis D.; Lark, Karl G.

    2002-01-01

    Evolution of mammalian skeletal structure can be rapid and the changes profound, as illustrated by the morphological diversity of the domestic dog. Here we use principal component analysis of skeletal variation in a population of Portuguese Water Dogs to reveal systems of traits defining skeletal structures. This analysis classifies phenotypic variation into independent components that can be used to dissect genetic networks regulating complex biological systems. We show that unlinked quantit...

  11. Identification of quantitative trait loci associated with bone traits and body weight in an F2 resource population of chickens*

    Directory of Open Access Journals (Sweden)

    Schreiweis Melissa A

    2005-11-01

    Full Text Available Abstract Bone fractures at the end of lay are a significant problem in egg-laying strains of hens. The objective of the current study was to identify quantitative trait loci (QTL associated with bone mineralization and strength in a chicken resource population. Layer (White Leghorn hens and broiler (Cobb-Cobb roosters lines were crossed to generate an F2 population of 508 hens over seven hatches, and 26 traits related to bone integrity, including bone mineral density (BMD and content (BMC, were measured. Genotypes of 120 microsatellite markers on 28 autosomal groups were determined, and interval mapping was conducted to identify QTL regions. Twenty-three tests representing three chromosomal regions (chromosomes 4, 10 and 27 contained significant QTL that surpassed the 5% genome-wise threshold, and 47 tests representing 15 chromosomes identified suggestive QTL that surpassed the 5% chromosome-wise threshold. Although no significant QTL influencing BMD and BMC were detected after adjusting for variation in body weight and egg production, multiple suggestive QTL were found. These results support previous experiments demonstrating an important genetic regulation of bone strength in chickens, but suggest the regulation may be due to the effects of multiple genes that each account for relatively small amounts of variation in bone strength.

  12. Identification of quantitative trait loci for the fatty acid composition in Korean native chicken.

    Science.gov (United States)

    Jin, Shil; Seo, Dongwon; Choi, Nu Ri; Manjula, Prabuddha; Cahyadi, Muhammad; Jung, Samooel; Jo, Cheorun; Lee, Jun Heon; Park, Hee Bok

    2018-01-26

    Fatty acid composition is one of the most important meat quality traits because it can contribute to functional, sensorial, and nutritional factors. In this study, quantitative trait locus (QTL) analyses for fatty acid composition traits were investigated in thigh and breast meat of Korean native chicken (KNC). In total, 18 fatty acid composition traits were investigated from each meat sample using 88 parents, and 595 F1 chicks of 20 week old. Genotype assessment was performed using 171 informative DNA markers on 26 autosomes. The KNC linkage map was constructed by CRI-MAP software, which calculated genetic distances, with map orders between markers. The half-sib and full-sib QTL analyses were performed using GridQTL and SOLAR programs, respectively. In total, 30 QTLs (12 in the thigh and 18 in the breast meat) were detected by the half-sib analysis and 7 QTLs (3 in the thigh and 4 in the breast meat) were identified by the full-sib analysis. With further verification of the QTL regions using additional markers and positional candidate gene studies, these results can provide valuable information for determining causative mutations affecting the fatty acid composition of KNC meat. Moreover, these findings may aid in the selection of birds with favorable fatty acid composition traits.

  13. Quantitative trait loci mapping in dairy cattle: review and meta-analysis

    Directory of Open Access Journals (Sweden)

    Raadsma Herman W

    2004-03-01

    Full Text Available Abstract From an extensive review of public domain information on dairy cattle quantitative trait loci (QTL, we have prepared a draft online QTL map for dairy production traits. Most publications (45 out of 55 reviewed reported QTL for the major milk production traits (milk, fat and protein yield, and fat and protein concentration (% and somatic cell score. Relatively few QTL studies have been reported for more complex traits such as mastitis, fertility and health. The collated QTL map shows some chromosomal regions with a high density of QTL, as well as a substantial number of QTL at single chromosomal locations. To extract the most information from these published records, a meta-analysis was conducted to obtain consensus on QTL location and allelic substitution effect of these QTL. This required modification and development of statistical methodologies. The meta-analysis indicated a number of consensus regions, the most striking being two distinct regions affecting milk yield on chromosome 6 at 49 cM and 87 cM explaining 4.2 and 3.6 percent of the genetic variance of milk yield, respectively. The first of these regions (near marker BM143 affects five separate milk production traits (protein yield, protein percent, fat yield, fat percent, as well as milk yield.

  14. Mapping quantitative trait loci affecting Arabidopsis thaliana seed morphology features extracted computationally from images.

    Science.gov (United States)

    Moore, Candace R; Gronwall, David S; Miller, Nathan D; Spalding, Edgar P

    2013-01-01

    Seeds are studied to understand dispersal and establishment of the next generation, as units of agricultural yield, and for other important reasons. Thus, elucidating the genetic architecture of seed size and shape traits will benefit basic and applied plant biology research. This study sought quantitative trait loci (QTL) controlling the size and shape of Arabidopsis thaliana seeds by computational analysis of seed phenotypes in recombinant inbred lines derived from the small-seeded Landsberg erecta × large-seeded Cape Verde Islands accessions. On the order of 10(3) seeds from each recombinant inbred line were automatically measured with flatbed photo scanners and custom image analysis software. The eight significant QTL affecting seed area explained 63% of the variation, and overlapped with five of the six major-axis (length) QTL and three of the five minor-axis (width) QTL, which accounted for 57% and 38% of the variation in those traits, respectively. Because the Arabidopsis seed is exalbuminous, lacking an endosperm at maturity, the results are relatable to embryo length and width. The Cvi allele generally had a positive effect of 2.6-4.0%. Analysis of variance showed heritability of the three traits ranged between 60% and 73%. Repeating the experiment with 2.2 million seeds from a separate harvest of the RIL population and approximately 0.5 million seeds from 92 near-isogenic lines confirmed the aforementioned results. Structured for download are files containing phenotype measurements, all sets of seed images, and the seed trait measuring tool.

  15. Genetic mapping of quantitative trait loci for milk production in sheep.

    Science.gov (United States)

    Mateescu, R G; Thonney, M L

    2010-10-01

    A backcross pedigree using dairy East Friesian rams and non-dairy Dorset ewes was established specifically to map quantitative trait loci (QTL) affecting milk production in sheep. Ninety nine microsatellite markers of an initial set of 120 were successfully genotyped and informative on 188 animals of this backcross pedigree. Test-day milk records on individual ewes were used to estimate several milk yield related traits, including peak milk yield and cumulative milk yield to 50 (MY50), 100 (MY100) and 250 days (MY250). These traits, as well as estimated breeding value of backcross ewes extracted from the genetic evaluation file of the entire flock, were used in interval mapping. Ovine chromosomes 2, 12, 18, 20 and 24 were identified to harbour putative QTL for different measures of milk production. The QTL on Ovis aries chromosomes (OAR) 2 and 20 mapped to locations where similar trait QTL have already been mapped in other studies, whereas QTL on OAR 12, 18 and 24 were unique to our backcross pedigree and have not been reported previously. In addition, all identified QTL regions were syntenic with bovine chromosomal segments revealed to harbour QTL affecting milk production traits, providing supporting evidence for the QTL identified here. © 2010 The Authors, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.

  16. Attack behaviors in mice: from factorial structure to quantitative trait loci mapping.

    Science.gov (United States)

    Roubertoux, Pierre L; Guillot, Pascale-Valérie; Mortaud, Stéphane; Pratte, Michel; Jamon, Marc; Cohen-Salmon, Charles; Tordjman, Sylvie

    2005-12-05

    The emergence or non-emergence of attack behavior results from interaction between the genotype and the conditions under which the mice are tested. Inbred mice of the same strain reared or housed under conditions do not react the same way; reactions also vary according to the place selected for testing and the different opponents. A factor analysis showed that the attack behavior in non-isolated males, tested in neutral area covaried with high testosterone and steroid sulfatase and low brain 5-hydroxytriptamine (5-HT), beta-endorphin and Adrenocorticotropic Hormone (ACTH) concentration, whereas, for isolated males tested in their own housing cage, it covaried with high testosterone activity and low brain 5-HT concentration. A wide genome scan was performed with two independent populations derived from C57BL/6J and NZB/BlNJ, each being reared, housed and tested under highly contrasting conditions, as described above, and confronted with A/J standard males. Common Quantitative Trait Loci emerged for two rearing/testing conditions. For rattling latency we detected Quantitative Trait Loci on Mus musculus chromosome 8 (MMU8) (at 44, LOD score=3.51 and 47 cM, LOD score=6.22, for the first and the second conditions) and on MMU12 (at 39 cM, LOD score=3.69 and at 41 cM, LOD score=2.99, respectively). For the number of attacks, Quantitative Trait Loci were common: on MMU11 at 39 cM LOD score=4.51 and 45 cM, LOD score=3.05, respectively, and on MMU12 (17 cM, LOD score=2.71 and 24 cM, LOD score=3.10). The steroid sulfatase gene (Sts), located on the X-Y pairing region, was linked, but only in non-isolated males, tested in neutral area for rattling latency, first attack latency, and number of attacks (LOD scores=4.9, 4.79 and 3.57, respectively). We found also that the Quantitative Trait Locus encompassing Sts region interacted with other Quantitative Trait Loci. These results indicate that attack behavior measured in different rearing and testing conditions have different

  17. Combining Ability And Heterosis For Some Quantitative Traits In Experimental Maize Hybrids

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    Abul Kalam Azad Mohammad

    2014-12-01

    Full Text Available In rabi season 2012, six diversed maize inbred lines were crossed in all possible combinations without reciprocals by using a half diallel mating design to obtain 15 single cross. Inbred parents and their F1 single crosses with a check were evaluated in rabi season 2013 to evaluate the role of general and specific combining ability and heterosis for some quantitative traits. Significant general combining ability variances was observed only for cob height and specific combining ability variances were observed for plant height, cob height, cob length, cob girth, number of kernels per cob, cob weight and hundred grain weight. The GCA/SCA ratio was less than unity for all studied traits except shelling percentage; this means that these traits are pre-dominantly controlled by non-additive gene action. Based on GCA estimates, it could be concluded that the best combiners were ML01, ML05 and ML29 inbred lines for most of the studied traits. This result indicated that these inbred lines could be considered as good combiners for improving these traits. Significant positive SCA effects were found for all studied traits except number of kernels per row and shelling percentage. Based on SCA effects, it could be concluded that the crosses ML01×ML02, ML02×ML05, ML02×ML29 and ML05×ML15 could be exploited by the maize breeders to increase maize yield. Three F1 hybrids such as ML02×ML15, ML02×ML29 and ML05×ML15 proved to be the outstanding hybrids to immediate further steps for commercial cultivation. In a conclusive decision the F1 hybrid, ML02×ML29 was the best combination as evaluated through combining ability and standard heterosis.

  18. Quantitative Trait Loci for Mercury Accumulation in Maize (Zea mays L.) Identified Using a RIL Population: e107243

    National Research Council Canada - National Science Library

    Zhongjun Fu; Weihua Li; Qinbin Zhang; Long Wang; Xiaoxiang Zhang; Guiliang Song; Zhiyuan Fu; Dong Ding; Zonghua Liu; Jihua Tang

    2014-01-01

      To investigate the genetic mechanism of mercury accumulation in maize (Zea mays L.), a population of 194 recombinant inbred lines derived from an elite hybrid Yuyu 22, was used to identify quantitative trait loci...

  19. The power to detect genetic linkage for quantitative traits in the Utah CEPH pedigrees.

    Science.gov (United States)

    Malhotra, Alka; Cromer, Kevin; Leppert, Mark F; Hasstedt, Sandra J

    2005-01-01

    Quantitative trait phenotypes and linked marker genotypes were simulated for a range of models with different sets of assumptions based on displacement, prevalence, and heritability of the trait in 30 Utah Centre d'Etude du Polymorphisme Humain (CEPH) families. The gain in power by the addition of 15 families was also estimated by extrapolation. Power was evaluated using both parametric single locus (PSL) models and variance components (VC) methods for two situations: (1) a single marker with 75% heterozygosity and a recombination fraction of 0.05, and (2) a fully informative marker as an approximation to multipoint analysis. When the simulation and analysis models were both dominant with the same prevalence, power > or =80% for lod >3 was estimated when quantitative trait locus variance was > or =40% with a displacement of 2.5 or 3. Power was 5-15% lower for recessive models compared to dominant models. With the addition of 15 families, an average increase in power of 17% and 22% was estimated for the dominant and recessive models, respectively. In PSL analyses, power was estimated at < or =20% when the dominance was misspecified. This investigation delineates parameter conditions under which this unique sample affords adequate power to detect linkage using both PSL and VC methods.

  20. Large-scale in silico mapping of complex quantitative traits in inbred mice.

    Directory of Open Access Journals (Sweden)

    Pengyuan Liu

    2007-07-01

    Full Text Available Understanding the genetic basis of common disease and disease-related quantitative traits will aid in the development of diagnostics and therapeutics. The processs of gene discovery can be sped up by rapid and effective integration of well-defined mouse genome and phenome data resources. We describe here an in silico gene-discovery strategy through genome-wide association (GWA scans in inbred mice with a wide range of genetic variation. We identified 937 quantitative trait loci (QTLs from a survey of 173 mouse phenotypes, which include models of human disease (atherosclerosis, cardiovascular disease, cancer and obesity as well as behavioral, hematological, immunological, metabolic, and neurological traits. 67% of QTLs were refined into genomic regions <0.5 Mb with approximately 40-fold increase in mapping precision as compared with classical linkage analysis. This makes for more efficient identification of the genes that underlie disease. We have identified two QTL genes, Adam12 and Cdh2, as causal genetic variants for atherogenic diet-induced obesity. Our findings demonstrate that GWA analysis in mice has the potential to resolve multiple tightly linked QTLs and achieve single-gene resolution. These high-resolution QTL data can serve as a primary resource for positional cloning and gene identification in the research community.

  1. Familial aggregation of quantitative autistic traits in multiplex versus simplex autism.

    Science.gov (United States)

    Virkud, Yamini V; Todd, Richard D; Abbacchi, Anna M; Zhang, Yi; Constantino, John N

    2009-04-05

    Recent research has suggested that the mode of inheritance for simplex autism (SA, one individual in the family affected) may be distinct from that for multiplex autism (MA, two or more individuals affected). Since sub clinical autistic traits have been observed in "unaffected" relatives of children with autism, we explored whether the distributions of such traits in families supported differential modes of genetic transmission for SA and MA autism. We measured patterns of familial aggregation of quantitative autistic traits (QAT) in children and parents in 80 SA families and 210 MA families, using the Social Responsiveness Scale. When considering all SA and MA siblings who scored below a uniform quantitative (clinical-level) severity threshold, MA brothers exhibited a distinct pathological shift in the distribution, compared to SA brothers (P families. Significant spousal correlations for QAT-suggestive of assortative mating-were observed in both SA and MA families, but neither group was characterized by a greater-than-chance level of concordant elevation among spousal pairs in this volunteer sample. Among male first degree relatives, there exist distinct patterns of QAT manifestation for simplex versus multiplex autism. These findings are consistent with the results of molecular genetic studies that have suggested differential modes of intergenerational transmission for SA and MA. Characterization of QAT and other endophenotypes among close relatives may be useful for reducing sample heterogeneity in future genetic and neurobiologic studies of autism. (c) 2008 Wiley-Liss, Inc.

  2. Comparative mapping of quantitative trait loci associated with waterlogging tolerance in barley (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    Zhou Meixue

    2008-08-01

    Full Text Available Abstract Background Resistance to soil waterlogging stress is an important plant breeding objective in high rainfall or poorly drained areas across many countries in the world. The present study was conducted to identify quantitative trait loci (QTLs associated with waterlogging tolerance (e.g. leaf chlorosis, plant survival and biomass reduction in barley and compare the QTLs identified across two seasons and in two different populations using a composite map constructed with SSRs, RFLP and Diversity Array Technology (DArT markers. Results Twenty QTLs for waterlogging tolerance related traits were found in the two barley double haploid (DH populations. Several of these QTLs were validated through replication of experiments across seasons or by co-location across populations. Some of these QTLs affected multiple waterlogging tolerance related traits, for example, QTL Qwt4-1 contributed not only to reducing barley leaf chlorosis, but also increasing plant biomass under waterlogging stress, whereas other QTLs controlled both leaf chlorosis and plant survival. Conclusion Improving waterlogging tolerance in barley is still at an early stage compared with other traits. QTLs identified in this study have made it possible to use marker assisted selection (MAS in combination with traditional field selection to significantly enhance barley breeding for waterlogging tolerance. There may be some degree of homoeologous relationship between QTLs controlling barley waterlogging tolerance and that in other crops as discussed in this study.

  3. Smoothing of the bivariate LOD score for non-normal quantitative traits.

    Science.gov (United States)

    Buil, Alfonso; Dyer, Thomas D; Almasy, Laura; Blangero, John

    2005-12-30

    Variance component analysis provides an efficient method for performing linkage analysis for quantitative traits. However, type I error of variance components-based likelihood ratio testing may be affected when phenotypic data are non-normally distributed (especially with high values of kurtosis). This results in inflated LOD scores when the normality assumption does not hold. Even though different solutions have been proposed to deal with this problem with univariate phenotypes, little work has been done in the multivariate case. We present an empirical approach to adjust the inflated LOD scores obtained from a bivariate phenotype that violates the assumption of normality. Using the Collaborative Study on the Genetics of Alcoholism data available for the Genetic Analysis Workshop 14, we show how bivariate linkage analysis with leptokurtotic traits gives an inflated type I error. We perform a novel correction that achieves acceptable levels of type I error.

  4. PROC QTL—A SAS Procedure for Mapping Quantitative Trait Loci

    Science.gov (United States)

    Hu, Zhiqiu; Xu, Shizhong

    2009-01-01

    Statistical analysis system (SAS) is the most comprehensive statistical analysis software package in the world. It offers data analysis for almost all experiments under various statistical models. Each analysis is performed using a particular subroutine, called a procedure (PROC). For example, PROC ANOVA performs analysis of variances. PROC QTL is a user-defined SAS procedure for mapping quantitative trait loci (QTL). It allows users to perform QTL mapping for continuous and discrete traits within the SAS platform. Users of PROC QTL are able to take advantage of all existing features offered by the general SAS software, for example, data management and graphical treatment. The current version of PROC QTL can perform QTL mapping for all line crossing experiments using maximum likelihood (ML), least square (LS), iteratively reweighted least square (IRLS), Fisher scoring (FISHER), Bayesian (BAYES), and empirical Bayes (EBAYES) methods. PMID:20037656

  5. Quantitative trait loci define genes and pathways underlying genetic variation in longevity.

    Science.gov (United States)

    Shmookler Reis, Robert J; Kang, Ping; Ayyadevara, Srinivas

    2006-10-01

    Quantitative trait locus (QTL) mapping provides a means to discover and roughly position regions of the genome that harbor genes responsible for natural variation in a complex trait. QTL mapping has been utilized extensively in the pursuit of genes contributing to longevity, chiefly in two animal models, the nematode Caenorhabditis elegans and the dipteran insect Drosophila melanogaster. Research on both species has demonstrated that a relatively small set of loci accounts for most of their genetic variance in lifespan. QTL mapping complements the discovery of longevity genes by mutagenesis screens, because the two procedures are predicted to unveil overlapping but distinct types of genes. We argue that information gained from animal models, even invertebrates, can greatly facilitate the process of gene identification and testing of homologous genes in humans.

  6. Influence of a quantitative trait locus on mouse chromosome 19 to the light-adapted electroretinogram.

    Science.gov (United States)

    Reynolds, Alison L; Danciger, Michael; Farrar, G Jane; Humphries, Peter; Kenna, Paul F

    2008-09-01

    Both implicit time and amplitude of the cone-mediated electroretinographic (ERG) b-wave differ significantly between the C57BL/6JOlaHsd and 129S2/SvHsd inbred mouse strains. The purpose of this work was to undertake a quantitative genetics study to localize the gene or genes involved. Implicit time and amplitude of the a- and b-waves of the single-flash and flicker cone-mediated ERG were recorded as the quantitative traits in reciprocal backcrossed populations. A genome-wide scan was performed with 106 polymorphic markers. Map Manager (release QTXb20) was used to analyze the data and make phenotype-genotype correlations. A quantitative trait locus (QTL) of major effect in controlling variation in both implicit time and amplitude of the cone-mediated ERG localized to the middle of chromosome 19. Mapping of a QTL influencing both implicit time and b-wave amplitude of the light-adapted ERG represents an initial step toward identifying the gene(s) responsible for this phenotypic variation.

  7. Natural selection on quantitative immune defence traits: a comparison between theory and data.

    Science.gov (United States)

    Seppälä, O

    2015-01-01

    Parasites present a threat for free-living species and affect several ecological and evolutionary processes. Immune defence is the main physiological barrier against infections, and understanding its evolution is central for predicting disease dynamics. I review theoretical predictions and empirical data on natural selection on quantitative immune defence traits in the wild. Evolutionary theory predicts immune traits to be under stabilizing selection owing to trade-offs between immune function and life-history traits. Empirical data, however, support mainly positive directional selection, but also show variation in the form of selection among study systems, immune traits and fitness components. I argue that the differences between theory and empirical data may at least partly arise from methodological difficulties in testing stabilizing selection as well as measuring fitness. I also argue that the commonness of positive directional selection and the variation in selection may be caused by several biological factors. First, selection on immune function may show spatial and temporal variation as epidemics are often local/seasonal. Second, factors affecting the range of phenotypic variation in immune traits could alter potential for selection. Third, different parasites may impose different selective pressures depending on their characteristics. Fourth, condition dependence of immune defence can obscure trade-offs related to it, thus possibly modifying observed selection gradients. Fifth, nonimmunological defences could affect the form of selection by reducing the benefits of strong immune function. To comprehensively understand the evolution of immune defence, the role of above factors should be considered in future studies. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  8. Identification of Quantitative Trait Loci for Resistance to RSIVD in Red Sea Bream (Pagrus major).

    Science.gov (United States)

    Sawayama, Eitaro; Tanizawa, Shiho; Kitamura, Shin-Ichi; Nakayama, Kei; Ohta, Kohei; Ozaki, Akiyuki; Takagi, Motohiro

    2017-12-01

    Red sea bream iridoviral disease (RSIVD) is a major viral disease in red sea bream farming in Japan. Previously, we identified one candidate male individual of red sea bream that was significantly associated with convalescent individuals after RSIVD. The purpose of this study is to identify the quantitative trait loci (QTL) linked to the RSIVD-resistant trait for future marker-assisted selection (MAS). Two test families were developed using the candidate male in 2014 (Fam-2014) and 2015 (Fam-2015). These test families were challenged with RSIV, and phenotypes were evaluated. Then, de novo genome sequences of red sea bream were obtained through next-generation sequencing, and microsatellite markers were searched and selected for linkage map construction. One immune-related gene, MHC class IIβ, was also used for linkage map construction. Of the microsatellite markers searched, 148 and 197 were mapped on 23 and 27 linkage groups in the female and male linkage maps, respectively, covering approximately 65% of genomes in both sexes. One QTL linked to an RSIVD-resistant trait was found in linkage group 2 of the candidate male in Fam-2014, and the phenotypic variance of the QTL was 31.1%. The QTL was closely linked to MHC class IIβ. Moreover, the QTL observed in Fam-2014 was also significantly linked to an RSIVD-resistant trait in the candidate male of Fam-2015. Our results suggest that the RSIVD-resistant trait in the candidate male was controlled by one major QTL closely linked to the MHC class IIβ gene and could be useful for MAS of red sea bream.

  9. [The study of tomato fruit weight quantitative trait locus and its application in genetics teaching].

    Science.gov (United States)

    Wang, Hai-yan

    2015-08-01

    The classical research cases, which have greatly promoted the development of genetics in history, can be combined with the content of courses in genetics teaching to train students' ability of scientific thinking and genetic analysis. The localization and clone of gene controlling tomato fruit weight is a pioneer work in quantitative trait locus (QTL) studies and represents a complete process of QTL research in plants. Application of this integrated case in genetics teaching, which showed a wonderful process of scientific discovery and the fascination of genetic research, has inspired students' interest in genetics and achieved a good teaching effect.

  10. Design database for quantitative trait loci (QTL) data warehouse, data mining, and meta-analysis.

    Science.gov (United States)

    Hu, Zhi-Liang; Reecy, James M; Wu, Xiao-Lin

    2012-01-01

    A database can be used to warehouse quantitative trait loci (QTL) data from multiple sources for comparison, genomic data mining, and meta-analysis. A robust database design involves sound data structure logistics, meaningful data transformations, normalization, and proper user interface designs. This chapter starts with a brief review of relational database basics and concentrates on issues associated with curation of QTL data into a relational database, with emphasis on the principles of data normalization and structure optimization. In addition, some simple examples of QTL data mining and meta-analysis are included. These examples are provided to help readers better understand the potential and importance of sound database design.

  11. Fine mapping of quantitative trait loci for mastitis resistance on bovine chromosome 11

    DEFF Research Database (Denmark)

    Schulman, N F; Sahana, G; Iso-Touru, T

    2009-01-01

    Quantitative trait loci (QTL) affecting clinical mastitis (CM) and somatic cell score (SCS) were mapped on bovine chromosome 11. The mapping population consisted of 14 grandsire families belonging to three Nordic red cattle breeds: Finnish Ayrshire (FA), Swedish Red and White (SRB) and Danish Red....... The families had previously been shown to segregate for udder health QTL. A total of 524 progeny tested bulls were included in the analysis. A linkage map including 33 microsatellite and five SNP markers was constructed. We performed combined linkage disequilibrium and linkage analysis (LDLA) using the whole...

  12. Expression quantitative trait loci reveals genes and pathways associated with boar taint in pigs

    DEFF Research Database (Denmark)

    Drag, Markus; Hansen, Mathias Brygger; Kadarmideen, Haja

    Boar taint (BT) is an offensive odour or taste of meat from a proportion of non-castrated male pigs due to skatole and androstenone accumulation in adipose tissue. Castration is an effective strategy to avoid BT but is currently under debate due to animal welfare concerns. This study aimed...... to functionally characterise and evaluate important expression quantitative trait loci (eQTL) to identify potential causal mechanisms of BT for use in optimised breeding for reduced BT without castration. Danish Landrace male pigs (n=48) with low, medium and high genetic merit of BT were slaughtered at 100 kg...

  13. Identification of quantitative trait loci for yield and yield related traits in groundnut (Arachis hypogaea L.) under different water regimes in Niger and Senegal.

    Science.gov (United States)

    Faye, Issa; Pandey, Manish K; Hamidou, Falalou; Rathore, Abhishek; Ndoye, Ousmane; Vadez, Vincent; Varshney, Rajeev K

    Yield under drought stress is a highly complex trait with large influence to even a minor fluctuation in the environmental conditions. Genomics-assisted breeding holds great promise for improving such complex traits more efficiently in less time, but requires markers associated with the trait of interest. In this context, a recombinant inbred line mapping population (TAG 24 × ICGV 86031) was used to identify markers associated with quantitative trait loci (QTLs) for yield and yield related traits at two important locations of West Africa under well watered and water stress conditions. Among the traits analyzed under WS condition, the harvest index (HI) and the haulm yield (HYLD) were positively correlated with the pod yield (PYLD) and showed intermediate broad sense heritability. QTL analysis using phenotyping and genotyping data resulted in identification of 52 QTLs. These QTLs had low phenotypic variance (meter reading, percentage of sound mature kernels, 100 kernel weight, shelling percentage, HI, HYLD and PYLD. Interestingly, few QTLs identified in this study were also overlapped with previously reported QTLs detected for drought tolerance related traits identified earlier in Indian environmental conditions using the same mapping population. Accumulating these many small-effect QTLs into a single genetic background is nearly impossible through marker-assisted backcrossing and even marker-assisted recurrent selection. Under such circumstances, the deployment of genomic selection is the most appropriate approach for improving such complex traits with more precision and in less time.

  14. Genetic dissection of milk yield traits and mastitis resistance quantitative trait loci on chromosome 20 in dairy cattle.

    Science.gov (United States)

    Kadri, Naveen K; Guldbrandtsen, Bernt; Lund, Mogens S; Sahana, Goutam

    2015-12-01

    Intense selection to increase milk yield has had negative consequences for mastitis incidence in dairy cattle. Due to low heritability of mastitis resistance and an unfavorable genetic correlation with milk yield, a reduction in mastitis through traditional breeding has been difficult to achieve. Here, we examined quantitative trait loci (QTL) that segregate for clinical mastitis and milk yield on Bos taurus autosome 20 (BTA20) to determine whether both traits are affected by a single polymorphism (pleiotropy) or by multiple closely linked polymorphisms. In the latter but not the former situation, undesirable genetic correlation could potentially be broken by selecting animals that have favorable variants for both traits. First, we performed a within-breed association study using a haplotype-based method in Danish Holstein cattle (HOL). Next, we analyzed Nordic Red dairy cattle (RDC) and Danish Jersey cattle (JER) with the goal of determining whether these QTL identified in Holsteins were segregating across breeds. Genotypes for 12,566 animals (5,966 HOL, 5,458 RDC, and 1,142 JER) were determined by using the Illumina Bovine SNP50 BeadChip (50K; Illumina, San Diego, CA), which identifies 1,568 single nucleotide polymorphisms on BTA20. Data were combined, phased, and clustered into haplotype states, followed by within- and across-breed haplotype-based association analyses using a linear mixed model. Association signals for both clinical mastitis and milk yield peaked in the 26- to 40-Mb region on BTA20 in HOL. Single-variant association analyses were carried out in the QTL region using whole sequence level variants imputed from references of 2,036 HD genotypes (BovineHD BeadChip; Illumina) and 242 whole-genome sequences. The milk QTL were also segregating in RDC and JER on the BTA20-targeted region; however, an indication of differences in the causal factor(s) was observed across breeds. A previously reported F279Y mutation (rs385640152) within the growth hormone

  15. Whole-genome mapping of agronomic and metabolic traits to identify novel quantitative trait Loci in bread wheat grown in a water-limited environment.

    Science.gov (United States)

    Hill, Camilla B; Taylor, Julian D; Edwards, James; Mather, Diane; Bacic, Antony; Langridge, Peter; Roessner, Ute

    2013-07-01

    Drought is a major environmental constraint responsible for grain yield losses of bread wheat (Triticum aestivum) in many parts of the world. Progress in breeding to improve complex multigene traits, such as drought stress tolerance, has been limited by high sensitivity to environmental factors, low trait heritability, and the complexity and size of the hexaploid wheat genome. In order to obtain further insight into genetic factors that affect yield under drought, we measured the abundance of 205 metabolites in flag leaf tissue sampled from plants of 179 cv Excalibur/Kukri F1-derived doubled haploid lines of wheat grown in a field experiment that experienced terminal drought stress. Additionally, data on 29 agronomic traits that had been assessed in the same field experiment were used. A linear mixed model was used to partition and account for nongenetic and genetic sources of variation, and quantitative trait locus analysis was used to estimate the genomic positions and effects of individual quantitative trait loci. Comparison of the agronomic and metabolic trait variation uncovered novel correlations between some agronomic traits and the levels of certain primary metabolites, including metabolites with either positive or negative associations with plant maturity-related or grain yield-related traits. Our analyses demonstrate that specific regions of the wheat genome that affect agronomic traits also have distinct effects on specific combinations of metabolites. This approach proved valuable for identifying novel biomarkers for the performance of wheat under drought and could facilitate the identification of candidate genes involved in drought-related responses in bread wheat.

  16. A quantitative review of pollination syndromes: do floral traits predict effective pollinators?

    Science.gov (United States)

    Rosas-Guerrero, Víctor; Aguilar, Ramiro; Martén-Rodríguez, Silvana; Ashworth, Lorena; Lopezaraiza-Mikel, Martha; Bastida, Jesús M; Quesada, Mauricio

    2014-03-01

    The idea of pollination syndromes has been largely discussed but no formal quantitative evaluation has yet been conducted across angiosperms. We present the first systematic review of pollination syndromes that quantitatively tests whether the most effective pollinators for a species can be inferred from suites of floral traits for 417 plant species. Our results support the syndrome concept, indicating that convergent floral evolution is driven by adaptation to the most effective pollinator group. The predictability of pollination syndromes is greater in pollinator-dependent species and in plants from tropical regions. Many plant species also have secondary pollinators that generally correspond to the ancestral pollinators documented in evolutionary studies. We discuss the utility and limitations of pollination syndromes and the role of secondary pollinators to understand floral ecology and evolution. © 2014 John Wiley & Sons Ltd/CNRS.

  17. Identification of quantitative trait loci associated with boiled seed hardness in soybean

    Science.gov (United States)

    Hirata, Kaori; Masuda, Ryoichi; Tsubokura, Yasutaka; Yasui, Takeshi; Yamada, Tetsuya; Takahashi, Koji; Nagaya, Taiko; Sayama, Takashi; Ishimoto, Masao; Hajika, Makita

    2014-01-01

    Boiled seed hardness is an important factor in the processing of soybean food products such as nimame and natto. Little information is available on the genetic basis for boiled seed hardness, despite the wide variation in this trait. DNA markers linked to the gene controlling this trait should be useful in soybean breeding programs because of the difficulty of its evaluation. In this report, quantitative trait locus (QTL) analysis was performed to reveal the genetic factors associated with boiled seed hardness using a recombinant inbred line population developed from a cross between two Japanese cultivars, ‘Natto-shoryu’ and ‘Hyoukei-kuro 3’, which differ largely in boiled seed hardness, which in ‘Natto-shoryu’ is about twice that of ‘Hyoukei-kuro 3’. Two significantly stable QTLs, qHbs3-1 and qHbs6-1, were identified on chromosomes 3 and 6, for which the ‘Hyoukei-kuro 3’ alleles contribute to decrease boiled seed hardness for both QTLs. qHbs3-1 also showed significant effects in progeny of a residual heterozygous line and in a different segregating population. Given its substantial effect on boiled seed hardness, SSR markers closely linked to qHbs3-1, such as BARCSOYSSR_03_0165 and BARCSOYSSR_03_0185, could be useful for marker-assisted selection in soybean breeding. PMID:25914591

  18. Effect of genetic architecture on the prediction accuracy of quantitative traits in samples of unrelated individuals.

    Science.gov (United States)

    Morgante, Fabio; Huang, Wen; Maltecca, Christian; Mackay, Trudy F C

    2018-02-10

    Predicting complex phenotypes from genomic data is a fundamental aim of animal and plant breeding, where we wish to predict genetic merits of selection candidates; and of human genetics, where we wish to predict disease risk. While genomic prediction models work well with populations of related individuals and high linkage disequilibrium (LD) (e.g., livestock), comparable models perform poorly for populations of unrelated individuals and low LD (e.g., humans). We hypothesized that low prediction accuracies in the latter situation may occur when the genetics architecture of the trait departs from the infinitesimal and additive architecture assumed by most prediction models. We used simulated data for 10,000 lines based on sequence data from a population of unrelated, inbred Drosophila melanogaster lines to evaluate this hypothesis. We show that, even in very simplified scenarios meant as a stress test of the commonly used Genomic Best Linear Unbiased Predictor (G-BLUP) method, using all common variants yields low prediction accuracy regardless of the trait genetic architecture. However, prediction accuracy increases when predictions are informed by the genetic architecture inferred from mapping the top variants affecting main effects and interactions in the training data, provided there is sufficient power for mapping. When the true genetic architecture is largely or partially due to epistatic interactions, the additive model may not perform well, while models that account explicitly for interactions generally increase prediction accuracy. Our results indicate that accounting for genetic architecture can improve prediction accuracy for quantitative traits.

  19. Quantitative trait loci associated with chemical composition of the chicken carcass.

    Science.gov (United States)

    Nones, K; Ledur, M C; Zanella, E L; Klein, C; Pinto, L F B; Moura, A S A M T; Ruy, D C; Baron, E E; Ambo, M; Campos, R L R; Boschiero, C; Burt, D W; Coutinho, L L

    2012-10-01

    Major objectives of the poultry industry are to increase meat production and to reduce carcass fatness, mainly abdominal fat. Information on growth performance and carcass composition are important for the selection of leaner meat chickens. To enhance our understanding of the genetic architecture underlying the chemical composition of chicken carcasses, an F(2) population developed from a broiler × layer cross was used to map quantitative trait loci (QTL) affecting protein, fat, water and ash contents in chicken carcasses. Two genetic models were applied in the QTL analysis: the line-cross and the half-sib models, both using the regression interval mapping method. Six significant and five suggestive QTL were mapped in the line-cross analysis, and four significant and six suggestive QTL were mapped in the half-sib analysis. A total of eleven QTL were mapped for fat (ether extract), five for protein, four for ash and one for water contents in the carcass using both analyses. No study to date has reported QTL for carcass chemical composition in chickens. Some QTL mapped here for carcass fat content match, as expected, QTL regions previously associated with abdominal fat in the same or in different populations, and novel QTL for protein, ash and water contents in the carcass are presented here. The results described here also reinforce the need for fine mapping and to perform multi-trait analyses to better understand the genetic architecture of these traits. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

  20. Quantitative trait loci × environment interactions for plant morphology vary over ontogeny in Brassica rapa.

    Science.gov (United States)

    Dechaine, Jennifer M; Brock, Marcus T; Iniguez-Luy, Federico L; Weinig, Cynthia

    2014-01-01

    Growth in plants occurs via the addition of repeating modules, suggesting that the genetic architecture of similar subunits may vary between earlier- and later-developing modules. These complex environment × ontogeny interactions are not well elucidated, as studies examining quantitative trait loci (QTLs) expression over ontogeny have not included multiple environments. Here, we characterized the genetic architecture of vegetative traits and onset of reproduction over ontogeny in recombinant inbred lines of Brassica rapa in the field and glasshouse. The magnitude of genetic variation in plasticity of seedling internodes was greater than in those produced later in ontogeny. We correspondingly detected that QTLs for seedling internode length were environment-specific, whereas later in ontogeny the majority of QTLs affected internode lengths in all treatments. The relationship between internode traits and onset of reproduction varied with environment and ontogenetic stage. This relationship was observed only in the glasshouse environment and was largely attributable to one environment-specific QTL. Our results provide the first evidence of a QTL × environment × ontogeny interaction, and provide QTL resolution for differences between early- and later-stage plasticity for stem elongation. These results also suggest potential constraints on morphological evolution in early vs later modules as a result of associations with reproductive timing. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  1. Little effect of HSP90 inhibition on the quantitative wing traits variation in Drosophila melanogaster.

    Science.gov (United States)

    Takahashi, Kazuo H

    2017-02-01

    Drosophila wings have been a model system to study the effect of HSP90 on quantitative trait variation. The effect of HSP90 inhibition on environmental buffering of wing morphology varies among studies while the genetic buffering effect of it was examined in only one study and was not detected. Variable results so far might show that the genetic background influences the environmental and genetic buffering effect of HSP90. In the previous studies, the number of the genetic backgrounds used is limited. To examine the effect of HSP90 inhibition with a larger number of genetic backgrounds than the previous studies, 20 wild-type strains of Drosophila melanogaster were used in this study. Here I investigated the effect of HSP90 inhibition on the environmental buffering of wing shape and size by assessing within-individual and among-individual variations, and as a result, I found little or very weak effects on environmental and genetic buffering. The current results suggest that the role of HSP90 as a global regulator of environmental and genetic buffering is limited at least in quantitative traits.

  2. Quantitative Trait Locus Mapping of Melanization in the Plant Pathogenic Fungus Zymoseptoria tritici

    Science.gov (United States)

    Lendenmann, Mark H.; Croll, Daniel; Stewart, Ethan L.; McDonald, Bruce A.

    2014-01-01

    Melanin plays an important role in virulence and antimicrobial resistance in several fungal pathogens. The wheat pathogen Zymoseptoria tritici is important worldwide, but little is known about the genetic architecture of pathogenicity, including the production of melanin. Because melanin production can exhibit complex inheritance, we used quantitative trait locus (QTL) mapping in two crosses to identify the underlying genes. Restriction site−associated DNA sequencing was used to genotype 263 (cross 1) and 261 (cross 2) progeny at ~8500 single-nucleotide polymorphisms and construct two dense linkage maps. We measured gray values, representing degrees of melanization, for single-spore colonies growing on Petri dishes by using a novel image-processing approach that enabled high-throughput phenotyping. Because melanin production can be affected by stress, each offspring was grown in two stressful environments and one control environment. We detected six significant QTL in cross 1 and nine in cross 2, with three QTL shared between the crosses. Different QTL were identified in different environments and at different colony ages. By obtaining complete genome sequences for the four parents and analyzing sequence variation in the QTL confidence intervals, we identified 16 candidate genes likely to affect melanization. One of these candidates was PKS1, a polyketide synthase gene known to play a role in the synthesis of dihydroxynaphthalene melanin. Three candidate quantitative trait nucleotides were identified in PKS1. Many of the other candidate genes were not previously associated with melanization. PMID:25360032

  3. Chromosomes 18 and X are quantitative trait loci for nephrotic-range proteinuria in rats.

    Science.gov (United States)

    Schachter, Asher D; Ichimura, Takaharu; Kohane, Isaac S

    2005-12-01

    Numerous cellular and molecular perturbations have been studied to elucidate the pathogenic mechanisms underlying nephrotic-range proteinuria, which may in turn shed light on disease-specific mechanisms. We have analyzed the publicly available data from the PhysGen partial panel of consomic rats to determine whether there are quantitative trait loci that associate with nephrotic-range proteinuria. As of this writing, consomic rat strains subjected to the renal protocol have been bred by the Program for Genomic Applications for 15 of the 22 rat chromosomes for both genders, predominantly with the Brown-Norway (BN) and Dahl salt-sensitive (SS) strains as parents. We defined chromosomes of interest as consomic SS-xBN strains whose phenotype measurements differed significantly from SS but not BN strains, stratified by gender. We filtered and clustered differentially expressed genes by function in renal tissue from relevant strains. Proteinuria was significantly higher in male SS vs. male SS-18BN, and it was significantly higher in male SS vs. female SS. Functional clustering of differentially expressed genes yielded two specific functional clusters: apoptosis (p=0.022) and angiogenesis (p=0.046). Gene expression profiles demonstrated differential expression of apoptotic and angiogenic genes. However, TUNEL stains of renal tissue showed no significant difference in the number of apoptotic nuclei. We conclude that chromosomes 18 and X are quantitative trait loci for nephrotic-range proteinuria in rats.

  4. Quantitative trait analysis of yeast biodiversity yields novel gene tools for metabolic engineering.

    Science.gov (United States)

    Hubmann, Georg; Foulquié-Moreno, Maria R; Nevoigt, Elke; Duitama, Jorge; Meurens, Nicolas; Pais, Thiago M; Mathé, Lotte; Saerens, Sofie; Nguyen, Huyen Thi Thanh; Swinnen, Steve; Verstrepen, Kevin J; Concilio, Luigi; de Troostembergh, Jean-Claude; Thevelein, Johan M

    2013-05-01

    Engineering of metabolic pathways by genetic modification has been restricted largely to enzyme-encoding structural genes. The product yield of such pathways is a quantitative genetic trait. Out of 52 Saccharomyces cerevisiae strains phenotyped in small-scale fermentations, we identified strain CBS6412 as having unusually low glycerol production and higher ethanol yield as compared to an industrial reference strain. We mapped the QTLs underlying this quantitative trait with pooled-segregant whole-genome sequencing using 20 superior segregants selected from a total of 257. Plots of SNP variant frequency against SNP chromosomal position revealed one major and one minor locus. Downscaling of the major locus and reciprocal hemizygosity analysis identified an allele of SSK1, ssk1(E330N…K356N), expressing a truncated and partially mistranslated protein, as causative gene. The diploid CBS6412 parent was homozygous for ssk1(E330N…K356N). This allele affected growth and volumetric productivity less than the gene deletion. Introduction of the ssk1(E330N…K356N) allele in the industrial reference strain resulted in stronger reduction of the glycerol/ethanol ratio compared to SSK1 deletion and also compromised volumetric productivity and osmotolerance less. Our results show that polygenic analysis of yeast biodiversity can provide superior novel gene tools for metabolic engineering. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. The genetic basis of adaptive population differentiation: A quantitative trait locus analysis of fitness traits in two wild barley populations from contrasting habitats

    NARCIS (Netherlands)

    Verhoeven, K.J.F.; Vanhala, T.K.; Biere, A.; Nevo, E.; Damme, van J.M.M.

    2004-01-01

    We used a quantitative trait locus (QTL) approach to study the genetic basis of population differentiation in wild barley, Hordeum spontaneum. Several ecotypes are recognized in this model species, and population genetic studies and reciprocal transplant experiments have indicated the role of local

  6. Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction.

    Science.gov (United States)

    Brøndum, R F; Su, G; Janss, L; Sahana, G; Guldbrandtsen, B; Boichard, D; Lund, M S

    2015-06-01

    This study investigated the effect on the reliability of genomic prediction when a small number of significant variants from single marker analysis based on whole genome sequence data were added to the regular 54k single nucleotide polymorphism (SNP) array data. The extra markers were selected with the aim of augmenting the custom low-density Illumina BovineLD SNP chip (San Diego, CA) used in the Nordic countries. The single-marker analysis was done breed-wise on all 16 index traits included in the breeding goals for Nordic Holstein, Danish Jersey, and Nordic Red cattle plus the total merit index itself. Depending on the trait's economic weight, 15, 10, or 5 quantitative trait loci (QTL) were selected per trait per breed and 3 to 5 markers were selected to tag each QTL. After removing duplicate markers (same marker selected for more than one trait or breed) and filtering for high pairwise linkage disequilibrium and assaying performance on the array, a total of 1,623 QTL markers were selected for inclusion on the custom chip. Genomic prediction analyses were performed for Nordic and French Holstein and Nordic Red animals using either a genomic BLUP or a Bayesian variable selection model. When using the genomic BLUP model including the QTL markers in the analysis, reliability was increased by up to 4 percentage points for production traits in Nordic Holstein animals, up to 3 percentage points for Nordic Reds, and up to 5 percentage points for French Holstein. Smaller gains of up to 1 percentage point was observed for mastitis, but only a 0.5 percentage point increase was seen for fertility. When using a Bayesian model accuracies were generally higher with only 54k data compared with the genomic BLUP approach, but increases in reliability were relatively smaller when QTL markers were included. Results from this study indicate that the reliability of genomic prediction can be increased by including markers significant in genome-wide association studies on whole genome

  7. Expected Genetic Gain for several Quantitative Traits in Alfalfa (Medicago sativa L.

    Directory of Open Access Journals (Sweden)

    Hassan MONIRIFAR

    2011-03-01

    Full Text Available In order to determine genetic gain for some quantitative traits in alfalfa ecotypes an experiment was conducted during cropping seasons of 2001-2007 at East Azarbaijan Agricultural and Natural Resources Research Center, Tabriz, Iran. Twenty nine native ecotypes collected from northwest of Iran and an improved variety were used in a polycross nursery. A randomized complete block design was used with 12 replications to ensure the random mating in the polycross nursery. The 30 half-sib families resulted from polycross nursery were planted individually in pots and 30 day old seedlings transplanted in the field and various traits were measured for three cropping seasons in a polycross test. The results of data analysis showed large variations among ecotypes for the traits studied. This indicates that successful selection for desired traits among their progenies is possible. Based on general combining ability, especially for fresh and dry yield, several ecotypes, including �Satellou�, �Gara-yonje�, �Almard�, �Legan�, �Baftan�, �Khaje�, �Sivan�, �Ilan jouj�, �Dizaj Safar Ali�, �Khosrovang� and �Garababa� were selected as promising parents for developing synthetic variety. The narrow�sense heritability values for fresh yield, dry matter, plant height, fresh leaf to stem and dry leaf to stem ratios were about 60%, 59%, 50%, 11% and 19%, respectively. Using selection intensity of 30%, an increase in fresh yield and dry matter yields were estimated to be 3.2 and 1.58 t/ha, respectively.

  8. Predicting complex quantitative traits with Bayesian neural networks: a case study with Jersey cows and wheat

    Directory of Open Access Journals (Sweden)

    Okut Hayrettin

    2011-10-01

    Full Text Available Abstract Background In the study of associations between genomic data and complex phenotypes there may be relationships that are not amenable to parametric statistical modeling. Such associations have been investigated mainly using single-marker and Bayesian linear regression models that differ in their distributions, but that assume additive inheritance while ignoring interactions and non-linearity. When interactions have been included in the model, their effects have entered linearly. There is a growing interest in non-parametric methods for predicting quantitative traits based on reproducing kernel Hilbert spaces regressions on markers and radial basis functions. Artificial neural networks (ANN provide an alternative, because these act as universal approximators of complex functions and can capture non-linear relationships between predictors and responses, with the interplay among variables learned adaptively. ANNs are interesting candidates for analysis of traits affected by cryptic forms of gene action. Results We investigated various Bayesian ANN architectures using for predicting phenotypes in two data sets consisting of milk production in Jersey cows and yield of inbred lines of wheat. For the Jerseys, predictor variables were derived from pedigree and molecular marker (35,798 single nucleotide polymorphisms, SNPS information on 297 individually cows. The wheat data represented 599 lines, each genotyped with 1,279 markers. The ability of predicting fat, milk and protein yield was low when using pedigrees, but it was better when SNPs were employed, irrespective of the ANN trained. Predictive ability was even better in wheat because the trait was a mean, as opposed to an individual phenotype in cows. Non-linear neural networks outperformed a linear model in predictive ability in both data sets, but more clearly in wheat. Conclusion Results suggest that neural networks may be useful for predicting complex traits using high

  9. Predicting complex quantitative traits with Bayesian neural networks: a case study with Jersey cows and wheat.

    Science.gov (United States)

    Gianola, Daniel; Okut, Hayrettin; Weigel, Kent A; Rosa, Guilherme Jm

    2011-10-07

    In the study of associations between genomic data and complex phenotypes there may be relationships that are not amenable to parametric statistical modeling. Such associations have been investigated mainly using single-marker and Bayesian linear regression models that differ in their distributions, but that assume additive inheritance while ignoring interactions and non-linearity. When interactions have been included in the model, their effects have entered linearly. There is a growing interest in non-parametric methods for predicting quantitative traits based on reproducing kernel Hilbert spaces regressions on markers and radial basis functions. Artificial neural networks (ANN) provide an alternative, because these act as universal approximators of complex functions and can capture non-linear relationships between predictors and responses, with the interplay among variables learned adaptively. ANNs are interesting candidates for analysis of traits affected by cryptic forms of gene action. We investigated various Bayesian ANN architectures using for predicting phenotypes in two data sets consisting of milk production in Jersey cows and yield of inbred lines of wheat. For the Jerseys, predictor variables were derived from pedigree and molecular marker (35,798 single nucleotide polymorphisms, SNPS) information on 297 individually cows. The wheat data represented 599 lines, each genotyped with 1,279 markers. The ability of predicting fat, milk and protein yield was low when using pedigrees, but it was better when SNPs were employed, irrespective of the ANN trained. Predictive ability was even better in wheat because the trait was a mean, as opposed to an individual phenotype in cows. Non-linear neural networks outperformed a linear model in predictive ability in both data sets, but more clearly in wheat. Results suggest that neural networks may be useful for predicting complex traits using high-dimensional genomic information, a situation where the number of unknowns

  10. Mapping Quantitative Trait Loci affecting biochemical and morphological fruit properties in eggplant (Solanum melongena L.

    Directory of Open Access Journals (Sweden)

    Laura eToppino

    2016-03-01

    Full Text Available Eggplant berries are a source of health-promoting metabolites including antioxidant and nutraceutical compounds, mainly anthocyanins and chlorogenic acid; however, they also contain some anti-nutritional compounds such as steroidal glycoalkaloids (SGA and saponins, which are responsible for the bitter taste of the flesh and with potential toxic effects on humans. Up to now, Quantitative Trait Loci (QTL for the metabolic content are far from being characterized in eggplant, thus hampering the application of breeding programs aimed at improving its fruit quality. Here we report on the identification of some QTL for the fruit metabolic content in an F2 intraspecific mapping population of 156 individuals, obtained by crossing the eggplant breeding lines ‘305E40’ x ‘67/3’. The same population was previously employed for the development of a RAD-tag based linkage map and the identification of QTL associated to morphological and physiological traits. The mapping population was biochemically characterized for both fruit basic qualitative data, like dry matter, °Brix, sugars and organic acids, as well as for health-related compounds such chlorogenic acid, (the main flesh monomeric phenol, the two peel anthocyanins (i.e. delphinidin-3-rutinoside (D3R and delphinidin-3-(p-coumaroylrutinoside-5-glucoside (nasunin and the two main steroidal glycoalkaloids, solasonine and solamargine. For most of the traits, one major QTL (PVE ≥ 10% was spotted and putative orthologies with other Solanaceae crops are discussed. The present results supply valuable information to eggplant breeders on the inheritance of key fruit quality traits, thus providing potential tools to assist future breeding programs.

  11. Molecular and quantitative trait variation within and among small fragmented populations of the endangered plant species Psilopeganum sinense.

    Science.gov (United States)

    Ye, Qigang; Tang, Feiyan; Wei, Na; Yao, Xiaohong

    2014-01-01

    Natural selection and genetic drift are important evolutionary forces in determining genetic and phenotypic differentiation in plant populations. The extent to which these two distinct evolutionary forces affect locally adaptive quantitative traits has been well studied in common plant and animal species. However, we know less about how quantitative traits respond to selection pressures and drift in endangered species that have small population sizes and fragmented distributions. To address this question, this study assessed the relative strengths of selection and genetic drift in shaping population differentiation of phenotypic traits in Psilopeganum sinense, a naturally rare and recently endangered plant species. Population differentiation at five quantitative traits (QST) obtained from a common garden experiment was compared with differentiation at putatively neutral microsatellite markers (FST) in seven populations of P. sinense. QST estimates were derived using a Bayesian hierarchical variance component method. Trait-specific QST values were equal to or lower than FST. Neutral genetic diversity was not correlated with quantitative genetic variation within the populations of P. sinense. Despite the prevalent empirical evidence for QST > FST, the results instead suggest a definitive role of stabilizing selection and drift leading to phenotypic differentiation among small populations. Three traits exhibited a significantly lower QST relative to FST, suggesting that populations of P. sinense might have experienced stabilizing selection for the same optimal phenotypes despite large geographical distances between populations and habitat fragmentation. For the other two traits, QST estimates were of the same magnitude as FST, indicating that divergence in these traits could have been achieved by genetic drift alone. The lack of correlation between molecular marker and quantitative genetic variation suggests that sophisticated considerations are required for the

  12. Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding

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    Yong-Bi Fu

    2017-07-01

    Full Text Available Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding.

  13. Identification of quantitative trait loci for growth and carcass composition in cattle.

    Science.gov (United States)

    Casas, E; Keele, J W; Shackelford, S D; Koohmaraie, M; Stone, R T

    2004-02-01

    A genomic screening to detect quantitative trait loci (QTL) affecting growth, carcass composition and meat quality traits was pursued. Two hundred nineteen microsatellite markers were genotyped on 176 of 620 (28%) progeny from a Brahman x Angus sire mated to mostly MARC III dams. Selective genotyping, based on retail product yield (%) and fat yield (%), was used to select individuals to be genotyped. Traits included in the study were birth weight (kg), hot carcass weight (kg), retail product yield, fat yield, marbling score (400 = slight00 and 500 = small00), USDA yield grade, and estimated kidney, heart and pelvic fat (%). The QTL were classified as significant when the expected number of false positives (ENFP) was less than 0.05 (F-statistic greater than 17.3), and suggestive when the ENFP was ENFP = 0.02) was detected for marbling score at centimorgan (cM) 54 on chromosome 2. Suggestive QTL were detected for fat yield at 50 cM, for retail product yield at 53 cM, and for USDA yield grade at 63 cM on chromosome 1, for marbling score at 56 cM, for retail product yield at 70 cM, and for estimated kidney, heart and pelvic fat at 79 cM on chromosome 3, for marbling score at 44 cM, for hot carcass weight at 49 cM, and for estimated kidney, heart and pelvic fat at 62 cM on chromosome 16, and for fat yield at 35 cM on chromosome 17. Two suggestive QTL for birth weight were identified, one at 12 cM on chromosome 20 and the other at 56 cM on chromosome 21. An additional suggestive QTL was detected for retail product yield, for fat yield, and for USDA yield grade at 26 cM on chromosome 26. Results presented here represent the initial search for quantitative trait loci in this family. Validation of detected QTL in other populations will be necessary.

  14. Mapping quantitative trait loci for innate immune response in the pig.

    Science.gov (United States)

    Uddin, M J; Cinar, M U; Grosse-Brinkhaus, C; Tesfaye, D; Tholen, E; Juengst, H; Looft, C; Wimmers, K; Phatsara, C; Schellander, K

    2011-04-01

    The aim of the present study was to detect quantitative trait loci (QTL) for the serum levels of cytokines and Toll-like receptors as traits related to innate immunity in pig. For this purpose, serum concentration of interleukin 2 (IL2), interleukin 10 (IL10), interferon-gamma (IFNG), Toll-like receptor 2 (TLR2) and Toll-like receptor 9 (TLR9) were measured in blood samples obtained from F(2) piglets (n = 334) of a Duroc × Piétrain resource population (DUPI) after Mycoplasma hypopneumoniae (Mh), tetanus toxoid (TT) and Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) vaccination at 6, 9 and 15 weeks of age. Animals were genotyped at 82 genetic markers covering all autosomes. QTL analysis was performed under the line cross F(2) model using QTL Express and 33 single QTL were detected on almost all porcine autosomes. Among the single QTL, eight, twelve and thirteen QTL were identified for innate immune traits in response to Mh, TT and PRRSV vaccine, respectively. Besides single QTL, six QTL were identified by a two-QTL model, of which two for TLR9_TT were in coupling phase and one for IL10_PRRSV was in repulsion phase. All QTL were significant at 5% chromosome-wide level including one and seven at 5% genome- and 1% chromosome-wide level significance. All innate immune traits are influenced by multiple chromosomal regions implying multiple gene action. Some of the identified QTL coincided with previously reported QTL for immune response and disease resistance, and the newly identified QTL are potentially involved in the immune function. The immune traits were also influenced by environmental factors like year of birth, age, parity and litter size. The results of this work shed new light on the genetic background of innate immune response and these findings will be helpful to identify candidate genes in these QTL regions related to immune competence and disease resistance in pigs. © 2011 Blackwell Publishing Ltd.

  15. Heritability and quantitative genetic divergence of serotiny, a fire-persistence plant trait.

    Science.gov (United States)

    Hernández-Serrano, Ana; Verdú, Miguel; Santos-Del-Blanco, Luís; Climent, José; González-Martínez, Santiago C; Pausas, Juli G

    2014-09-01

    Although it is well known that fire acts as a selective pressure shaping plant phenotypes, there are no quantitative estimates of the heritability of any trait related to plant persistence under recurrent fires, such as serotiny. In this study, the heritability of serotiny in Pinus halepensis is calculated, and an evaluation is made as to whether fire has left a selection signature on the level of serotiny among populations by comparing the genetic divergence of serotiny with the expected divergence of neutral molecular markers (QST-FST comparison). A common garden of P. halepensis was used, located in inland Spain and composed of 145 open-pollinated families from 29 provenances covering the entire natural range of P. halepensis in the Iberian Peninsula and Balearic Islands. Narrow-sense heritability (h(2)) and quantitative genetic differentiation among populations for serotiny (QST) were estimated by means of an 'animal model' fitted by Bayesian inference. In order to determine whether genetic differentiation for serotiny is the result of differential natural selection, QST estimates for serotiny were compared with FST estimates obtained from allozyme data. Finally, a test was made of whether levels of serotiny in the different provenances were related to different fire regimes, using summer rainfall as a proxy for fire regime in each provenance. Serotiny showed a significant narrow-sense heritability (h(2)) of 0·20 (credible interval 0·09-0·40). Quantitative genetic differentiation among provenances for serotiny (QST = 0·44) was significantly higher than expected under a neutral process (FST = 0·12), suggesting adaptive differentiation. A significant negative relationship was found between the serotiny level of trees in the common garden and summer rainfall of their provenance sites. Serotiny is a heritable trait in P. halepensis, and selection acts on it, giving rise to contrasting serotiny levels among populations depending on the fire regime, and

  16. Variation in CHI3LI in relation to type 2 diabetes and related quantitative traits.

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    Camilla Noelle Rathcke

    Full Text Available CHI3LI encoding the inflammatory glycoprotein YKL-40 is located on chromosome 1q32.1. YKL-40 is involved in inflammatory processes and patients with Type 2 Diabetes (T2D have elevated circulating YKL-40 levels which correlate with their level of insulin resistance. Interestingly, it has been reported that rs10399931 (-329 G/A of CHI3LI contributes to the inter-individual plasma YKL-40 levels in patients with sarcoidosis, and that rs4950928 (-131 C/G is a susceptibility polymorphism for asthma and a decline in lung function. We hypothesized that single nucleotide polymorphisms (SNPs or haplotypes thereof the CHI3LI locus might influence risk of T2D. The aim of the present study was to investigate the putative association between SNPs and haplotype blocks of CHI3LI and T2D and T2D related quantitative traits.Eleven SNPs of CHI3LI were genotyped in 6514 individuals from the Inter99 cohort and 2924 individuals from the outpatient clinic at Steno Diabetes Center. In cas-control studies a total of 2345 T2D patients and 5302 individuals with a normal glucose tolerance test were examined. We found no association between rs10399931 (OR, 0.98 (CI, 0.88-1.10, p = 0.76, rs4950928 (0.98 (0.87-1.10, p = 0.68 or any of the other SNPs with T2D. Similarly, we found no significant association between any of the 11 tgSNPs and T2D related quantitative traits, all p>0.14. None of the identified haplotype blocks of CHI3LI showed any association with T2D, all p>0.16.None of the examined SNPs or haplotype blocks of CHI3LI showed any association with T2D or T2D related quantitative traits. Estimates of insulin resistance and dysregulated glucose homeostasis in T2D do not seem to be accounted for by the examined variations of CHI3LI.

  17. Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution.

    Science.gov (United States)

    Rohlfs, Rori V; Nielsen, Rasmus

    2015-09-01

    A number of methods have been developed for modeling the evolution of a quantitative trait on a phylogeny. These methods have received renewed interest in the context of genome-wide studies of gene expression, in which the expression levels of many genes can be modeled as quantitative traits. We here develop a new method for joint analyses of quantitative traits within- and between species, the Expression Variance and Evolution (EVE) model. The model parameterizes the ratio of population to evolutionary expression variance, facilitating a wide variety of analyses, including a test for lineage-specific shifts in expression level, and a phylogenetic ANOVA that can detect genes with increased or decreased ratios of expression divergence to diversity, analogous to the famous Hudson Kreitman Aguadé (HKA) test used to detect selection at the DNA level. We use simulations to explore the properties of these tests under a variety of circumstances and show that the phylogenetic ANOVA is more accurate than the standard ANOVA (no accounting for phylogeny) sometimes used in transcriptomics. We then apply the EVE model to a mammalian phylogeny of 15 species typed for expression levels in liver tissue. We identify genes with high expression divergence between species as candidates for expression level adaptation, and genes with high expression diversity within species as candidates for expression level conservation and/or plasticity. Using the test for lineage-specific expression shifts, we identify several candidate genes for expression level adaptation on the catarrhine and human lineages, including genes putatively related to dietary changes in humans. We compare these results to those reported previously using a model which ignores expression variance within species, uncovering important differences in performance. We demonstrate the necessity for a phylogenetic model in comparative expression studies and show the utility of the EVE model to detect expression divergence

  18. Genetic Map Construction and Quantitative Trait Locus (QTL) Detection of Growth-Related Traits in Litopenaeus vannamei for Selective Breeding Applications

    Science.gov (United States)

    Andriantahina, Farafidy; Liu, Xiaolin; Huang, Hao

    2013-01-01

    Growth is a priority trait from the point of view of genetic improvement. Molecular markers linked to quantitative trait loci (QTL) have been regarded as useful for marker-assisted selection (MAS) in complex traits as growth. Using an intermediate F2 cross of slow and fast growth parents, a genetic linkage map of Pacific whiteleg shrimp, Litopenaeusvannamei, based on amplified fragment length polymorphisms (AFLP) and simple sequence repeats (SSR) markers was constructed. Meanwhile, QTL analysis was performed for growth-related traits. The linkage map consisted of 451 marker loci (429 AFLPs and 22 SSRs) which formed 49 linkage groups with an average marker space of 7.6 cM; they spanned a total length of 3627.6 cM, covering 79.50% of estimated genome size. 14 QTLs were identified for growth-related traits, including three QTLs for body weight (BW), total length (TL) and partial carapace length (PCL), two QTLs for body length (BL), one QTL for first abdominal segment depth (FASD), third abdominal segment depth (TASD) and first abdominal segment width (FASW), which explained 2.62 to 61.42% of phenotypic variation. Moreover, comparison of linkage maps between L. vannamei and Penaeusjaponicus was applied, providing a new insight into the genetic base of QTL affecting the growth-related traits. The new results will be useful for conducting MAS breeding schemes in L. vannamei. PMID:24086466

  19. Genetic map construction and quantitative trait locus (QTL detection of growth-related traits in Litopenaeus vannamei for selective breeding applications.

    Directory of Open Access Journals (Sweden)

    Farafidy Andriantahina

    Full Text Available Growth is a priority trait from the point of view of genetic improvement. Molecular markers linked to quantitative trait loci (QTL have been regarded as useful for marker-assisted selection (MAS in complex traits as growth. Using an intermediate F2 cross of slow and fast growth parents, a genetic linkage map of Pacific whiteleg shrimp, Litopenaeusvannamei, based on amplified fragment length polymorphisms (AFLP and simple sequence repeats (SSR markers was constructed. Meanwhile, QTL analysis was performed for growth-related traits. The linkage map consisted of 451 marker loci (429 AFLPs and 22 SSRs which formed 49 linkage groups with an average marker space of 7.6 cM; they spanned a total length of 3627.6 cM, covering 79.50% of estimated genome size. 14 QTLs were identified for growth-related traits, including three QTLs for body weight (BW, total length (TL and partial carapace length (PCL, two QTLs for body length (BL, one QTL for first abdominal segment depth (FASD, third abdominal segment depth (TASD and first abdominal segment width (FASW, which explained 2.62 to 61.42% of phenotypic variation. Moreover, comparison of linkage maps between L. vannamei and Penaeusjaponicus was applied, providing a new insight into the genetic base of QTL affecting the growth-related traits. The new results will be useful for conducting MAS breeding schemes in L. vannamei .

  20. A quantitative trait locus mixture model that avoids spurious LOD score peaks.

    Science.gov (United States)

    Feenstra, Bjarke; Skovgaard, Ib M

    2004-06-01

    In standard interval mapping of quantitative trait loci (QTL), the QTL effect is described by a normal mixture model. At any given location in the genome, the evidence of a putative QTL is measured by the likelihood ratio of the mixture model compared to a single normal distribution (the LOD score). This approach can occasionally produce spurious LOD score peaks in regions of low genotype information (e.g., widely spaced markers), especially if the phenotype distribution deviates markedly from a normal distribution. Such peaks are not indicative of a QTL effect; rather, they are caused by the fact that a mixture of normals always produces a better fit than a single normal distribution. In this study, a mixture model for QTL mapping that avoids the problems of such spurious LOD score peaks is presented.

  1. Developmental Patterning as a Quantitative Trait: Genetic Modulation of the Hoxb6 Mutant Skeletal Phenotype.

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    Claudia Kappen

    Full Text Available The process of patterning along the anterior-posterior axis in vertebrates is highly conserved. The function of Hox genes in the axis patterning process is particularly well documented for bone development in the vertebral column and the limbs. We here show that Hoxb6, in skeletal elements at the cervico-thoracic junction, controls multiple independent aspects of skeletal pattern, implicating discrete developmental pathways as substrates for this transcription factor. In addition, we demonstrate that Hoxb6 function is subject to modulation by genetic factors. These results establish Hox-controlled skeletal pattern as a quantitative trait modulated by gene-gene interactions, and provide evidence that distinct modifiers influence the function of conserved developmental genes in fundamental patterning processes.

  2. Linkage of DNA Methylation Quantitative Trait Loci to Human Cancer Risk

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    Holger Heyn

    2014-04-01

    Full Text Available Epigenetic regulation and, in particular, DNA methylation have been linked to the underlying genetic sequence. DNA methylation quantitative trait loci (meQTL have been identified through significant associations between the genetic and epigenetic codes in physiological and pathological contexts. We propose that interrogating the interplay between polymorphic alleles and DNA methylation is a powerful method for improving our interpretation of risk alleles identified in genome-wide association studies that otherwise lack mechanistic explanation. We integrated patient cancer risk genotype data and genome-scale DNA methylation profiles of 3,649 primary human tumors, representing 13 solid cancer types. We provide a comprehensive meQTL catalog containing DNA methylation associations for 21% of interrogated cancer risk polymorphisms. Differentially methylated loci harbor previously reported and as-yet-unidentified cancer genes. We suggest that such regulation at the DNA level can provide a considerable amount of new information about the biology of cancer-risk alleles.

  3. Fine mapping quantitative trait loci under selective phenotyping strategies based on linkage and linkage disequilibrium criteria

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P; Lund, M S

    2009-01-01

    disequilibrium-based sampling criteria (LDC) for selecting individuals to phenotype are compared to random phenotyping in a quantitative trait loci (QTL) verification experiment using stochastic simulation. Several strategies based on LAC and LDC for selecting the most informative 30%, 40% or 50% of individuals......, in order to estimate unbiased QTL parameters based on LAC in a large half-sib family, prior information on QTL position was required. The LDC improved the accuracy to estimate the QTL position but not significantly compared to random phenotyping with the same sample size. When applying LDC (all phenotyping......In fine mapping of a large-scale experimental population where collection of phenotypes are very expensive, difficult to record or time-demanding, selective phenotyping could be used to phenotype the most informative individuals. Linkage analyses based sampling criteria (LAC) and linkage...

  4. SplicePlot: a utility for visualizing splicing quantitative trait loci.

    Science.gov (United States)

    Wu, Eric; Nance, Tracy; Montgomery, Stephen B

    2014-04-01

    RNA sequencing has provided unprecedented resolution of alternative splicing and splicing quantitative trait loci (sQTL). However, there are few tools available for visualizing the genotype-dependent effects of splicing at a population level. SplicePlot is a simple command line utility that produces intuitive visualization of sQTLs and their effects. SplicePlot takes mapped RNA sequencing reads in BAM format and genotype data in VCF format as input and outputs publication-quality Sashimi plots, hive plots and structure plots, enabling better investigation and understanding of the role of genetics on alternative splicing and transcript structure. Source code and detailed documentation are available at http://montgomerylab.stanford.edu/spliceplot/index.html under Resources and at Github. SplicePlot is implemented in Python and is supported on Linux and Mac OS. A VirtualBox virtual machine running Ubuntu with SplicePlot already installed is also available.

  5. Evolution of Quantitative Traits under a Migration-Selection Balance: When Does Skew Matter?

    Science.gov (United States)

    Débarre, Florence; Yeaman, Sam; Guillaume, Frédéric

    2015-10-01

    Quantitative-genetic models of differentiation under migration-selection balance often rely on the assumption of normally distributed genotypic and phenotypic values. When a population is subdivided into demes with selection toward different local optima, migration between demes may result in asymmetric, or skewed, local distributions. Using a simplified two-habitat model, we derive formulas without a priori assuming a Gaussian distribution of genotypic values, and we find expressions that naturally incorporate higher moments, such as skew. These formulas yield predictions of the expected divergence under migration-selection balance that are more accurate than models assuming Gaussian distributions, which illustrates the importance of incorporating these higher moments to assess the response to selection in heterogeneous environments. We further show with simulations that traits with loci of large effect display the largest skew in their distribution at migration-selection balance.

  6. Cold sweetening in diploid potato: mapping quantitative trait loci and candidate genes.

    Science.gov (United States)

    Menéndez, Cristina M; Ritter, Enrique; Schäfer-Pregl, Ralf; Walkemeier, Birgit; Kalde, Alexandra; Salamini, Francesco; Gebhardt, Christiane

    2002-01-01

    A candidate gene approach has been used as a first step to identify the molecular basis of quantitative trait variation in potato. Sugar content of tubers upon cold storage was the model trait chosen because the metabolic pathways involved in starch and sugar metabolism are well known and many of the genes have been cloned. Tubers of two F(1) populations of diploid potato grown in six environments were evaluated for sugar content after cold storage. The populations were genotyped with RFLP, AFLP, and candidate gene markers. QTL analysis revealed that QTL for glucose, fructose, and sucrose content were located on all potato chromosomes. Most QTL for glucose content mapped to the same positions as QTL for fructose content. QTL explaining >10% of the variability for reducing sugars were located on linkage groups I, III, VII, VIII, IX, and XI. QTL consistent across populations and/or environments were identified. QTL were linked to genes encoding invertase, sucrose synthase 3, sucrose phosphate synthase, ADP-glucose pyrophosphorylase, sucrose transporter 1, and a putative sucrose sensor. The results suggest that allelic variants of enzymes operating in carbohydrate metabolic pathways contribute to the genetic variation in cold sweetening. PMID:12454085

  7. Mapping of quantitative trait loci affecting resistance/susceptibility to Sarcocystis miescheriana in swine.

    Science.gov (United States)

    Reiner, Gerald; Kliemt, Damaris; Willems, Hermann; Berge, Thomas; Fischer, Reiner; Köhler, Florian; Hepp, Sabine; Hertrampf, Barbara; Daugschies, Arwid; Geldermann, Hermann; Mackenstedt, Ute; Zahner, Horst

    2007-05-01

    The outcome of infectious diseases in vertebrates is under genetic control at least to some extent. In swine, e.g., marked differences in resistance/susceptibility to Sarcocystis miescheriana have been shown between Chinese Meishan and European Pietrain pigs, and these differences are associated with high heritabilities. A first step toward the identification of genes and polymorphisms causal for these differences may be the mapping of quantitative trait loci (QTLs). Considering clinical, immunological, and parasitological traits in the above model system, this survey represents the first QTL study on parasite resistance in pigs. QTL mapping was performed in 139 F(2) pigs of a Meishan/Pietrain family infected with S. miescheriana. Fourteen genome-wide significant QTLs were mapped to several chromosomal areas. Among others, major QTLs were identified for bradyzoite numbers in skeletal muscles (F = 17.4; p < 0.001) and for S. miescheriana-specific plasma IgG(2) levels determined 42 days p.i. (F = 20.9; p < 0.001). The QTLs were mapped to different regions of chromosome 7, i.e., to the region of the major histocompatibility complex (bradyzoites) and to an immunoglobulin heavy chain cluster, respectively. These results provide evidence for a direct and causal role for gene variants within these gene clusters (cis-acting) in differences in resistance to S. miescheriana.

  8. Limits to behavioral evolution: the quantitative genetics of a complex trait under directional selection.

    Science.gov (United States)

    Careau, Vincent; Wolak, Matthew E; Carter, Patrick A; Garland, Theodore

    2013-11-01

    Replicated selection experiments provide a powerful way to study how "multiple adaptive solutions" may lead to differences in the quantitative-genetic architecture of selected traits and whether this may translate into differences in the timing at which evolutionary limits are reached. We analyze data from 31 generations (n=17,988) of selection on voluntary wheel running in house mice. The rate of initial response, timing of selection limit, and height of the plateau varied significantly between sexes and among the four selected lines. Analyses of litter size and realized selection differentials seem to rule out counterposing natural selection as a cause of the selection limits. Animal-model analyses showed that although the additive genetic variance was significantly lower in selected than control lines, both before and after the limits, the decrease was not sufficient to explain the limits. Moreover, directional selection promoted a negative covariance between additive and maternal genetic variance over the first 10 generations. These results stress the importance of replication in selection studies of higher-level traits and highlight the fact that long-term predictions of response to selection are not necessarily expected to be linear because of the variable effects of selection on additive genetic variance and maternal effects. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  9. Mapping of imprinted quantitative trait loci using immortalized F2 populations.

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    Yongxian Wen

    Full Text Available Mapping of imprinted quantitative trait loci (iQTLs is helpful for understanding the effects of genomic imprinting on complex traits in animals and plants. At present, the experimental designs and corresponding statistical methods having been proposed for iQTL mapping are all based on temporary populations including F2 and BC1, which can be used only once and suffer some other shortcomings respectively. In this paper, we propose a framework for iQTL mapping, including methods of interval mapping (IM and composite interval mapping (CIM based on conventional low-density genetic maps and point mapping (PM and composite point mapping (CPM based on ultrahigh-density genetic maps, using an immortalized F2 (imF2 population generated by random crosses between recombinant inbred lines or doubled haploid lines. We demonstrate by simulations that imF2 populations are very desirable and the proposed statistical methods (especially CIM and CPM are very powerful for iQTL mapping, with which the imprinting effects as well as the additive and dominance effects of iQTLs can be unbiasedly estimated.

  10. Identification of quantitative trait loci regulating haematopoietic parameters in B6AKRF2 mice.

    Science.gov (United States)

    van Os, Ronald; Ausema, Albertina; Noach, Estelle J K; van Pelt, Kyrjon; Dontje, Bert J H; Vellenga, Edo; de Haan, Gerald

    2006-01-01

    The haematopoietic system is a complex organised tissue with a hierarchical structure. Identification of organisational pathways within the haematopoietic system is relevant for a better understanding of haematopoiesis in health and disease. We have analysed numerous haematopoietic parameters in two panels of a total of 157 genetically distinct B6AKRF2 mice, derived from an intercross between AKR and C57Bl/6 mice, strains known to differ in various stem cell traits. The major objective of our study was to assess the extent to which various haematopoietic parameters, such as stem cell numbers, progenitor cell cycling, progenitor cell mobilisation and neutrophil numbers in blood and bone marrow are coregulated. The genotypes of these mice were used to search for genetic loci that regulate these parameters. We found significant quantitative trait loci (QTL) associated with the number of stem cells (CAFC-35) in the bone marrow and the number of neutrophils in the blood. However, most haematopoietic parameters appeared to be controlled by non-heritable (epigenetic) factors, or by multiple QTLs. Our study reveals striking differences in structure of the haematopoietic hierarchy between individual mice. Surprisingly, stem and progenitor cell pool size and proliferation rate, as well as peripheral blood cell counts are all independently regulated.

  11. Six quantitative trait loci influence task thresholds for hygienic behaviour in honeybees (Apis mellifera).

    Science.gov (United States)

    Oxley, Peter R; Spivak, Marla; Oldroyd, Benjamin P

    2010-04-01

    Honeybee hygienic behaviour provides colonies with protection from many pathogens and is an important model system of the genetics of a complex behaviour. It is a textbook example of complex behaviour under simple genetic control: hygienic behaviour consists of two components--uncapping a diseased brood cell, followed by removal of the contents--each of which are thought to be modulated independently by a few loci of medium to large effect. A worker's genetic propensity to engage in hygienic tasks affects the intensity of the stimulus required before she initiates the behaviour. Genetic diversity within colonies leads to task specialization among workers, with a minority of workers performing the majority of nest-cleaning tasks. We identify three quantitative trait loci that influence the likelihood that workers will engage in hygienic behaviour and account for up to 30% of the phenotypic variability in hygienic behaviour in our population. Furthermore, we identify two loci that influence the likelihood that a worker will perform uncapping behaviour only, and one locus that influences removal behaviour. We report the first candidate genes associated with engaging in hygienic behaviour, including four genes involved in olfaction, learning and social behaviour, and one gene involved in circadian locomotion. These candidates will allow molecular characterization of this distinctive behavioural mode of disease resistance, as well as providing the opportunity for marker-assisted selection for this commercially significant trait.

  12. Bayesian analysis of quantitative traits in popcorn (Zea mays L. through four cycles of recurrent selection

    Directory of Open Access Journals (Sweden)

    Antonio Teixeira do Amaral Junior

    2016-10-01

    Full Text Available A Bayesian analysis of genetic parameters for quantitative traits was carried out in full-sib families of popcorn through four cycles (C5, C6, C7, and C8 of recurrent selection. The parameters of Bayesian model were estimated using the independence chain algorithm. Grain yield and plant height were found to be moderately heritable ranging from 0.25 to 0.48 and 0.45 to 0.58, respectively. The highest heritability estimates were found for popping expansion volume at C5 ($ \\hat{h}_{C_5}^{2} $ = 0.71, and C7 ($ \\hat{h}_{C_7}^{2} $ = 0.63. The response of recurrent selection was 30.5 and 32.3% for grain yield and popping expansion volume, respectively. In C8, predicted genetic advances (from the Bayesian prediction of genotypic values were 4.8, 4.3, and 2.9% for plant height, grain yield, and popping expansion volume, respectively. The significant genetic variability among popcorn families in successive cycles of recurrent selection has sustained continued genetic progress in breeding for the traits of interest.

  13. Quantifying and correcting for the winner's curse in quantitative-trait association studies.

    Science.gov (United States)

    Xiao, Rui; Boehnke, Michael

    2011-04-01

    Quantitative traits (QT) are an important focus of human genetic studies both because of interest in the traits themselves and because of their role as risk factors for many human diseases. For large-scale QT association studies including genome-wide association studies, investigators usually focus on genetic loci showing significant evidence for SNP-QT association, and genetic effect size tends to be overestimated as a consequence of the winner's curse. In this paper, we study the impact of the winner's curse on QT association studies in which the genetic effect size is parameterized as the slope in a linear regression model. We demonstrate by analytical calculation that the overestimation in the regression slope estimate decreases as power increases. To reduce the ascertainment bias, we propose a three-parameter maximum likelihood method and then simplify this to a one-parameter method by excluding nuisance parameters. We show that both methods reduce the bias when power to detect association is low or moderate, and that the one-parameter model generally results in smaller variance in the estimate. © 2011 Wiley-Liss, Inc.

  14. Identification of quantitative trait loci and candidate genes for cadmium tolerance in Populus

    Energy Technology Data Exchange (ETDEWEB)

    Induri, Brahma R [West Virginia University; Ellis, Danielle R [West Virginia University; Slavov, Goncho T. [West Virginia University; Yin, Tongming [ORNL; Zhang, Xinye [ORNL; Tuskan, Gerald A [ORNL; DiFazio, Steven P [West Virginia University

    2012-01-01

    Understanding genetic variation for the response of Populus to heavy metals like cadmium (Cd) is an important step in elucidating the underlying mechanisms of tolerance. In this study, a pseudo-backcross pedigree of Populus trichocarpa Torr. & Gray and Populus deltoides Bart. was characterized for growth and performance traits after Cd exposure. A total of 16 quantitative trait loci (QTL) at logarithm of odds (LOD) ratio 2.5 were detected for total dry weight, its components and root volume. Major QTL for Cd responses were mapped to two different linkage groups and the relative allelic effects were in opposing directions on the two chromosomes, suggesting differential mechanisms at these two loci. The phenotypic variance explained by Cd QTL ranged from 5.9 to 11.6% and averaged 8.2% across all QTL. A whole-genome microarray study led to the identification of nine Cd-responsive genes from these QTL. Promising candidates for Cd tolerance include an NHL repeat membrane-spanning protein, a metal transporter and a putative transcription factor. Additional candidates in the QTL intervals include a putative homolog of a glutamate cysteine ligase, and a glutathione-S-transferase. Functional characterization of these candidate genes should enhance our understanding of Cd metabolism and transport and phytoremediation capabilities of Populus.

  15. Generation mean analysis for quantitative traits in sesame (Sesamum indicum L. crosses

    Directory of Open Access Journals (Sweden)

    Vijayarajan Sharmila

    2007-01-01

    Full Text Available To study the nature and magnitude of gene effects for yield and its components in sesame (Sesamum indicum L. we carried out generation mean analysis using the following four crosses of different sesame cultivars: VS 9510 x Co1; NIC 7907 x TMV 3; Cianno 13/10x VRI 1; and Si 1115/1 x TMV 3. The P1, P2, F1, F2, BC1 and BC2 of these generations were studied for seven quantitative traits. The analysis showed the presence of additive, dominance and epistatic gene interactions. The additive dominance model was adequate for plant height in the NIC 7907 x TMV3 and Si 1115/1x TMV 3 crosses and for capsule length in the VS 9510 x Co1, NIC 7907 x TMV 3 and Si 1115/1 x TMV 3 crosses. An epistatic digenic model was assumed for the remaining crosses. Duplicate-type epistasis played a greater role than complementary epistasis. The study revealed the importance of both additive and non-additive types of gene action for all the traits studied.

  16. Statistical distributions of test statistics used for quantitative trait association mapping in structured populations

    Directory of Open Access Journals (Sweden)

    Teyssèdre Simon

    2012-11-01

    Full Text Available Abstract Background Spurious associations between single nucleotide polymorphisms and phenotypes are a major issue in genome-wide association studies and have led to underestimation of type 1 error rate and overestimation of the number of quantitative trait loci found. Many authors have investigated the influence of population structure on the robustness of methods by simulation. This paper is aimed at developing further the algebraic formalization of power and type 1 error rate for some of the classical statistical methods used: simple regression, two approximate methods of mixed models involving the effect of a single nucleotide polymorphism (SNP and a random polygenic effect (GRAMMAR and FASTA and the transmission/disequilibrium test for quantitative traits and nuclear families. Analytical formulae were derived using matrix algebra for the first and second moments of the statistical tests, assuming a true mixed model with a polygenic effect and SNP effects. Results The expectation and variance of the test statistics and their marginal expectations and variances according to the distribution of genotypes and estimators of variance components are given as a function of the relationship matrix and of the heritability of the polygenic effect. These formulae were used to compute type 1 error rate and power for any kind of relationship matrix between phenotyped and genotyped individuals for any level of heritability. For the regression method, type 1 error rate increased with the variability of relationships and with heritability, but decreased with the GRAMMAR method and was not affected with the FASTA and quantitative transmission/disequilibrium test methods. Conclusions The formulae can be easily used to provide the correct threshold of type 1 error rate and to calculate the power when designing experiments or data collection protocols. The results concerning the efficacy of each method agree with simulation results in the literature but were

  17. Radial basis function regression methods for predicting quantitative traits using SNP markers.

    Science.gov (United States)

    Long, Nanye; Gianola, Daniel; Rosa, Guilherme J M; Weigel, Kent A; Kranis, Andreas; González-Recio, Oscar

    2010-06-01

    A challenge when predicting total genetic values for complex quantitative traits is that an unknown number of quantitative trait loci may affect phenotypes via cryptic interactions. If markers are available, assuming that their effects on phenotypes are additive may lead to poor predictive ability. Non-parametric radial basis function (RBF) regression, which does not assume a particular form of the genotype-phenotype relationship, was investigated here by simulation and analysis of body weight and food conversion rate data in broilers. The simulation included a toy example in which an arbitrary non-linear genotype-phenotype relationship was assumed, and five different scenarios representing different broad sense heritability levels (0.1, 0.25, 0.5, 0.75 and 0.9) were created. In addition, a whole genome simulation was carried out, in which three different gene action modes (pure additive, additive+dominance and pure epistasis) were considered. In all analyses, a training set was used to fit the model and a testing set was used to evaluate predictive performance. The latter was measured by correlation and predictive mean-squared error (PMSE) on the testing data. For comparison, a linear additive model known as Bayes A was used as benchmark. Two RBF models with single nucleotide polymorphism (SNP)-specific (RBF I) and common (RBF II) weights were examined. Results indicated that, in the presence of complex genotype-phenotype relationships (i.e. non-linearity and non-additivity), RBF outperformed Bayes A in predicting total genetic values using SNP markers. Extension of Bayes A to include all additive, dominance and epistatic effects could improve its prediction accuracy. RBF I was generally better than RBF II, and was able to identify relevant SNPs in the toy example.

  18. Localization of quantitative trait loci for diapause and other photoperiodically regulated life history traits important in adaptation to seasonally varying environments.

    Science.gov (United States)

    Tyukmaeva, Venera I; Veltsos, Paris; Slate, Jon; Gregson, Emma; Kauranen, Hannele; Kankare, Maaria; Ritchie, Michael G; Butlin, Roger K; Hoikkala, Anneli

    2015-06-01

    Seasonally changing environments at high latitudes present great challenges for the reproduction and survival of insects, and photoperiodic cues play an important role in helping them to synchronize their life cycle with prevalent and forthcoming conditions. We have mapped quantitative trait loci (QTL) responsible for the photoperiodic regulation of four life history traits, female reproductive diapause, cold tolerance, egg-to-eclosion development time and juvenile body weight in Drosophila montana strains from different latitudes in Canada and Finland. The F2 progeny of the cross was reared under a single photoperiod (LD cycle 16:8), which the flies from the Canadian population interpret as early summer and the flies from the Finnish population as late summer. The analysis revealed a unique QTL for diapause induction on the X chromosome and several QTL for this and the other measured traits on the 4th chromosome. Flies' cold tolerance, egg-to-eclosion development time and juvenile body weight had several QTL also on the 2nd, 3rd and 5th chromosome, some of the peaks overlapping with each other. These results suggest that while the downstream output of females' photoperiodic diapause response is partly under a different genetic control from that of the other traits in the given day length, all traits also share some QTL, possibly involving genes with pleiotropic effects and/or multiple tightly linked genes. Nonoverlapping QTL detected for some of the traits also suggest that the traits are potentially capable of independent evolution, even though this may be restricted by epistatic interactions and/or correlations and trade-offs between the traits. © 2015 John Wiley & Sons Ltd.

  19. Field-Based High-Throughput Plant Phenotyping Reveals the Temporal Patterns of Quantitative Trait Loci Associated with Stress-Responsive Traits in Cotton.

    Science.gov (United States)

    Pauli, Duke; Andrade-Sanchez, Pedro; Carmo-Silva, A Elizabete; Gazave, Elodie; French, Andrew N; Heun, John; Hunsaker, Douglas J; Lipka, Alexander E; Setter, Tim L; Strand, Robert J; Thorp, Kelly R; Wang, Sam; White, Jeffrey W; Gore, Michael A

    2016-04-07

    The application of high-throughput plant phenotyping (HTPP) to continuously study plant populations under relevant growing conditions creates the possibility to more efficiently dissect the genetic basis of dynamic adaptive traits. Toward this end, we employed a field-based HTPP system that deployed sets of sensors to simultaneously measure canopy temperature, reflectance, and height on a cotton (Gossypium hirsutum L.) recombinant inbred line mapping population. The evaluation trials were conducted under well-watered and water-limited conditions in a replicated field experiment at a hot, arid location in central Arizona, with trait measurements taken at different times on multiple days across 2010-2012. Canopy temperature, normalized difference vegetation index (NDVI), height, and leaf area index (LAI) displayed moderate-to-high broad-sense heritabilities, as well as varied interactions among genotypes with water regime and time of day. Distinct temporal patterns of quantitative trait loci (QTL) expression were mostly observed for canopy temperature and NDVI, and varied across plant developmental stages. In addition, the strength of correlation between HTPP canopy traits and agronomic traits, such as lint yield, displayed a time-dependent relationship. We also found that the genomic position of some QTL controlling HTPP canopy traits were shared with those of QTL identified for agronomic and physiological traits. This work demonstrates the novel use of a field-based HTPP system to study the genetic basis of stress-adaptive traits in cotton, and these results have the potential to facilitate the development of stress-resilient cotton cultivars. Copyright © 2016 Pauli et al.

  20. Mapping loci influencing blood pressure in the Framingham pedigrees using model-free LOD score analysis of a quantitative trait.

    Science.gov (United States)

    Knight, Jo; North, Bernard V; Sham, Pak C; Curtis, David

    2003-12-31

    This paper presents a method of performing model-free LOD-score based linkage analysis on quantitative traits. It is implemented in the QMFLINK program. The method is used to perform a genome screen on the Framingham Heart Study data. A number of markers that show some support for linkage in our study coincide substantially with those implicated in other linkage studies of hypertension. Although the new method needs further testing on additional real and simulated data sets we can already say that it is straightforward to apply and may offer a useful complementary approach to previously available methods for the linkage analysis of quantitative traits.

  1. Quantitative Trait Locus Mapping in Dairy Cattle by Means of Selective Milk DNA Pooling Using Dinucleotide Microsatellite Markers: Analysis of Milk Protein Percentage

    National Research Council Canada - National Science Library

    Lipkin, Ehud; Mosig, Mathias O; Darvasi, Ariel; Ezra, Ephraim; Shalom, A; Friedmann, Adam; Soller, Morris

    1998-01-01

    "Selective DNA pooling" accomplishes quantitative trait locus (QTL) mapping through densitometric estimates of marker allele frequencies in pooled DNA samples of phenotypically extreme individuals. With poly(TG...

  2. Evaluation of breeding strategies for polledness in dairy cattle using a newly developed simulation framework for quantitative and Mendelian traits.

    Science.gov (United States)

    Scheper, Carsten; Wensch-Dorendorf, Monika; Yin, Tong; Dressel, Holger; Swalve, Herrmann; König, Sven

    2016-06-29

    Intensified selection of polled individuals has recently gained importance in predominantly horned dairy cattle breeds as an alternative to routine dehorning. The status quo of the current polled breeding pool of genetically-closely related artificial insemination sires with lower breeding values for performance traits raises questions regarding the effects of intensified selection based on this founder pool. We developed a stochastic simulation framework that combines the stochastic simulation software QMSim and a self-designed R program named QUALsim that acts as an external extension. Two traits were simulated in a dairy cattle population for 25 generations: one quantitative (QMSim) and one qualitative trait with Mendelian inheritance (i.e. polledness, QUALsim). The assignment scheme for qualitative trait genotypes initiated realistic initial breeding situations regarding allele frequencies, true breeding values for the quantitative trait and genetic relatedness. Intensified selection for polled cattle was achieved using an approach that weights estimated breeding values in the animal best linear unbiased prediction model for the quantitative trait depending on genotypes or phenotypes for the polled trait with a user-defined weighting factor. Selection response for the polled trait was highest in the selection scheme based on genotypes. Selection based on phenotypes led to significantly lower allele frequencies for polled. The male selection path played a significantly greater role for a fast dissemination of polled alleles compared to female selection strategies. Fixation of the polled allele implies selection based on polled genotypes among males. In comparison to a base breeding scenario that does not take polledness into account, intensive selection for polled substantially reduced genetic gain for this quantitative trait after 25 generations. Reducing selection intensity for polled males while maintaining strong selection intensity among females

  3. A genome scan for quantitative trait loci and imprinted regions affecting reproduction in pigs.

    Science.gov (United States)

    Holl, J W; Cassady, J P; Pomp, D; Johnson, R K

    2004-12-01

    Quantitative trait loci for reproductive traits in a three-generation resource population of a cross between low-indexing pigs from a control line and high-indexing pigs from a line selected 10 generations for increased index of ovulation rate and embryonic survival are reported. Phenotypic data were collected in F2 females for birth weight (BWT, n = 428), weaning weight (WWT, n = 405), age at puberty (AP, n = 295), ovulation rate (OR, n = 423), number of fully formed pigs (FF, n = 370), number of pigs born alive (NBA, n = 370), number of mummified pigs (MUM, n = 370), and number of stillborn pigs (NSB, n = 370). Grandparent, F1, and F2 animals were genotyped for 151 microsatellite markers. Sixteen putative QTL (P reproductive traits were identified in previous analyses of these data with single QTL line-cross models. Data were reanalyzed with multiple QTL models, including imprinting effects. Data also were analyzed with half-sib models. Permutation was used to establish genome-wide significance levels ( = 0.01, 0.05, and 0.10). Thirty-one putative QTL for reproductive traits and two QTL for birth weight were identified (P < 0.10). One Mendelian QTL for FF (P < 0.05), one for NBA (P < 0.05), three for NSB (P < 0.05), three for NN (P < 0.05), seven for AP (P < 0.10), five for MUM (P < 0.10), and one for BWT (P < 0.10) were found. Partial imprinting of QTL affecting OR (P < 0.01), BWT (P < 0.05), and MUM (P < 0.05) was detected. There were four paternally expressed QTL for NN (P < 0.10) and one each for AP (P < 0.05) and MUM (P < 0.10). Maternally expressed QTL affecting NSB (P < 0.10), NN (P < 0.10), and MUM (P < 0.10) were detected. No QTL were detected with half-sib analyses. Multiple QTL models with imprinting effects are more appropriate for analyzing F2 data than single Mendelian QTL line-cross models.

  4. Quantitative trait loci map for growth and morphometric traits using a channel catfish x blue catfish interspecific hybrid system.

    Science.gov (United States)

    Hutson, A M; Liu, Z; Kucuktas, H; Umali-Maceina, G; Su, B; Dunham, R A

    2014-05-01

    Head length, head depth, head width, body depth, body width, caudal depth, and caudal width and total length and BW were measured for 71 backcross full sibs between the interspecific backcross F1 (female channel catfish [Ictalurus punctatus] × male blue catfish [Ictalurus furcatus]) female × blue catfish male. Body measurements were corrected for both size and the relationship between relative body shape and size, which is critical but usually ignored in fish research. Amplified fragment length polymorphism analysis was used for construction of a QTL map with 44 linkage groups. Eleven of 44 linkage groups had at least 1 significant QTL (P ≤ 0.05) and 11 of 44 at P = 0.10. Linkage group 19 was unique as it had multiple QTL for every trait measured, except for caudal width for which no QTL was identified on any linkage group. Approximately half of the markers measured were associated with positive effects (increase in size) on the traits and half had negative effects (decrease in size). Linkage groups 5, 9, 18, 20, 39, and 40 were significant for multiple traits and always had a trait negative effect. Total length is represented on the map by the most linkage groups and the most markers. The linkage relationships found among BW, total length, and the 7 morphometric traits indicated that multiple trait marker-assisted selection to simultaneously increase BW body depth, body width, and caudal depth while decreasing the head traits with the goal to increase body weight and carcass yield would be very difficult. Multiple genetic enhancement approaches would likely be needed to simultaneously improve BW and body conformation.

  5. Fabp7 maps to a quantitative trait locus for a schizophrenia endophenotype.

    Directory of Open Access Journals (Sweden)

    Akiko Watanabe

    2007-11-01

    Full Text Available Deficits in prepulse inhibition (PPI are a biological marker for schizophrenia. To unravel the mechanisms that control PPI, we performed quantitative trait loci (QTL analysis on 1,010 F2 mice derived by crossing C57BL/6 (B6 animals that show high PPI with C3H/He (C3 animals that show low PPI. We detected six major loci for PPI, six for the acoustic startle response, and four for latency to response peak, some of which were sex-dependent. A promising candidate on the Chromosome 10-QTL was Fabp7 (fatty acid binding protein 7, brain, a gene with functional links to the N-methyl-D-aspartic acid (NMDA receptor and expression in astrocytes. Fabp7-deficient mice showed decreased PPI and a shortened startle response latency, typical of the QTL's proposed effects. A quantitative complementation test supported Fabp7 as a potential PPI-QTL gene, particularly in male mice. Disruption of Fabp7 attenuated neurogenesis in vivo. Human FABP7 showed altered expression in schizophrenic brains and genetic association with schizophrenia, which were both evident in males when samples were divided by sex. These results suggest that FABP7 plays a novel and crucial role, linking the NMDA, neurodevelopmental, and glial theories of schizophrenia pathology and the PPI endophenotype, with larger or overt effects in males. We also discuss the results from the perspective of fetal programming.

  6. A Conceptual Framework for Mapping Quantitative Trait Loci Regulating Ontogenetic Allometry

    Science.gov (United States)

    Li, Hongying; Huang, Zhongwen; Gai, Junyi; Wu, Song; Zeng, Yanru; Li, Qin; Wu, Rongling

    2007-01-01

    Although ontogenetic changes in body shape and its associated allometry has been studied for over a century, essentially nothing is known about their underlying genetic and developmental mechanisms. One of the reasons for this ignorance is the unavailability of a conceptual framework to formulate the experimental design for data collection and statistical models for data analyses. We developed a framework model for unraveling the genetic machinery for ontogenetic changes of allometry. The model incorporates the mathematical aspects of ontogenetic growth and allometry into a maximum likelihood framework for quantitative trait locus (QTL) mapping. As a quantitative platform, the model allows for the testing of a number of biologically meaningful hypotheses to explore the pleiotropic basis of the QTL that regulate ontogeny and allometry. Simulation studies and real data analysis of a live example in soybean have been performed to investigate the statistical behavior of the model and validate its practical utilization. The statistical model proposed will help to study the genetic architecture of complex phenotypes and, therefore, gain better insights into the mechanistic regulation for developmental patterns and processes in organisms. PMID:18043752

  7. Novel autism subtype-dependent genetic variants are revealed by quantitative trait and subphenotype association analyses of published GWAS data.

    Science.gov (United States)

    Hu, Valerie W; Addington, Anjene; Hyman, Alexander

    2011-04-27

    The heterogeneity of symptoms associated with autism spectrum disorders (ASDs) has presented a significant challenge to genetic analyses. Even when associations with genetic variants have been identified, it has been difficult to associate them with a specific trait or characteristic of autism. Here, we report that quantitative trait analyses of ASD symptoms combined with case-control association analyses using distinct ASD subphenotypes identified on the basis of symptomatic profiles result in the identification of highly significant associations with 18 novel single nucleotide polymorphisms (SNPs). The symptom categories included deficits in language usage, non-verbal communication, social development, and play skills, as well as insistence on sameness or ritualistic behaviors. Ten of the trait-associated SNPs, or quantitative trait loci (QTL), were associated with more than one subtype, providing partial replication of the identified QTL. Notably, none of the novel SNPs is located within an exonic region, suggesting that these hereditary components of ASDs are more likely related to gene regulatory processes (or gene expression) than to structural or functional changes in gene products. Seven of the QTL reside within intergenic chromosomal regions associated with rare copy number variants that have been previously reported in autistic samples. Pathway analyses of the genes associated with the QTL identified in this study implicate neurological functions and disorders associated with autism pathophysiology. This study underscores the advantage of incorporating both quantitative traits as well as subphenotypes into large-scale genome-wide analyses of complex disorders.

  8. Novel autism subtype-dependent genetic variants are revealed by quantitative trait and subphenotype association analyses of published GWAS data.

    Directory of Open Access Journals (Sweden)

    Valerie W Hu

    Full Text Available The heterogeneity of symptoms associated with autism spectrum disorders (ASDs has presented a significant challenge to genetic analyses. Even when associations with genetic variants have been identified, it has been difficult to associate them with a specific trait or characteristic of autism. Here, we report that quantitative trait analyses of ASD symptoms combined with case-control association analyses using distinct ASD subphenotypes identified on the basis of symptomatic profiles result in the identification of highly significant associations with 18 novel single nucleotide polymorphisms (SNPs. The symptom categories included deficits in language usage, non-verbal communication, social development, and play skills, as well as insistence on sameness or ritualistic behaviors. Ten of the trait-associated SNPs, or quantitative trait loci (QTL, were associated with more than one subtype, providing partial replication of the identified QTL. Notably, none of the novel SNPs is located within an exonic region, suggesting that these hereditary components of ASDs are more likely related to gene regulatory processes (or gene expression than to structural or functional changes in gene products. Seven of the QTL reside within intergenic chromosomal regions associated with rare copy number variants that have been previously reported in autistic samples. Pathway analyses of the genes associated with the QTL identified in this study implicate neurological functions and disorders associated with autism pathophysiology. This study underscores the advantage of incorporating both quantitative traits as well as subphenotypes into large-scale genome-wide analyses of complex disorders.

  9. Testing for biases in selection on avian reproductive traits and partitioning direct and indirect selection using quantitative genetic models.

    Science.gov (United States)

    Reed, Thomas E; Gienapp, Phillip; Visser, Marcel E

    2016-10-01

    Key life history traits such as breeding time and clutch size are frequently both heritable and under directional selection, yet many studies fail to document microevolutionary responses. One general explanation is that selection estimates are biased by the omission of correlated traits that have causal effects on fitness, but few valid tests of this exist. Here, we show, using a quantitative genetic framework and six decades of life-history data on two free-living populations of great tits Parus major, that selection estimates for egg-laying date and clutch size are relatively unbiased. Predicted responses to selection based on the Robertson-Price Identity were similar to those based on the multivariate breeder's equation (MVBE), indicating that unmeasured covarying traits were not missing from the analysis. Changing patterns of phenotypic selection on these traits (for laying date, linked to climate change) therefore reflect changing selection on breeding values, and genetic constraints appear not to limit their independent evolution. Quantitative genetic analysis of correlational data from pedigreed populations can be a valuable complement to experimental approaches to help identify whether apparent associations between traits and fitness are biased by missing traits, and to parse the roles of direct versus indirect selection across a range of environments. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  10. Genetic and Quantitative Trait Locus Analysis for Bio-Oil Compounds after Fast Pyrolysis in Maize Cobs.

    Directory of Open Access Journals (Sweden)

    Brandon Jeffrey

    Full Text Available Fast pyrolysis has been identified as one of the biorenewable conversion platforms that could be a part of an alternative energy future, but it has not yet received the same attention as cellulosic ethanol in the analysis of genetic inheritance within potential feedstocks such as maize. Ten bio-oil compounds were measured via pyrolysis/gas chromatography-mass spectrometry (Py/GC-MS in maize cobs. 184 recombinant inbred lines (RILs of the intermated B73 x Mo17 (IBM Syn4 population were analyzed in two environments, using 1339 markers, for quantitative trait locus (QTL mapping. QTL mapping was performed using composite interval mapping with significance thresholds established by 1000 permutations at α = 0.05. 50 QTL were found in total across those ten traits with R2 values ranging from 1.7 to 5.8%, indicating a complex quantitative inheritance of these traits.

  11. Mapping quantitative trait loci for tissue culture response in VCS3M-DH population of Brassica rapa

    NARCIS (Netherlands)

    Seo, M.S.; Jin, M.; Lee, S.S.; Kwon, S.J.; Mun, J.H.; Park, B.S.; Visser, R.G.F.; Bonnema, A.B.; Sohn, S.H.

    2013-01-01

    Quantitative trait loci (QTL) controlling callus induction and plant regeneration were identified in the VCS3M-DH population of Brassica rapa. The VCS3M-DH population showed wide and continuous variation in callus induction and shoot regeneration. Significant coefficient correlations were detected

  12. Mapping quantitative trait loci controlling early growth in a (longleaf pine × slash pine) × slash pine BC1 family

    Science.gov (United States)

    C. Weng; Thomas L. Kubisiak; C. Dana. Nelson; M. Stine

    2002-01-01

    Random amplified polymorphic DNA (RAPD) markers were employed to map the genome and quantitative trait loci controlling the early growth of a pine hybrid F1 tree (Pinus palustris Mill. × P. elliottii Engl.) and a recurrent slash pine tree (P. ellottii Engl.) in a (longleaf pine × slash pine...

  13. Robust quantitative trait association tests in the parent-offspring triad design: conditional likelihood-based approaches.

    Science.gov (United States)

    Wang, J-Y; Tai, J J

    2009-03-01

    Association studies, based on either population data or familial data, have been widely applied to mapping of genes underlying complex diseases. In family-based association studies, using case-parent triad families, the popularly used transmission/disequilibrium test (TDT) was proposed for avoidance of spurious association results caused by other confounders such as population stratification. Originally, the TDT was developed for analysis of binary disease data. Extending it to allow for quantitative trait analysis of complex diseases and for robust analysis of binary diseases against the uncertainty of mode of inheritance has been thoroughly discussed. Nevertheless, studies on robust analysis of quantitative traits for complex diseases received relatively less attention. In this paper, we use parent-offspring triad families to demonstrate the feasibility of establishment of the robust candidate-gene association tests for quantitative traits. We first introduce the score statistics from the conditional likelihoods based on parent-offspring triad data under various genetic models. By applying two existing robust procedures we then construct the robust association tests for analysis of quantitative traits. Simulations are conducted to evaluate empirical type I error rates and powers of the proposed robust tests. The results show that these robust association tests do exhibit robustness against the effect of misspecification of the underlying genetic model on testing powers.

  14. Mapping of quantitative trait loci associated with partial resistance to phytophthora sojae and flooding tolerance in soybean

    Science.gov (United States)

    Phytophthora root rot (PRR) caused by Phytophthora sojae Kaufm. & Gerd. and flooding can limit growth and productivity, of soybean [Glycine max (L.) Merr.], especially on poorly drained soils. The primary objective of this research project was to map quantitative trait loci (QTL) associated with f...

  15. Effects of long-term averaging of quantitative blood pressure traits on the detection of genetic associations

    NARCIS (Netherlands)

    S.K. Ganesh (Santhi); D.I. Chasman (Daniel); M.G. Larson (Martin); X. Guo (Xiuqing); G.C. Verwoert (Germaine); J.C. Bis (Joshua); X. Gu (Xiangjun); G.D. Smith; M.-L. Yang (Min-Lee); Y. Zhang (Yan); G.B. Ehret (Georg); L.M. Rose (Lynda); S.J. Hwang; G.J. Papanicolau (George); E.J.G. Sijbrands (Eric); K. Rice (Kenneth); G. Eiriksdottir (Gudny); V. Pihur (Vasyl); P.M. Ridker (Paul); R.S. Vasan (Ramachandran Srini); C. Newton-Cheh (Christopher); L.J. Raffel (Leslie); N. Amin (Najaf); J.I. Rotter (Jerome); K. Liu (Kiang); L.J. Launer (Lenore); M. Xu (Ming); M. Caulfield (Mark); A.C. Morrison (Alanna); A.D. Johnson (Andrew); D. Vaidya (Dhananjay); A. Dehghan (Abbas); G. Li (Guo); C. Bouchard (Claude); T.B. Harris (Tamara); H. Zhang (He); E.A. Boerwinkle (Eric); D.S. Siscovick (David); W. Gao (Wei); A.G. Uitterlinden (André); F. Rivadeneira Ramirez (Fernando); A. Hofman (Albert); E.M. Schmidt (Ellen); O.H. Franco (Oscar); Y. Huo (Yong); J.C.M. Witteman (Jacqueline); P. Munroe (Patricia); V. Gudnason (Vilmundur); W. Palmas (Walter); C.M. van Duijn (Cornelia); M. Fornage (Myriam); D. Levy (Daniel); B.M. Psaty (Bruce); A. Chakravarti (Aravinda)

    2014-01-01

    textabstractBlood pressure (BP) is a heritable, quantitative trait with intraindividual variability and susceptibility to measurement error. Genetic studies of BP generally use single-visit measurements and thus cannot remove variability occurring over months or years. We leveraged the idea that

  16. Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs

    DEFF Research Database (Denmark)

    Drag, Markus; Hansen, Mathias Brygger; Kadarmideen, Haja

    2018-01-01

    to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at ~100 kg. Gene expression...

  17. Quantitative trait loci affecting oil content, oil composition, and other agronomically important traits in Oat (Avena sativa L.)

    Science.gov (United States)

    Groat oil content and composition are important determinants of oat quality. We investigated these traits in a population of 146 recombinant inbred lines from a cross between 'Dal' (high oil) and 'Exeter' (low oil). A linkage map consisting of 475 DArT markers spanning 1271.8 cM across 40 linkage gr...

  18. Comparison of single-marker and multi-marker tests in rare variant association studies of quantitative traits

    Science.gov (United States)

    Yilmaz, Yildiz E.; Pischon, Tobias

    2017-01-01

    In genetic association studies of rare variants, low statistical power and potential violations of established estimator properties are among the main challenges of association tests. Multi-marker tests (MMTs) have been proposed to target these challenges, but any comparison with single-marker tests (SMTs) has to consider that their aim is to identify causal genomic regions instead of variants. Valid power comparisons have been performed for the analysis of binary traits indicating that MMTs have higher power, but there is a lack of conclusive studies for quantitative traits. The aim of our study was therefore to fairly compare SMTs and MMTs in their empirical power to identify the same causal loci associated with a quantitative trait. The results of extensive simulation studies indicate that previous results for binary traits cannot be generalized. First, we show that for the analysis of quantitative traits, conventional estimation methods and test statistics of single-marker approaches have valid properties yielding association tests with valid type I error, even when investigating singletons or doubletons. Furthermore, SMTs lead to more powerful association tests for identifying causal genes than MMTs when the effect sizes of causal variants are large, and less powerful tests when causal variants have small effect sizes. For moderate effect sizes, whether SMTs or MMTs have higher power depends on the sample size and percentage of causal SNVs. For a more complete picture, we also compare the power in studies of quantitative and binary traits, and the power to identify causal genes with the power to identify causal rare variants. In a genetic association analysis of systolic blood pressure in the Genetic Analysis Workshop 19 data, SMTs yielded smaller p-values compared to MMTs for most of the investigated blood pressure genes, and were least influenced by the definition of gene regions. PMID:28562689

  19. Network-based group variable selection for detecting expression quantitative trait loci (eQTL

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    Zhang Xuegong

    2011-06-01

    Full Text Available Abstract Background Analysis of expression quantitative trait loci (eQTL aims to identify the genetic loci associated with the expression level of genes. Penalized regression with a proper penalty is suitable for the high-dimensional biological data. Its performance should be enhanced when we incorporate biological knowledge of gene expression network and linkage disequilibrium (LD structure between loci in high-noise background. Results We propose a network-based group variable selection (NGVS method for QTL detection. Our method simultaneously maps highly correlated expression traits sharing the same biological function to marker sets formed by LD. By grouping markers, complex joint activity of multiple SNPs can be considered and the dimensionality of eQTL problem is reduced dramatically. In order to demonstrate the power and flexibility of our method, we used it to analyze two simulations and a mouse obesity and diabetes dataset. We considered the gene co-expression network, grouped markers into marker sets and treated the additive and dominant effect of each locus as a group: as a consequence, we were able to replicate results previously obtained on the mouse linkage dataset. Furthermore, we observed several possible sex-dependent loci and interactions of multiple SNPs. Conclusions The proposed NGVS method is appropriate for problems with high-dimensional data and high-noise background. On eQTL problem it outperforms the classical Lasso method, which does not consider biological knowledge. Introduction of proper gene expression and loci correlation information makes detecting causal markers more accurate. With reasonable model settings, NGVS can lead to novel biological findings.

  20. Combining quantitative genetic footprinting and trait enrichment analysis to identify fitness determinants of a bacterial pathogen.

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    Travis J Wiles

    Full Text Available Strains of Extraintestinal Pathogenic Escherichia c oli (ExPEC exhibit an array of virulence strategies and are a major cause of urinary tract infections, sepsis and meningitis. Efforts to understand ExPEC pathogenesis are challenged by the high degree of genetic and phenotypic variation that exists among isolates. Determining which virulence traits are widespread and which are strain-specific will greatly benefit the design of more effective therapies. Towards this goal, we utilized a quantitative genetic footprinting technique known as transposon insertion sequencing (Tn-seq in conjunction with comparative pathogenomics to functionally dissect the genetic repertoire of a reference ExPEC isolate. Using Tn-seq and high-throughput zebrafish infection models, we tracked changes in the abundance of ExPEC variants within saturated transposon mutant libraries following selection within distinct host niches. Nine hundred and seventy bacterial genes (18% of the genome were found to promote pathogen fitness in either a niche-dependent or independent manner. To identify genes with the highest therapeutic and diagnostic potential, a novel Trait Enrichment Analysis (TEA algorithm was developed to ascertain the phylogenetic distribution of candidate genes. TEA revealed that a significant portion of the 970 genes identified by Tn-seq have homologues more often contained within the genomes of ExPEC and other known pathogens, which, as suggested by the first axiom of molecular Koch's postulates, is considered to be a key feature of true virulence determinants. Three of these Tn-seq-derived pathogen-associated genes--a transcriptional repressor, a putative metalloendopeptidase toxin and a hypothetical DNA binding protein--were deleted and shown to independently affect ExPEC fitness in zebrafish and mouse models of infection. Together, the approaches and observations reported herein provide a resource for future pathogenomics-based research and highlight the

  1. Combining quantitative genetic footprinting and trait enrichment analysis to identify fitness determinants of a bacterial pathogen.

    Science.gov (United States)

    Wiles, Travis J; Norton, J Paul; Russell, Colin W; Dalley, Brian K; Fischer, Kael F; Mulvey, Matthew A

    2013-01-01

    Strains of Extraintestinal Pathogenic Escherichia c oli (ExPEC) exhibit an array of virulence strategies and are a major cause of urinary tract infections, sepsis and meningitis. Efforts to understand ExPEC pathogenesis are challenged by the high degree of genetic and phenotypic variation that exists among isolates. Determining which virulence traits are widespread and which are strain-specific will greatly benefit the design of more effective therapies. Towards this goal, we utilized a quantitative genetic footprinting technique known as transposon insertion sequencing (Tn-seq) in conjunction with comparative pathogenomics to functionally dissect the genetic repertoire of a reference ExPEC isolate. Using Tn-seq and high-throughput zebrafish infection models, we tracked changes in the abundance of ExPEC variants within saturated transposon mutant libraries following selection within distinct host niches. Nine hundred and seventy bacterial genes (18% of the genome) were found to promote pathogen fitness in either a niche-dependent or independent manner. To identify genes with the highest therapeutic and diagnostic potential, a novel Trait Enrichment Analysis (TEA) algorithm was developed to ascertain the phylogenetic distribution of candidate genes. TEA revealed that a significant portion of the 970 genes identified by Tn-seq have homologues more often contained within the genomes of ExPEC and other known pathogens, which, as suggested by the first axiom of molecular Koch's postulates, is considered to be a key feature of true virulence determinants. Three of these Tn-seq-derived pathogen-associated genes--a transcriptional repressor, a putative metalloendopeptidase toxin and a hypothetical DNA binding protein--were deleted and shown to independently affect ExPEC fitness in zebrafish and mouse models of infection. Together, the approaches and observations reported herein provide a resource for future pathogenomics-based research and highlight the diversity of

  2. Quantitative trait loci mapping reveals candidate pathways regulating cell cycle duration in Plasmodium falciparum

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    Siwo Geoffrey

    2010-10-01

    Full Text Available Abstract Background Elevated parasite biomass in the human red blood cells can lead to increased malaria morbidity. The genes and mechanisms regulating growth and development of Plasmodium falciparum through its erythrocytic cycle are not well understood. We previously showed that strains HB3 and Dd2 diverge in their proliferation rates, and here use quantitative trait loci mapping in 34 progeny from a cross between these parent clones along with integrative bioinformatics to identify genetic loci and candidate genes that control divergences in cell cycle duration. Results Genetic mapping of cell cycle duration revealed a four-locus genetic model, including a major genetic effect on chromosome 12, which accounts for 75% of the inherited phenotype variation. These QTL span 165 genes, the majority of which have no predicted function based on homology. We present a method to systematically prioritize candidate genes using the extensive sequence and transcriptional information available for the parent lines. Putative functions were assigned to the prioritized genes based on protein interaction networks and expression eQTL from our earlier study. DNA metabolism or antigenic variation functional categories were enriched among our prioritized candidate genes. Genes were then analyzed to determine if they interact with cyclins or other proteins known to be involved in the regulation of cell cycle. Conclusions We show that the divergent proliferation rate between a drug resistant and drug sensitive parent clone is under genetic regulation and is segregating as a complex trait in 34 progeny. We map a major locus along with additional secondary effects, and use the wealth of genome data to identify key candidate genes. Of particular interest are a nucleosome assembly protein (PFL0185c, a Zinc finger transcription factor (PFL0465c both on chromosome 12 and a ribosomal protein L7Ae-related on chromosome 4 (PFD0960c.

  3. Genome-Assisted Prediction of Quantitative Traits Using the R Package sommer.

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    Giovanny Covarrubias-Pazaran

    Full Text Available Most traits of agronomic importance are quantitative in nature, and genetic markers have been used for decades to dissect such traits. Recently, genomic selection has earned attention as next generation sequencing technologies became feasible for major and minor crops. Mixed models have become a key tool for fitting genomic selection models, but most current genomic selection software can only include a single variance component other than the error, making hybrid prediction using additive, dominance and epistatic effects unfeasible for species displaying heterotic effects. Moreover, Likelihood-based software for fitting mixed models with multiple random effects that allows the user to specify the variance-covariance structure of random effects has not been fully exploited. A new open-source R package called sommer is presented to facilitate the use of mixed models for genomic selection and hybrid prediction purposes using more than one variance component and allowing specification of covariance structures. The use of sommer for genomic prediction is demonstrated through several examples using maize and wheat genotypic and phenotypic data. At its core, the program contains three algorithms for estimating variance components: Average information (AI, Expectation-Maximization (EM and Efficient Mixed Model Association (EMMA. Kernels for calculating the additive, dominance and epistatic relationship matrices are included, along with other useful functions for genomic analysis. Results from sommer were comparable to other software, but the analysis was faster than Bayesian counterparts in the magnitude of hours to days. In addition, ability to deal with missing data, combined with greater flexibility and speed than other REML-based software was achieved by putting together some of the most efficient algorithms to fit models in a gentle environment such as R.

  4. Mapping quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm

    Science.gov (United States)

    Singh, Rajinder; Tan, Soon G; Panandam, Jothi M; Rahman, Rahimah Abdul; Ooi, Leslie CL; Low, Eng-Ti L; Sharma, Mukesh; Jansen, Johannes; Cheah, Suan-Choo

    2009-01-01

    Background Marker Assisted Selection (MAS) is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials. Results A map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026) and a Nigerian E. guinneensis (T128). A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E. guineensis) map, 252 markers (199 AFLP, 38 RFLP and 15 SSR) could be ordered in 21 linkage groups (1815 cM). Interval mapping and multiple-QTL model (MQM) mapping (also known as composite interval mapping, CIM) were used to detect quantitative trait loci (QTLs) controlling oil quality (measured in terms of iodine value and fatty acid composition). At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV), myristic acid (C14:0), palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), oleic acid (C18:1) and linoleic acid (C18:2) content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3. A minor QTL

  5. Mapping quantitative trait loci (QTLs for fatty acid composition in an interspecific cross of oil palm

    Directory of Open Access Journals (Sweden)

    Sharma Mukesh

    2009-08-01

    Full Text Available Abstract Background Marker Assisted Selection (MAS is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials. Results A map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026 and a Nigerian E. guinneensis (T128. A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E. guineensis map, 252 markers (199 AFLP, 38 RFLP and 15 SSR could be ordered in 21 linkage groups (1815 cM. Interval mapping and multiple-QTL model (MQM mapping (also known as composite interval mapping, CIM were used to detect quantitative trait loci (QTLs controlling oil quality (measured in terms of iodine value and fatty acid composition. At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV, myristic acid (C14:0, palmitic acid (C16:0, palmitoleic acid (C16:1, stearic acid (C18:0, oleic acid (C18:1 and linoleic acid (C18:2 content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3

  6. Quantitative trait loci associated with the immune response to a bovine respiratory syncytial virus vaccine.

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    Richard J Leach

    Full Text Available Infectious disease is an important problem for animal breeders, farmers and governments worldwide. One approach to reducing disease is to breed for resistance. This linkage study used a Charolais-Holstein F2 cattle cross population (n = 501 which was genotyped for 165 microsatellite markers (covering all autosomes to search for associations with phenotypes for Bovine Respiratory Syncytial Virus (BRSV specific total-IgG, IgG1 and IgG2 concentrations at several time-points pre- and post-BRSV vaccination. Regions of the bovine genome which influenced the immune response induced by BRSV vaccination were identified, as well as regions associated with the clearance of maternally derived BRSV specific antibodies. Significant positive correlations were detected within traits across time, with negative correlations between the pre- and post-vaccination time points. The whole genome scan identified 27 Quantitative Trait Loci (QTL on 13 autosomes. Many QTL were associated with the Thymus Helper 1 linked IgG2 response, especially at week 2 following vaccination. However the most significant QTL, which reached 5% genome-wide significance, was on BTA 17 for IgG1, also 2 weeks following vaccination. All animals had declining maternally derived BRSV specific antibodies prior to vaccination and the levels of BRSV specific antibody prior to vaccination were found to be under polygenic control with several QTL detected.Heifers from the same population (n = 195 were subsequently immunised with a 40-mer Foot-and-Mouth Disease Virus peptide (FMDV in a previous publication. Several of these QTL associated with the FMDV traits had overlapping peak positions with QTL in the current study, including the QTL on BTA23 which included the bovine Major Histocompatibility Complex (BoLA, and QTL on BTA9 and BTA24, suggesting that the genes underlying these QTL may control responses to multiple antigens. These results lay the groundwork for future investigations to identify the

  7. Quantitative trait analysis of the development of pulmonary tolerance to inhaled zinc oxide in mice

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    Gordon Terry

    2005-07-01

    Full Text Available Abstract Background Individuals may develop tolerance to the induction of adverse pulmonary effects following repeated exposures to inhaled toxicants. Previously, we demonstrated that genetic background plays an important role in the development of pulmonary tolerance to inhaled zinc oxide (ZnO in inbred mouse strains, as assessed by polymorphonuclear leukocytes (PMNs, macrophages, and total protein in bronchoalveolar lavage (BAL phenotypes. The BALB/cByJ (CBy and DBA/2J (D2 strains were identified as tolerant and non-tolerant, respectively. The present study was designed to identify candidate genes that control the development of pulmonary tolerance to inhaled ZnO. Methods Genome-wide linkage analyses were performed on a CByD2F2 mouse cohort phenotyped for BAL protein, PMNs, and macrophages following 5 consecutive days of exposure to 1.0 mg/m3 inhaled ZnO for 3 hours/day. A haplotype analysis was carried out to determine the contribution of each quantitative trait locus (QTL and QTL combination to the overall BAL protein phenotype. Candidate genes were identified within each QTL interval using the positional candidate gene approach. Results A significant quantitative trait locus (QTL on chromosome 1, as well as suggestive QTLs on chromosomes 4 and 5, for the BAL protein phenotype, was established. Suggestive QTLs for the BAL PMN and macrophage phenotypes were also identified on chromosomes 1 and 5, respectively. Analysis of specific haplotypes supports the combined effect of three QTLs in the overall protein phenotype. Toll-like receptor 5 (Tlr5 was identified as an interesting candidate gene within the significant QTL for BAL protein on chromosome 1. Wild-derived Tlr5-mutant MOLF/Ei mice were tolerant to BAL protein following repeated ZnO exposure. Conclusion Genetic background is an important influence in the acquisition of pulmonary tolerance to BAL protein, PMNs, and macrophages following ZnO exposure. Promising candidate genes exist within

  8. Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping

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    Huang Yung-Fen

    2012-02-01

    Full Text Available Abstract Background Proanthocyanidins (PAs, or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL analysis on a 191-individual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a diversity panel of 141 grapevine cultivars in order to identify causal SNPs. Results Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes (VvLAR1, VvMYBPA2, VvCHI1, VvMYBPA1 showed at least one significant association with PA variables, especially VvLAR1 revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the diversity panel. Conclusions This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA

  9. The adaptation rate of a quantitative trait in an environmental gradient

    Science.gov (United States)

    Hermsen, R.

    2016-12-01

    The spatial range of a species habitat is generally determined by the ability of the species to cope with biotic and abiotic variables that vary in space. Therefore, the species range is itself an evolvable property. Indeed, environmental gradients permit a mode of evolution in which range expansion and adaptation go hand in hand. This process can contribute to rapid evolution of drug resistant bacteria and viruses, because drug concentrations in humans and livestock treated with antibiotics are far from uniform. Here, we use a minimal stochastic model of discrete, interacting organisms evolving in continuous space to study how the rate of adaptation of a quantitative trait depends on the steepness of the gradient and various population parameters. We discuss analytical results for the mean-field limit as well as extensive stochastic simulations. These simulations were performed using an exact, event-driven simulation scheme that can deal with continuous time-, density- and coordinate-dependent reaction rates and could be used for a wide variety of stochastic systems. The results reveal two qualitative regimes. If the gradient is shallow, the rate of adaptation is limited by dispersion and increases linearly with the gradient slope. If the gradient is steep, the adaptation rate is limited by mutation. In this regime, the mean-field result is highly misleading: it predicts that the adaptation rate continues to increase with the gradient slope, whereas stochastic simulations show that it in fact decreases with the square root of the slope. This discrepancy underscores the importance of discreteness and stochasticity even at high population densities; mean-field results, including those routinely used in quantitative genetics, should be interpreted with care.

  10. Mapping quantitative trait loci (QTL in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep

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    Lam Mary K

    2009-10-01

    Full Text Available Abstract An (Awassi × Merino × Merino backcross family of 172 ewes was used to map quantitative trait loci (QTL for different milk production traits on a framework map of 200 loci across all autosomes. From five previously proposed mathematical models describing lactation curves, the Wood model was considered the most appropriate due to its simplicity and its ability to determine ovine lactation curve characteristics. Derived milk traits for milk, fat, protein and lactose yield, as well as percentage composition and somatic cell score were used for single and two-QTL approaches using maximum likelihood estimation and regression analysis. A total of 15 significant (P P http://crcidp.vetsci.usyd.edu.au/cgi-bin/gbrowse/oaries_genome/. Many of the QTL for milk production traits have been reported on chromosomes 1, 3, 6, 16 and 20. Those on chromosomes 3 and 20 are in strong agreement with the results reported here. In addition, novel QTL were found on chromosomes 7, 8, 9, 14, 22 and 24. In a cross-species comparison, we extended the meta-assembly by comparing QTL regions of sheep and cattle, which provided strong evidence for synteny conservation of QTL regions for milk, fat, protein and somatic cell score data between cattle and sheep.

  11. Measuring quantitative autism traits in families: informant effect or intergenerational transmission?

    Science.gov (United States)

    De la Marche, Wouter; Noens, Ilse; Kuppens, Sofie; Spilt, Jantine L; Boets, Bart; Steyaert, Jean

    2015-04-01

    Autism spectrum disorders (ASD) have a high degree of heritability, but there is still much debate about specific causal genes and pathways. To gain insight into patterns of transmission, research has focused on the relatedness of quantitative autism traits (QAT) between family members, mostly using questionnaires. Yet, different kinds of bias may influence research results. In this paper, we focus on possible informant effects and, taking these into account, on possible intergenerational transmission of QAT. This study used multiple informant data retrieved via the Social Responsiveness Scale from 170 families with at least one member with ASD. Using intraclass correlations (ICCs) and mixed model analyses, we investigated inter-informant agreement and differences between parent and teacher reports on children and between self- and other-reports on adults. Using structural equation modelling (SEM), we investigated the relatedness of QAT between family members in ASD families. Parent-teacher agreement about social responsiveness was poor, especially for children with ASD, though agreement between parents was moderate to strong for affected and unaffected children. Agreement between self- and other-report in adult men was good, but only moderate in women. Agreement did not differ between adults with and without ASD. While accounting for informant effects, our SEM results corroborated the assortative mating theory and the intergenerational transmission of QAT from both fathers and mothers to their offspring.

  12. Linkage disequilibrium fine mapping of quantitative trait loci: A simulation study

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    Pérez-Enciso Miguel

    2003-09-01

    Full Text Available Abstract Recently, the use of linkage disequilibrium (LD to locate genes which affect quantitative traits (QTL has received an increasing interest, but the plausibility of fine mapping using linkage disequilibrium techniques for QTL has not been well studied. The main objectives of this work were to (1 measure the extent and pattern of LD between a putative QTL and nearby markers in finite populations and (2 investigate the usefulness of LD in fine mapping QTL in simulated populations using a dense map of multiallelic or biallelic marker loci. The test of association between a marker and QTL and the power of the test were calculated based on single-marker regression analysis. The results show the presence of substantial linkage disequilibrium with closely linked marker loci after 100 to 200 generations of random mating. Although the power to test the association with a frequent QTL of large effect was satisfactory, the power was low for the QTL with a small effect and/or low frequency. More powerful, multi-locus methods may be required to map low frequent QTL with small genetic effects, as well as combining both linkage and linkage disequilibrium information. The results also showed that multiallelic markers are more useful than biallelic markers to detect linkage disequilibrium and association at an equal distance.

  13. Mapping a Quantitative Trait Locus (QTL conferring pyrethroid resistance in the African malaria vector Anopheles funestus

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    Hunt Richard H

    2007-01-01

    Full Text Available Abstract Background Pyrethroid resistance in Anopheles funestus populations has led to an increase in malaria transmission in southern Africa. Resistance has been attributed to elevated activities of cytochrome P450s but the molecular basis underlying this metabolic resistance is unknown. Microsatellite and SNP markers were used to construct a linkage map and to detect a quantitative trait locus (QTL associated with pyrethroid resistance in the FUMOZ-R strain of An. funestus from Mozambique. Results By genotyping 349 F2 individuals from 11 independent families, a single major QTL, rp1, at the telomeric end of chromosome 2R was identified. The rp1 QTL appears to present a major effect since it accounts for more than 60% of the variance in susceptibility to permethrin. This QTL has a strong additive genetic effect with respect to susceptibility. Candidate genes associated with pyrethroid resistance in other species were physically mapped to An. funestus polytene chromosomes. This showed that rp1 is genetically linked to a cluster of CYP6 cytochrome P450 genes located on division 9 of chromosome 2R and confirmed earlier reports that pyrethroid resistance in this strain is not associated with target site mutations (knockdown resistance. Conclusion We hypothesize that one or more of these CYP6 P450s clustered on chromosome 2R confers pyrethroid resistance in the FUMOZ-R strain of An. funestus.

  14. Quantitative trait loci in Anopheles gambiae controlling the encapsulation response against Plasmodium cynomolgi Ceylon

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    Luna Coralia

    2003-10-01

    Full Text Available Abstract Background Anopheles gambiae females are the world's most successful vectors of human malaria. However, a fraction of these mosquitoes is refractory to Plasmodium development. L3-5, a laboratory selected refractory strain, encapsulates transforming ookinetes/early oocysts of a wide variety of Plasmodium species. Previous studies on these mosquitoes showed that one major (Pen1 and two minor (Pen2, Pen3 autosomal dominant quantitative trait loci (QTLs control the melanotic encapsulation response against P. cynomolgi B, a simian malaria originating in Malaysia. Results We have investigated the response of L3-5 to infection with P. cynomolgi Ceylon, a different but related parasite species, in crosses with the susceptible strain 4Arr. Refractoriness to this parasite is incompletely recessive. Infection and genotyping of F2 intercross females at genome-spanning microsatellite loci revealed that 3 autosomal QTLs control encapsulation of this species. Two loci map to the regions containing Pen2 and Pen3. The novel QTL maps to chromosome 3R, probably to polytene division 32 or 33. Thus the relative contribution of any QTL to oocyst encapsulation varies with the species of parasite. Further, different QTLs were most readily identified in different F2 families. This, like the F1 data, suggests that L3-5 is not genetically homogeneous and that somewhat different pathways may be used to achieve an encapsulation response. Conclusion We have shown here that different QTLs are involved in responses against different Plasmodium parasites.

  15. Well posedness and maximum entropy approximation for the dynamics of quantitative traits

    KAUST Repository

    Boďová, Katarína

    2017-11-06

    We study the Fokker–Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker–Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain’s boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker–Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one.

  16. Identification of quantitative trait loci for osteoarthritis of hip joints in dogs.

    Science.gov (United States)

    Mateescu, Raluca G; Burton-Wurster, Nancy I; Tsai, Kate; Phavaphutanon, Janjira; Zhang, Zhiwu; Murphy, Keith E; Lust, George; Todhunter, Rory J

    2008-10-01

    To identify quantitative trait loci (QTL) associated with osteoarthritis (OA) of hip joints of dogs by use of a whole-genome microsatellite scan. 116 founder, backcross, F1, and F2 dogs from a crossbred pedigree. Necropsy scores and an optimized set of 342 microsatellite markers were used for interval mapping by means of a combined backcross and F2 design module from an online statistical program. Breed and sex were included in the model as fixed effects. Age of dog at necropsy and body weight at 8 months of age were also included in the model as covariates. The chromosomal location at which the highest F score was obtained was considered the best estimate of a QTL position. Chromosome-wide significance thresholds were determined empirically from 10,000 permutations of marker genotypes. 4 chromosomes contained putative QTL for OA of hip joints in dogs at the 5% chromosome-wide significance threshold: chromosomes 5, 18, 23, and 31. Osteoarthritis of canine hip joints is a complex disease to which many genes and environmental factors contribute. Identification of contributing QTL is a strategy to elucidate the genetic mechanisms that underlie this disease. Refinement of the putative QTL and subsequent candidate gene studies are needed to identify the genes involved in the disease process.

  17. A two-locus model of spatially varying stabilizing or directional selection on a quantitative trait.

    Science.gov (United States)

    Geroldinger, Ludwig; Bürger, Reinhard

    2014-06-01

    The consequences of spatially varying, stabilizing or directional selection on a quantitative trait in a subdivided population are studied. A deterministic two-locus two-deme model is employed to explore the effects of migration, the degree of divergent selection, and the genetic architecture, i.e., the recombination rate and ratio of locus effects, on the maintenance of genetic variation. The possible equilibrium configurations are determined as functions of the migration rate. They depend crucially on the strength of divergent selection and the genetic architecture. The maximum migration rates are investigated below which a stable fully polymorphic equilibrium or a stable single-locus polymorphism can exist. Under stabilizing selection, but with different optima in the demes, strong recombination may facilitate the maintenance of polymorphism. However usually, and in particular with directional selection in opposite direction, the critical migration rates are maximized by a concentrated genetic architecture, i.e., by a major locus and a tightly linked minor one. Thus, complementing previous work on the evolution of genetic architectures in subdivided populations subject to diversifying selection, it is shown that concentrated architectures may aid the maintenance of polymorphism. Conditions are obtained when this is the case. Finally, the dependence of the phenotypic variance, linkage disequilibrium, and various measures of local adaptation and differentiation on the parameters is elaborated. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  18. Identification of context-dependent expression quantitative trait loci in whole blood.

    Science.gov (United States)

    Zhernakova, Daria V; Deelen, Patrick; Vermaat, Martijn; van Iterson, Maarten; van Galen, Michiel; Arindrarto, Wibowo; van 't Hof, Peter; Mei, Hailiang; van Dijk, Freerk; Westra, Harm-Jan; Bonder, Marc Jan; van Rooij, Jeroen; Verkerk, Marijn; Jhamai, P Mila; Moed, Matthijs; Kielbasa, Szymon M; Bot, Jan; Nooren, Irene; Pool, René; van Dongen, Jenny; Hottenga, Jouke J; Stehouwer, Coen D A; van der Kallen, Carla J H; Schalkwijk, Casper G; Zhernakova, Alexandra; Li, Yang; Tigchelaar, Ettje F; de Klein, Niek; Beekman, Marian; Deelen, Joris; van Heemst, Diana; van den Berg, Leonard H; Hofman, Albert; Uitterlinden, André G; van Greevenbroek, Marleen M J; Veldink, Jan H; Boomsma, Dorret I; van Duijn, Cornelia M; Wijmenga, Cisca; Slagboom, P Eline; Swertz, Morris A; Isaacs, Aaron; van Meurs, Joyce B J; Jansen, Rick; Heijmans, Bastiaan T; 't Hoen, Peter A C; Franke, Lude

    2017-01-01

    Genetic risk factors often localize to noncoding regions of the genome with unknown effects on disease etiology. Expression quantitative trait loci (eQTLs) help to explain the regulatory mechanisms underlying these genetic associations. Knowledge of the context that determines the nature and strength of eQTLs may help identify cell types relevant to pathophysiology and the regulatory networks underlying disease. Here we generated peripheral blood RNA-seq data from 2,116 unrelated individuals and systematically identified context-dependent eQTLs using a hypothesis-free strategy that does not require previous knowledge of the identity of the modifiers. Of the 23,060 significant cis-regulated genes (false discovery rate (FDR) ≤ 0.05), 2,743 (12%) showed context-dependent eQTL effects. The majority of these effects were influenced by cell type composition. A set of 145 cis-eQTLs depended on type I interferon signaling. Others were modulated by specific transcription factors binding to the eQTL SNPs.

  19. Quantitative trait loci mapping of metal concentrations in leaves of the maize IBM population.

    Science.gov (United States)

    Zdunić, Zvonimir; Grljušić, Sonja; Ledenčan, Tatjana; Duvnjak, Tomislav; Simić, Domagoj

    2014-06-01

    Characterizing concentrations of several beneficiary and toxic metals in maize leaves is of importance for ionomic studies and for silage production. The intermated B73 × Mo17 maize population (IBM) was evaluated for concentrations of eight metals (cadmium - Cd, copper - Cu, iron - Fe, potassium - K, magnesium - Mg, manganese - Mn, strontium - Sr and zinc - Zn) in ear-leaf to map quantitative trait loci (QTL) with 2161 molecular markers across the genome. QTL analysis revealed nine significant QTLs for concentrations of Cd, Cu, Fe, K, Mg and Sr combined over two environments. Median resolution for the QTL interval was less than 1 cM on a regular F2 map, which is a big improvement compared with the prior mapping (8 cM). The highest LOD scores of 15.52 and 15.31 were detected for K and Cd concentrations, respectively, explaining more than 20 percent of the phenotypic variance. No QTLs were found to be colocalized. QTL mapping in the IBM population did not confirm our earlier QTL results demonstrating considerable QTL ×genetic background interaction. The only exception is confirmation of the major QTL for Cd accumulation on chromosome 2. Our results could facilitate further genetic and physical mapping of genes for metal accumulation in maize. © 2014 The Authors.

  20. RAS1, a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis

    KAUST Repository

    Ren, Zhonghai

    2010-03-08

    Soil salinity limits agricultural production and is a major obstacle for feeding the growing world population. We used natural genetic variation in salt tolerance among different Arabidopsis accessions to map a major quantitative trait locus (QTL) for salt tolerance and abscisic acid (ABA) sensitivity during seed germination and early seedling growth. A recombinant inbred population derived from Landsberg erecta (Ler; salt and ABA sensitive) x Shakdara (Sha; salt and ABA resistant) was used for QTL mapping. High-resolution mapping and cloning of this QTL, Response to ABA and Salt 1 (RAS1), revealed that it is an ABA- and salt stress-inducible gene and encodes a previously undescribed plant-specific protein. A premature stop codon results in a truncated RAS1 protein in Sha. Reducing the expression of RAS1 by transfer-DNA insertion in Col or RNA interference in Ler leads to decreased salt and ABA sensitivity, whereas overexpression of the Ler allele but not the Sha allele causes increased salt and ABA sensitivity. Our results suggest that RAS1 functions as a negative regulator of salt tolerance during seed germination and early seedling growth by enhancing ABA sensitivity and that its loss of function contributes to the increased salt tolerance of Sha.

  1. Multi-QTL mapping for quantitative traits using epistatic distorted markers.

    Directory of Open Access Journals (Sweden)

    Shang-Qian Xie

    Full Text Available The interaction between segregation distortion loci (SDL has been often observed in all kinds of mapping populations. However, little has been known about the effect of epistatic SDL on quantitative trait locus (QTL mapping. Here we proposed a multi-QTL mapping approach using epistatic distorted markers. Using the corrected linkage groups, epistatic SDL was identified. Then, these SDL parameters were used to correct the conditional probabilities of QTL genotypes, and these corrections were further incorporated into the new QTL mapping approach. Finally, a set of simulated datasets and a real data in 304 mouse F2 individuals were used to validate the new method. As compared with the old method, the new one corrects genetic distance between distorted markers, and considers epistasis between two linked SDL. As a result, the power in the detection of QTL is higher for the new method than for the old one, and significant differences for estimates of QTL parameters between the two methods were observed, except for QTL position. Among two QTL for mouse weight, one significant difference for QTL additive effect between the above two methods was observed, because epistatic SDL between markers C66 and T93 exists (P = 2.94e-4.

  2. Congenital sensorineural deafness in dalmatian dogs associated with quantitative trait loci.

    Science.gov (United States)

    Kluth, Susanne; Distl, Ottmar

    2013-01-01

    A genome-wide association study (GWAS) was performed for 235 Dalmatian dogs using the canine Illumina high density bead chip to identify quantitative trait loci (QTL) associated with canine congenital sensorineural deafness (CCSD). Data analysis was performed for all Dalmatian dogs and in addition, separately for brown-eyed and blue-eyed dogs because of the significant influence of eye colour on CCSD in Dalmatian dogs. Mixed linear model analysis (MLM) revealed seven QTL with experiment-wide significant associations (-log10P>5.0) for CCSD in all Dalmatian dogs. Six QTL with experiment-wide significant associations for CCSD were found in brown-eyed Dalmatian dogs and in blue-eyed Dalmatian dogs, four experiment-wide significant QTL were detected. The experiment-wide CCSD-associated SNPs explained 82% of the phenotypic variance of CCSD. Five CCSD-loci on dog chromosomes (CFA) 6, 14, 27, 29 and 31 were in close vicinity of genes shown as causative for hearing loss in human and/or mouse.

  3. Congenital sensorineural deafness in dalmatian dogs associated with quantitative trait loci.

    Directory of Open Access Journals (Sweden)

    Susanne Kluth

    Full Text Available A genome-wide association study (GWAS was performed for 235 Dalmatian dogs using the canine Illumina high density bead chip to identify quantitative trait loci (QTL associated with canine congenital sensorineural deafness (CCSD. Data analysis was performed for all Dalmatian dogs and in addition, separately for brown-eyed and blue-eyed dogs because of the significant influence of eye colour on CCSD in Dalmatian dogs. Mixed linear model analysis (MLM revealed seven QTL with experiment-wide significant associations (-log10P>5.0 for CCSD in all Dalmatian dogs. Six QTL with experiment-wide significant associations for CCSD were found in brown-eyed Dalmatian dogs and in blue-eyed Dalmatian dogs, four experiment-wide significant QTL were detected. The experiment-wide CCSD-associated SNPs explained 82% of the phenotypic variance of CCSD. Five CCSD-loci on dog chromosomes (CFA 6, 14, 27, 29 and 31 were in close vicinity of genes shown as causative for hearing loss in human and/or mouse.

  4. Mapping quantitative trait loci for canine hip dysplasia in German Shepherd dogs.

    Science.gov (United States)

    Marschall, Yvonne; Distl, Ottmar

    2007-12-01

    Canine hip dysplasia (CHD) is a common hereditary developmental disease of the coxofemoral joints. CHD is characterized by subluxation of the femoral head and deformation of the acetabulum leading to a painful osteoarthrosis. Analyses of mode of inheritance have shown the involvement of a major gene in expression of CHD in German Shepherd dogs. Thus, a whole genome scan for quantitative trait loci (QTL) was performed in German Shepherd dogs. For this purpose 11 paternal half-sib families, including a total of 459 purebred German Shepherd dogs with sires, dams, and offspring, were genotyped for 261 microsatellites. These markers were equidistantly distributed over all 38 autosomes and the X chromosome with an average marker distance of 11.7 cM. The mean observed heterozygosity of the marker set was 50%. The CHD status for the dogs was scored according to the official rules of the Fédération Cynologique Internationale. At the genome-wide level of significance at p dogs.

  5. Evaluation of quantitative trait loci for hip dysplasia in Labrador Retrievers.

    Science.gov (United States)

    Phavaphutanon, Janjira; Mateescu, Raluca G; Tsai, Kate L; Schweitzer, Peter A; Corey, Elizabeth E; Vernier-Singer, Margaret A; Williams, Alma J; Dykes, Nathan L; Murphy, Keith E; Lust, George; Todhunter, Rory J

    2009-09-01

    To identify the quantitative trait loci (QTL) that contribute to hip dysplasia in dogs. 192 Labrador Retrievers. Hip dysplasia was measured by use of the Norberg angle (NA), dorsolateral subluxation (DLS) score, and distraction index (DI). Genome-wide screening was conducted by use of 276 unique microsatellites. Linkage analysis was performed with a variance-based linear model. Logarithm of the odds (LOD) scores were reported when values were > 2.0. Canis familiaris autosomes (CFAs) 01, 02, 10, 20, 22, and 32 harbored significant QTL at LOD scores > 2.0. Among the 6 QTL, the QTL on CFA02 had not been reported to harbor QTL for hip dysplasia. The highest LOD score of 3.32 on CFA20 contributed to the second principal component of the DLS score and NA of the right hip joint. The QTL that was mapped on CFA01 (LOD score of 3.13 at 55 centimorgans) was located on the same chromosome reported to harbor a QTL for hip dysplasia in Portuguese Water Dogs and German Shepherd Dogs. In this study, CFAs 10, 20, 22, and 32 harbored QTL for hip dysplasia that have been identified in a Labrador Retriever-Greyhound pedigree and in German Shepherd Dogs. Multiple QTL were clearly involved with hip dysplasia. Identification of these QTL will enable fine-resolution mapping and subsequent assessment of candidate genes within the refined intervals to enable researchers to develop genetic screening tests and preventative and novel therapeutic regimens.

  6. Optimal selection for multiple quantitative trait loci and contributions of individuals using genetic algorithm

    Science.gov (United States)

    Tang, G.; Lin, P.; Xu, C.; Xue, J.; Liu, T.; Wang, Z.; Li, X.

    2011-01-01

    Two methods (Scheme A and Scheme B) were developed to optimize the relative weights on quantitative trait loci (QTL) and contributions of selected individuals simultaneously to maximize selection response while constraining the rate of inbreeding to the rate observed in gene assisted selection (GAS). In Scheme A, both the relative weights give to QTL and contributions of the selected individuals were optimized using a genetic algorithm. The possible solutions for relative weights of QTL and contributions of the selected individuals were encoded simultaneously. A physical selection population was used to evaluate the fitness of each encoded solution using stochastic simulation with 50 replicates. The fitness of each solution was the mean of all replicates for accumulative discounted sum of genetic means of all generations in physical selection population. In Scheme B, the optimization for relative weights on QTL was similar to Scheme A, and also was implemented based on a genetic algorithm. However, unlike Scheme A, an optimal contribution algorithm (OC) was used to optimize contributions of selection candidates. When compared with GAS, Schemes A and B resulted in up to 15.88 and 22.26% extra discounted sum of genetic value of all generations in a long planning horizon, respectively. Compared GAS+OC and Scheme B, most of the increase (about 78%) in genetic gain was produced by only optimizing contributions of selected individuals. The optimization for relative weight given to QTL just avoided the long-term loss (about 22%) observed in GAS scheme. PMID:22577484

  7. Sequence variation and genetic evolution at the human F12 locus: mapping quantitative trait nucleotides that influence FXII plasma levels.

    Science.gov (United States)

    Calafell, Francesc; Almasy, Laura; Sabater-Lleal, Maria; Buil, Alfonso; Mordillo, Carolina; Ramírez-Soriano, Anna; Sikora, Martin; Souto, Juan Carlos; Blangero, John; Fontcuberta, Jordi; Soria, José Manuel

    2010-02-01

    The level of Factor XII (FXII) is an important phenotype that exhibits a high genetic component and is associated with thrombotic disease. In a genome-wide linkage scan, we demonstrated that the F12 gene represents a quantitative trait locus (QTL) that influences FXII levels. The current study investigated the genetic architecture of the F12 gene to locate polymorphism(s) responsible for the variation of FXII levels. Re-sequencing of the F12 gene in 40 unrelated individuals (selected from the tails of normal distribution of FXII levels) identified 26 polymorphisms which were genotyped in 398 individuals belonging to 21 families from the GAIT Project. By a measured genotype association analysis, eight of 26 SNPs showed significant P-values less than 10(-5) (after multiple test correction) with FXII levels. In addition, the Bayesian Quantitative Trait Nucleotide method, which infers those polymorphisms most likely to have a direct influence on the trait under study, provided evidence that only rs1801020 variation accounted for the variance attributed to this QTL. Moreover, we have analyzed the evolutionary processes that produced the variation in F12 gene and concluded that is evolutionarily neutral and that the T allele of the rs1801020 appeared approximately 100 000 years ago and spread to most human populations rising to high frequencies by genetic drift. Our study provides a template for future genetic studies of human quantitative traits, as we move beyond QTL localization to the polymorphisms responsible for the variation of important biomedical phenotypes.

  8. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture.

    Science.gov (United States)

    Topp, Christopher N; Iyer-Pascuzzi, Anjali S; Anderson, Jill T; Lee, Cheng-Ruei; Zurek, Paul R; Symonova, Olga; Zheng, Ying; Bucksch, Alexander; Mileyko, Yuriy; Galkovskyi, Taras; Moore, Brad T; Harer, John; Edelsbrunner, Herbert; Mitchell-Olds, Thomas; Weitz, Joshua S; Benfey, Philip N

    2013-04-30

    Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala × Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r(2) = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops.

  9. Virulence attributes and hyphal growth of C. neoformans are quantitative traits and the MATalpha allele enhances filamentation.

    Directory of Open Access Journals (Sweden)

    Xiaorong Lin

    2006-11-01

    Full Text Available Cryptococcus neoformans is a fungal human pathogen with a bipolar mating system. It undergoes a dimorphic transition from a unicellular yeast to hyphal filamentous growth during mating and monokaryotic fruiting. The traditional sexual cycle that leads to the production of infectious basidiospores involves cells of both alpha and a mating type. Monokaryotic fruiting is a modified form of sexual reproduction that involves cells of the same mating type, most commonly alpha, which is the predominant mating type in both the environment and clinical isolates. However, some a isolates can also undergo monokaryotic fruiting. To determine whether mating type and other genetic loci contribute to the differences in fruiting observed between alpha and a cells, we applied quantitative trait loci (QTL mapping to an inbred population of F2 progeny. We discovered that variation in hyphal length produced during fruiting is a quantitative trait resulting from the combined effects of multiple genetic loci, including the mating type (MAT locus. Importantly, the alpha allele of the MAT locus enhanced hyphal growth compared with the a allele. Other virulence traits, including melanization and growth at 39 degrees C, also are quantitative traits that share a common QTL with hyphal growth. The Mac1 transcription factor, encoded in this common QTL, regulates copper homeostasis. MAC1 allelic differences contribute to phenotypic variation, and mac1Delta mutants exhibit defects in filamentation, melanin production, and high temperature growth. Further characterization of these QTL regions will reveal additional quantitative trait genes controlling biological processes central to fungal development and pathogenicity.

  10. Porcine OGN and ASPN: mapping, polymorphisms and use for quantitative trait loci identification for growth and carcass traits in a Meishan x Piétrain intercross.

    Science.gov (United States)

    Stratil, A; Van Poucke, M; Bartenschlager, H; Knoll, A; Yerle, M; Peelman, L J; Kopecný, M; Geldermann, H

    2006-08-01

    The porcine orthologues of human chromosome HSA9q22.31 genes osteoglycin (OGN) and asporin (ASPN) were mapped to porcine chromosome SSC3 using linkage analysis and a somatic cell hybrid panel. This mapping was refined to SSC3q11 using fluorescence in situ hybridization. These results confirm the existence of a small conserved synteny group between SSC3 and HSA9. Polymorphisms were revealed in both genes, including a pentanucleotide microsatellite (SCZ003) in OGN and two single nucleotide polymorphisms (AM181682.1:g.780G>T and AM181682.1:g.825T>C) in ASPN. The two genes were included in a set of markers for quantitative trait loci (QTL) mapping on SSC3 in the Hohenheim Meishan x Piétrain F2 family. Major QTL for growth and carcass traits were centred in the ASPN-SW902 region.

  11. IDENTIFICATION OF A MAJOR QUANTITATIVE TRAIT LOCUS CONFERRING RICE BLAST RESISTANCE USING RECOMBINANT INBRED LINES

    Directory of Open Access Journals (Sweden)

    Sobrizal Sobrizal

    2013-05-01

    Full Text Available Blast disease caused by Pyricularia oryzae is one of the limiting factors for rice production world wide. The use of resistant varieties for managing blast disease is considered as the most eco-friendly approaches. However, their resistances may be broken down within a few years due to the appearance of new virulent blast races in the field. The objective of the present study was to identify the quantitative trait locus (QTL conferring resistance to blast disease using 126 recombinant inbred (RI lines originated from a crossing of a durably resistant upland rice genotype (Laka and a highly susceptible rice accession cultivar (Kencana Bali. The RI population was developed through a single seed descent method from 1997 to 2004. Resistance of the RI lines was evaluated for blast in an endemic area of Sukabumi, West Java, in 2005. Disease intensity of the blast was examined following the standard evaluation system developed by the International Rice Research Institute (IRRI. At the same year the RI lines were analyzed with 134 DNA markers. Results of the study showed that one major QTL was found to be associated with blast resistance, and this QTL was located near RM2136 marker on the long arm of chromosome 11. This QTL explained 87% of the phenotypic variation with 37% additive effect. The map position of this QTL differed from that of a partial resistant gene, Pi34, identified previously on chromosome 11 in the Japanese durably resistant variety, Chubu 32. The QTL, however, was almost at the same position as that of the multiple allele-resistant gene, Pik. Therefore, an allelic test should be conducted to clarify the allelic relationship between QTL identified in this study and the Pik. The RI lines are the permanent segregating population that could be very useful for analysing phenotypic variations of important agronomic traits possibly owned by the RI lines. The major QTL identified in this study could be used as a genetic resource in

  12. High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping

    Directory of Open Access Journals (Sweden)

    Esteras Cristina

    2012-02-01

    Full Text Available Abstract Background Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species. The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP, was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL. Results We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo × Scallop (subsp. ovifera. The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. Conclusion Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research

  13. High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping.

    Science.gov (United States)

    Esteras, Cristina; Gómez, Pedro; Monforte, Antonio J; Blanca, José; Vicente-Dólera, Nelly; Roig, Cristina; Nuez, Fernando; Picó, Belén

    2012-02-22

    Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species.The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in

  14. A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit

    National Research Council Canada - National Science Library

    L. Bermúdez; U. Urias; D. Milstein; L. Kamenetzky; R. Asis; A. R. Fernie; M. A. Van Sluys; F. Carrari; M. Rossi

    2008-01-01

    In tomato, numerous wild-related species have been demonstrated to be untapped sources of valuable genetic variability, including pathogen-resistance genes, nutritional, and industrial quality traits...

  15. Strategies on Sample Size Determination and Qualitative and Quantitative Traits Integration to Construct Core Collection of Rice (Oryza sativa

    Directory of Open Access Journals (Sweden)

    Xiao-ling LI

    2011-03-01

    Full Text Available The development of a core collection could enhance the utilization of germplasm collections in crop improvement programs and simplify their management. Selection of an appropriate sampling strategy is an important prerequisite to construct a core collection with appropriate size in order to adequately represent the genetic spectrum and maximally capture the genetic diversity in available crop collections. The present study was initiated to construct nested core collections to determine the appropriate sample size to represent the genetic diversity of rice landrace collection based on 15 quantitative traits and 34 qualitative traits of 2 262 rice accessions. The results showed that 50–225 nested core collections, whose sampling rate was 2.2%–9.9%, were sufficient to maintain the maximum genetic diversity of the initial collections. Of these, 150 accessions (6.6% could capture the maximal genetic diversity of the initial collection. Three data types, i.e. qualitative traits (QT1, quantitative traits (QT2 and integrated qualitative and quantitative traits (QTT, were compared for their efficiency in constructing core collections based on the weighted pair-group average method combined with stepwise clustering and preferred sampling on adjusted Euclidean distances. Every combining scheme constructed eight rice core collections (225, 200, 175, 150, 125, 100, 75 and 50. The results showed that the QTT data was the best in constructing a core collection as indicated by the genetic diversity of core collections. A core collection constructed only on the information of QT1 could not represent the initial collection effectively. QTT should be used together to construct a productive core collection.

  16. Quantitative trait locus affecting birth weight on bovine chromosome 5 in a F2 Gyr x Holstein population

    Directory of Open Access Journals (Sweden)

    Gustavo Gasparin

    2005-12-01

    Full Text Available Segregation between a genetic marker and a locus influencing a quantitative trait in a well delineated population is the basis for success in mapping quantitative trait loci (QTL. To detect bovine chromosome 5 (BTA5 birth weight QTL we genotyped 294 F2 Gyr (Bos indicus x Holstein (Bos taurus crossbreed cattle for five microsatellite markers. A linkage map was constructed for the markers and an interval analysis for the presence of QTL was performed. The linkage map indicated differences in the order of two markers relative to the reference map (http://www.marc.usda.gov. Interval analysis detected a QTL controlling birth weight (p < 0.01 at 69 centimorgans (cM from the most centromeric marker with an effect of 0.32 phenotypic standard-error. These results support other studies with crossbred Bos taurus x Bos indicus populations.

  17. Quantitative Trait Loci from Two Genotypes of Oat (Avena sativa) Conditioning Resistance to Puccinia coronata.

    Science.gov (United States)

    Babiker, Ebrahiem M; Gordon, Tyler C; Jackson, Eric W; Chao, Shiaoman; Harrison, Stephen A; Carson, Martin L; Obert, Don E; Bonman, J Michael

    2015-02-01

    Developing oat cultivars with partial resistance to crown rust would be beneficial and cost-effective for disease management. Two recombinant inbred-line populations were generated by crossing the susceptible cultivar Provena with two partially resistant sources, CDC Boyer and breeding line 94197A1-9-2-2-2-5. A third mapping population was generated by crossing the partially resistant sources to validate the quantitative trait locus (QTL) results. The three populations were evaluated for crown rust severity in the field at Louisiana State University (LSU) in 2009 and 2010 and at the Cereal Disease Laboratory (CDL) in St. Paul, MN, in 2009, 2010, and 2011. An iSelect platform assay containing 5,744 oat single nucleotide polymorphisms was used to genotype the populations. From the 2009 CDL test, linkage analyses revealed two QTLs for partial resistance in the Provena/CDC Boyer population on chromosome 19A. One of the 19A QTLs was also detected in the 2009 LSU test. Another QTL was detected on chromosome 12D in the CDL 2009 test. In the Provena/94197A1-9-2-2-2-5 population, only one QTL was detected, on chromosome 13A, in the CDL 2011 test. The 13A QTL from the Provena/94197A1-9-2-2-2-5 population was validated in the CDC Boyer/94197A1-9-2-2-2-5 population in the CDL 2010 and 2011 tests. Comparative analysis of the significant marker sequences with the rice genome database revealed 15 candidate genes for disease resistance on chromosomes 4 and 6 of rice. These genes could be potential targets for cloning from the two resistant parents.

  18. Quantitative trait locus mapping of acute functional tolerance in the LXS recombinant inbred strains.

    Science.gov (United States)

    Bennett, Beth; Larson, Colin; Richmond, Phillip A; Odell, Aaron T; Saba, Laura M; Tabakoff, Boris; Dowell, Robin; Radcliffe, Richard A

    2015-04-01

    We previously reported that acute functional tolerance (AFT) to the hypnotic effects of alcohol was significantly correlated with drinking in the dark (DID) in the LXS recombinant inbred panel, but only in mice that had been pretreated with alcohol. Here, we have conducted quantitative trait locus (QTL) mapping for AFT. DNA sequencing of the progenitor ILS and ISS strains and microarray analyses were also conducted to identify candidate genes and functional correlates. LXS mice were given either saline or alcohol (5 g/kg) on day 1 and then tested for loss of righting reflex AFT on day 2. QTLs were mapped using standard procedures. Two microarray analyses from brain were conducted: (i) naïve LXS mice and (ii) an alcohol treatment time course in the ILS and ISS. The full genomes of the ILS and ISS were sequenced to a depth of approximately 30×. A significant QTL for AFT in the alcohol pretreatment group was mapped to distal chromosome 4; numerous suggestive QTLs were also mapped. Preference drinking and DID have previously been mapped to the chromosome 4 locus. The credible interval of the significant chromosome 4 QTL spanned 23 Mb and included 716 annotated genes of which 150 had at least 1 nonsynonymous single nucleotide polymorphism or small indel that differed between the ILS and ISS; expression of 48 of the genes was cis-regulated. Enrichment analysis indicated broad functional categories underlying AFT, including proteolysis, transcription regulation, chromatin modification, protein kinase activity, and apoptosis. The chromosome 4 QTL is a key region containing possibly pleiotropic genes for AFT and drinking behavior. Given that the region contains many viable candidates and a large number of the genes in the interval fall into 1 or more of the enriched functional categories, we postulate that many genes of varying effect size contribute to the observed QTL effect. Copyright © 2015 by the Research Society on Alcoholism.

  19. A powerful test of parent-of-origin effects for quantitative traits using haplotypes.

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    Rui Feng

    Full Text Available Imprinting is an epigenetic phenomenon where the same alleles have unequal transcriptions and thus contribute differently to a trait depending on their parent of origin. This mechanism has been found to affect a variety of human disorders. Although various methods for testing parent-of-origin effects have been proposed in linkage analysis settings, only a few are available for association analysis and they are usually restricted to small families and particular study designs. In this study, we develop a powerful maximum likelihood test to evaluate the parent-of-origin effects of SNPs on quantitative phenotypes in general family studies. Our method incorporates haplotype distribution to take advantage of inter-marker LD information in genome-wide association studies (GWAS. Our method also accommodates missing genotypes that often occur in genetic studies. Our simulation studies with various minor allele frequencies, LD structures, family sizes, and missing schemes have uniformly shown that using the new method significantly improves the power of detecting imprinted genes compared with the method using the SNP at the testing locus only. Our simulations suggest that the most efficient strategy to investigate parent-of-origin effects is to recruit one parent and as many offspring as possible under practical constraints. As a demonstration, we applied our method to a dataset from the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN to test the parent-of-origin effects of the SNPs within the PPARGC1A, MTP and FABP2 genes on diabetes-related phenotypes, and found that several SNPs in the MTP gene show parent-of-origin effects on insulin and glucose levels.

  20. Quantitative trait loci associated with longevity of lettuce seeds under conventional and controlled deterioration storage conditions

    Science.gov (United States)

    Schwember, Andrés R.; Bradford, Kent J.

    2010-01-01

    Lettuce (Lactuca sativa L.) seeds have poor shelf life and exhibit thermoinhibition (fail to germinate) above ∼25°C. Seed priming (controlled hydration followed by drying) alleviates thermoinhibition by increasing the maximum germination temperature, but reduces lettuce seed longevity. Controlled deterioration (CD) or accelerated ageing storage conditions (i.e. elevated temperature and relative humidity) are used to study seed longevity and to predict potential seed lifetimes under conventional storage conditions. Seeds produced in 2002 and 2006 of a recombinant inbred line (RIL) population derived from a cross between L. sativa cv. Salinas×L. serriola accession UC96US23 were utilized to identify quantitative trait loci (QTLs) associated with seed longevity under CD and conventional storage conditions. Multiple longevity-associated QTLs were identified under both conventional and CD storage conditions for control (non-primed) and primed seeds. However, seed longevity was poorly correlated between the two storage conditions, suggesting that deterioration processes under CD conditions are not predictive of ageing in conventional storage conditions. Additionally, the same QTLs were not identified when RIL populations were grown in different years, indicating that lettuce seed longevity is strongly affected by production environment. Nonetheless, a major QTL on chromosome 4 [Seed longevity 4.1 (Slg4.1)] was responsible for almost 23% of the phenotypic variation in viability of the conventionally stored control seeds of the 2006 RIL population, with improved longevity conferred by the Salinas allele. QTL analyses may enable identification of mechanisms responsible for the sensitivity of primed seeds to CD conditions and breeding for improved seed longevity. PMID:20693410

  1. The Expression Quantitative Trait Loci in Immune Pathways and their Effect on Cutaneous Melanoma Prognosis.

    Science.gov (United States)

    Vogelsang, Matjaz; Martinez, Carlos N; Rendleman, Justin; Bapodra, Anuj; Malecek, Karolina; Romanchuk, Artur; Kazlow, Esther; Shapiro, Richard L; Berman, Russell S; Krogsgaard, Michelle; Osman, Iman; Kirchhoff, Tomas

    2016-07-01

    The identification of personalized germline markers with biologic relevance for the prediction of cutaneous melanoma prognosis is highly demanded but to date, it has been largely unsuccessful. As melanoma progression is controlled by host immunity, here we present a novel approach interrogating immunoregulatory pathways using the genome-wide maps of expression quantitative trait loci (eQTL) to reveal biologically relevant germline variants modulating cutaneous melanoma outcomes. Using whole genome eQTL data from a healthy population, we identified 385 variants significantly impacting the expression of 268 immune-relevant genes. The 40 most significant eQTLs were tested in a prospective cohort of 1,221 patients with cutaneous melanoma for their association with overall (OS) and recurrence-free survival using Cox regression models. We identified highly significant associations with better melanoma OS for rs6673928, impacting IL19 expression (HR, 0.56; 95% CI, 0.41-0.77; P = 0.0002) and rs6695772, controlling the expression of BATF3 (HR, 1.64; 95% CI, 1.19-2.24; P = 0.0019). Both associations map in the previously suspected melanoma prognostic locus at 1q32. Furthermore, we show that their combined effect on melanoma OS is substantially enhanced reaching the level of clinical applicability (HR, 1.92; 95% CI, 1.43-2.60; P = 2.38e-5). Our unique approach of interrogating lymphocyte-specific eQTLs reveals novel and biologically relevant immunomodulatory eQTL predictors of cutaneous melanoma prognosis that are independent of current histopathologic markers. The significantly enhanced combined effect of identified eQTLs suggests the personalized utilization of both SNPs in a clinical setting, strongly indicating the promise of the proposed design for the discovery of prognostic or risk germline markers in other cancers. Clin Cancer Res; 22(13); 3268-80. ©2016 AACR. ©2016 American Association for Cancer Research.

  2. Detection of quantitative trait loci for resistance/susceptibility to pseudorabies virus in swine.

    Science.gov (United States)

    Reiner, Gerald; Melchinger, Elke; Kramarova, Marcela; Pfaff, Eberhardt; Büttner, Matthias; Saalmüller, Armin; Geldermann, Hermann

    2002-01-01

    This study describes genetic differences in resistance/susceptibility to pseudorabies virus (PrV) between European Large White and Chinese Meishan pigs, with a mapping of quantitative trait loci (QTL) obtained from a genome-wide scan in F(2) animals. Eighty-nine F(2) pigs were challenged intranasally at 12 weeks with 10(5) p.f.u. of the wild-type PrV strain NIA-3. For QTL analysis, 85 microsatellite markers, evenly spaced on the 18 porcine autosomes and on the pseudoautosomal region of the X chromosome, were genotyped. All pigs developed clinical signs, i.e. fever, from 3 to 7 days p.i. The pure-bred Large White pigs, the F(1) and three-quarters of the F(2) animals, but none of the Meishan pigs, developed neurological symptoms and died or were euthanized. QTLs for appearance/non-appearance of neurological symptoms were found on chromosomes 9, 5, 6 and 13. They explained 10.6-17.9% of F(2) phenotypic variance. QTL effects for rectal temperature after PrV challenge were found on chromosomes 2, 4, 8, 10, 11 and 16. Effects on chromosomes 9, 10 and 11 were significant on a genome-wide level. The results present chromosomal regions that are associated with presence/absence of neurological symptoms as well as temperature course after intranasal challenge with NIA-3. The QTLs are in proximity to important candidate genes that are assumed to play crucial roles in host defence against PrV.

  3. Introgression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars.

    Science.gov (United States)

    Concibido, V C; La Vallee, B; McLaird, P; Pineda, N; Meyer, J; Hummel, L; Yang, J; Wu, K; Delannay, X

    2003-02-01

    The value of exotic germplasm in broadening the genetic base of most crops has been demonstrated many times. However, the difficulties involved in working with exotic germplasm have limited their utility in plant breeding. Unwanted linkages often thwart the successful incorporation of beneficial exotic genes into commercial lines. Thus, the use of exotics in traditional breeding makes the process of crop improvement a tedious, time-consuming and expensive endeavor. The availability of molecular markers makes it possible to isolate specific genomic regions and transfer them into commercial varieties with minimal linkage drag. We found a yield-enhancing quantitative trait locus (QTL) from Glycine soja (Siebold and Zucc.) by evaluating a population of 265 BC(2) individuals from a cross between HS-1 and PI 407305. The yield QTL was located on linkage group B2(U26) of the soybean [Glycine max (L.) Merrill] genetic linkage map. In a 2-year, multi-location study, individuals carrying the PI 407305 haplotype at the QTL locus demonstrated a 9.4% yield advantage over individuals that did not contain the exotic haplotype. When tested in a more uniform "HS-1-like" background in two locations, we observed an 8% yield advantage for lines that carry the PI 407305 haplotype. We further assessed the QTL effect in various elite soybean genetic backgrounds. The yield effect was consistently observed in only two of six genetic backgrounds. Individuals carrying the PI 407305 haplotype at the QTL locus had a 9% yield advantage in yield trials across locations. Despite the limited adaptability of this yield-QTL across genetic backgrounds, this study demonstrates the potential of exotic germplasm for yield enhancement in soybean.

  4. A narrow quantitative trait locus in C. elegans coordinately affects longevity, thermotolerance, and resistance to paraquat

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    Anthony eVertino

    2011-09-01

    Full Text Available By linkage mapping of quantitative trait loci, we previously identified at least 11 natural genetic variants that significantly modulate C. elegans lifespan, many of which would have eluded discovery by knockdown or mutation screens. A region on chromosome IV between markers stP13 and stP35 had striking effects on longevity in three interstrain crosses (each P < 1E–9. In order to define the limits of that interval, we have now constructed two independent lines by marker-based selection during 20 backcross generations, isolating the stP13–stP35 interval from strain Bergerac-BO in a CL2a background. These congenic lines differed significantly from CL2a in lifespan, assayed in two environments (each P<0.001. We then screened for exchange of flanking markers to isolate recombinants that partition this region, because fine mapping the boundaries for overlapping heteroallelic spans can greatly narrow the implicated interval. Recombinants carrying the CL2a allele at stP35 were consistently long-lived compared to those retaining the Bergerac-BO allele (P<0.001, and more resistant to temperature elevation and paraquat (each ~1.7-fold, P<0.0001, but gained little protection from ultraviolet or peroxide stresses. Two rounds of recombinant screening, followed by fine-mapping of break-points and survival testing, narrowed the interval to 0.18 Mb (13.35–13.53 Mb containing 26 putative genes and 6 small-nuclear RNAs – a manageable number of targets for functional assessment.

  5. Replication and narrowing of gene expression quantitative trait loci using inbred mice.

    Science.gov (United States)

    Gatti, Daniel M; Harrill, Alison H; Wright, Fred A; Threadgill, David W; Rusyn, Ivan

    2009-07-01

    Gene expression quantitative trait locus (eQTL) mapping has become a powerful tool in systems biology. While many authors have made important discoveries using this approach, one persistent challenge in eQTL studies is the selection of loci and genes that should receive further biological investigation. In this study we compared eQTL generated from gene expression profiling in the livers of two panels of mouse strains: 41 BXD recombinant inbred and 36 Mouse Diversity Panel (MDP) strains. Cis-eQTL, loci in which the transcript and its maximum QTL are colocated, have been shown to be more reproducible than trans-eQTL, which are not colocated with the transcript. We observed that between 9.9 and 12.1% of cis-eQTL and between 2.0 and 12.6% of trans-eQTL replicated between the two panels depending on the degree of statistical stringency. Notably, a significant eQTL hotspot on distal chromosome 12 observed in the BXD panel was reproduced in the MDP. Furthermore, the shorter linkage disequilibrium in the MDP strains allowed us to considerably narrow the locus and limit the number of candidate genes to a cluster of Serpin genes, which code for extracellular proteases. We conclude that this strategy has some utility in increasing confidence and resolution in eQTL mapping studies; however, due to the high false-positive rate in the MDP, eQTL mapping in inbred strains is best carried out in combination with an eQTL linkage study.

  6. Expression quantitative trait loci for PAX8 contributes to the prognosis of hepatocellular carcinoma.

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    Shijie Ma

    Full Text Available Paired-box family member PAX8 encodes a transcription factor that has a role in cell differentiation and cell growth and may participate in the prognosis of hepatocellular carcinoma (HCC. By bioinformatics analysis, we identified several single nucleotide polymorphisms (SNPs within a newly identified long non-coding RNA (lncRNA AC016683.6 as expression quantitative trait loci (eQTLs for PAX8. Hence, we hypothesized that PAX8eQTLs in lncRNA AC016683.6 may influence the HCC prognosis. We then performed a case-only study to assess the association between the two SNPs as well as the prognosis of HCC in 331 HBV-positive HCC patients without surgical treatment. Cox proportional hazard models were used for survival analysis with adjustments for the age, gender, smoking status, drinking status, Barcelona-Clinic Liver Cancer (BCLC stage, and chemotherapy or TACE (transcatheter hepatic arterial chemoembolization status. We found that the G allele of rs1110839 and the T allele of rs4848320 in PAX8was significantly associated with a better prognosis compared with the T allele of rs1110839 and the C allele of rs4848320 (adjusted HR = 0.74, 95% CI = 0.61-0.91, P = 0.004 for rs1110839 and adjusted HR = 0.71, 95% CI = 0.54-0.94, P = 0.015 for rs4848320 in the additive model. Furthermore, the combined effect of the variant genotypes for these two SNPs was more prominent in patients with the BCLC-C stage orpatients with chemotherapy or TACE. Although the exact biological function remains to be explored, our findings suggest a possible association of PAX8eQTLs in lncRNA AC016683.6 with the HCC prognosis inthe Chinese population. Further large and functional studies are needed to confirm our findings.

  7. Identification of quantitative trait loci controlling linolenic acid concentration in PI483463 (Glycine soja).

    Science.gov (United States)

    Ha, Bo-Keun; Kim, Hyun-Jee; Velusamy, Vijayanand; Vuong, Tri D; Nguyen, Henry T; Shannon, J Grover; Lee, Jeong-Dong

    2014-07-01

    The QTLs controlling alpha-linolenic acid concentration from wild soybean were mapped on nine soybean chromosomes with various phenotypic variations. New QTLs for alpha-linolenic acid were detected in wild soybean. Alpha-linolenic acid (ALA) is a polyunsaturated fatty acid desired in human and animal diets. Some wild soybean (Glycine soja) genotypes are high in ALA. The objective of this study was to identify quantitative trait loci (QTLs) controlling ALA concentration in a wild soybean accession, PI483463. In total, 188 recombinant inbred lines of F5:6, F5:7, and F5:8 generations derived from a cross of wild soybean PI483463 (~15 % ALA) and cultivar Hutcheson (~9 % ALA) were planted in four environments. Harvested seeds were used to measure fatty acid concentration. Single nucleotide polymorphism markers of the universal soybean linkage panel (USLP 1.0) and simple sequence repeat markers were used for molecular genotyping. Nine putative QTLs were identified that controlled ALA concentration by model-based composite interval mapping and mapped to different soybean chromosomes. The QTLs detected in four environments explained 2.4-7.9 % of the total phenotypic variation (PV). Five QTLs, qALA5_3, qALA6_1, qALA14_1, qALA15_1, and qALA17_1, located on chromosomes 5, 6, 14, 15, and 17 were identified by model-based composite interval mapping and composite interval mapping in two individual environments. Among them, qALA6_1 showed the highest contribution to the PV with 10.0-10.2 % in two environments. The total detected QTLs for additive and epistatic effects explained 52.4 % of the PV for ALA concentration. These findings will provide useful information for understanding genetic structure and marker-assisted breeding programs to increase ALA concentration in seeds derived from wild soybean PI483463.

  8. Quantitative trait locus analysis identifies Gabra3 as a regulator of behavioral despair in mice

    Science.gov (United States)

    Miller, Brooke H.; Schultz, Laura E.; Long, Bradley C.

    2010-01-01

    The Tail Suspension Test (TST), which measures behavioral despair, is widely used as an animal model of human depressive disorders and antidepressant efficacy. In order to identify novel genes involved in the regulation of TST performance, we crossed an inbred strain exhibiting low immobility in the TST (RIIIS/J) with two high-immobility strains (C57BL/6J and NZB/BlNJ) to create two distinct F2 hybrid populations. All F2 offspring (n = 655) were genotyped at high density with a panel of SNP markers. Whole-genome interval mapping of the F2 populations identified statistically significant quantitative trait loci (QTLs) on mouse chromosomes (MMU) 4, 6, and X. Microarray analysis of hippocampal gene expression in the three parental strains was used to identify potential candidate genes within the MMUX QTLs identified in the NZB/BlNJ × RIIIS/J cross. Expression of Gabra3, which encodes the GABAA receptor α3 subunit, was robust in the hippocampus of B6 and RIIIS mice but absent from NZB hippocampal tissue. To verify the role of Gabra3 in regulating TST behavior in vivo, mice were treated with SB-205384, a positive modulator of the α3 subunit. SB-205384 significantly reduced TST immobility in B6 mice without affecting general activity, but it had no effect on behavior in NZB mice. This work suggests that GABRA3 regulates a behavioral endophenotype of depression and establishes this gene as a viable new target for the study and treatment of human depression. Electronic supplementary material The online version of this article (doi:10.1007/s00335-010-9266-6) contains supplementary material, which is available to authorized users. PMID:20512339

  9. Mapping Quantitative Trait Loci (QTL for Resistance to Late Blight in Tomato

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    Dilip R. Panthee

    2017-07-01

    Full Text Available Late blight caused by Phytophthora infestans (Montagne, Bary is a devastating disease of tomato worldwide. There are three known major genes, Ph-1, Ph-2, and Ph-3, conferring resistance to late blight. In addition to these three genes, it is also believed that there are additional factors or quantitative trait loci (QTL conferring resistance to late blight. Precise molecular mapping of all those major genes and potential QTL is important in the development of suitable molecular markers and hence, marker-assisted selection (MAS. The objective of the present study was to map the genes and QTL associated with late blight resistance in a tomato population derived from intra-specific crosses. To achieve this objective, a population, derived from the crossings of NC 1CELBR × Fla. 7775, consisting of 250 individuals at F2 and F2-derived families, were evaluated in replicated trials. These were conducted at Mountain Horticultural Crops Reseach & Extension Center (MHCREC at Mills River, NC, and Mountain Research Staion (MRS at Waynesville, NC in 2011, 2014, and 2015. There were two major QTL associated with late blight resistance located on chromosomes 9 and 10 with likelihood of odd (LOD scores of more than 42 and 6, explaining 67% and 14% of the total phenotypic variation, respectively. The major QTLs are probably caused by the Ph-2 and Ph-3 genes. Furthermore, there was a minor QTL on chromosomes 12, which has not been reported before. This minor QTL may be novel and may be worth investigating further. Source of resistance to Ph-2, Ph-3, and this minor QTL traces back to line L3707, or Richter’s Wild Tomato. The combination of major genes and minor QTL may provide a durable resistance to late blight in tomato.

  10. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

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    Fagen Li

    Full Text Available Dense genetic maps, along with quantitative trait loci (QTLs detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR, expressed sequence tag (EST derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS, and diversity arrays technology (DArT markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age and wood density (56 months were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

  11. Association Mapping of Malting Quality Quantitative Trait Loci in Winter Barley: Positive Signals from Small Germplasm Arrays

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    Lucía Gutiérrez

    2011-11-01

    Full Text Available Malting quality comprises one of the most economically relevant set of traits in barley ( L.. It is a complex phenotype, expensive and difficult to measure, that would benefit from a marker-assisted selection strategy. Malting quality is a target of the U.S. Barley Coordinated Agricultural Project (CAP and development of winter habit malting barley varieties is a key objective of the U.S. barley research community. The objective of this work was to detect quantitative trait loci (QTL for malting quality traits in a winter breeding program that is a component of the U.S. Barley CAP. We studied the association between five malting quality traits and 3072 single nucleotide polymorphisms (SNPs from the barley oligonucleotide pool assay (BOPA 1 and 2, assayed in advanced inbred lines from the Oregon State University (OSU breeding program from three germplasm arrays (CAP I, CAP II, and CAP III. After comparing 16 models we selected a structured association model with posterior probabilities inferred from software STRUCTURE (QK approach to use on all germplasm arrays. Most of the marker-trait associations are germplasm- and environment-specific and close to previously mapped genes and QTL relevant for malt and beer quality. We found alleles fixed by random genetic drift, novel unmasked alleles, and genetic-background interaction. In a relatively small population size study we provide strong evidence for detecting true QTL.

  12. Quantitative Trait Locus Analysis of Seed Germination and Seedling Vigor in Brassica rapa Reveals QTL Hotspots and Epistatic Interactions

    Science.gov (United States)

    Basnet, Ram K.; Duwal, Anita; Tiwari, Dev N.; Xiao, Dong; Monakhos, Sokrat; Bucher, Johan; Visser, Richard G. F.; Groot, Steven P. C.; Bonnema, Guusje; Maliepaard, Chris

    2015-01-01

    The genetic basis of seed germination and seedling vigor is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded vegetable-type pak choi. We identified 26 QTL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigor under non-stress and salt stress conditions illustrating the polygenic nature of these traits. QTLs for multiple traits co-localized and we identified eight hotspots for quantitative trait loci (QTL) of seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 mapped at the B. rapa Flowering Locus C (BrFLC2). Another hotspot on A05 with salt stress specific QTLs co-located with the B. rapa Fatty acid desaturase 2 (BrFAD2) locus. Epistatic interactions were observed between QTL hotspots for seed germination on A02 and A10 and with a salt tolerance QTL on A05. These results contribute to the understanding of the genetics of seed quality and seeding vigor in B. rapa and can offer tools for Brassica breeding. PMID:26648948

  13. Mapping quantitative trait loci associated with chilling requirement, heat requirement and bloom date in peach (Prunus persica).

    Science.gov (United States)

    Fan, Shenghua; Bielenberg, Douglas G; Zhebentyayeva, Tetyana N; Reighard, Gregory L; Okie, William R; Holland, Doron; Abbott, Albert G

    2010-03-01

    *Chilling requirement, together with heat requirement, determines the bloom date, which has an impact on the climatic distribution of the genotypes of tree species. The molecular basis of floral bud chilling requirement is poorly understood, despite its importance to the adaptation and production of fruit trees. In addition, the genetic nature of heat requirement and the genetic interrelationships among chilling requirement, heat requirement and bloom date remain unclear. *A peach (Prunus persica) F(2) population of 378 genotypes developed from two genotypes with contrasting chilling requirements was used for linkage map construction and quantitative trait loci (QTL) mapping. The floral bud chilling and heat requirements of each genotype were evaluated over 2 yr and the bloom date was scored over 4 yr. *Twenty QTLs with additive effects were identified for three traits, including one major QTL for chilling requirement and two major QTLs for bloom date. The majority of QTLs colocalized with QTLs for other trait(s). In particular, one genomic region of 2 cM, pleiotropic for the three traits, overlapped with the sequenced peach EVG region. *This first report on the QTL mapping of floral bud chilling requirement will facilitate marker-assisted breeding for low chilling requirement cultivars and the map-based cloning of genes controlling chilling requirement. The extensive colocalization of QTLs suggests that there may be one unified temperature sensing and action system regulating chilling requirement, heat requirement and bloom date together.

  14. Quantitative Trait Locus Analysis of Seed Germination and Seedling Vigor in Brassica rapa Reveals QTL Hotspots and Epistatic Interactions.

    Science.gov (United States)

    Basnet, Ram K; Duwal, Anita; Tiwari, Dev N; Xiao, Dong; Monakhos, Sokrat; Bucher, Johan; Visser, Richard G F; Groot, Steven P C; Bonnema, Guusje; Maliepaard, Chris

    2015-01-01

    The genetic basis of seed germination and seedling vigor is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded vegetable-type pak choi. We identified 26 QTL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigor under non-stress and salt stress conditions illustrating the polygenic nature of these traits. QTLs for multiple traits co-localized and we identified eight hotspots for quantitative trait loci (QTL) of seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 mapped at the B. rapa Flowering Locus C (BrFLC2). Another hotspot on A05 with salt stress specific QTLs co-located with the B. rapa Fatty acid desaturase 2 (BrFAD2) locus. Epistatic interactions were observed between QTL hotspots for seed germination on A02 and A10 and with a salt tolerance QTL on A05. These results contribute to the understanding of the genetics of seed quality and seeding vigor in B. rapa and can offer tools for Brassica breeding.

  15. Quantitative Trait Loci for Yield and Yield-Related Traits in Spring Barley Populations Derived from Crosses between European and Syrian Cultivars.

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    Krzysztof Mikołajczak

    Full Text Available In response to climatic changes, breeding programmes should be aimed at creating new cultivars with improved resistance to water scarcity. The objective of this study was to examine the yield potential of barley recombinant inbred lines (RILs derived from three cross-combinations of European and Syrian spring cultivars, and to identify quantitative trait loci (QTLs for yield-related traits in these populations. RILs were evaluated in field experiments over a period of three years (2011 to 2013 and genotyped with simple sequence repeat (SSR and single nucleotide polymorphism (SNP markers; a genetic map for each population was constructed and then one consensus map was developed. Biological interpretation of identified QTLs was achieved by reference to Ensembl Plants barley gene space. Twelve regions in the genomes of studied RILs were distinguished after QTL analysis. Most of the QTLs were identified on the 2H chromosome, which was the hotspot region in all three populations. Syrian parental cultivars contributed alleles decreasing traits' values at majority of QTLs for grain weight, grain number, spike length and time to heading, and numerous alleles increasing stem length. The phenomic and molecular approaches distinguished the lines with an acceptable grain yield potential combining desirable features or alleles from their parents, that is, early heading from the Syrian breeding line (Cam/B1/CI08887//CI05761 and short plant stature from the European semidwarf cultivar (Maresi.

  16. Quantitative trait loci for plant height in Maresi × CamB barley population and their associations with yield-related traits under different water regimes.

    Science.gov (United States)

    Mikołajczak, Krzysztof; Kuczyńska, Anetta; Krajewski, Paweł; Sawikowska, Aneta; Surma, Maria; Ogrodowicz, Piotr; Adamski, Tadeusz; Krystkowiak, Karolina; Górny, Andrzej G; Kempa, Michał; Szarejko, Iwona; Guzy-Wróbelska, Justyna; Gudyś, Kornelia

    2017-02-01

    High-yielding capacity of the modern barley varieties is mostly dependent on the sources of semi-dwarfness associated with the sdw1/denso locus. The objective of the study was to identify quantitative trait loci (QTLs) associated with the plant height and yield potential of barley recombinant inbred lines (RILs) grown under various soil moisture regimes. The plant material was developed from a hybrid between the Maresi (European cv.) and CamB (Syrian cv.). A total of 103 QTLs affecting analysed traits were detected and 36 of them showed stable effects over environments. In total, ten QTLs were found to be significant only under water shortage conditions. Nine QTLs affecting the length of main stem were detected on 2H-6H chromosomes. In four of the detected QTLs, alleles contributed by Maresi had negative effects on that trait, the most significant being the QLSt-3H.1-1 in the 3H.1 linkage group. The close linkage between QTLs identified around the sdw1/denso locus, with positive alleles contributed by Maresi, indicates that the semi-dwarf cv. Maresi could serve as a donor of favourable traits resulting in grain yield improvement, also under water scarcity. Molecular analyses revealed that the Syrian cv. also contributed alleles which increased the yield potential. Available barley resources of genomic annotations were employed to the biological interpretation of detected QTLs. This approach revealed 26 over-represented Gene Ontology terms. In the projected support intervals of QGWSl-5H.3-2 and QLSt-5H.3 on the chromosome 5H, four genes annotated to 'response to stress' were found. It suggests that these QTL-regions may be involved in a response of plant to a wide range of environmental disturbances.

  17. Identification of Quantitative Trait Loci Controlling Root and Shoot Traits Associated with Drought Tolerance in a Lentil (Lens culinaris Medik.) Recombinant Inbred Line Population.

    Science.gov (United States)

    Idrissi, Omar; Udupa, Sripada M; De Keyser, Ellen; McGee, Rebecca J; Coyne, Clarice J; Saha, Gopesh C; Muehlbauer, Fred J; Van Damme, Patrick; De Riek, Jan

    2016-01-01

    Drought is one of the major abiotic stresses limiting lentil productivity in rainfed production systems. Specific rooting patterns can be associated with drought avoidance mechanisms that can be used in lentil breeding programs. In all, 252 co-dominant and dominant markers were used for Quantitative Trait Loci (QTL) analysis on 132 lentil recombinant inbred lines based on greenhouse experiments for root and shoot traits during two seasons under progressive drought-stressed conditions. Eighteen QTLs controlling a total of 14 root and shoot traits were identified. A QTL-hotspot genomic region related to a number of root and shoot characteristics associated with drought tolerance such as dry root biomass, root surface area, lateral root number, dry shoot biomass and shoot length was identified. Interestingly, a QTL (QRSratioIX-2.30) related to root-shoot ratio, an important trait for drought avoidance, explaining the highest phenotypic variance of 27.6 and 28.9% for the two consecutive seasons, respectively, was detected. This QTL was closed to the co-dominant SNP marker TP6337 and also flanked by the two SNP TP518 and TP1280. An important QTL (QLRNIII-98.64) related to lateral root number was found close to TP3371 and flanked by TP5093 and TP6072 SNP markers. Also, a QTL (QSRLIV-61.63) associated with specific root length was identified close to TP1873 and flanked by F7XEM6b SRAP marker and TP1035 SNP marker. These two QTLs were detected in both seasons. Our results could be used for marker-assisted selection in lentil breeding programs targeting root and shoot characteristics conferring drought avoidance as an efficient alternative to slow and labor-intensive conventional breeding methods.

  18. Identification of quantitative trait loci controlling root and shoot traits associated with drought tolerance in a lentil (Lens culinaris Medik. recombinant inbred line population

    Directory of Open Access Journals (Sweden)

    Omar Idrissi

    2016-08-01

    Full Text Available Drought is one of the major abiotic stresses limiting lentil productivity in rainfed production systems. Specific rooting patterns can be associated with drought avoidance mechanisms that can be used in lentil breeding programs. In all, 252 co-dominant and dominant markers were used for Quantitative Trait Loci (QTL analysis on 132 lentil recombinant inbred lines based on greenhouse experiments for root and shoot traits during two seasons under progressive drought-stressed conditions. Eighteen QTLs controlling a total of 14 root and shoot traits were identified. A QTL-hotspot genomic region related to a number of root and shoot characteristics associated with drought tolerance such as dry root biomass, root surface area, lateral root number, dry shoot biomass and shoot length was identified. Interestingly, a QTL related to root-shoot ratio, an important trait for drought avoidance, explaining the highest phenotypic variance of 27.6 % and 28.9 % for the two consecutive seasons, respectively, was detected. This QTL was closed to the co-dominant SNP marker TP6337 and also flanked by the two SNP TP518 and TP1280. An important QTL related to lateral root number was found close to TP3371 and flanked by TP5093 and TP6072 SNP markers. Also, a QTL associated with specific root length was identified close to TP1873 and flanked by F7XEM6b SRAP marker and TP1035 SNP marker. These two QTLs were detected in both seasons. Our results could be used for marker-assisted selection in lentil breeding programs targeting root and shoot characteristics conferring drought avoidance as an efficient alternative to slow and labour-intensive conventional breeding methods.

  19. Comparison of Quantitative Trait Loci for Adaptive Traits Between Oak and Chestnut Based on an Expressed Sequence Tag Consensus Map

    Science.gov (United States)

    Casasoli, Manuela; Derory, Jeremy; Morera-Dutrey, Caroline; Brendel, Oliver; Porth, Ilga; Guehl, Jean-Marc; Villani, Fiorella; Kremer, Antoine

    2006-01-01

    A comparative genetic and QTL mapping was performed between Quercus robur L. and Castanea sativa Mill., two major forest tree species belonging to the Fagaceae family. Oak EST-derived markers (STSs) were used to align the 12 linkage groups of the two species. Fifty-one and 45 STSs were mapped in oak and chestnut, respectively. These STSs, added to SSR markers previously mapped in both species, provided a total number of 55 orthologous molecular markers for comparative mapping within the Fagaceae family. Homeologous genomic regions identified between oak and chestnut allowed us to compare QTL positions for three important adaptive traits. Colocation of the QTL controlling the timing of bud burst was significant between the two species. However, conservation of QTL for height growth was not supported by statistical tests. No QTL for carbon isotope discrimination was conserved between the two species. Putative candidate genes for bud burst can be identified on the basis of colocations between EST-derived markers and QTL. PMID:16204213

  20. Identification of a Putative Quantitative Trait Gene for Resistance to Obesity in Mice Using Transcriptome Analysis and Causal Inference Tests.

    Directory of Open Access Journals (Sweden)

    Akira Ishikawa

    Full Text Available It is still challenging to identify causal genes governing obesity. Pbwg1.5, a quantitative trait locus (QTL for resistance to obesity, was previously discovered from wild Mus musculus castaneus mice and was fine-mapped to a 2.1-Mb genomic region of mouse chromosome 2, where no known gene with an effect on white adipose tissue (WAT has been reported. The aim of this study was to identify a strong candidate gene for Pbwg1.5 by an integration approach of transcriptome analysis (RNA-sequencing followed by real-time PCR analysis and the causal inference test (CIT, a statistical method to infer causal relationships between diplotypes, gene expression and trait values. Body weight, body composition and biochemical traits were measured in F2 mice obtained from an intercross between the C57BL/6JJcl strain and a congenic strain carrying Pbwg1.5 on the C57BL/6JJcl background. The F2 mice showed significant diplotype differences in 12 traits including body weight, WAT weight and serum cholesterol/triglyceride levels. The transcriptome analysis revealed that Ly75, Pla2r1, Fap and Gca genes were differentially expressed in the liver and that Fap, Ifih1 and Grb14 were differentially expressed in WAT. However, CITs indicated statistical evidence that only the liver Ly75 gene mediated between genotype and WAT. Ly75 expression was negatively associated with WAT weight. The results suggested that Ly75 is a putative quantitative trait gene for the obesity-resistant Pbwg1.5 QTL discovered from the wild M. m. castaneus mouse. The finding provides a novel insight into a better understanding of the genetic basis for prevention of obesity.

  1. Identification of a Putative Quantitative Trait Gene for Resistance to Obesity in Mice Using Transcriptome Analysis and Causal Inference Tests.

    Science.gov (United States)

    Ishikawa, Akira

    2017-01-01

    It is still challenging to identify causal genes governing obesity. Pbwg1.5, a quantitative trait locus (QTL) for resistance to obesity, was previously discovered from wild Mus musculus castaneus mice and was fine-mapped to a 2.1-Mb genomic region of mouse chromosome 2, where no known gene with an effect on white adipose tissue (WAT) has been reported. The aim of this study was to identify a strong candidate gene for Pbwg1.5 by an integration approach of transcriptome analysis (RNA-sequencing followed by real-time PCR analysis) and the causal inference test (CIT), a statistical method to infer causal relationships between diplotypes, gene expression and trait values. Body weight, body composition and biochemical traits were measured in F2 mice obtained from an intercross between the C57BL/6JJcl strain and a congenic strain carrying Pbwg1.5 on the C57BL/6JJcl background. The F2 mice showed significant diplotype differences in 12 traits including body weight, WAT weight and serum cholesterol/triglyceride levels. The transcriptome analysis revealed that Ly75, Pla2r1, Fap and Gca genes were differentially expressed in the liver and that Fap, Ifih1 and Grb14 were differentially expressed in WAT. However, CITs indicated statistical evidence that only the liver Ly75 gene mediated between genotype and WAT. Ly75 expression was negatively associated with WAT weight. The results suggested that Ly75 is a putative quantitative trait gene for the obesity-resistant Pbwg1.5 QTL discovered from the wild M. m. castaneus mouse. The finding provides a novel insight into a better understanding of the genetic basis for prevention of obesity.

  2. An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci.

    Science.gov (United States)

    Ju, Jin Hyun; Shenoy, Sushila A; Crystal, Ronald G; Mezey, Jason G

    2017-05-01

    Genome-wide expression Quantitative Trait Loci (eQTL) studies in humans have provided numerous insights into the genetics of both gene expression and complex diseases. While the majority of eQTL identified in genome-wide analyses impact a single gene, eQTL that impact many genes are particularly valuable for network modeling and disease analysis. To enable the identification of such broad impact eQTL, we introduce CONFETI: Confounding Factor Estimation Through Independent component analysis. CONFETI is designed to address two conflicting issues when searching for broad impact eQTL: the need to account for non-genetic confounding factors that can lower the power of the analysis or produce broad impact eQTL false positives, and the tendency of methods that account for confounding factors to model broad impact eQTL as non-genetic variation. The key advance of the CONFETI framework is the use of Independent Component Analysis (ICA) to identify variation likely caused by broad impact eQTL when constructing the sample covariance matrix used for the random effect in a mixed model. We show that CONFETI has better performance than other mixed model confounding factor methods when considering broad impact eQTL recovery from synthetic data. We also used the CONFETI framework and these same confounding factor methods to identify eQTL that replicate between matched twin pair datasets in the Multiple Tissue Human Expression Resource (MuTHER), the Depression Genes Networks study (DGN), the Netherlands Study of Depression and Anxiety (NESDA), and multiple tissue types in the Genotype-Tissue Expression (GTEx) consortium. These analyses identified both cis-eQTL and trans-eQTL impacting individual genes, and CONFETI had better or comparable performance to other mixed model confounding factor analysis methods when identifying such eQTL. In these analyses, we were able to identify and replicate a few broad impact eQTL although the overall number was small even when applying CONFETI. In

  3. The sensitivity of murine spermiogenesis to miglustat is a quantitative trait: a pharmacogenetic study

    Directory of Open Access Journals (Sweden)

    Boomkamp Stephanie

    2007-01-01

    parental strains. Conclusion The effects of miglustat on spermatogenesis in mice are strain-dependent, while in rabbits the drug is ineffective. Evaluation of interstrain hybrid mice indicated that the sensitivity of spermatogenesis to miglustat is a quantitative trait. These studies pave the way for identifying the genetic factors underlying the strain/species differences in the effect of miglustat.

  4. Qualitative and quantitative dermatoglyphic traits in patients with breast cancer: a prospective clinical study

    Directory of Open Access Journals (Sweden)

    Tuteja Amita

    2007-03-01

    Full Text Available Abstract Background Breast cancer is one of the most extensively studied cancers and its genetic basis is well established. Dermatoglyphic traits are formed under genetic control early in development but may be affected by environmental factors during first trimester of pregnancy. They however do not change significantly thereafter, thus maintaining stability not greatly affected by age. These patterns may represent the genetic make up of an individual and therefore his/her predisposition to certain diseases. Patterns of dermatoglyphics have been studied in various congenital disorders like Down's syndrome and Kleinfelter syndrome. The prints can thus represent a non-invasive anatomical marker of breast cancer risk and thus facilitate early detection and treatment. Methods The study was conducted on 60 histo-pathologically confirmed breast cancer patients and their digital dermatoglyphic patterns were studied to assess their association with the type and onset of breast cancer. Simultaneously 60 age-matched controls were also selected that had no self or familial history of a diagnosed breast cancer and the observations were recorded. The differences of qualitative (dermatoglyphic patterns data were tested for their significance using the chi-square test, and for quantitative (ridge counts and pattern intensity index data using the t- test. Results It was observed that six or more whorls in the finger print pattern were statistically significant among the cancer patients as compared to controls. It was also seen that whorls in the right ring finger and right little finger were found increased among the cases as compared to controls. The differences between mean pattern intensity index of cases and controls were found to be statistically significant. Conclusion The dermatoglyphic patterns may be utilized effectively to study the genetic basis of breast cancer and may also serve as a screening tool in the high-risk population. In a developing

  5. Application of a Bayesian dominance model improves power in quantitative trait genome-wide association analysis.

    Science.gov (United States)

    Bennewitz, Jörn; Edel, Christian; Fries, Ruedi; Meuwissen, Theo H E; Wellmann, Robin

    2017-01-14

    Multi-marker methods, which fit all markers simultaneously, were originally tailored for genomic selection purposes, but have proven to be useful also in association analyses, especially the so-called BayesC Bayesian methods. In a recent study, BayesD extended BayesC towards accounting for dominance effects and improved prediction accuracy and persistence in genomic selection. The current study investigated the power and precision of BayesC and BayesD in genome-wide association studies by means of stochastic simulations and applied these methods to a dairy cattle dataset. The simulation protocol was designed to mimic the genetic architecture of quantitative traits as realistically as possible. Special emphasis was put on the joint distribution of the additive and dominance effects of causative mutations. Additive marker effects were estimated by BayesC and additive and dominance effects by BayesD. The dependencies between additive and dominance effects were modelled in BayesD by choosing appropriate priors. A sliding-window approach was used. For each window, the R. Fernando window posterior probability of association was calculated and this was used for inference purpose. The power to map segregating causal effects and the mapping precision were assessed for various marker densities up to full sequence information and various window sizes. Power to map a QTL increased with higher marker densities and larger window sizes. This held true for both methods. Method BayesD had improved power compared to BayesC. The increase in power was between -2 and 8% for causative genes that explained more than 2.5% of the genetic variance. In addition, inspection of the estimates of genomic window dominance variance allowed for inference about the magnitude of dominance at significant associations, which remains hidden in BayesC analysis. Mapping precision was not substantially improved by BayesD. BayesD improved power, but precision only slightly. Application of BayesD needs large

  6. A meta-analysis of quantitative trait loci for abiotic and biotic stress resistance in tetraploid cotton.

    Science.gov (United States)

    Abdelraheem, Abdelraheem; Liu, Feng; Song, Mingzhou; Zhang, Jinfa F

    2017-12-01

    The number and location of mapped quantitative trait loci (QTL) depend on genetic populations and testing environments. The identification of consistent QTL across genetic backgrounds and environments is a pre-requisite to marker-assisted selection. This study analyzed a total of 661 abiotic and biotic stress resistance QTL based on our previous work and other publications using the meta-analysis software Biomercator. It identified chromosomal regions containing QTL clusters for different resistance traits and hotspots for a particular resistance trait in cotton from 98 QTL for drought tolerance under greenhouse (DT) and 150 QTL in field conditions (FDT), 80 QTL for salt tolerance in the greenhouse conditions (ST), 201 QTL for resistance to Verticillium wilt (VW, Verticillium dahliae), 47 QTL for resistance to Fusarium wilt (FW, Fusarium oxysporum f. sp. vasinfectum), and 85 QTL for resistance to root-knot nematodes (RKN, Meloiodogyne incognita) and reniform nematodes (RN, Rotylenchulus reniformis). The traits used in QTL mapping for abiotic stress tolerance included morphological traits-plant height and fresh and dry shoot and root weights, physiological traits-chlorophyll content, osmotic potential, carbon isotope ratio, stomatal conductance, photosynthetic rate, transpiration, canopy temperature, and leaf area index, agronomic traits-seedcotton yield, lint yield, boll weight, and lint percent, and fiber quality traits-fiber length, uniformity, strength, elongation, and micronaire. The results showed that resistance QTL are not uniformly distributed across the cotton genome; some chromosomes carried disproportionally more QTL, QTL clusters, or hotspots. Twenty-three QTL clusters were found on 15 chromosomes (c3, c4, c5, c6, c7, c11, c14, c15, c16, c19, c20, c23, c24, c25, and c26). Moreover, 28 QTL hotshots were associated with different resistance traits including one hotspot on c4 for Verticillium wilt resistance, two QTL hotspots on c24 for chlorophyll

  7. Quantitative Genetic Analysis of Seed Vigour and Pre-Emergence Seedling Growth Traits in Brassica oleracea

    National Research Council Canada - National Science Library

    Mary Bettey; W. E. Finch-Savage; G. J. King; J. R. Lynn

    2000-01-01

    ..., and should therefore be considered in crop improvement. We measured traits associated with seed vigour and pre-emergence seedling growth in a segregating population of 105 doubled haploid Brassica oleracea lines...

  8. Cancer survivorship and sexual orientation.

    Science.gov (United States)

    Boehmer, Ulrike; Miao, Xiaopeng; Ozonoff, Al

    2011-08-15

    Lesbian, gay, and bisexual populations are not part of cancer surveillance, resulting in scarce information about the cancer survivorship of these populations. To address this information gap, the authors examined the prevalence of cancer survivorship by sexual orientation and cancer survivors' self-reported health by sexual orientation. The authors explored these issues by analyzing pooled data from the California Health Interview survey from 2001, 2003, and 2005. By using descriptive statistics and logistic regressions, they examined the cancer prevalence in men and women by sexual orientation and subsequently compared the self-reported health of male and female cancer survivors by sexual orientation. Among women, the authors found no significant differences in cancer prevalence by sexual orientation, but lesbian and bisexual female cancer survivors had 2.0 and 2.3× the odds of reporting fair or poor health compared with heterosexual female cancer survivors. Among men, we found significant differences in cancer prevalence, with gay men having 1.9× the odds of reporting a cancer diagnosis compared with heterosexual men. There were no differences by sexual orientation in male cancer survivors' self-reported health. Our novel findings suggest sex differences in the impact of cancer on lesbian, gay, and bisexual cancer survivors. Lesbian and bisexual cancer survivors need to be targeted by programs and services to assist these cancer survivors in improving their health perceptions, whereas healthcare providers and public health agencies need to be made aware of the higher prevalence of cancer in gay men to prevent future cancers through increased screening and primary prevention. Copyright © 2011 American Cancer Society.

  9. Quantitative trait loci and candidate genes associated with starch pasting viscosity characteristics in cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Thanyasiriwat, T; Sraphet, S; Whankaew, S; Boonseng, O; Bao, J; Lightfoot, D A; Tangphatsornruang, S; Triwitayakorn, K

    2014-01-01

    Starch pasting viscosity is an important quality trait in cassava (Manihot esculenta Crantz) cultivars. The aim here was to identify loci and candidate genes associated with the starch pasting viscosity. Quantitative trait loci (QTL) mapping for seven pasting viscosity parameters was carried out using 100 lines of an F1 mapping population from a cross between two cassava cultivars Huay Bong 60 and Hanatee. Starch samples were obtained from roots of cassava grown in 2008 and 2009 at Rayong, and in 2009 at Lop Buri province, Thailand. The traits showed continuous distribution among the F1 progeny with transgressive variation. Fifteen QTL were identified from mean trait data, with Logarithm of Odds (LOD) values from 2.77-13.01 and phenotype variations explained (PVE) from10.0-48.4%. In addition, 48 QTL were identified in separate environments. The LOD values ranged from 2.55-8.68 and explained 6.6-43.7% of phenotype variation. The loci were located on 19 linkage groups. The most important QTL for pasting temperature (PT) (qPT.1LG1) from mean trait values showed largest effect with highest LOD value (13.01) and PVE (48.4%). The QTL co-localised with PT and pasting time (PTi) loci that were identified in separate environments. Candidate genes were identified within the QTL peak regions. However, the major genes of interest, encoding the family of glycosyl or glucosyl transferases and hydrolases, were located at the periphery of QTL peaks. The loci identified could be effectively applied in breeding programmes to improve cassava starch quality. Alleles of candidate genes should be further studied in order to better understand their effects on starch quality traits. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

  10. Identification of major quantitative trait loci underlying floral pollination syndrome divergence in Penstemon

    OpenAIRE

    Wessinger, Carolyn A.; Hileman, Lena C.; Rausher, Mark D.

    2014-01-01

    Distinct floral pollination syndromes have emerged multiple times during the diversification of flowering plants. For example, in western North America, a hummingbird pollination syndrome has evolved more than 100 times, generally from within insect-pollinated lineages. The hummingbird syndrome is characterized by a suite of floral traits that attracts and facilitates pollen movement by hummingbirds, while at the same time discourages bee visitation. These floral traits generally include larg...

  11. Optical characterization of red blood cells from individuals with sickle cell trait and disease in Tanzania using quantitative phase imaging

    CERN Document Server

    Jung, JaeHwang; Lee, KyeoReh; Kazyoba, Paul E; Yoon, Jonghee; Massaga, Julius J; Kim, Kyoohyun; Kim, Dong-Jin; Park, YongKeun

    2016-01-01

    Sickle cell disease (SCD) is common across Sub-Saharan Africa. However, the investigation of SCD in this area has been significantly limited mainly due to the lack of research facilities and skilled personnel. Here, we present optical measurements of individual red blood cells (RBCs) from healthy individuals and individuals with SCD and sickle cell trait in Tanzania using the quantitative phase imaging technique. By employing a quantitative phase imaging unit (QPIU), an existing microscope in a clinic is transformed into a powerful quantitative phase microscope providing measurements on the morphological, biochemical, and biomechanical properties of individual cells. The present approach will open up new opportunities for cost-effective investigation and diagnosis of several diseases in low resource environments.

  12. Optical characterization of red blood cells from individuals with sickle cell trait and disease in Tanzania using quantitative phase imaging

    Science.gov (United States)

    Jung, Jaehwang; Matemba, Lucas E.; Lee, Kyeoreh; Kazyoba, Paul E.; Yoon, Jonghee; Massaga, Julius J.; Kim, Kyoohyun; Kim, Dong-Jin; Park, Yongkeun

    2016-08-01

    Sickle cell disease (SCD) is common across Sub-Saharan Africa. However, the investigation of SCD in this area has been significantly limited mainly due to the lack of research facilities and skilled personnel. Here, we present optical measurements of individual red blood cells from healthy individuals and individuals with SCD and sickle cell trait in Tanzania using the quantitative phase imaging technique. By employing a quantitative phase imaging unit, an existing microscope in a clinic is transformed into a powerful quantitative phase microscope providing measurements on the morphological, biochemical, and biomechanical properties of individual cells. The present approach will open up new opportunities for cost-effective investigation and diagnosis of several diseases in low resource environments.

  13. Environmental stress-dependent effects of deletions encompassing Hsp70Ba on canalization and quantitative trait asymmetry in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Kazuo H Takahashi

    Full Text Available Hsp70 genes may influence the expression of wing abnormalities in Drosophila melanogaster but their effects on variability in quantitative characters and developmental instability are unclear. In this study, we focused on one of the six Hsp70 genes, Hsp70Ba, and investigated its effects on within- and among-individual variability in orbital bristle number, sternopleural bristle number, wing size and wing shape under different environmental conditions. To do this, we studied a newly constructed deletion, Df(3RED5579, which encompasses Hsp70Ba and nine non-Hsp genes, in the heterozygous condition and another, Hsp70Ba(304, which deletes only Hsp70Ba, in the homozygous condition. We found no significant effect of both deletions on within-individual variation quantified by fluctuating asymmetry (FA of morphological traits. On the other hand, the Hsp70Ba(304/Hsp70Ba(304 genotype significantly increased among-individual variation quantified by coefficient of variation (CV of bristle number and wing size in female, while the Df(3RED5579 heterozygote showed no significant effect. The expression level of Hsp70Ba in the deletion heterozygote was 6 to 20 times higher than in control homozygotes, suggesting that the overexpression of Hsp70Ba did not influence developmental stability or canalization significantly. These findings suggest that the absence of expression of Hsp70Ba increases CV of some morphological traits and that HSP70Ba may buffer against environmental perturbations on some quantitative traits.

  14. Robust Joint Analysis with Data Fusion in Two-Stage Quantitative Trait Genome-Wide Association Studies

    Science.gov (United States)

    Pan, Ying; Fung, Wing-Kam

    2013-01-01

    Genome-wide association studies (GWASs) in identifying the disease-associated genetic variants have been proved to be a great pioneering work. Two-stage design and analysis are often adopted in GWASs. Considering the genetic model uncertainty, many robust procedures have been proposed and applied in GWASs. However, the existing approaches mostly focused on binary traits, and few work has been done on continuous (quantitative) traits, since the statistical significance of these robust tests is difficult to calculate. In this paper, we develop a powerful F-statistic-based robust joint analysis method for quantitative traits using the combined raw data from both stages in the framework of two-staged GWASs. Explicit expressions are obtained to calculate the statistical significance and power. We show using simulations that the proposed method is substantially more robust than the F-test based on the additive model when the underlying genetic model is unknown. An example for rheumatic arthritis (RA) is used for illustration. PMID:24288575

  15. Sequential Elimination of Major-Effect Contributors Identifies Additional Quantitative Trait Loci Conditioning High-Temperature Growth in Yeast

    Science.gov (United States)

    Sinha, Himanshu; David, Lior; Pascon, Renata C.; Clauder-Münster, Sandra; Krishnakumar, Sujatha; Nguyen, Michelle; Shi, Getao; Dean, Jed; Davis, Ronald W.; Oefner, Peter J.; McCusker, John H.; Steinmetz, Lars M.

    2008-01-01

    Several quantitative trait loci (QTL) mapping strategies can successfully identify major-effect loci, but often have poor success detecting loci with minor effects, potentially due to the confounding effects of major loci, epistasis, and limited sample sizes. To overcome such difficulties, we used a targeted backcross mapping strategy that genetically eliminated the effect of a previously identified major QTL underlying high-temperature growth (Htg) in yeast. This strategy facilitated the mapping of three novel QTL contributing to Htg of a clinically derived yeast strain. One QTL, which is linked to the previously identified major-effect QTL, was dissected, and NCS2 was identified as the causative gene. The interaction of the NCS2 QTL with the first major-effect QTL was background dependent, revealing a complex QTL architecture spanning these two linked loci. Such complex architecture suggests that more genes than can be predicted are likely to contribute to quantitative traits. The targeted backcrossing approach overcomes the difficulties posed by sample size, genetic linkage, and epistatic effects and facilitates identification of additional alleles with smaller contributions to complex traits. PMID:18780730

  16. Environmental Stress-Dependent Effects of Deletions Encompassing Hsp70Ba on Canalization and Quantitative Trait Asymmetry in Drosophila melanogaster

    Science.gov (United States)

    Takahashi, Kazuo H.; Daborn, Phillip J.; Hoffmann, Ary A.; Takano-Shimizu, Toshiyuki

    2011-01-01

    Hsp70 genes may influence the expression of wing abnormalities in Drosophila melanogaster but their effects on variability in quantitative characters and developmental instability are unclear. In this study, we focused on one of the six Hsp70 genes, Hsp70Ba, and investigated its effects on within-and among-individual variability in orbital bristle number, sternopleural bristle number, wing size and wing shape under different environmental conditions. To do this, we studied a newly constructed deletion, Df(3R)ED5579, which encompasses Hsp70Ba and nine non-Hsp genes, in the heterozygous condition and another, Hsp70Ba304, which deletes only Hsp70Ba, in the homozygous condition. We found no significant effect of both deletions on within-individual variation quantified by fluctuating asymmetry (FA) of morphological traits. On the other hand, the Hsp70Ba304/Hsp70Ba304 genotype significantly increased among-individual variation quantified by coefficient of variation (CV) of bristle number and wing size in female, while the Df(3R)ED5579 heterozygote showed no significant effect. The expression level of Hsp70Ba in the deletion heterozygote was 6 to 20 times higher than in control homozygotes, suggesting that the overexpression of Hsp70Ba did not influence developmental stability or canalization significantly. These findings suggest that the absence of expression of Hsp70Ba increases CV of some morphological traits and that HSP70Ba may buffer against environmental perturbations on some quantitative traits. PMID:21541022

  17. A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.

    Directory of Open Access Journals (Sweden)

    Schaffer Arthur

    2011-07-01

    Full Text Available Abstract Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L. over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS. Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org, an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability

  18. A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.).

    Science.gov (United States)

    Diaz, Aurora; Fergany, Mohamed; Formisano, Gelsomina; Ziarsolo, Peio; Blanca, José; Fei, Zhanjun; Staub, Jack E; Zalapa, Juan E; Cuevas, Hugo E; Dace, Gayle; Oliver, Marc; Boissot, Nathalie; Dogimont, Catherine; Pitrat, Michel; Hofstede, René; van Koert, Paul; Harel-Beja, Rotem; Tzuri, Galil; Portnoy, Vitaly; Cohen, Shahar; Schaffer, Arthur; Katzir, Nurit; Xu, Yong; Zhang, Haiying; Fukino, Nobuko; Matsumoto, Satoru; Garcia-Mas, Jordi; Monforte, Antonio J

    2011-07-28

    A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in a broad array of

  19. Complex interactions of new quantitative trait loci, Sluc1, Sluc2, Sluc3, and Sluc4, that influence the susceptibility to lung cancer in the mouse

    NARCIS (Netherlands)

    Fijneman, Remond J.A.; Vries, Sandra S. de; Jansen, Ritsert C.; Demant, Peter

    1996-01-01

    Many complex traits, including susceptibility to lung cancer, are controlled by multiple genes - quantitative trait loci (QTLs). We facilitated the mapping of QTLs by making use of recombinant congenic strains (RCS), a system of mouse inbred strains in which the genetic complexity is reduced, and by

  20. Comparison of gene-based rare variant association mapping methods for quantitative traits in a bovine population with complex familial relationships

    NARCIS (Netherlands)

    Zhang, Qianqian; Guldbrandtsen, Bernt; Calus, Mario P.L.; Lund, Mogens Sandø; Sahana, Goutam

    2016-01-01

    Background: There is growing interest in the role of rare variants in the variation of complex traits due to increasing evidence that rare variants are associated with quantitative traits. However, association methods that are commonly used for mapping common variants are not effective to map

  1. Oxidative stress survival in a clinical Saccharomyces cerevisiae isolate is influenced by a major quantitative trait nucleotide.

    Science.gov (United States)

    Diezmann, Stephanie; Dietrich, Fred S

    2011-07-01

    One of the major challenges in characterizing eukaryotic genetic diversity is the mapping of phenotypes that are the cumulative effect of multiple alleles. We have investigated tolerance of oxidative stress in the yeast Saccharomyces cerevisiae, a trait showing phenotypic variation in the population. Initial crosses identified that this is a quantitative trait. Microorganisms experience oxidative stress in many environments, including during infection of higher eukaryotes. Natural variation in oxidative stress tolerance is an important aspect of response to oxidative stress exerted by the human immune system and an important trait in microbial pathogens. A clinical isolate of the usually benign yeast S. cerevisiae was found to survive oxidative stress significantly better than the laboratory strain. We investigated the genetic basis of increased peroxide survival by crossing those strains, phenotyping 1500 segregants, and genotyping of high-survival segregants by hybridization of bulk and single segregant DNA to microarrays. This effort has led to the identification of an allele of the transcription factor Rds2 as contributing to stress response. Rds2 has not previously been associated with the survival of oxidative stress. The identification of its role in the oxidative stress response here is an example of a specific trait that appears to be beneficial to Saccharomyces cerevisiae when growing as a pathogen. Understanding the role of this fungal-specific transcription factor in pathogenicity will be important in deciphering how fungi infect and colonize the human host and could eventually lead to a novel drug target.

  2. Quantitative Trait Locus Analysis for Deep-Sowing Germination Ability in the Maize IBM Syn10 DH Population.

    Science.gov (United States)

    Liu, Hongjun; Zhang, Lin; Wang, Jiechen; Li, Changsheng; Zeng, Xing; Xie, Shupeng; Zhang, Yongzhong; Liu, Sisi; Hu, Songlin; Wang, Jianhua; Lee, Michael; Lübberstedt, Thomas; Zhao, Guangwu

    2017-01-01

    Deep-sowing is an effective measure to ensure seeds absorbing water from deep soil layer and emerging normally in arid and semiarid regions. However, existing varieties demonstrate poor germination ability in deep soil layer and some key quantitative trait loci (QTL) or genes related to deep-sowing germination ability remain to be identified and analyzed. In this study, a high-resolution genetic map based on 280 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population which comprised 6618 bin markers was used for the QTL analysis of deep-sowing germination related traits. The results showed significant differences in germination related traits under deep-sowing condition (12.5 cm) and standard-germination condition (2 cm) between two parental lines. In total, 8, 11, 13, 15, and 18 QTL for germination rate, seedling length, mesocotyl length, plumule length, and coleoptile length were detected for the two sowing conditions, respectively. These QTL explained 2.51-7.8% of the phenotypic variance with LOD scores ranging from 2.52 to 7.13. Additionally, 32 overlapping QTL formed 11 QTL clusters on all chromosomes except for chromosome 8, indicating the minor effect genes have a pleiotropic role in regulating various traits. Furthermore, we identified six candidate genes related to deep-sowing germination ability, which were co-located in the cluster regions. The results provide a basis for molecular marker assisted breeding and functional study in deep-sowing germination ability of maize.

  3. A genome-screen experiment to detect quantitative trait loci affecting resistance to facial eczema disease in sheep.

    Science.gov (United States)

    Phua, S H; Dodds, K G; Morris, C A; Henry, H M; Beattie, A E; Garmonsway, H G; Towers, N R; Crawford, A M

    2009-02-01

    Facial eczema (FE) is a secondary photosensitization disease arising from liver cirrhosis caused by the mycotoxin sporidesmin. The disease affects sheep, cattle, deer and goats, and costs the New Zealand sheep industry alone an estimated NZ$63M annually. A long-term sustainable solution to this century-old FE problem is to breed for disease-resistant animals by marker-assisted selection. As a step towards finding a diagnostic DNA test for FE sensitivity, we have conducted a genome-scan experiment to screen for quantitative trait loci (QTL) affecting this trait in Romney sheep. Four F(1) sires, obtained from reciprocal matings of FE resistant and susceptible selection-line animals, were used to generate four outcross families. The resulting half-sib progeny were artificially challenged with sporidesmin to phenotype their FE traits measured in terms of their serum levels of liver-specific enzymes, namely gamma-glutamyl transferase and glutamate dehydrogenase. In a primary screen using selective genotyping on extreme progeny of each family, a total of 244 DNA markers uniformly distributed over all 26 ovine autosomes (with an autosomal genome coverage of 79-91%) were tested for linkage to the FE traits. Data were analysed using Haley-Knott regression. The primary screen detected one significant and one suggestive QTL on chromosomes 3 and 8 respectively. Both the significant and suggestive QTL were followed up in a secondary screen where all progeny were genotyped and analysed; the QTL on chromosome 3 was significant in this analysis.

  4. Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog Ranitomeya imitator

    DEFF Research Database (Denmark)

    Vestergaard, Jacob Schack; Twomey, Evan; Larsen, Rasmus

    2015-01-01

    The number of genes controlling mimetic traits has been a topic of much research and discussion. In this paper, we examine a mimetic, dendrobatid frog Ranitomeya imitator, which harbours extensive phenotypic variation with multiple mimetic morphs, not unlike the celebrated Heliconius system....... However, the genetic basis for this polymorphism is unknown, and not easy to determine using standard experimental approaches, for this hard-to-breed species. To circumvent this problem, we first develop a new protocol for automatic quantification of complex colour pattern phenotypes from images. Using...... this method, which has the potential to be applied in many other systems, we define a phenotype associated with differences in colour pattern between different mimetic morphs. We then proceed to develop a maximum-likelihood method for estimating the number of genes affecting a quantitative trait segregating...

  5. Lesbian, Gay, Bisexual, and Transgender (LGBT) Survivorship.

    Science.gov (United States)

    Kamen, Charles

    2018-02-01

    To discuss lesbian, gay, bisexual, and transgender (LGBT)-specific survivorship issues including: integrating sexual and gender minority identities with cancer survivor identities; coordinating medical care and disclosing identities to health care providers; dealing with late effects of treatment; and addressing LGBT family and relationship issues. Published articles, quotes from an online survey of 311 LGBT survivors. The transition from active cancer treatment to survivorship presents challenges, and LGBT cancer survivors may face additional challenges as they enter the survivorship phase. Oncology nurses can improve the quality of survivorship care delivered to LGBT survivors and their caregivers by addressing the disparities and gaps in health care. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. The use of metabolomic quantitative trait locus mapping and osmotic adjustment traits for the improvement of crop yields under environmental stresses.

    Science.gov (United States)

    Abdelrahman, Mostafa; Burritt, David J; Tran, Lam-Son Phan

    2017-06-28

    an emphasis on the use of metabolomic quantitative trait locus mapping and osmotic adjustment agronomic traits, for the improvement of crop yields under environmental stresses. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Two novel quantitative trait linkage analysis statistics based on the posterior probability of linkage: application to the COGA families.

    Science.gov (United States)

    Bartlett, Christopher W; Vieland, Veronica J

    2005-12-30

    In this paper we apply two novel quantitative trait linkage statistics based on the posterior probability of linkage (PPL) to chromosome 4 from the GAW 14 COGA dataset. Our approaches are advantageous since they use the full likelihood, use full phenotypic information, do not assume normality at the population level or require population/sample parameter estimates; and like other forms of the PPL, they are specifically tailored to accumulate linkage evidence, either for or against linkage, across multiple sets of heterogeneous data. The first statistic uses all quantitative trait (QT) information from the pedigree (QT-posterior probability of linkage, PPL); we applied the QT-PPL to the trait ecb21 (resting electroencephalogram). The second statistic allows simultaneous incorporation of dichotomous trait data into the QT analysis via a threshold model (QTT-PPL); we applied the QTT-PPL to combined data on ecb21 and ALDX1. We obtained a QT-PPL of 96% at GABRB1 and a QT-PPL of 18% at FABP2 while the QTT-PPL was 4% and 2% at the same two loci, respectively. By comparison, the variance-components (VC) method, as implemented in SOLAR, yielded multipoint VC LOD scores of 2.05 and 2.21 at GABRB1 and FABP2, respectively; no other VC LODs were greater than 2. The QTT-PPL was only 4% at GABARB1, which might suggest that the underlying ecb21 gene does not also cause ALDX1, although features of the data complicate interpretation of this result.

  8. Genetic interrelationship among nutritional and quantitative traits in the vegetable amaranth

    Directory of Open Access Journals (Sweden)

    Sudhir Shukla

    2010-01-01

    Full Text Available The present investigation was conducted to elucidate the interrelationship among various agronomic andquality traits and their direct and indirect effect on foliage yield in 39 distinct cultivars of vegetable amaranth (A. tricolor.Among the agronomic traits, plant height and number of inflorescence exhibited significant positive association with foliageyield, while chlorophyll a, chlorophyll b, carotenoid, fiber and ascorbic acid were positively correlated with foliage yield.Chlorophyll a and chlorophyll b exhibited significant positive association with carotenoid, fiber and ascorbic acid. Ascorbicacid was positively correlated with fiber and carotenoid. Protein was associated with plant height, branches per plant and 500seed weight. Chlorophyll a, carotenoid and inflorescence length revealed high positive direct effect on foliage yield, whilebranches plant-1, leaf size, seed yield, chlorophyll b, moisture content and ascorbic acid showed negative path coefficient withfoliage yield. Suitable traits have been marked out to enhance foliage yield in vegetable amaranth.

  9. Cancer Survivorship for Primary Care Annotated Bibliography.

    Science.gov (United States)

    Westfall, Matthew Y; Overholser, Linda; Zittleman, Linda; Westfall, John M

    2015-06-01

    Long-term cancer survivorship care is a relatively new and rapidly advancing field of research. Increasing cancer survivorship rates have created a huge population of long-term cancer survivors whose cancer-specific needs challenge healthcare infrastructure and highlight a significant deficit of knowledge and guidelines in transitional care from treatment to normalcy/prolonged survivorship. As the paradigm of cancer care has changed from a fixation on the curative to the maintenance on long-term overall quality of life, so to, has the delineation of responsibility between oncologists and primary care physicians (PCPs). As more patients enjoy long-term survival, PCPs play a more comprehensive role in cancer care following acute treatment. To this end, this annotated bibliography was written to provide PCPs and other readers with an up-to-date and robust base of knowledge on long-term cancer survivorship, including definitions and epidemiological information as well as specific considerations and recommendations on physical, psychosocial, sexual, and comorbidity needs of survivors. Additionally, significant information is included on survivorship care, specifically Survivorship Care Plans (SPCs) and their evolution, utilization by oncologists and PCPs, and current gaps, as well as an introduction to patient navigation programs. Given rapid advancements in cancer research, this bibliography is meant to serve as current baseline reference outlining the state of the science.

  10. Refinement of a quantitative trait locus on equine chromosome 5 responsible for fetlock osteochondrosis in Hanoverian warmblood horses.

    Science.gov (United States)

    Lampe, V; Dierks, C; Distl, O

    2009-08-01

    In this report, we provide 29 new informative microsatellites distributed over a region of 21 Mb on horse chromosome (ECA) 5 and refine a quantitative trait locus (QTL) for fetlock osteochondrosis dissecans (OCD) to a genome-wide significant interval between 78.03 and 90.23 Mb on ECA5. Genotyping was performed in 211 Hanoverian warmblood horses from 14 paternal half-sib groups. Within this OCD-QTL, collagen type XXIV alpha 1 was identified as a potential functional candidate gene for equine osteochondrosis. This report is a further step towards unravelling the genes that cause equine osteochondrosis.

  11. Construction of a dense genetic linkage map and mapping quantitative trait loci for economic traits of a doubled haploid population of Pyropia haitanensis (Bangiales, Rhodophyta).

    Science.gov (United States)

    Xu, Yan; Huang, Long; Ji, Dehua; Chen, Changsheng; Zheng, Hongkun; Xie, Chaotian

    2015-09-21

    Pyropia haitanensis is one of the most economically important mariculture crops in China. A high-density genetic map has not been published yet and quantitative trait locus (QTL) mapping has not been undertaken for P. haitanensis because of a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) was developed recently for large-scale, high resolution de novo marker discovery and genotyping. In this study, SLAF-seq was used to obtain mass length polymorphic markers to construct a high-density genetic map for P. haitanensis. In total, 120.33 Gb of data containing 75.21 M pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 75.50-fold in the male parent, 74.02-fold in the female parent, and 6.14-fold average in each double haploid individual. In total, 188,982 SLAFs were detected, of which 6731 were length polymorphic SLAFs that could be used to construct a genetic map. The final map included 4550 length polymorphic markers that were combined into 740 bins on five linkage groups, with a length of 874.33 cM and an average distance of 1.18 cM between adjacent bins. This map was used for QTL mapping to identify chromosomal regions associated with six economically important traits: frond length, width, thickness, fresh weight, growth rates of frond length and growth rates of fresh weight. Fifteen QTLs were identified for these traits. The value of phenotypic variance explained by an individual QTL ranged from 9.59 to 16.61 %, and the confidence interval of each QTL ranged from 0.97 cM to 16.51 cM. The first high-density genetic linkage map for P. haitanensis was constructed, and fifteen QTLs associated with six economically important traits were identified. The results of this study not only provide a platform for gene and QTL fine mapping, map-based gene isolation, and molecular breeding for P. haitanensis, but will also serve as a reference for positioning sequence scaffolds on a physical

  12. Quantitative studies of DNA methylation and gene expression in neuropsychiatric traits

    NARCIS (Netherlands)

    van Eijk, K.R.

    2014-01-01

    Research has shown that besides genes and environment, epigenetic factors are also playing a role in the development of traits and diseases. Epigenetic changes do not affect the underlying DNA sequence, but affect its structure and is thought to play a major role in regulation of gene expression.

  13. Mapping of quantitative trait loci for oil content in cottonseed kernel

    Indian Academy of Sciences (India)

    However, till date, QTL mapping and genetic analysis related to this trait in cotton have only been conducted in the tetraploid embryo genome. In the current experiment, an IF2 population of cottonseed kernels from the random crossing of 188 intraspecific recombinant inbred lines which were derived from the hybrid of two ...

  14. Mapping quantitative trait loci in plant breeding populations : Use of parental haplotype sharing

    NARCIS (Netherlands)

    Jansen, Ritsert C.; Jannink, Jean-Luc; Beavis, William D.

    2003-01-01

    Applied breeding programs evaluate large numbers of progeny derived from multiple related crosses for a wide range of agronomic traits and for tens to hundreds of molecular markers. This study was conducted to determine how these phenotypic and genetic data could be used for routinely mapping

  15. Discovery of quantitative trait loci for resistance to parasitic nematode infection in sheep: I. Analysis of outcross pedigrees

    Directory of Open Access Journals (Sweden)

    Greer Gordon J

    2006-07-01

    Full Text Available Abstract Background Currently most pastoral farmers rely on anthelmintic drenches to control gastrointestinal parasitic nematodes in sheep. Resistance to anthelmintics is rapidly increasing in nematode populations such that on some farms none of the drench families are now completely effective. It is well established that host resistance to nematode infection is a moderately heritable trait. This study was undertaken to identify regions of the genome, quantitative trait loci (QTL that contain genes affecting resistance to parasitic nematodes. Results Rams obtained from crossing nematode parasite resistant and susceptible selection lines were used to derive five large half-sib families comprising between 348 and 101 offspring per sire. Total offspring comprised 940 lambs. Extensive measurements for a range of parasite burden and immune function traits in all offspring allowed each lamb in each pedigree to be ranked for relative resistance to nematode parasites. Initially the 22 most resistant and 22 most susceptible progeny from each pedigree were used in a genome scan that used 203 microsatellite markers spread across all sheep autosomes. This study identified 9 chromosomes with regions showing sufficient linkage to warrant the genotyping of all offspring. After genotyping all offspring with markers covering Chromosomes 1, 3, 4, 5, 8, 12, 13, 22 and 23, the telomeric end of chromosome 8 was identified as having a significant QTL for parasite resistance as measured by the number of Trichostrongylus spp. adults in the abomasum and small intestine at the end of the second parasite challenge. Two further QTL for associated immune function traits of total serum IgE and T. colubiformis specific serum IgG, at the end of the second parasite challenge, were identified on chromosome 23. Conclusion Despite parasite resistance being a moderately heritable trait, this large study was able to identify only a single significant QTL associated with it. The QTL

  16. Plastic expression of heterochrony quantitative trait loci (hQTLs) for leaf growth in the common bean (Phaseolus vulgaris).

    Science.gov (United States)

    Jiang, Libo; Clavijo, Jose A; Sun, Lidan; Zhu, Xuli; Bhakta, Mehul S; Gezan, Salvador A; Carvalho, Melissa; Vallejos, C Eduardo; Wu, Rongling

    2015-08-01

    Heterochrony, that is, evolutionary changes in the relative timing of developmental events and processes, has emerged as a key concept that links evolution and development. Genes associated with heterochrony encode molecular components of developmental timing mechanisms. However, our understanding of how heterochrony genes alter the expression of heterochrony in response to environmental changes remains very limited. We applied functional mapping to find quantitative trait loci (QTLs) responsible for growth trajectories of leaf area and leaf mass in the common bean (Phaseolus vulgaris) grown in two contrasting environments. We identified three major QTLs pleiotropically expressed under the two environments. Further characterization of the temporal pattern of these QTLs indicates that they are heterochrony QTLs (hQTLs) in terms of their role in influencing four heterochronic parameters: the timing of the inflection point, the timing of maximum acceleration and deceleration, and the duration of linear growth. The pattern of gene action by the hQTLs on each parameter was unique, being environmentally dependent and varying between two allometrically related leaf growth traits. These results provide new insights into the complexity of genetic mechanisms that control trait formation in plants and provide novel findings that will be of use in studying the evolutionary trends. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  17. Effects of Long-Term Averaging of Quantitative Blood Pressure Traits on the Detection of Genetic Associations

    Science.gov (United States)

    Ganesh, Santhi K.; Chasman, Daniel I.; Larson, Martin G.; Guo, Xiuqing; Verwoert, Germain; Bis, Joshua C.; Gu, Xiangjun; Smith, Albert V.; Yang, Min-Lee; Zhang, Yan; Ehret, Georg; Rose, Lynda M.; Hwang, Shih-Jen; Papanicolau, George J.; Sijbrands, Eric J.; Rice, Kenneth; Eiriksdottir, Gudny; Pihur, Vasyl; Ridker, Paul M.; Vasan, Ramachandran S.; Newton-Cheh, Christopher; Newton-Cheh, Christopher; Johnson, Toby; Gateva, Vesela; Tobin, Martin D.; Bochud, Murielle; Coin, Lachlan; Najjar, Samer S.; Zhao, Jing Hua; Heath, Simon C.; Eyheramendy, Susana; Papadakis, Konstantinos; Voight, Benjamin F.; Scott, Laura J.; Zhang, Feng; Farrall, Martin; Tanaka, Toshiko; Wallace, Chris; Chambers, John C.; Khaw, Kay-Tee; Nilsson, Peter; van der Harst, Pim; Polidoro, Silvia; Grobbee, Diederick E.; Onland-Moret, N. Charlotte; Bots, Michiel L.; Wain, Louise V.; Elliott, Katherine S.; Teumer, Alexander; Luan, Jian’an; Lucas, Gavin; Kuusisto, Johanna; Burton, Paul R.; Hadley, David; McArdle, Wendy L.; Brown, Morris; Dominiczak, Anna; Newhouse, Stephen J.; Samani, Nilesh J.; Webster, John; Zeggini, Eleftheria; Beckmann, Jacques S.; Bergmann, Sven; Lim, Noha; Song, Kijoung; Vollenweider, Peter; Waeber, Gerard; Waterworth, Dawn M.; Yuan, Xin; Groop, Leif; Orho-Melander, Marju; Allione, Alessandra; Di Gregorio, Alessandra; Guarrera, Simonetta; Panico, Salvatore; Ricceri, Fulvio; Romanazzi, Valeria; Sacerdote, Carlotta; Vineis, Paolo; Barroso, Inês; Sandhu, Manjinder S.; Luben, Robert N.; Crawford, Gabriel J.; Jousilahti, Pekka; Perola, Markus; Boehnke, Michael; Bonnycastle, Lori L.; Collins, Francis S.; Jackson, Anne U.; Mohlke, Karen L.; Stringham, Heather M.; Valle, Timo T.; Willer, Cristen J.; Bergman, Richard N.; Morken, Mario A.; Döring, Angela; Gieger, Christian; Illig, Thomas; Meitinger, Thomas; Org, Elin; Pfeufer, Arne; Wichmann, H. Erich; Kathiresan, Sekar; Marrugat, Jaume; O’Donnell, Christopher J.; Schwartz, Stephen M.; Siscovick, David S.; Subirana, Isaac; Freimer, Nelson B.; Hartikainen, Anna-Liisa; McCarthy, Mark I.; O’Reilly, Paul F.; Peltonen, Leena; Pouta, Anneli; de Jong, Paul E.; Snieder, Harold; van Gilst, Wiek H.; Clarke, Robert; Goel, Anuj; Hamsten, Anders; Peden, John F.; Seedorf, Udo; Syvänen, Ann-Christine; Tognoni, Giovanni; Lakatta, Edward G.; Sanna, Serena; Scheet, Paul; Schlessinger, David; Scuteri, Angelo; Dörr, Marcus; Ernst, Florian; Felix, Stephan B.; Homuth, Georg; Lorbeer, Roberto; Reffelmann, Thorsten; Rettig, Rainer; Völker, Uwe; Galan, Pilar; Gut, Ivo G.; Hercberg, Serge; Lathrop, G. Mark; Zeleneka, Diana; Deloukas, Panos; Soranzo, Nicole; Williams, Frances M.; Zhai, Guangju; Salomaa, Veikko; Laakso, Markku; Elosua, Roberto; Forouhi, Nita G.; Völzke, Henry; Uiterwaal, Cuno S.; van der Schouw, Yvonne T; Numans, Mattijs E.; Matullo, Giuseppe; Navis, Gerjan; Berglund, Göran; Bingham, Sheila A.; Kooner, Jaspal S.; Paterson, Andrew D.; Connell, John M.; Bandinelli, Stefania; Ferrucci, Luigi; Watkins, Hugh; Spector, Tim D.; Tuomilehto, Jaakko; Altshuler, David; Strachan, David P.; Laan, Maris; Meneton, Pierre; Wareham, Nicholas J.; Uda, Manuela; Jarvelin, Marjo-Riitta; Mooser, Vincent; Melander, Olle; Loos, Ruth J.F.; Elliott, Paul; Abecasis, Gonçalo R.; Caulfield, Mark; Munroe, Patricia B.; Raffel, Leslie J.; Amin, Najaf; Rotter, Jerome I.; Liu, Kiang; Launer, Lenore J.; Xu, Ming; Caulfield, Mark; Morrison, Alanna C.; Johnson, Andrew D.; Vaidya, Dhananjay; Dehghan, Abbas; Li, Guo; Bouchard, Claude; Harris, Tamara B.; Zhang, He; Boerwinkle, Eric; Siscovick, David S.; Gao, Wei; Uitterlinden, Andre G.; Rivadeneira, Fernando; Hofman, Albert; Willer, Cristen J.; Franco, Oscar H.; Huo, Yong; Witteman, Jacqueline C.M.; Munroe, Patricia B.; Gudnason, Vilmundur; Palmas, Walter; van Duijn, Cornelia; Fornage, Myriam; Levy, Daniel; Psaty, Bruce M.; Chakravarti, Aravinda

    2014-01-01

    Blood pressure (BP) is a heritable, quantitative trait with intraindividual variability and susceptibility to measurement error. Genetic studies of BP generally use single-visit measurements and thus cannot remove variability occurring over months or years. We leveraged the idea that averaging BP measured across time would improve phenotypic accuracy and thereby increase statistical power to detect genetic associations. We studied systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP) averaged over multiple years in 46,629 individuals of European ancestry. We identified 39 trait-variant associations across 19 independent loci (p associations (in four loci) uniquely identified by our LTA analyses included those of SBP and MAP at 2p23 (rs1275988, near KCNK3), DBP at 2q11.2 (rs7599598, in FER1L5), and PP at 6p21 (rs10948071, near CRIP3) and 7p13 (rs2949837, near IGFBP3). Replication analyses conducted in cohorts with single-visit BP data showed positive replication of associations and a nominal association (p association studies. Using LTA analysis, we identified genetic loci influencing BP. LTA might be one way of increasing the power of genetic associations for continuous traits in extant samples for other phenotypes that are measured serially over time. PMID:24975945

  18. Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies.

    Science.gov (United States)

    Bolormaa, Sunduimijid; Pryce, Jennie E; Kemper, Kathryn E; Hayes, Ben J; Zhang, Yuandan; Tier, Bruce; Barendse, William; Reverter, Antonio; Goddard, Mike E

    2013-10-29

    The apparent effect of a single nucleotide polymorphism (SNP) on phenotype depends on the linkage disequilibrium (LD) between the SNP and a quantitative trait locus (QTL). However, the phase of LD between a SNP and a QTL may differ between Bos indicus and Bos taurus because they diverged at least one hundred thousand years ago. Here, we test the hypothesis that the apparent effect of a SNP on a quantitative trait depends on whether the SNP allele is inherited from a Bos taurus or Bos indicus ancestor. Phenotype data on one or more traits and SNP genotype data for 10 181 cattle from Bos taurus, Bos indicus and composite breeds were used. All animals had genotypes for 729 068 SNPs (real or imputed). Chromosome segments were classified as originating from B. indicus or B. taurus on the basis of the haplotype of SNP alleles they contained. Consequently, SNP alleles were classified according to their sub-species origin. Three models were used for the association study: (1) conventional GWAS (genome-wide association study), fitting a single SNP effect regardless of subspecies origin, (2) interaction GWAS, fitting an interaction between SNP and subspecies-origin, and (3) best variable GWAS, fitting the most significant combination of SNP and sub-species origin. Fitting an interaction between SNP and subspecies origin resulted in more significant SNPs (i.e. more power) than a conventional GWAS. Thus, the effect of a SNP depends on the subspecies that the allele originates from. Also, most QTL segregated in only one subspecies, suggesting that many mutations that affect the traits studied occurred after divergence of the subspecies or the mutation became fixed or was lost in one of the subspecies. The results imply that GWAS and genomic selection could gain power by distinguishing SNP alleles based on their subspecies origin, and that only few QTL segregate in both B. indicus and B. taurus cattle. Thus, the QTL that segregate in current populations likely resulted from

  19. Exploring the quantitative nature of empathy, systemising and autistic traits using factor mixture modelling.

    Science.gov (United States)

    Grove, Rachel; Baillie, Andrew; Allison, Carrie; Baron-Cohen, Simon; Hoekstra, Rosa A

    2015-11-01

    Autism research has previously focused on either identifying a latent dimension or searching for subgroups. Research assessing the concurrently categorical and dimensional nature of autism is needed. To investigate the latent structure of autism and identify meaningful subgroups in a sample spanning the full spectrum of genetic vulnerability. Factor mixture models were applied to data on empathy, systemising and autistic traits from individuals on the autism spectrum, parents and general population controls. A two-factor three-class model was identified, with two factors measuring empathy and systemising. Class one had high systemising and low empathy scores and primarily consisted of individuals with autism. Mainly comprising controls and parents, class three displayed high empathy scores and lower systemising scores, and class two showed balanced scores on both measures of systemising and empathy. Autism is best understood as a dimensional construct, but meaningful subgroups can be identified based on empathy, systemising and autistic traits. © The Royal College of Psychiatrists 2015.

  20. Statistical correction of the Winner's Curse explains replication variability in quantitative trait genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    Cameron Palmer

    2017-07-01

    Full Text Available Genome-wide association studies (GWAS have identified hundreds of SNPs responsible for variation in human quantitative traits. However, genome-wide-significant associations often fail to replicate across independent cohorts, in apparent inconsistency with their apparent strong effects in discovery cohorts. This limited success of replication raises pervasive questions about the utility of the GWAS field. We identify all 332 studies of quantitative traits from the NHGRI-EBI GWAS Database with attempted replication. We find that the majority of studies provide insufficient data to evaluate replication rates. The remaining papers replicate significantly worse than expected (p < 10-14, even when adjusting for regression-to-the-mean of effect size between discovery- and replication-cohorts termed the Winner's Curse (p < 10-16. We show this is due in part to misreporting replication cohort-size as a maximum number, rather than per-locus one. In 39 studies accurately reporting per-locus cohort-size for attempted replication of 707 loci in samples with similar ancestry, replication rate matched expectation (predicted 458, observed 457, p = 0.94. In contrast, ancestry differences between replication and discovery (13 studies, 385 loci cause the most highly-powered decile of loci to replicate worse than expected, due to difference in linkage disequilibrium.

  1. Identification and Characterization of Quantitative Trait Loci for Shattering in Japonica Rice Landrace Jiucaiqing from Taihu Lake Valley, China

    Directory of Open Access Journals (Sweden)

    Jinping Cheng

    2016-11-01

    Full Text Available Easy shattering reduces yield from grain loss during rice ( L. harvest. We characterized a nonshattering rice landrace Jiucaiqing from Taihu Lake valley in China. The breaking tensile strength (BTS; grams force, gf of the grain pedicel was measured using a digital force gauge to evaluate the degree of shattering at 0, 7, 14, 21, 28, and 35 d after heading (DAH. The BTS of Jiucaiqing did not significantly decrease with increasing DAH, maintaining a level of 152.2 to 195.9 gf, while that of IR26 decreased greatly during 0 to 14 DAH and finally stabilized at ∼100 gf. Then the chromosome segment substitution lines (CSSLs and near isogenic lines (NILs of Jiucaiqing in IR26 background were developed for quantitative trait loci (QTL mapping. Four putative QTL (, , , and for shattering were detected, and the was confirmed on chromosome 1. We further mapped to a 98.4-kb region, which contains 14 genes. Os01g62920 was considered to be a strong candidate for , which colocated with . Further quantitative real-time polymerase chain reaction (PCR analyses confirmed that the QTL can significantly decrease the expression of shattering related genes (, , , , and especially at the middle development stage at 10 and 15 cm panicle length, which causes rice shattering decrease. The elite allele and the NIL with desirable agronomic traits identified in this study could be useful for rice breeding.

  2. I.4 Screening Experimental Designs for Quantitative Trait Loci, Association Mapping, Genotype-by Environment Interaction, and Other Investigations

    Science.gov (United States)

    Federer, Walter T.; Crossa, José

    2012-01-01

    Crop breeding programs using conventional approaches, as well as new biotechnological tools, rely heavily on data resulting from the evaluation of genotypes in different environmental conditions (agronomic practices, locations, and years). Statistical methods used for designing field and laboratory trials and for analyzing the data originating from those trials need to be accurate and efficient. The statistical analysis of multi-environment trails (MET) is useful for assessing genotype × environment interaction (GEI), mapping quantitative trait loci (QTLs), and studying QTL × environment interaction (QEI). Large populations are required for scientific study of QEI, and for determining the association between molecular markers and quantitative trait variability. Therefore, appropriate control of local variability through efficient experimental design is of key importance. In this chapter we present and explain several classes of augmented designs useful for achieving control of variability and assessing genotype effects in a practical and efficient manner. A popular procedure for unreplicated designs is the one known as “systematically spaced checks.” Augmented designs contain “c” check or standard treatments replicated “r” times, and “n” new treatments or genotypes included once (usually) in the experiment. PMID:22675304

  3. Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato[OPEN

    Science.gov (United States)

    Alseekh, Saleh; Tohge, Takayuki; Wendenberg, Regina; Scossa, Federico; Omranian, Nooshin; Li, Jie; Kleessen, Sabrina; Giavalisco, Patrick; Pleban, Tzili; Mueller-Roeber, Bernd; Zamir, Dani; Nikoloski, Zoran; Fernie, Alisdair R.

    2015-01-01

    A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism. PMID:25770107

  4. Quantitative trait loci mapping of heat tolerance in broccoli (Brassica oleracea var. italica) using genotyping-by-sequencing.

    Science.gov (United States)

    Branham, Sandra E; Stansell, Zachary J; Couillard, David M; Farnham, Mark W

    2017-03-01

    Five quantitative trait loci and one epistatic interaction were associated with heat tolerance in a doubled haploid population of broccoli evaluated in three summer field trials. Predicted rising global temperatures due to climate change have generated a demand for crops that are resistant to yield and quality losses from heat stress. Broccoli (Brassica oleracea var. italica) is a cool weather crop with high temperatures during production decreasing both head quality and yield. Breeding for heat tolerance in broccoli has potential to both expand viable production areas and extend the growing season but breeding efficiency is constrained by limited genetic information. A doubled haploid (DH) broccoli population segregating for heat tolerance was evaluated for head quality in three summer fields in Charleston, SC, USA. Multiple quantitative trait loci (QTL) mapping of 1,423 single nucleotide polymorphisms developed through genotyping-by-sequencing identified five QTL and one positive epistatic interaction that explained 62.1% of variation in heat tolerance. The QTL identified here can be used to develop markers for marker-assisted selection and to increase our understanding of the molecular mechanisms underlying plant response to heat stress.

  5. Hybrid vigour and gene action for two quantitative traits of castor ...

    African Journals Online (AJOL)

    Five homozygous lines of castor plant, namely RS1-Om, RN1-Om, RTl-2m, RSl- Owm, and RNl- Omb, were crossed to raise F1, F2, BC1, and BC2 generations. The hybrids were tested for hybrid vigour for two metric traits, viz; number of pods per plant and seed yield per plant. Highly significant hybrid vigour was detected ...

  6. Characterization of Three Indica Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci Identification

    OpenAIRE

    Lijun Meng; Longbiao Guo; Kimberly Ponce; Xiangqian Zhao; Guoyou Ye

    2016-01-01

    Three new rice ( L.) multiparent advanced generation intercross (MAGIC) populations were developed using eight elite rice varieties from different breeding programs. These three populations were two recombinant inbred line (RIL) populations derived from two 4-way crosses, DC1 and DC2, and one RIL population derived from an 8-way cross. These populations were genotyped using an Illumina Infinium rice 6K SNP chip. The potential of the three MAGIC populations in identifying marker–trait associa...

  7. Genetic mapping of quantitative trait loci underlying flowering time in chrysanthemum (Chrysanthemum morifolium.

    Directory of Open Access Journals (Sweden)

    Fei Zhang

    Full Text Available Flowering time is an important trait in chrysanthemum, but its genetic basis remains poorly understood. An intra-specific mapping population bred from the cross between the autumn-flowering cultivar 'Yuhualuoying' and the summer-flowering 'Aoyunhanxiao' was used to determine the number and relative effect of QTL segregating for five measures of flowering time. From flowering time data recorded over two consecutive seasons, 35 additive QTL were detected, each explaining between 5.8% and 22.7% of the overall phenotypic variance. Of these, 13 were detected in both years. Nine genomic regions harboring QTL for at least two of the five traits were identified. Ten pairs of loci epistatically determined the flowering time, but their contribution to the overall phenotypic variance was less than for the additive QTL. The results suggest that flowering time in chrysanthemum is principally governed by main effect QTL but that epistasis also contributes to the genetic architecture of the trait, and the major QTL identified herein are useful in our ongoing efforts to streamline the improvement of chrysanthemum via the use of molecular methodology.

  8. Genetic mapping of quantitative trait loci underlying flowering time in chrysanthemum (Chrysanthemum morifolium).

    Science.gov (United States)

    Zhang, Fei; Chen, Sumei; Jiang, Jiafu; Guan, Zhiyong; Fang, Weimin; Chen, Fadi

    2013-01-01

    Flowering time is an important trait in chrysanthemum, but its genetic basis remains poorly understood. An intra-specific mapping population bred from the cross between the autumn-flowering cultivar 'Yuhualuoying' and the summer-flowering 'Aoyunhanxiao' was used to determine the number and relative effect of QTL segregating for five measures of flowering time. From flowering time data recorded over two consecutive seasons, 35 additive QTL were detected, each explaining between 5.8% and 22.7% of the overall phenotypic variance. Of these, 13 were detected in both years. Nine genomic regions harboring QTL for at least two of the five traits were identified. Ten pairs of loci epistatically determined the flowering time, but their contribution to the overall phenotypic variance was less than for the additive QTL. The results suggest that flowering time in chrysanthemum is principally governed by main effect QTL but that epistasis also contributes to the genetic architecture of the trait, and the major QTL identified herein are useful in our ongoing efforts to streamline the improvement of chrysanthemum via the use of molecular methodology.

  9. Evaluation of Qualitative and Quantitative Traits of Maize (cv. 604 Under Drought Stress and Plant Density

    Directory of Open Access Journals (Sweden)

    Parvaneh Vafa

    2014-05-01

    Full Text Available In order to study the effects of drought stress and plant density on yield and yields Components of maize (cv. 604, an experiment was conducted as a split plot based on randomized complete block design with four replications in Ilam station, Iran during 2007-2008 growing season. The treatment were three levels of irrigation (90, 120 and 150 evaporation (mm from pan (Class A as main plots, four planting densities (90000, 100000, 110000 and 125000 plants ha-1 as sub plot. The results showed that different levels of irrigation on the most of measured traits were significant at 1% probability level. Level of irrigation 90 mm evaporation (mm from pan had a highest a number grain per row, 1000 kernel weight, grain yield and biologic yield other than traits. Between plating density the most of measured traits were significant. The highest grain yield, row per ear, number grain per row, biologic yield and harvest index obtained in 110000 plants ha-1. Interaction effect of irrigation Ч plant density was effect on grain yield. The highest grain yield from 90 mm evaporationЧ110000 plants ha-1 and the lowest grain yield from 150 mm evaporationЧ90000 plants ha-1.

  10. Genetic mapping of quantitative trait loci for aseasonal reproduction in sheep.

    Science.gov (United States)

    Mateescu, R G; Thonney, M L

    2010-10-01

    The productivity and economic prosperity of sheep farming could benefit greatly from more effective methods of selection for year-round lambing. Identification of QTL for aseasonal reproduction in sheep could lead to more accurate selection and faster genetic improvement. One hundred and twenty microsatellite markers were genotyped on 159 backcross ewes from a Dorset × East Friesian crossbred pedigree. Interval mapping was undertaken to map the QTL underlying several traits describing aseasonal reproduction including the number of oestrous cycles, maximum level of progesterone prior to breeding, pregnancy status determined by progesterone level, pregnancy status determined by ultrasound, lambing status and number of lambs born. Seven chromosomes (1, 3, 12, 17, 19, 20 and 24) were identified to harbour putative QTL for one or more component traits used to describe aseasonal reproduction. Ovine chromosomes 12, 17, 19 and 24 harbour QTL significant at the 5% chromosome-wide level, chromosomes 3 and 20 harbour QTL that exceeded the threshold at the 1% chromosome-wide level, while the QTL identified on chromosome 1 exceeded the 1% experiment-wide significance level. These results are a first step towards understanding the genetic mechanism of this complex trait and show that variation in aseasonal reproduction is associated with multiple chromosomal regions. © 2010 The Authors, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.

  11. Quantitative trait loci (QTL study identifies novel genomic regions associated to Chiari-like malformation in Griffon Bruxellois dogs.

    Directory of Open Access Journals (Sweden)

    Philippe Lemay

    Full Text Available Chiari-like malformation (CM is a developmental abnormality of the craniocervical junction that is common in the Griffon Bruxellois (GB breed with an estimated prevalence of 65%. This disease is characterized by overcrowding of the neural parenchyma at the craniocervical junction and disturbance of cerebrospinal fluid (CSF flow. The most common clinical sign is pain either as a direct consequence of CM or neuropathic pain as a consequence of secondary syringomyelia. The etiology of CM remains unknown but genetic factors play an important role. To investigate the genetic complexity of the disease, a quantitative trait locus (QTL approach was adopted. A total of 14 quantitative skull and atlas measurements were taken and were tested for association to CM. Six traits were found to be associated to CM and were subjected to a whole-genome association study using the Illumina canine high density bead chip in 74 GB dogs (50 affected and 24 controls. Linear and mixed regression analyses identified associated single nucleotide polymorphisms (SNPs on 5 Canis Familiaris Autosomes (CFAs: CFA2, CFA9, CFA12, CFA14 and CFA24. A reconstructed haplotype of 0.53 Mb on CFA2 strongly associated to the height of the cranial fossa (diameter F and an haplotype of 2.5 Mb on CFA14 associated to both the height of the rostral part of the caudal cranial fossa (AE and the height of the brain (FG were significantly associated to CM after 10 000 permutations strengthening their candidacy for this disease (P = 0.0421, P = 0.0094 respectively. The CFA2 QTL harbours the Sall-1 gene which is an excellent candidate since its orthologue in humans is mutated in Townes-Brocks syndrome which has previously been associated to Chiari malformation I. Our study demonstrates the implication of multiple traits in the etiology of CM and has successfully identified two new QTL associated to CM and a potential candidate gene.

  12. A Quantitative Trait Locus Analysis of Social Responsiveness in Multiplex Autism Families

    National Research Council Canada - National Science Library

    Todd, Richard D; Geschwind, Daniel H; Duvall, Jacqueline A; Constantino, John N; Lu, Ake; Cantor, Rita M

    2007-01-01

    ... focused on social relatedness. Method: A nonparametric quantitative genome scan was performed using the Social Responsiveness Scale in a cohort of about 100 families with two or more autistic probands from the Autism Genetic Resource...

  13. Quantitative trait loci mapping of phenotypic plasticity and genotype-environment interactions in plant and insect performance.

    Science.gov (United States)

    Tétard-Jones, C; Kertesz, M A; Preziosi, R F

    2011-05-12

    Community genetic studies generally ignore the plasticity of the functional traits through which the effect is passed from individuals to the associated community. However, the ability of organisms to be phenotypically plastic allows them to rapidly adapt to changing environments and plasticity is commonly observed across all taxa. Owing to the fitness benefits of phenotypic plasticity, evolutionary biologists are interested in its genetic basis, which could explain how phenotypic plasticity is involved in the evolution of species interactions. Two current ideas exist: (i) phenotypic plasticity is caused by environmentally sensitive loci associated with a phenotype; (ii) phenotypic plasticity is caused by regulatory genes that simply influence the plasticity of a phenotype. Here, we designed a quantitative trait loci (QTL) mapping experiment to locate QTL on the barley genome associated with barley performance when the environment varies in the presence of aphids, and the composition of the rhizosphere. We simultaneously mapped aphid performance across variable rhizosphere environments. We mapped main effects, QTL × environment interaction (QTL×E), and phenotypic plasticity (measured as the difference in mean trait values) for barley and aphid performance onto the barley genome using an interval mapping procedure. We found that QTL associated with phenotypic plasticity were co-located with main effect QTL and QTL×E. We also located phenotypic plasticity QTL that were located separately from main effect QTL. These results support both of the current ideas of how phenotypic plasticity is genetically based and provide an initial insight into the functional genetic basis of how phenotypically plastic traits may still be important sources of community genetic effects.

  14. Genetic architecture of contemporary adaptation to biotic invasions: quantitative trait locus mapping of beak reduction in soapberry bugs.

    Science.gov (United States)

    Yu, Y; Andrés, Jose A

    2014-02-19

    Biological invasions can result in new selection pressures driven by the establishment of new biotic interactions. The response of exotic and native species to selection depends critically on the genetic architecture of ecologically relevant traits. In the Florida peninsula, the soapberry bug (Jadera haematoloma) has colonized the recently introduced Chinese flametree, Koelreuteria elegans, as a host plant. Driven by feeding efficiency, the populations associated with this new host have differentiated into a new bug ecomorph characterized by short beaks more appropriate for feeding on the flattened pods of the Chinese flametree. In this study, we have generated a three-generation pedigree from crossing the long-beaked and short-beaked ecomorphs to construct a de novo linkage map and to locate putative quantitative trait locus (QTL) controlling beak length and body size in J. haematoloma. Using amplified fragment-length polymorphism markers and a two-way pseudo-testcross design, we have produced two parental maps in six linkage groups, covering the known number of chromosomes. QTL analysis revealed one significant QTL for beak length on a maternal linkage group and the corresponding paternal linkage group. Three QTL were found for body size. Through single marker regression analysis, nine single markers that could not be placed on the map were also found to be significantly associated with one or both of the two traits. Interestingly, the most significant body size QTL co-localized with the beak length QTL, suggesting linkage disequilibrium or pleiotropic effects of related traits. Our results suggest an oligogenic control of beak length.

  15. Quantitative Trait Locus Analysis for Deep-Sowing Germination Ability in the Maize IBM Syn10 DH Population

    Science.gov (United States)

    Liu, Hongjun; Zhang, Lin; Wang, Jiechen; Li, Changsheng; Zeng, Xing; Xie, Shupeng; Zhang, Yongzhong; Liu, Sisi; Hu, Songlin; Wang, Jianhua; Lee, Michael; Lübberstedt, Thomas; Zhao, Guangwu

    2017-01-01

    Deep-sowing is an effective measure to ensure seeds absorbing water from deep soil layer and emerging normally in arid and semiarid regions. However, existing varieties demonstrate poor germination ability in deep soil layer and some key quantitative trait loci (QTL) or genes related to deep-sowing germination ability remain to be identified and analyzed. In this study, a high-resolution genetic map based on 280 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population which comprised 6618 bin markers was used for the QTL analysis of deep-sowing germination related traits. The results showed significant differences in germination related traits under deep-sowing condition (12.5 cm) and standard-germination condition (2 cm) between two parental lines. In total, 8, 11, 13, 15, and 18 QTL for germination rate, seedling length, mesocotyl length, plumule length, and coleoptile length were detected for the two sowing conditions, respectively. These QTL explained 2.51–7.8% of the phenotypic variance with LOD scores ranging from 2.52 to 7.13. Additionally, 32 overlapping QTL formed 11 QTL clusters on all chromosomes except for chromosome 8, indicating the minor effect genes have a pleiotropic role in regulating various traits. Furthermore, we identified six candidate genes related to deep-sowing germination ability, which were co-located in the cluster regions. The results provide a basis for molecular marker assisted breeding and functional study in deep-sowing germination ability of maize. PMID:28588594

  16. Effect of Regulated Deficit Irrigation (RDI and Partial Root zone Drying (PRD on Quantitative and Qualitative Traits of Strawberry

    Directory of Open Access Journals (Sweden)

    A. Shahnazari

    2016-02-01

    Full Text Available Introduction: Deficit irrigation (DI is a suitable solution to gain acceptable and economic performance by using minimum amount of water. The partial root zone drying (PRD method introduced in Australia for the first time and its goal was controlling the vine’s excessive growth. This goal gained by alternative drying the rootzone. Basically the theory of PRD method, is expanding the plant’s roots by applying alternative stress on different sides of the roots. So the plants with PRD irrigation method can have different root system in comparison with other irrigation methods. At this method the plant’s condition would be OK by uptaking water from wet side, and the roots at the dry side can release abscisic acid hormone which decrease the stomatal conductance and consequently the water use efficiency would be increase.There had been studies on the effect of water tension on strawberry. The previous studies on strawberry indicated that the water stress can increase the plant’s brix concentration and some of plant acids.The awareness of the impact of water deficit stress on strawberry plant quantity and quality is essential for irrigation and product management, and at the current study, effect of different deficit irrigation methods on quantitative and qualitative traits of strawberry have been evaluated. The focus at the current study was on the qualitative traits. Materials and Methods: The present study was conducted in one of strawberry farms of Babolsar city in 2012 to evaluate the effects of deficit irrigation and partial root zone drying on quantitative and qualitative traits of strawberry plants. Three Irrigation treatments were studied: Full Irrigation (FI, Regulated Deficit Irrigation (RDI75% at 75% level of plants water requirementand Partial Root zone Drying (PRD75% at 75% level of plants water requirement. The study was conducted in a randomized complete block design with three replications. Irrigation was continued until the

  17. Genetic Parameters and Combining Ability Effects of Parents for Seed Yield and other Quantitative Traits in Black Gram [Vigna mungo (L. Hepper

    Directory of Open Access Journals (Sweden)

    Supriyo CHAKRABORTY

    2010-06-01

    Full Text Available Line x tester analysis was carried out in black gram [Vigna mungo (L. Hepper], an edible legume, to estimate the gca (general combining ability effects of parents (3 lines and 3 testers and the SCA (specific combining ability effects of 9 crosses for seed yield and other eleven quantitative traits. Though additive and nonadditive gene actions governed the expression of quantitative traits, the magnitude of nonadditive gene action was higher than that of additive gene action for each quantitative trait. Two parents viz. �UG157� and �DPU915� were good general combiners. Two crosses namely �PDB 88-31�/�DPU 915� and �PLU 277�/�KAU7� had high per se performance along with positive significant SCA effect for seed yield/plant. The degree of dominance revealed overdominance for all the traits except clusters/plant with partial dominance. The predictability ratio also revealed the predominant role of nonadditive gene action in the genetic control of quantitative traits. Narrow sense heritability was also low for each trait. Recurrent selection or biparental mating followed by selection which can exploit both additive and nonadditive gene actions would be of interest for yield improvement in black gram. Due to presence of high magnitude of nonadditive gene action, heterosis breeding could also be attempted to develop low cost hybrid variety using genetic male sterility system in black gram.

  18. Genetic Parameters and Combining Ability Effects of Parents for Seed Yield and other Quantitative Traits in Black Gram [Vigna mungo (L. Hepper

    Directory of Open Access Journals (Sweden)

    Supriyo CHAKRABORTY

    2010-06-01

    Full Text Available Line x tester analysis was carried out in black gram [Vigna mungo (L. Hepper], an edible legume, to estimate the gca (general combining ability effects of parents (3 lines and 3 testers and the SCA (specific combining ability effects of 9 crosses for seed yield and other eleven quantitative traits. Though additive and nonadditive gene actions governed the expression of quantitative traits, the magnitude of nonadditive gene action was higher than that of additive gene action for each quantitative trait. Two parents viz. UG157 and DPU915 were good general combiners. Two crosses namely PDB 88-31/DPU 915 and PLU 277/KAU7 had high per se performance along with positive significant SCA effect for seed yield/plant. The degree of dominance revealed overdominance for all the traits except clusters/plant with partial dominance. The predictability ratio also revealed the predominant role of nonadditive gene action in the genetic control of quantitative traits. Narrow sense heritability was also low for each trait. Recurrent selection or biparental mating followed by selection which can exploit both additive and nonadditive gene actions would be of interest for yield improvement in black gram. Due to presence of high magnitude of nonadditive gene action, heterosis breeding could also be attempted to develop low cost hybrid variety using genetic male sterility system in black gram.

  19. Genome-wide linkage analysis for identifying quantitative trait loci involved in the regulation of lipoprotein a (Lpa) levels.

    Science.gov (United States)

    López, Sonia; Buil, Alfonso; Ordoñez, Jordi; Souto, Juan Carlos; Almasy, Laura; Lathrop, Mark; Blangero, John; Blanco-Vaca, Francisco; Fontcuberta, Jordi; Soria, José Manuel

    2008-11-01

    Lipoprotein Lp(a) levels are highly heritable and are associated with cardiovascular risk. We performed a genome-wide linkage analysis to delineate the genomic regions that influence the concentration of Lp(a) in families from the Genetic Analysis of Idiopathic Thrombophilia (GAIT) Project. Lp(a) levels were measured in 387 individuals belonging to 21 extended Spanish families. A total of 485 DNA microsatellite markers were genotyped to provide a 7.1 cM genetic map. The variance component linkage method was used to evaluate linkage and to detect quantitative trait loci (QTLs). The main QTL that showed strong evidence of linkage with Lp(a) levels was located at the structural gene for apo(a) on chromosome 6 (LOD score=13.8). Interestingly, another QTL influencing Lp(a) concentration was located on chromosome 2 with an LOD score of 2.01. This region contains several candidate genes. One of them is the tissue factor pathway inhibitor (TFPI), which has antithrombotic action and also has the ability to bind lipoproteins. However, quantitative trait association analyses performed with 12 SNPs in TFPI gene revealed no association with Lp(a) levels. Our study confirms previous results on the genetic basis of Lp(a) levels. In addition, we report a new QTL on chromosome 2 involved in the quantitative variation of Lp(a). These data should serve as the basis for further detection of candidate genes and to elucidate the relationship between the concentration of Lp(a) and cardiovascular risk.

  20. Genetic Variants Associated With Quantitative Glucose Homeostasis Traits Translate to Type 2 Diabetes in Mexican Americans: The GUARDIAN (Genetics Underlying Diabetes in Hispanics) Consortium.

    Science.gov (United States)

    Palmer, Nicholette D; Goodarzi, Mark O; Langefeld, Carl D; Wang, Nan; Guo, Xiuqing; Taylor, Kent D; Fingerlin, Tasha E; Norris, Jill M; Buchanan, Thomas A; Xiang, Anny H; Haritunians, Talin; Ziegler, Julie T; Williams, Adrienne H; Stefanovski, Darko; Cui, Jinrui; Mackay, Adrienne W; Henkin, Leora F; Bergman, Richard N; Gao, Xiaoyi; Gauderman, James; Varma, Rohit; Hanis, Craig L; Cox, Nancy J; Highland, Heather M; Below, Jennifer E; Williams, Amy L; Burtt, Noel P; Aguilar-Salinas, Carlos A; Huerta-Chagoya, Alicia; Gonzalez-Villalpando, Clicerio; Orozco, Lorena; Haiman, Christopher A; Tsai, Michael Y; Johnson, W Craig; Yao, Jie; Rasmussen-Torvik, Laura; Pankow, James; Snively, Beverly; Jackson, Rebecca D; Liu, Simin; Nadler, Jerry L; Kandeel, Fouad; Chen, Yii-Der I; Bowden, Donald W; Rich, Stephen S; Raffel, Leslie J; Rotter, Jerome I; Watanabe, Richard M; Wagenknecht, Lynne E

    2015-05-01

    Insulin sensitivity, insulin secretion, insulin clearance, and glucose effectiveness exhibit strong genetic components, although few studies have examined their genetic architecture or influence on type 2 diabetes (T2D) risk. We hypothesized that loci affecting variation in these quantitative traits influence T2D. We completed a multicohort genome-wide association study to search for loci influencing T2D-related quantitative traits in 4,176 Mexican Americans. Quantitative traits were measured by the frequently sampled intravenous glucose tolerance test (four cohorts) or euglycemic clamp (three cohorts), and random-effects models were used to test the association between loci and quantitative traits, adjusting for age, sex, and admixture proportions (Discovery). Analysis revealed a significant (P genetic factors, potentially delineating genomic components of these quantitative traits that drive the risk for T2D. © 2015 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

  1. Genetic Control and Heterosis of Quantitative Traits in Several Local Eggplant Genotypes

    Directory of Open Access Journals (Sweden)

    Ndueso Michael AKPAN

    2017-12-01

    Full Text Available The present study was performed to assess the nature of gene action governing inheritance of agronomic traits in eggplant genotypes and extent of mid parent heterosis (MPH and better parent heterosis (BPH in six eggplant hybrids generated from four superior and optimally divergent genotypes of eggplant namely ‘Yalo’, ‘Uyo’, ‘K3’ and ‘Iyoyo’ selected from the germplasm and were crossed in 4×4 half diallel mating design. The six hybrids were found to show a significant (p< 0.05 positive MPH in yield traits and the highest was obtained in the hybrid ‘Yalo’ × ‘K3’ for number of fruits per plant (158.90% and ‘K3’ × ‘Iyoyo’ for fruit yield per plant (63.14% and fruit yield per hectare (62.20 %. The hybrid combinations ‘Yalo’ × ‘K3’ and ‘K3’ × ‘Iyoyo’ had significant positive BPH for the number of fruits per plant, 104.08% and 42.43%, respectively. For fruit yield per plant, the hybrid combination ‘Yalo’ × ‘K3’ (7.93%, ‘Uyo’ × ‘K3’ (8.48% and ‘K3’ × ‘Iyoyo’ (12.26% had significant positive BPH. However, the hybrid ‘K3’ × ‘Iyoyo’ (11.51% showed significant positive BPH in fruit yield per hectare. Dominance and dominance × dominance gene effect were found to be positively higher in magnitude in all crosses for number of fruits per plant, fruit yield per plant and fruit yield per hectare. The prevalence of dominance and dominance × dominance gene effect in the yield traits indicate heterosis breeding as the best breeding method to improve the productivity of eggplant.

  2. Heritability and gene effects for yield related quantitative traits in eggplant

    Directory of Open Access Journals (Sweden)

    Chintan Mistry

    2016-12-01

    Full Text Available Knowledge of gene actions and their relative contribution in expression of characters is of great importance. Therefore, four crosses were made among the six parents viz., Doli-5 × GBL-1 (cross 1, Doli-5 × KS-331 (cross 2, Pusa Uttam × KS-331 (cross 3 and AB 07-02 × GOB 1 (cross 4 to study gene actions responsible for inheritance of twelve fruit yield traits. The generation mean analysis in six populations revealed significant digenic interactions for all the characters in majority of the crosses studied. Character-cross combination revealed the adequacy of simple additive dominance model for plant height (in cross 1, primary branches per plant (in cross 2, secondary branches per plant (in cross 3, fruit length (in cross 2, fruit girth (in cross 3 and pedicel length (in cross 3 indicating the absence of non-allelic interactions. Most of the crosses for all the yield traits showed low magnitude of dominance and environmental variances, revealing higher heritabilities. Duplicate epistasis effects controlled all traits in different cross-combinations suggesting the mild selection intensity in the earlier generations while intense in later generations. However, in few cases average dominance ratio was more than unity indicated the importance of dominance gene effects. These results indicated that for eggplant improvement, additive variation is of great importance and makes it possible to successfully select better individuals in segregating populations, since the selective gains will depend only on gametic variation. For this reason, backcross, pedigree, single-seed descent or gametic selection methods are recommended for advancing the segregating populations.

  3. Evaluation of pea varieties based on correlation of quantitative traits and indices

    Directory of Open Access Journals (Sweden)

    О. І. Присяжнюк

    2016-12-01

    Full Text Available Purpose. To evaluate pea plants productivity and determine the degree of correlation among the main agronomic characters in pea varieties. Methods. Structural and statistical analysis. Results. Evaluation of pea samples in terms of indices of plant productivity elements level based on correlation analysis and single-factor indices appliance provided insight into the ratio of one trait share per unit of another one. It was defined that some correlations among the elements of productivity was not only moderate and weak, but they also changed their sign that could be the evidence of growth conditions influence on structural relationships bet­ween some traits and, consequently, redistribution of their contributions to the formation of variety productivity. Positive and very close relationship of many traits was revealed, particularly between plant height and the height of the plant up to the first bean, the number of nodes and the number of sterile nodes (r = 0,95–0,97. Methodological aspects of the variety model creation were considered, that may be useful not only in pea breeding but also for improving the techno­logy of its cultivation. Conclusions. Correlation relationships were established between the number of beans and the number of fruiting nodes and the number of carpophores containing 2 beans (r = 0,86–0,88, seed mass and plant mass (r = 0,81, the number of seeds per plant and plant mass and seed mass per plant (r = 0,78–0,81, the number of certified seeds and the number of seeds per plant (r = 0,84, the average number of beans per fertile node and the number of carpophores containing 2 beans (r = 0,74 that makes it possible to use them in assessing the productivity of plants.

  4. Issues in adult blood cancer survivorship care.

    Science.gov (United States)

    Bugos, Kelly G

    2015-02-01

    To describe the current literature and future directions of survivorship care for the adult blood cancer population including unique features, identification of needs, practice guidelines, care models and the implications for nursing. Peer reviewed literature, government and national advocacy organization reports, professional organization guidelines. Adult blood cancer survivors are a heterogeneous population that often receives complicated treatments to live a longer life. Survivorship needs among this population are often unmet throughout the cancer care continuum. The limited research literature and guidelines point to survivorship care strategies from the day of diagnosis to enhance long-term outcomes and improve quality of life. Nurses are experts in symptom management and central to preventing, detecting, measuring, educating, and treating the effects of cancer and its treatment. Moreover, nurses are key to implementing strategies to support blood cancer survivors, families, and caregivers from the day of diagnosis to the last day of life. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Pattern of quantitative inheritance of yield and component traits in opium poppy (Papaver somniferum L.

    Directory of Open Access Journals (Sweden)

    Maurya Krishna Nand

    2014-01-01

    Full Text Available Generation mean analysis of cross NB-5x58/1 and its reciprocal cross was carried out to understand the nature of gene action in opium poppy. The significance of A, B, C and D scaling tests indicated presence of non-allelic interaction in the inheritance of traits except capsule size and husk yield/plant for reciprocal cross. Additive as well as dominance components of gene action were found in both the crosses. Most of the traits had greater non fixable dominance ‘h’ and dominance x dominance effects ‘l’ than fixable additive (d and additive x additive effects (i except leaves/plant, branches/plant, capsules/plant, stem diameter, capsule weight/plant, husk yield/plant, opium yield/plant, codeine and narcotine content which showed greater importance of additive (d and additive x additive effects (i effects. Inter-mating of the best parents, diallel selective mating or biparental mating in early segregating generations followed by recurrent selections were suggested for genetic improvement of opium poppy.

  6. Evaluation of Quantitative and Qualitative Traits of Some Apricot Cultivars Grown in Zanjan Region

    Directory of Open Access Journals (Sweden)

    sanaz molaie

    2017-02-01

    Full Text Available Introduction Apricot (Prunus armeniaca L. has special position in Iran fruit culture industry. In terms of cultivation and producing, Iran is one of the major countries in the world but in terms of export Iran is ranked 23. For this reason, research on necessities of fruit culture industries and access to new cultivars by breeding project is required. Obviously, paying attention to quality and quantity of products and using of local germplasm that known completely, played a significant role in this project. Apricot with genomic feature 2n=16, has extensive diversity due to sexual propagation and cultivation in different areas. Central Asia and Caucasian groups of apricot that involving Iranian and Turkish cultivars, have greatest phenotypic variations, while European group including cultivars that cultivated in North America, Australia and South Africa have the lowest diversity. Climate adaptation, increasing of fruits quality, self-compatibility and resistance to diseases are the most important goals of apricot breeding. Of course, the quality of fruits depends on sugar and acid balance and special aroma. One of the important targets of apricot breeding is introduce and develop of cultivars that can be cultivated in extensive areas. Target of recent study is primary evaluating of morphological and pomological traits of some cultivar and genotypes of apricot grown in Zanjan province. In order to introduce the cultivars that produces fruit with high quality and complete scientific researches to selection of ideal cultivars in this region for future. Method and material: This research carried out on four cultivars (Badami, Daneshkadeh, Shekarpareh, Shahroodi and two genotypes (C and D and was conducted in a completely randomize design with three replications. Evaluating of tree, branch, leaf, flower and some fruit traits performed based on existing descriptor. For determining some important pomological traits, fruits harvested in commercial time

  7. On the detection of imprinted quantitative trait loci in experimental crosses of outbred species

    NARCIS (Netherlands)

    Koning, de D.J.; Bovenhuis, H.; Arendonk, van J.A.M.

    2002-01-01

    In this article, the quantitative genetic aspects of imprinted genes and statistical properties of methods to detect imprinted QTL are studied. Different models to detect imprinted QTL and to distinguish between imprinted and Mendelian QTL were compared in a simulation study. Mendelian and imprinted

  8. On the detection of imprinting quantitative trait loci in experimental crosses of outbred species

    NARCIS (Netherlands)

    Koning, de D.J.; Bovenhuis, H.; Arendonk, van J.A.M.

    2002-01-01

    In this article, the quantitative genetic aspects of imprinted genes and statistical properties of methods to detect imprinted QTL are studied. Different models to detect imprinted QTL and to distinguish between imprinted and Mendelian QTL were compared in a simulation study. Mendelian and imprinted

  9. Multilocus association testing of quantitative traits based on partial least-squares analysis.

    Directory of Open Access Journals (Sweden)

    Feng Zhang

    Full Text Available Because of combining the genetic information of multiple loci, multilocus association studies (MLAS are expected to be more powerful than single locus association studies (SLAS in disease genes mapping. However, some researchers found that MLAS had similar or reduced power relative to SLAS, which was partly attributed to the increased degrees of freedom (dfs in MLAS. Based on partial least-squares (PLS analysis, we develop a MLAS approach, while avoiding large dfs in MLAS. In this approach, genotypes are first decomposed into the PLS components that not only capture majority of the genetic information of multiple loci, but also are relevant for target traits. The extracted PLS components are then regressed on target traits to detect association under multilinear regression. Simulation study based on real data from the HapMap project were used to assess the performance of our PLS-based MLAS as well as other popular multilinear regression-based MLAS approaches under various scenarios, considering genetic effects and linkage disequilibrium structure of candidate genetic regions. Using PLS-based MLAS approach, we conducted a genome-wide MLAS of lean body mass, and compared it with our previous genome-wide SLAS of lean body mass. Simulations and real data analyses results support the improved power of our PLS-based MLAS in disease genes mapping relative to other three MLAS approaches investigated in this study. We aim to provide an effective and powerful MLAS approach, which may help to overcome the limitations of SLAS in disease genes mapping.

  10. Identification of Quantitative Trait Loci (QTL) and Candidate Genes for Cadmium Tolerance in Populus

    Energy Technology Data Exchange (ETDEWEB)

    Induri, Brahma R [West Virginia University; Ellis, Danielle R [West Virginia University; Slavov, Gancho [West Virginia University; Yin, Tongming [ORNL; Muchero, Wellington [ORNL; Tuskan, Gerald A [ORNL; DiFazio, Stephen P [West Virginia University

    2012-01-01

    Knowledge of genetic variation in response of Populus to heavy metals like cadmium (Cd) is an important step in understanding the underlying mechanisms of tolerance. In this study, a pseudo-backcross pedigree of Populus trichocarpa and Populus deltoides was characterized for Cd exposure. The pedigree showed significant variation for Cd tolerance thus enabling the identification of relatively tolerant and susceptible genotypes for intensive characterization. A total of 16 QTLs at logarithm of odds (LOD) ratio > 2.5, were found to be associated with total dry weight, its components, and root volume. Four major QTLs for total dry weight were mapped to different linkage groups in control (LG III) and Cd conditions (LG XVI) and had opposite allelic effects on Cd tolerance, suggesting that these genomic regions were differentially controlled. The phenotypic variation explained by Cd QTL for all traits under study varied from 5.9% to 11.6% and averaged 8.2% across all QTL. Leaf Cd contents also showed significant variation suggesting the phytoextraction potential of Populus genotypes, though heritability of this trait was low (0.22). A whole-genome microarray study was conducted by using two genotypes with extreme responses for Cd tolerance in the above study and differentially expressed genes were identified. Candidate genes including CAD2 (CADMIUM SENSITIVE 2), HMA5 (HEAVY METAL ATPase5), ATGTST1 (Arabidopsis thaliana Glutathione S-Transferase1), ATGPX6 (Glutathione peroxidase 6), and ATMRP 14 (Arabidopsis thaliana Multidrug Resistance associated Protein 14) were identified from QTL intervals and microarray study. Functional characterization of these candidate genes could enhance phytoremediation capabilities of Populus.

  11. A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population

    Science.gov (United States)

    2011-01-01

    Background Cassava (Manihot esculenta Crantz) can produce cyanide, a toxic compound, without self-injury. That ability was called the cyanogenic potential (CN). This project aimed to identify quantitative trait loci (QTL) associated with the CN in an outbred population derived from 'Hanatee' × 'Huay Bong 60', two contrasting cultivars. CN was evaluated in 2008 and in 2009 at Rayong province, and in 2009 at Lop Buri province, Thailand. CN was measured using a picrate paper kit. QTL analysis affecting CN was performed with 303 SSR markers. Results The phenotypic values showed continuous variation with transgressive segregation events with more (115 ppm) and less CN (15 ppm) than either parent ('Hanatee' had 33 ppm and 'Huay Bong 60' had 95 ppm). The linkage map consisted of 303 SSR markers, on 27 linkage groups with a map that encompassed 1,328 cM. The average marker interval was 5.8 cM. Five QTL underlying CN were detected. CN08R1from 2008 at Rayong, CN09R1and CN09R2 from 2009 at Rayong, and CN09L1 and CN09L2 from 2009 at Lop Buri were mapped on linkage group 2, 5, 10 and 11, respectively. Among all the identified QTL, CN09R1 was the most significantly associated with the CN trait with LOD score 5.75 and explained the greatest percentage of phenotypic variation (%Expl.) of 26%. Conclusions Five new QTL affecting CN were successfully identified from 4 linkage groups. Discovery of these QTL can provide useful markers to assist in cassava breeding and studying genes affecting the trait. PMID:21609492

  12. Effects of long-term averaging of quantitative blood pressure traits on the detection of genetic associations.

    Science.gov (United States)

    Ganesh, Santhi K; Chasman, Daniel I; Larson, Martin G; Guo, Xiuqing; Verwoert, Germain; Bis, Joshua C; Gu, Xiangjun; Smith, Albert V; Yang, Min-Lee; Zhang, Yan; Ehret, Georg; Rose, Lynda M; Hwang, Shih-Jen; Papanicolau, George J; Sijbrands, Eric J; Rice, Kenneth; Eiriksdottir, Gudny; Pihur, Vasyl; Ridker, Paul M; Vasan, Ramachandran S; Newton-Cheh, Christopher; Raffel, Leslie J; Amin, Najaf; Rotter, Jerome I; Liu, Kiang; Launer, Lenore J; Xu, Ming; Caulfield, Mark; Morrison, Alanna C; Johnson, Andrew D; Vaidya, Dhananjay; Dehghan, Abbas; Li, Guo; Bouchard, Claude; Harris, Tamara B; Zhang, He; Boerwinkle, Eric; Siscovick, David S; Gao, Wei; Uitterlinden, Andre G; Rivadeneira, Fernando; Hofman, Albert; Willer, Cristen J; Franco, Oscar H; Huo, Yong; Witteman, Jacqueline C M; Munroe, Patricia B; Gudnason, Vilmundur; Palmas, Walter; van Duijn, Cornelia; Fornage, Myriam; Levy, Daniel; Psaty, Bruce M; Chakravarti, Aravinda

    2014-07-03

    Blood pressure (BP) is a heritable, quantitative trait with intraindividual variability and susceptibility to measurement error. Genetic studies of BP generally use single-visit measurements and thus cannot remove variability occurring over months or years. We leveraged the idea that averaging BP measured across time would improve phenotypic accuracy and thereby increase statistical power to detect genetic associations. We studied systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP) averaged over multiple years in 46,629 individuals of European ancestry. We identified 39 trait-variant associations across 19 independent loci (p < 5 × 10(-8)); five associations (in four loci) uniquely identified by our LTA analyses included those of SBP and MAP at 2p23 (rs1275988, near KCNK3), DBP at 2q11.2 (rs7599598, in FER1L5), and PP at 6p21 (rs10948071, near CRIP3) and 7p13 (rs2949837, near IGFBP3). Replication analyses conducted in cohorts with single-visit BP data showed positive replication of associations and a nominal association (p < 0.05). We estimated a 20% gain in statistical power with long-term average (LTA) as compared to single-visit BP association studies. Using LTA analysis, we identified genetic loci influencing BP. LTA might be one way of increasing the power of genetic associations for continuous traits in extant samples for other phenotypes that are measured serially over time. Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  13. Quantitative trait loci for thermal time to flowering and photoperiod responsiveness discovered in summer annual-type Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Matthew N Nelson

    Full Text Available Time of flowering is a key adaptive trait in plants and is conditioned by the interaction of genes and environmental cues including length of photoperiod, ambient temperature and vernalisation. Here we investigated the photoperiod responsiveness of summer annual-types of Brassica napus (rapeseed, canola. A population of 131 doubled haploid lines derived from a cross between European and Australian parents was evaluated for days to flowering, thermal time to flowering (measured in degree-days and the number of leaf nodes at flowering in a compact and efficient glasshouse-based experiment with replicated short and long day treatments. All three traits were under strong genetic control with heritability estimates ranging from 0.85-0.93. There was a very strong photoperiod effect with flowering in the population accelerated by 765 degree-days in the long day versus short day treatments. However, there was a strong genetic correlation of line effects (0.91 between the long and short day treatments and relatively low genotype x treatment interaction indicating that photoperiod had a similar effect across the population. Bivariate analysis of thermal time to flowering in short and long days revealed three main effect quantitative trait loci (QTLs that accounted for 57.7% of the variation in the population and no significant interaction QTLs. These results provided insight into the contrasting adaptations of Australian and European varieties. Both parents responded to photoperiod and their alleles shifted the population to earlier flowering under long days. In addition, segregation of QTLs in the population caused wide transgressive segregation in thermal time to flowering. Potential candidate flowering time homologues located near QTLs were identified with the aid of the Brassica rapa reference genome sequence. We discuss how these results will help to guide the breeding of summer annual types of B. napus adapted to new and changing environments.

  14. ffect of Nitrogen and Zinc Foliar Application on Quantitative Traits of Tea Rosslle (Hibiscus sabdariffa in Jiroft Zone

    Directory of Open Access Journals (Sweden)

    abdolreza raisi sarbijan

    2017-02-01

    increased with increasing amountof nitrogen up to N3 level. Theapplication of zinc fertilizer significantly increased the plant fresh weigh, plant dry weight, mucilage percentage and yield. The interactions of nitrogen and zinc improved the calycle, leaf dry weight, plant dry weight, and the highest calycle dry weight were achieved from N2Zn1 and N3Zn1 treatments. The results showed that any givenlevel of nitrogen fertilizer and zinc fertilizer increased growth, yieldand quantitative traits of Hibiscus tea, but the level of interaction between nitrogen and zinc fertilizer hada significant effect on growth traits of Hibiscus tea, and even reduced the growth and yield of quantitative traits. The nitrogen and the fertilizer mixture of nitrogen and zinc had a significant influence on Hibiscus tea quantitative traits. Nitrogen fertilizer with a higher level of performance and yield had the greatest effect on Hibiscus tea.The greatest impact of nitrogen fertilizer, zinc fertilizer and the fertilizer mixture of nitrogen and zinc on sepal fresh weight were215.481 gr, 209.935 gr and 216.893 gr respectively.The effect of nitrogen fertilizer, zinc fertilizer and fertilizer mixture of nitrogen and zinc on leaf fresh weight,leaf dry weight andsepals dry weight were 61.787 gr 13.378 gr and 19.482 gr respectively. Conclusion The results of this study showed thatin order to increase crop yield and quality,nitrogen fertilizer and spraying of manure on Hibiscus tea is recommended. Because of having useful properties in the treatment of diabetes, as well as the climate and soil conditions of Jiroft area, this plant is grown as a medicinal plant at a large scale. Since Jiroft region is a suitable place for growth of Hibiscus tea and due to the importance of medicinal plants, it recommend that this experiment should be repeated to evaluateplant characteristics.

  15. Boron toxicity in rice (Oryza sativa L.). I. Quantitative trait locus (QTL) analysis of tolerance to boron toxicity.

    Science.gov (United States)

    Ochiai, K; Uemura, S; Shimizu, A; Okumoto, Y; Matoh, T

    2008-06-01

    Boron toxicity tolerance of rice plants was studied. Modern japonica subspecies such as Koshihikari, Nipponbare, and Sasanishiki were tolerant, whereas indica subspecies such as Kasalath and IR36 were intolerant to excessive application of boron (B), even though their shoot B contents under B toxicity were not significantly different. Recombinant inbred lines (RILs) of japonica Nekken-1 and indica IR36 were used for quantitative trait locus (QTL) analysis to identify the gene responsible for B toxicity tolerance. A major QTL that could explain 45% of the phenotypic variation was detected in chromosome 4. The QTL was confirmed using a population derived from a recombinant inbred line which is heterogenic at the QTL region. The QTL was also confirmed in other chromosome segment substitution lines (CSSLs).

  16. Environmental and seasonal influences on red raspberry flavour volatiles and identification of quantitative trait loci (QTL) and candidate genes.

    Science.gov (United States)

    Paterson, Alistair; Kassim, Angzzas; McCallum, Susan; Woodhead, Mary; Smith, Kay; Zait, Dzeti; Graham, Julie

    2013-01-01

    Raspberry volatiles are important for perceptions of sensory quality, mould resistance and some have nutraceutical activities. Twelve raspberry character volatiles were quantified, 11 of them in fruit from two seasons, from plants from the Glen Moy × Latham mapping population growing in both open field and under cover (polytunnels). Effects of season and environment were examined for their impact on the content of α-ionone, α-ionol, β-ionone, β-damascenone, linalool, geraniol, benzyl alcohol, (Z)-3-hexenol, acetoin, acetic and hexanoic acids, whilst raspberry ketone was measured in one season. A significant variation was observed in fruit volatiles in all progeny between seasons and method of cultivation. Quantitative trait loci were determined and mapped to six of the seven linkage groups, as were candidate genes in the volatiles pathways.

  17. Combined use of phenotypic and genotypic information in sampling animalsfor genotyping in detection of quantitative trait loci

    DEFF Research Database (Denmark)

    Ansari-Mahyari, S; Berg, P

    2008-01-01

    Conventional selective genotyping which is using the extreme phenotypes (EP) was compared with alternative criteria to find the most informative animals for genotyping with respects to mapping quantitative trait loci (QTL). Alternative sampling strategies were based on minimizing the sampling error...... of the estimated QTL effect (MinERR) and maximizing likelihood ratio test (MaxLRT) using both phenotypic and genotypic information. In comparison, animals were randomly genotyped either within or across families. One hundred data sets were simulated each with 30 half-sib families and 120 daughters per family....... The strategies were compared in these datasets with respect to estimated effect and position of a QTL within a previously defined genomic region at genotyping 10, 20 or 30% of the animals. Combined linkage disequilibrium linkage analysis (LDLA) was applied in a variance component approach. Power to detect QTL...

  18. Stability of quantitative trait loci for growth and wood properties across multiple pedigrees and environments in Eucalyptus globulus.

    Science.gov (United States)

    Freeman, Jules S; Potts, Brad M; Downes, Geoffrey M; Pilbeam, David; Thavamanikumar, Saravanan; Vaillancourt, René E

    2013-06-01

    · Eucalypts are one of the most planted tree genera worldwide, and there is increasing interest in marker-assisted selection for tree improvement. Implementation of marker-assisted selection requires a knowledge of the stability of quantitative trait loci (QTLs). This study aims to investigate the stability of QTLs for wood properties and growth across contrasting sites and multiple pedigrees of Eucalyptus globulus. · Saturated linkage maps were constructed using 663 genotypes from four separate families, grown at three widely separated sites, and were employed to construct a consensus map. This map was used for QTL analysis of growth, wood density and wood chemical traits, including pulp yield. · Ninety-eight QTLs were identified across families and sites: 87 for wood properties and 11 for growth. These QTLs mapped to 38 discrete regions, some of which co-located with candidate genes. Although 16% of QTLs were verified across different families, 24% of wood property QTLs and 38% of growth QTLs exhibited significant genotype-by-environment interaction. · This study provides the most detailed assessment of the effect of environment and pedigree on QTL detection in the genus. Despite markedly different environments and pedigrees, many QTLs were stable, providing promising targets for the application of marker-assisted selection. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  19. High-Density Genetic Linkage Map Construction and Quantitative Trait Locus Mapping for Hawthorn (Crataegus pinnatifida Bunge).

    Science.gov (United States)

    Zhao, Yuhui; Su, Kai; Wang, Gang; Zhang, Liping; Zhang, Jijun; Li, Junpeng; Guo, Yinshan

    2017-07-14

    Genetic linkage maps are an important tool in genetic and genomic research. In this study, two hawthorn cultivars, Qiujinxing and Damianqiu, and 107 progenies from a cross between them were used for constructing a high-density genetic linkage map using the 2b-restriction site-associated DNA (2b-RAD) sequencing method, as well as for mapping quantitative trait loci (QTL) for flavonoid content. In total, 206,411,693 single-end reads were obtained, with an average sequencing depth of 57× in the parents and 23× in the progeny. After quality trimming, 117,896 high-quality 2b-RAD tags were retained, of which 42,279 were polymorphic; of these, 12,951 markers were used for constructing the genetic linkage map. The map contained 17 linkage groups and 3,894 markers, with a total map length of 1,551.97 cM and an average marker interval of 0.40 cM. QTL mapping identified 21 QTLs associated with flavonoid content in 10 linkage groups, which explained 16.30-59.00% of the variance. This is the first high-density linkage map for hawthorn, which will serve as a basis for fine-scale QTL mapping and marker-assisted selection of important traits in hawthorn germplasm and will facilitate chromosome assignment for hawthorn whole-genome assemblies in the future.

  20. A composite method for mapping quantitative trait loci without interference of female achiasmatic and gender effects in silkworm, Bombyx mori.

    Science.gov (United States)

    Li, C; Zuo, W; Tong, X; Hu, H; Qiao, L; Song, J; Xiong, G; Gao, R; Dai, F; Lu, C

    2015-08-01

    The silkworm, Bombyx mori, is an economically important insect that was domesticated more than 5000 years ago. Its major economic traits focused on by breeders are quantitative traits, and an accurate and efficient QTL mapping method is necessary to explore their genetic architecture. However, current widely used QTL mapping models are not well suited for silkworm because they ignore female achiasmate and gender effects. In this study, we propose a composite method combining rational population selection and special mapping methods to map QTL in silkworm. By determining QTL for cocoon shell weight (CSW), we demonstrated the effectiveness of this method. In the CSW mapping process, only 56 markers were used and five loci or chromosomes were detected, more than in previous studies. Additionally, loci on chromosomes 1 and 11 dominated and accounted for 35.10% and 15.03% of the phenotypic variance respectively. Unlike previous studies, epistasis was detected between loci on chromosomes 11 and 22. These mapping results demonstrate the power and convenience of this method for QTL mapping in silkworm, and this method may inspire the development of similar approaches for other species with special genetic characteristics. © 2015 Stichting International Foundation for Animal Genetics.

  1. Confirmatory factor analytic structure and measurement invariance of quantitative autistic traits measured by the social responsiveness scale-2.

    Science.gov (United States)

    Frazier, Thomas W; Ratliff, Kristin R; Gruber, Chris; Zhang, Yi; Law, Paul A; Constantino, John N

    2014-01-01

    Understanding the factor structure of autistic symptomatology is critical to the discovery and interpretation of causal mechanisms in autism spectrum disorder. We applied confirmatory factor analysis and assessment of measurement invariance to a large (N = 9635) accumulated collection of reports on quantitative autistic traits using the Social Responsiveness Scale, representing a broad diversity of age, severity, and reporter type. A two-factor structure (corresponding to social communication impairment and restricted, repetitive behavior) as elaborated in the updated Diagnostic and Statistical Manual of Mental Disorders (5th ed.; DSM-5) criteria for autism spectrum disorder exhibited acceptable model fit in confirmatory factor analysis. Measurement invariance was appreciable across age, sex, and reporter (self vs other), but somewhat less apparent between clinical and nonclinical populations in this sample comprised of both familial and sporadic autism spectrum disorders. The statistical power afforded by this large sample allowed relative differentiation of three factors among items encompassing social communication impairment (emotion recognition, social avoidance, and interpersonal relatedness) and two factors among items encompassing restricted, repetitive behavior (insistence on sameness and repetitive mannerisms). Cross-trait correlations remained extremely high, that is, on the order of 0.66-0.92. These data clarify domains of statistically significant factoral separation that may relate to partially-but not completely-overlapping biological mechanisms, contributing to variation in human social competency. Given such robust intercorrelations among symptom domains, understanding their co-emergence remains a high priority in conceptualizing common neural mechanisms underlying autistic syndromes.

  2. A quantitative trait locus for faecal worm egg and blood eosinophil counts on chromosome 23 in Australian goats.

    Science.gov (United States)

    Bolormaa, S; van der Werf, J H J; Walkden-Brown, S W; Marshall, K; Ruvinsky, A

    2010-06-01

    Three microsatellite markers on goat chromosome 23 adjacent to the MHC were used to test for quantitative trait loci (QTL) affecting faecal worm egg count (WEC) and leukocyte traits in ten Australian Angora and twelve Australian Cashmere half-sib families (n = 16-57 per family). Data were collected from 280 Angora and 347 Cashmere kids over a 3- and 4-year period. A putative QTL affecting trichostrongyle WEC was found in two small families at the 5% chromosome-wise threshold level. The biggest QTL effect for WEC of 1.65 standard deviations (sigma(p)) was found within the region of OarCP73-BM1258. A significant QTL affecting blood eosinophil counts at the 1% chromosome-wise threshold level was detected at marker BM1258 (at 26 cM) in two Angora and Cashmere families. The magnitude of the putative QTL was 0.69 and 0.85 sigma(p) in Angora and Cashmere families, respectively. Due to the comparatively low power of the study these findings should be viewed as indicative rather than definitive.

  3. Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease.

    Directory of Open Access Journals (Sweden)

    Steven G Potkin

    Full Text Available BACKGROUND: With the exception of APOE epsilon4 allele, the common genetic risk factors for sporadic Alzheimer's Disease (AD are unknown. METHODS AND FINDINGS: We completed a genome-wide association study on 381 participants in the ADNI (Alzheimer's Disease Neuroimaging Initiative study. Samples were genotyped using the Illumina Human610-Quad BeadChip. 516,645 unique Single Nucleotide Polymorphisms (SNPs were included in the analysis following quality control measures. The genotype data and raw genetic data are freely available for download (LONI, http://www.loni.ucla.edu/ADNI/Data/. Two analyses were completed: a standard case-control analysis, and a novel approach using hippocampal atrophy measured on MRI as an objectively defined, quantitative phenotype. A General Linear Model was applied to identify SNPs for which there was an interaction between the genotype and diagnosis on the quantitative trait. The case-control analysis identified APOE and a new risk gene, TOMM40 (translocase of outer mitochondrial membrane 40, at a genome-wide significance level of < or =10(-6 (10(-11 for a haplotype. TOMM40 risk alleles were approximately twice as frequent in AD subjects as controls. The quantitative trait analysis identified 21 genes or chromosomal areas with at least one SNP with a p-value < or =10(-6, which can be considered potential "new" candidate loci to explore in the etiology of sporadic AD. These candidates included EFNA5, CAND1, MAGI2, ARSB, and PRUNE2, genes involved in the regulation of protein degradation, apoptosis, neuronal loss and neurodevelopment. Thus, we identified common genetic variants associated with the increased risk of developing AD in the ADNI cohort, and present publicly available genome-wide data. Supportive evidence based on case-control studies and biological plausibility by gene annotation is provided. Currently no available sample with both imaging and genetic data is available for replication. CONCLUSIONS: Using

  4. Detection of quantitative trait loci for kernel oil and protein concentration in a B73 and Zheng58 maize cross.

    Science.gov (United States)

    Yang, Z; Li, X; Zhang, N; Zhang, Y N; Jiang, H W; Gao, J; Kuai, B K; Ding, Y L; Huang, X Q

    2016-09-30

    Maize (Zea mays L.) is one of the most important food crops throughout the world, and provides oil and proteins to humans and livestock. Kernel oil and protein content in maize are two complex quantitative traits. In order to identify quantitative trait loci (QTL) controlling oil and protein concentration in maize kernels, and to evaluate their genetic effects, QTL analysis was conducted on an F3:4 population derived from a cross between an inbred line with a low oil and protein concentration (Zheng58) and an inbred line with a higher oil and protein concentration (B73). A total of 189 polymorphic simple sequence repeat markers were used to construct a linkage map. Eleven QTLs for kernel oil concentration were detected on nine chromosomes, except for chromosome 9. A single QTL explained 4.6 to 11.1% of the phenotypic variance. Ten QTLs for kernel protein concentration were also detected on nine chromosomes, except for chromosome 9. A single QTL explained 4.2 to 11.4% of the phenotypic variance. Interestingly, novel QTLs for oil concentration (qOIL08-01 and qOIL10-01) and QTLs for protein concentration (qPRO01-01 and qPRO05-01) were specific to the population studied, which could explain 7.1 to 11.1% of the phenotypic variance. These results will provide better understanding of the genetic basis of oil and protein concentrations in maize. The markers closely linked with the QTLs will facilitate breeding of maize varieties with high oil and protein concentrations through molecular marker-assisted selection.

  5. Survivorship care planning after participation in communication skills training intervention for a consultation about lymphoma survivorship.

    Science.gov (United States)

    Banerjee, Smita C; Matasar, Matthew J; Bylund, Carma L; Horwitz, Steven; McLarney, Kara; Levin, Tomer; Jacobsen, Paul B; Parker, Patricia; Astrow, Alan; Kissane, David W

    2015-12-01

    A survivorship care plan refers to a written summary of the treatment received and recommendations regarding surveillance and management of late effects. To provide evaluation of a communication skills training (CST) intervention to enhance the transition of lymphoma survivors to cancer survivorship. Nineteen oncologists specializing in lymphoma treatment were recruited and completed a survivorship CST workshop, and two standardized patient assessments (SPAs), one pretraining and one posttraining. Significant improvements in SPA scores were observed in six of the seven SPA assessment categories: use of survivorship care plan, review of disease and treatment details, long-term effects, potential late effects, specific physician recommendations, and additional health maintenance recommendations. The intervention had significant effects on physicians' uptake of new strategies and skills, as measured through pre- and posttraining SPAs, as well as on the physicians' self-efficacy about having these conversations.

  6. Quantitative trait loci for resistance to trichostrongylid infection in Spanish Churra sheep

    Directory of Open Access Journals (Sweden)

    Primitivo Fermin San

    2009-10-01

    Full Text Available Abstract Background For ruminants reared on grazing systems, gastrointestinal nematode (GIN parasite infections represent the class of diseases with the greatest impact on animal health and productivity. Among the many possible strategies for controlling GIN infection, the enhancement of host resistance through the selection of resistant animals has been suggested by many authors. Because of the difficulty of routinely collecting phenotypic indicators of parasite resistance, information derived from molecular markers may be used to improve the efficiency of classical genetic breeding. Methods A total of 181 microsatellite markers evenly distributed along the 26 sheep autosomes were used in a genome scan analysis performed in a commercial population of Spanish Churra sheep to detect chromosomal regions associated with parasite resistance. Following a daughter design, we analysed 322 ewes distributed in eight half-sib families. The phenotypes studied included two faecal egg counts (LFEC0 and LFEC1, anti-Teladorsagia circumcincta LIV IgA levels (IgA and serum pepsinogen levels (Peps. Results The regression analysis revealed one QTL at the 5% genome-wise significance level on chromosome 6 for LFEC1 within the marker interval BM4621-CSN3. This QTL was found to be segregating in three out of the eight families analysed. Four other QTL were identified at the 5% chromosome-wise level on chromosomes 1, 10 and 14. Three of these QTL influenced faecal egg count, and the other one had an effect on IgA levels. Conclusion This study has successfully identified segregating QTL for parasite resistance traits in a commercial population. For some of the QTL detected, we have identified interesting coincidences with QTL previously reported in sheep, although most of those studies have been focused on young animals. Some of these coincidences might indicate that some common underlying loci affect parasite resistance traits in different sheep breeds. The

  7. Correlações entre caracteres quantitativos em milho pipoca Correlation among quantitative traits in popcorn maize

    Directory of Open Access Journals (Sweden)

    Valéria Carpentieri-Pípolo

    2002-12-01

    Full Text Available Em um programa de melhoramento, o conhecimento da grandeza das associações entre caracteres de interesse, é de fundamental importância na obtenção de populações melhoradas. O presente trabalho teve como objetivo determinar as correlações genotípicas, fenotípicas e ambientais entre caracteres quantitativos em milho pipoca. Foram avaliados nove genótipos de milho pipoca dispostos no campo em delineamento em blocos casualizados com oito repetições. Os genótipos UEL ZP, UEL SI e UEL PAP revelaram maiores capacidades de expansão (27,50; 27,15 e 24,40 respectivamente e número de grãos por volume (244,75; 248,50 e 248,75 respectivamente. A capacidade de expansão revelou correlação fenotípica positiva com o tamanho da pipoca e com o número de grãos por volume, e correlação negativa com massa de grãos por planta. Os caracteres massa de grãos por planta e peso total da espiga revelaram correlações fenotípicas e genotípicas positivas entre si, o que possibilita a utilização de um ou outro na seleção, optando-se pelo que melhor convier aos propósitos do programa de melhoramento.Knowledge of the size of the association among traits of interest is of fundamental importance in a breeding program to allow genetic progress. The genotypic, phenotypic and environment correlation were studied among quantitative traits of popcorn maize. Nine popcorn maize genotypes were assessed. A randomized complete block design with eight replications was used. The UEL ZP, UEL SI and UEL PAP. genotypes which had greatest expansion capacity (27.50; 27.15 and 24.20, respectively, also had the greatest values for the number of grains per volume (244.75; 248.50 and 248.75, respectively. The expansion capacity correlated positively with the popcorn size and with number of grains per volume and negatively with plant yield. The traits plant yield, and total ear weight showed positive phenotypic and genotypic correlation that permits the choice of

  8. Quantitative trait loci identified for blood chemistry components of an advanced intercross line of chickens under heat stress.

    Science.gov (United States)

    Van Goor, Angelica; Ashwell, Christopher M; Persia, Michael E; Rothschild, Max F; Schmidt, Carl J; Lamont, Susan J

    2016-04-14

    Heat stress in poultry results in considerable economic losses and is a concern for both animal health and welfare. Physiological changes occur during periods of heat stress, including changes in blood chemistry components. A highly advanced intercross line, created from a broiler (heat susceptible) by Fayoumi (heat resistant) cross, was exposed to daily heat cycles for seven days starting at 22 days of age. Blood components measured pre-heat treatment and on the seventh day of heat treatment included pH, pCO2, pO2, base excess, HCO3, TCO2, K, Na, ionized Ca, hematocrit, hemoglobin, sO2, and glucose. A genome-wide association study (GWAS) for these traits and their calculated changes was conducted to identify quantitative trait loci (QTL) using a 600 K SNP panel. There were significant increases in pH, base excess, HCO3, TCO2, ionized Ca, hematocrit, hemoglobin, and sO2, and significant decreases in pCO2 and glucose after 7 days of heat treatment. Heritabilities ranged from 0.01-0.21 for pre-heat measurements, 0.01-0.23 for measurements taken during heat, and 0.00-0.10 for the calculated change due to heat treatment. All blood components were highly correlated within measurement days, but not correlated between measurement days. The GWAS revealed 61 QTL for all traits, located on GGA (Gallus gallus chromosome) 1, 3, 6, 9, 10, 12-14, 17, 18, 21-28, and Z. A functional analysis of the genes in these QTL regions identified the Angiopoietin pathway as significant. The QTL that co-localized for three or more traits were on GGA10, 22, 26, 28, and Z and revealed candidate genes for birds' response to heat stress. The results of this study contribute to our knowledge of levels and heritabilities of several blood components of chickens under thermoneutral and heat stress conditions. Most components responded to heat treatment. Mapped QTL may serve as markers for genomic selection to enhance heat tolerance in poultry. The Angiopoietin pathway is likely involved in the

  9. Estimates of genetic and environmental contribution to 43 quantitative traits support sharing of a homogeneous environment in an isolated population from South Tyrol, Italy.

    Science.gov (United States)

    Marroni, Fabio; Grazio, Daniela; Pattaro, Cristian; Devoto, Marcella; Pramstaller, Peter

    2008-01-01

    As part of the genomic health care program 'GenNova', we measured 43 quantitative traits in 1,136 subjects living in three isolated villages in South Tyrol (Italy), for which extended genealogical information was available. Thirty-seven of the studied traits had been previously investigated in other populations, while six of them are, to the best of our knowledge, studied here for the first time. For all 43 traits we estimated narrow-sense heritability, individual-specific environmental effects, and shared environmental effects. Estimates of narrow-sense heritability were in good agreement with previous findings. We found significant heritability for all traits; after correcting for multiple testing, all traits except serum concentration of glutamic oxaloacetic transaminase (GOT) and potassium still showed significant heritability. In contrast, the effect of living in the same sibship or village (the so-called sibship and household effects, respectively) was significant for a few traits only, and after correcting for multiple testing no trait showed significant shared environment effect. We suggest that the sharing of a highly similar environment by the subjects included in this study explains the low contribution of the household effects to the overall trait variation. This peculiarity should provide an advantage in gene-mapping projects by reducing environmental bias. (c) 2007 S. Karger AG, Basel

  10. Effects of intraspecific diversity on survivorship, growth, and recruitment of the eastern oyster across sites.

    Science.gov (United States)

    Hanley, Torrance C; Hughes, A Randall; Williams, Bethany; Garland, Hanna; Kimbro, David L

    2016-06-01

    Intraspecific diversity, particularly of foundation species, can significantly affect population, community, and ecosystem processes. Examining how genetic diversity relates to demographic traits provides a key mechanistic link from genotypic and phenotypic variation of taxa with complex life histories to their population dynamics. We conducted a field experiment to assess how two metrics of intraspecific diversity (cohort diversity, the number of independent juvenile cohorts created from different adult source populations, and genetic relatedness, genetic similarity among individuals within and across cohorts) affect the survivorship, growth, and recruitment of the foundation species Crassostrea virginica. To assess the effects of both cohort diversity and genetic relatedness on oyster demographic traits under different environmental conditions, we manipulated juvenile oyster diversity and predator exposure (presence/absence of a cage) at two sites differing in resource availability and predation intensity. Differences in predation pressure between sites overwhelmingly determined post-settlement survivorship of oysters. However, in the absence of predation (i.e., cage treatment), one or both metrics of intraspecific diversity, in addition to site, influenced long-term survivorship, growth, and recruitment. While both cohort diversity and genetic relatedness were negatively associated with long-term survivorship, genetic relatedness alone showed a positive association with growth and cohort diversity alone showed a positive association with recruitment. Thus, our results demonstrate that in the absence of predation, intraspecific diversity can affect multiple demographic traits of a foundation species, but the relative importance of these effects depends on the environmental context. Moreover, the magnitude and direction of these effects vary depending on the diversity metric, cohort diversity or genetic relatedness, suggesting that although they are inversely

  11. Efficiency of genomic selection using Bayesian multimarker models for traits selected to reflect a wide range of heritabilities and frequencies of detected quantitative traits loci in mice

    DEFF Research Database (Denmark)

    Kapell, Dagmar NRG; Sorensen, Daniel; Su, Guosheng

    2012-01-01

    generally performed better than traditional polygenic selection, especially in the context of between family cross-validation. Reducing the number of markers considered to affect the trait did not significantly change PA for most traits, particularly in the case of within family cross...... families. Results Genomic selection showed a high predictive ability (PA) in comparison to traditional polygenic selection, especially for traits of moderate heritability and when cross-validation was between families. This occurred although the proportion of genomic variance of traits using genomic models...

  12. Characterization of Three Rice Multiparent Advanced Generation Intercross (MAGIC) Populations for Quantitative Trait Loci Identification.

    Science.gov (United States)

    Meng, Lijun; Guo, Longbiao; Ponce, Kimberly; Zhao, Xiangqian; Ye, Guoyou

    2016-07-01

    Three new rice ( L.) multiparent advanced generation intercross (MAGIC) populations were developed using eight elite rice varieties from different breeding programs. These three populations were two recombinant inbred line (RIL) populations derived from two 4-way crosses, DC1 and DC2, and one RIL population derived from an 8-way cross. These populations were genotyped using an Illumina Infinium rice 6K SNP chip. The potential of the three MAGIC populations in identifying marker-trait associations was demonstrated using the plant height (PH) and heading date (HD) measured in 2014. A population of 248 IRRI breeding lines and a population of 323 Chinese breeding lines were also included to compare genetic diversity and linkage disequilibrium (LD) pattern. Our study discovered that (i) the 8-way population had a higher gene diversity than the DC1, DC2, and IRRI populations; (ii) all three MAGIC populations showed no clear population structure; (iii) LD decayed to Chinese populations, respectively; and (iv) the 8-way population was more powerful than the DC1, DC2, and IRRI populations on QTL identification. The association analysis identified two and three QTL for PH and HD, respectively. Four of the five QTL had peak markers close to known genes. A novel QTL for PH was identified on chromosome 12 using the 8-way population. Therefore, our study suggests that the three new MAGIC populations are valuable resources for QTL identification. Copyright © 2016 Crop Science Society of America.

  13. On sharing quantitative trait GWAS results in an era of multiple-omics data and the limits of genomic privacy.

    Science.gov (United States)

    Im, Hae Kyung; Gamazon, Eric R; Nicolae, Dan L; Cox, Nancy J

    2012-04-06

    Recent advances in genome-scale, system-level measurements of quantitative phenotypes (transcriptome, metabolome, and proteome) promise to yield unprecedented biological insights. In this environment, broad dissemination of results from genome-wide association studies (GWASs) or deep-sequencing efforts is highly desirable. However, summary results from case-control studies (allele frequencies) have been withdrawn from public access because it has been shown that they can be used for inferring participation in a study if the individual's genotype is available. A natural question that follows is how much private information is contained in summary results from quantitative trait GWAS such as regression coefficients or p values. We show that regression coefficients for many SNPs can reveal the person's participation and for participants his or her phenotype with high accuracy. Our power calculations show that regression coefficients contain as much information on individuals as allele frequencies do, if the person's phenotype is rather extreme or if multiple phenotypes are available as has been increasingly facilitated by the use of multiple-omics data sets. These findings emphasize the need to devise a mechanism that allows data sharing that will facilitate scientific progress without sacrificing privacy protection. Copyright © 2012 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  14. Sources of uncertainty in cancer survivorship.

    Science.gov (United States)

    Miller, Laura E

    2012-12-01

    Previous research has demonstrated the common experience of illness-related uncertainty; however, little research has explored the specific sources of uncertainty throughout cancer survivorship. The purpose of this study is to investigate the experience of uncertainty for cancer survivors and their partners. Thus, the following research question is posed: What are the sources of uncertainty in cancer survivorship for survivors and partners? One-on-one interviews were conducted with 35 cancer survivors and 25 partners. Constant comparative methodologies were used to analyze the data. Participants described medical, personal, and social sources of uncertainty that persisted throughout survivorship. Medical sources of uncertainty included questions about the cancer diagnosis, treatment and prognosis. Personal sources of uncertainty included ambiguous valued identities and career-related questions. Social sources of uncertainty included unclear communicative, relational and familial consequences of illness. Survivors and partners in this study experienced uncertainty that persisted long after the completion of cancer treatment. The participants also described sources of uncertainty unique to this illness context. These results have important implications for health care providers and intervention developers and imply that chronic uncertainty should be managed throughout survivorship. The sources of uncertainty described in the current study have important implications for cancer survivors' management of uncertainty. Cancer survivors and their family members must first know the common sources of uncertainty to adaptively adjust to an uncertain survivorship trajectory. The present investigation provides insight into the uncertainty experiences of cancer survivors and implies that continued care may improve well-being after the completion of cancer treatment.

  15. Pursuing Normality: Reflections on Cancer Survivorship Care of Lymphoma Survivors.

    Science.gov (United States)

    Madsen, Louise S; Handberg, Charlotte

    2018-01-16

    The present study explored the reflections on cancer survivorship care of lymphoma survivors in active treatment. Lymphoma survivors have survivorship care needs, yet their participation in cancer survivorship care programs is still reported as low. The aim of this study was to understand the reflections on cancer survivorship care of lymphoma survivors to aid the future planning of cancer survivorship care and overcome barriers to participation. Data were generated in a hematological ward during 4 months of ethnographic fieldwork, including participant observation and 46 semistructured interviews with 9 lymphoma survivors. Interpretive description methodology and social practice theory guided the analytical framework. "Pursuing normality" was an overall finding and was comprised of 2 overarching patterns, "future prospects" and "survivorship care perceptions," both implying an influence on whether to participate in cancer survivorship care programs. Because of "pursuing normality," 8 of 9 participants opted out of cancer survivorship care programming due to prospects of "being cured" and perceptions of cancer survivorship care as "a continuation of the disease." The findings add to our understanding of possible barriers for participation in cancer survivorship care and outline important aspects to account for in the practice of health professionals. The study findings may guide practice to establish a systematic approach for providing information to cancer survivors regarding the possible management of their symptoms and of the content and purpose of cancer survivorship care.

  16. Dissecting Quantitative Trait Loci for Boron Efficiency across Multiple Environments in Brassica napus

    Science.gov (United States)

    Zhao, Zunkang; Wu, Likun; Nian, Fuzhao; Ding, Guangda; Shi, Taoxiong; Zhang, Didi; Shi, Lei; Xu, Fangsen; Meng, Jinling

    2012-01-01

    High yield is the most important goal in crop breeding, and boron (B) is an essential micronutrient for plants. However, B deficiency, leading to yield decreases, is an agricultural problem worldwide. Brassica napus is one of the most sensitive crops to B deficiency, and considerable genotypic variation exists among different cultivars in response to B deficiency. To dissect the genetic basis of tolerance to B deficiency in B. napus, we carried out QTL analysis for seed yield and yield-related traits under low and normal B conditions using the double haploid population (TNDH) by two-year and the BQDH population by three-year field trials. In total, 80 putative QTLs and 42 epistatic interactions for seed yield, plant height, branch number, pod number, seed number, seed weight and B efficiency coefficient (BEC) were identified under low and normal B conditions, singly explaining 4.15–23.16% and 0.53–14.38% of the phenotypic variation. An additive effect of putative QTLs was a more important controlling factor than the additive-additive effect of epistatic interactions. Four QTL-by-environment interactions and 7 interactions between epistatic interactions and the environment contributed to 1.27–4.95% and 1.17–3.68% of the phenotypic variation, respectively. The chromosome region on A2 of SYLB-A2 for seed yield under low B condition and BEC-A2 for BEC in the two populations was equivalent to the region of a reported major QTL, BE1. The B. napus homologous genes of Bra020592 and Bra020595 mapped to the A2 region and were speculated to be candidate genes for B efficiency. These findings reveal the complex genetic basis of B efficiency in B. napus. They provide a basis for the fine mapping and cloning of the B efficiency genes and for breeding B-efficient cultivars by marker-assisted selection (MAS). PMID:23028855

  17. Dissecting quantitative trait loci for boron efficiency across multiple environments in Brassica napus.

    Directory of Open Access Journals (Sweden)

    Zunkang Zhao

    Full Text Available High yield is the most important goal in crop breeding, and boron (B is an essential micronutrient for plants. However, B deficiency, leading to yield decreases, is an agricultural problem worldwide. Brassica napus is one of the most sensitive crops to B deficiency, and considerable genotypic variation exists among different cultivars in response to B deficiency. To dissect the genetic basis of tolerance to B deficiency in B. napus, we carried out QTL analysis for seed yield and yield-related traits under low and normal B conditions using the double haploid population (TNDH by two-year and the BQDH population by three-year field trials. In total, 80 putative QTLs and 42 epistatic interactions for seed yield, plant height, branch number, pod number, seed number, seed weight and B efficiency coefficient (BEC were identified under low and normal B conditions, singly explaining 4.15-23.16% and 0.53-14.38% of the phenotypic variation. An additive effect of putative QTLs was a more important controlling factor than the additive-additive effect of epistatic interactions. Four QTL-by-environment interactions and 7 interactions between epistatic interactions and the environment contributed to 1.27-4.95% and 1.17-3.68% of the phenotypic variation, respectively. The chromosome region on A2 of SYLB-A2 for seed yield under low B condition and BEC-A2 for BEC in the two populations was equivalent to the region of a reported major QTL, BE1. The B. napus homologous genes of Bra020592 and Bra020595 mapped to the A2 region and were speculated to be candidate genes for B efficiency. These findings reveal the complex genetic basis of B efficiency in B. napus. They provide a basis for the fine mapping and cloning of the B efficiency genes and for breeding B-efficient cultivars by marker-assisted selection (MAS.

  18. Characterization of Three Indica Rice Multiparent Advanced Generation Intercross (MAGIC Populations for Quantitative Trait Loci Identification

    Directory of Open Access Journals (Sweden)

    Lijun Meng

    2016-07-01

    Full Text Available Three new rice ( L. multiparent advanced generation intercross (MAGIC populations were developed using eight elite rice varieties from different breeding programs. These three populations were two recombinant inbred line (RIL populations derived from two 4-way crosses, DC1 and DC2, and one RIL population derived from an 8-way cross. These populations were genotyped using an Illumina Infinium rice 6K SNP chip. The potential of the three MAGIC populations in identifying marker–trait associations was demonstrated using the plant height (PH and heading date (HD measured in 2014. A population of 248 IRRI breeding lines and a population of 323 Chinese breeding lines were also included to compare genetic diversity and linkage disequilibrium (LD pattern. Our study discovered that (i the 8-way population had a higher gene diversity than the DC1, DC2, and IRRI populations; (ii all three MAGIC populations showed no clear population structure; (iii LD decayed to < 0.2 at about 2.5, 2.5, 1.25, 1.75, and 4.0 Mb for the DC1, DC2, 8-way, IRRI, and Chinese populations, respectively; and (iv the 8-way population was more powerful than the DC1, DC2, and IRRI populations on QTL identification. The association analysis identified two and three QTL for PH and HD, respectively. Four of the five QTL had peak markers close to known genes. A novel QTL for PH was identified on chromosome 12 using the 8-way population. Therefore, our study suggests that the three new MAGIC populations are valuable resources for QTL identification.

  19. Quantitative trait loci associated with functional stay-green SNU-SG1 in rice.

    Science.gov (United States)

    Yoo, Soo-Cheul; Cho, Sung-Hwan; Zhang, Haitao; Paik, Hyo-Chung; Lee, Chung-Hee; Li, Jinjie; Yoo, Jeong-Hoon; Lee, Byun-Woo; Koh, Hee-Jong; Seo, Hak Soo; Paek, Nam-Chon

    2007-08-31

    During monocarpic senescence in higher plants, functional stay-green delays leaf yellowing, maintaining photosynthetic competence, whereas nonfunctional stay-green retains leaf greenness without sustaining photosynthetic activity. Thus, functional stay-green is considered a beneficial trait that can increase grain yield in cereal crops. A stay-green japonica rice 'SNU-SG1' had a good seed-setting rate and grain yield, indicating the presence of a functional stay-green genotype. SNU-SG1 was crossed with two regular cultivars to determine the inheritance mode and identify major QTLs conferring stay-green in SNU-SG1. For QTL analysis, linkage maps with 100 and 116 DNA marker loci were constructed using selective genotyping with F2 and RIL (recombinant inbred line) populations, respectively. Molecular marker-based QTL analyses with both populations revealed that the functional stay-green phenotype of SNU-SG1 is regulated by several major QTLs accounting for a large portion of the genetic variation. Three main-effect QTLs located on chromosomes 7 and 9 were detected in both populations and a number of epistatic-effect QTLs were also found. The amount of variation explained by several digenic interactions was larger than that explained by main-effect QTLs. Two main-effect QTLs on chromosome 9 can be considered the target loci that most influence the functional stay-green in SNU-SG1. The functional stay-green QTLs may help develop low-input high-yielding rice cultivars by QTL-marker-assisted breeding with SNU-SG1.

  20. Bilaterally Asymmetric Effects of Quantitative Trait Loci (QTLs): QTLs That Affect Laxity in the Right Versus Left Coxofemoral (Hip) Joints of the Dog (Canis familiaris)

    OpenAIRE

    Chase, Kevin; Lawler, Dennis F.; Adler, Fred R.; Ostrander, Elaine A.; Lark, Karl G.

    2004-01-01

    In dogs hip joint laxity that can lead to degenerative joint disease (DJD) is frequent and heritable, providing a genetic model for some aspects of the human disease. We have used Portuguese water dogs (PWDs) to identify Quantitative trait loci (QTLs) that regulate laxity in the hip joint.A population of 286 PWDs, each characterized by ca. 500 molecular genetic markers, was analyzed for subluxation of the hip joint as measured by the Norberg angle, a quantitative radiographic measure of laxit...

  1. Detection of quantitative trait loci in Danish Holstein cattle affecting clinical mastitis, somatic cell score, udder conformation traits, and assessment of associated effects on milk yield

    DEFF Research Database (Denmark)

    Lund, M S; Guldbrandtsen, B; Buitenhuis, A J

    2008-01-01

    either a pleiotropic QTL affecting 2 traits or 2 QTL each affecting 1 trait gave some evidence to distinguish between these models. For Bos taurus autosome 5, the most likely models were a pleiotropic QTL affecting CM2, CM3, and SCS, and a linked QTL affecting fat yield index. For Bos taurus autosome 9...

  2. Genetic mapping of semi-polar metabolites in pepper fruits (Capsicum sp.): towards unravelling the molecular regulation of flavonoid quantitative trait loci

    NARCIS (Netherlands)

    Wahyuni, Y.; Stahl-Hermes, V.; Ballester, A.R.; Vos, de C.H.; Voorrips, R.E.; Maharijaya, A.; Molthoff, J.W.; Víquez Zamora, A.M.; Sudarmonowati, E.; Arisi, A.C.M.; Bino, R.J.; Bovy, A.G.

    2014-01-01

    Untargeted LCMS profiling of semi-polar metabolites followed by metabolite quantitative trait locus (mQTL) analysis was performed in ripe pepper fruits of 113 F2 plants derived from a cross between Capsicum annuum AC1979 (no. 19) and Capsicum chinense No. 4661 Selection (no. 18). The parental

  3. Genomewide rapid association using mixed model and regression: A fast and simple method for genomewide pedigree-based quantitative trait loci association analysis

    NARCIS (Netherlands)

    Y.S. Aulchenko (Yurii); D.-J. de Koning; C. Haley (Chris)

    2007-01-01

    textabstractFor pedigree-based quantitative trait loci (QTL) association analysis, a range of methods utilizing within-family variation such as transmission- disequilibrium test (TDT)-based methods have been developed. In scenarios where stratification is not a concern, methods exploiting

  4. Genes and quantitative trait loci (QTL) controlling trace element concentrations in perennial grasses grown on phytotoxic soil contaminated with heavy metals

    Science.gov (United States)

    Perennial grasses cover diverse soils throughout the world, including sites contaminated with heavy metals, producing forages that must be safe for livestock and wildlife. Chromosome regions known as quantitative trait loci (QTLs) controlling forage mineral concentrations were mapped in a populatio...

  5. Quantitative Autism Traits in First Degree Relatives: Evidence for the Broader Autism Phenotype in Fathers, but Not in Mothers and Siblings

    Science.gov (United States)

    De la Marche, Wouter; Noens, Ilse; Luts, Jan; Scholte, Evert; Van Huffel, Sabine; Steyaert, Jean

    2012-01-01

    Autism spectrum disorder (ASD) symptoms are present in unaffected relatives and individuals from the general population. Results are inconclusive, however, on whether unaffected relatives have higher levels of quantitative autism traits (QAT) or not. This might be due to differences in research populations, because behavioral data and molecular…

  6. Multi-ethnic meta-analysis identifies RAI1 as a possible obstructive sleep apnea related quantitative trait locus in men

    Science.gov (United States)

    Obstructive sleep apnea (OSA) is a common heritable disorder displaying marked sexual dimorphism in disease prevalence and progression. Previous genetic association studies have identified a few genetic loci associated with OSA and related quantitative traits, but they have only focused on single et...

  7. Imputation-based analysis of association studies: candidate regions and quantitative traits.

    Directory of Open Access Journals (Sweden)

    Bertrand Servin

    2007-07-01

    Full Text Available We introduce a new framework for the analysis of association studies, designed to allow untyped variants to be more effectively and directly tested for association with a phenotype. The idea is to combine knowledge on patterns of correlation among SNPs (e.g., from the International HapMap project or resequencing data in a candidate region of interest with genotype data at tag SNPs collected on a phenotyped study sample, to estimate ("impute" unmeasured genotypes, and then assess association between the phenotype and these estimated genotypes. Compared with standard single-SNP tests, this approach results in increased power to detect association, even in cases in which the causal variant is typed, with the greatest gain occurring when multiple causal variants are present. It also provides more interpretable explanations for observed associations, including assessing, for each SNP, the strength of the evidence that it (rather than another correlated SNP is causal. Although we focus on association studies with quantitative phenotype and a relatively restricted region (e.g., a candidate gene, the framework is applicable and computationally practical for whole genome association studies. Methods described here are implemented in a software package, Bim-Bam, available from the Stephens Lab website http://stephenslab.uchicago.edu/software.html.

  8. Genome-wide gene-environment interactions on quantitative traits using family data.

    Science.gov (United States)

    Sitlani, Colleen M; Dupuis, Josée; Rice, Kenneth M; Sun, Fangui; Pitsillides, Achilleas N; Cupples, L Adrienne; Psaty, Bruce M

    2016-07-01

    Gene-environment interactions may provide a mechanism for targeting interventions to those individuals who would gain the most benefit from them. Searching for interactions agnostically on a genome-wide scale requires large sample sizes, often achieved through collaboration among multiple studies in a consortium. Family studies can contribute to consortia, but to do so they must account for correlation within families by using specialized analytic methods. In this paper, we investigate the performance of methods that account for within-family correlation, in the context of gene-environment interactions with binary exposures and quantitative outcomes. We simulate both cross-sectional and longitudinal measurements, and analyze the simulated data taking family structure into account, via generalized estimating equations (GEE) and linear mixed-effects models. With sufficient exposure prevalence and correct model specification, all methods perform well. However, when models are misspecified, mixed modeling approaches have seriously inflated type I error rates. GEE methods with robust variance estimates are less sensitive to model misspecification; however, when exposures are infrequent, GEE methods require modifications to preserve type I error rate. We illustrate the practical use of these methods by evaluating gene-drug interactions on fasting glucose levels in data from the Framingham Heart Study, a cohort that includes related individuals.

  9. Mapping quantitative trait loci associated with leaf and stem pubescence in cotton.

    Science.gov (United States)

    Lacape, J-M; Nguyen, T B

    2005-01-01

    Leaf pubescence in cotton have a potential for insect pest management. Varying degrees of leaf trichome density in Gossypium species and cultivars have been associated to a series of five genes, referred to as t(1)-t(5). We used two segregating interspecific G. hirsutum x G. barbadense backcross populations developed in our laboratory to assess qualitatively and quantitatively leaf and stem pubescence. QTL analyses were performed using simple and composite interval mapping. Based on both types of measurements and under both types of QTL analyses, nine QTLs met permutation-based thresholds. The nine QTLs mapped to four different chromosome regions. Highest LOD values corresponded to the QTLs detected on c6 (four colocalized QTLs) and on D03 (two QTLs) for which the higher pubescence in the progeny derived from the pubescent G. hirsutum parent alleles. Conversely, on c17 (one QTL) and A01 (two QTLs), the G. hirsutum parental alleles affected negatively pubescence. These results combined with another published study confirm (1) the location in a center region of chromosome 6 of the t(1) locus as a major locus/gene determining leaf pubescence, and (2) additional genes located on seven additional chromosomes have been shown to impart trichome density either positively or negatively. The existence of a high density of PCR-based loci in most of the regions identified as harboring leaf pubescence QTLs, particularly that on chromosome 6, will facilitate future efforts for map-based cloning.

  10. Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation.

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    Damien C Croteau-Chonka

    Full Text Available Disease-associated loci identified through genome-wide association studies (GWAS frequently localize to non-coding sequence. We and others have demonstrated strong enrichment of such single nucleotide polymorphisms (SNPs for expression quantitative trait loci (eQTLs, supporting an important role for regulatory genetic variation in complex disease pathogenesis. Herein we describe our initial efforts to develop a predictive model of disease-associated variants leveraging eQTL information. We first catalogued cis-acting eQTLs (SNPs within 100 kb of target gene transcripts by meta-analyzing four studies of three blood-derived tissues (n = 586. At a false discovery rate < 5%, we mapped eQTLs for 6,535 genes; these were enriched for disease-associated genes (P < 10(-04, particularly those related to immune diseases and metabolic traits. Based on eQTL information and other variant annotations (distance from target gene transcript, minor allele frequency, and chromatin state, we created multivariate logistic regression models to predict SNP membership in reported GWAS. The complete model revealed independent contributions of specific annotations as strong predictors, including evidence for an eQTL (odds ratio (OR = 1.2-2.0, P < 10(-11 and the chromatin states of active promoters, different classes of strong or weak enhancers, or transcriptionally active regions (OR = 1.5-2.3, P < 10(-11. This complete prediction model including eQTL association information ultimately allowed for better discrimination of SNPs with higher probabilities of GWAS membership (6.3-10.0%, compared to 3.5% for a random SNP than the other two models excluding eQTL information. This eQTL-based prediction model of disease relevance can help systematically prioritize non-coding GWAS SNPs for further functional characterization.

  11. Detection of quantitative trait loci (QTL) related to grilsing and late sexual maturation in Atlantic salmon (Salmo salar).

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    Gutierrez, Alejandro P; Lubieniecki, Krzysztof P; Fukui, Steve; Withler, Ruth E; Swift, Bruce; Davidson, William S

    2014-02-01

    In Atlantic salmon aquaculture, early sexual maturation represents a major problem for producers. This is especially true for grilse, which mature after one sea winter before reaching a desirable harvest weight, rather than after two sea winters. Salmon maturing as grilse have a much lower market value than later maturing individuals. For this reason, most companies desire fish that grow fast and mature late. Marker-assisted selection has the potential to improve the efficiency of selection against early maturation and for late sexual maturation; however, studies identifying age of sexual maturation-related genetic markers are lacking for Atlantic salmon. Therefore, we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype five families from the Mainstream Canada broodstock program and search for SNPs associated with early (grilsing) or late sexual maturation. There were 529 SNP loci that were variable across all five families, and this was the set that was used for quantitative trait loci (QTL) analysis. GridQTL identified two chromosomes, Ssa10 and Ssa21, containing QTL related to grilsing. In contrast, only one QTL, on Ssa18, was found linked to late maturation in Atlantic salmon. Our previous work on these five families did not identify genome-wide significant growth-related QTL on Ssa10, Ssa21, or Ssa18. Therefore, taken together, these results suggest that both grilsing and late sexual maturation are controlled independently of one another and also from growth-related traits. The identification of genomic regions associated with grilsing or late sexual maturation provide an opportunity to incorporate this information into selective breeding programs that will enhance Atlantic salmon farming.

  12. Drought-related secondary metabolites of barley (Hordeum vulgare L.) leaves and their metabolomic quantitative trait loci.

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    Piasecka, Anna; Sawikowska, Aneta; Kuczyńska, Anetta; Ogrodowicz, Piotr; Mikołajczak, Krzysztof; Krystkowiak, Karolina; Gudyś, Kornelia; Guzy-Wróbelska, Justyna; Krajewski, Paweł; Kachlicki, Piotr

    2017-03-01

    Determining the role of plant secondary metabolites in stress conditions is problematic due to the diversity of their structures and the complexity of their interdependence with different biological pathways. Correlation of metabolomic data with the genetic background provides essential information about the features of metabolites. LC-MS analysis of leaf metabolites from 100 barley recombinant inbred lines (RILs) revealed that 98 traits among 135 detected phenolic and terpenoid compounds significantly changed their level as a result of drought stress. Metabolites with similar patterns of change were grouped in modules, revealing differences among RILs and parental varieties at early and late stages of drought. The most significant changes in stress were observed for ferulic and sinapic acid derivatives as well as acylated glycosides of flavones. The tendency to accumulate methylated compounds was a major phenomenon in this set of samples. In addition, the polyamine derivatives hordatines as well as terpenoid blumenol C derivatives were observed to be drought related. The correlation of drought-related compounds with molecular marker polymorphisms resulted in the definition of metabolomic quantitative trait loci in the genomic regions of single-nucleotide polymorphism 3101-111 and simple sequence repeat Bmag0692 with multiple linkages to metabolites. The associations pointed to genes related to the defence response and response to cold, heat and oxidative stress, but not to genes related to biosynthesis of the compounds. We postulate that the significant metabolites have a role as antioxidants, regulators of gene expression and modulators of protein function in barley during drought. © 2016 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

  13. The Effect of Planting Space and Harvesting Method on Quantitative and Qualitative Traits of Tomato (Lycopersicon esculentum Mill.

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    H Khazaei

    2016-02-01

    Full Text Available Introduction One time tomato harvesting, in addition to labor saving, provides a possibility of increasing the cultivated area which lead to increase the total output (1. Varieties of tomato that has multiple harvest usually have a lower density in farm compared to one time harvest (2. In the late 1940s, the processing tomato industry in California was concerned that expected shortage of labor would prevent harvest of its increasing tomato production. Commercial use of the new variety and the new harvesting method, began in early 1960s. New harvesting method had a labor requirement of 2.9 hours per ton, compared with 5.3 hours per ton for hand-harvest in several times. Total labor use for the crop dropped from 13.5 million hours in the hand-harvest years to about 3.8 million hours per year in 1997, while fruit yield increased 4-fold (3. Materials and Methods This study was carried out in two years (2010-2011 at Mazrae Nemone Astan Ghods Razavi using a factorial experiment based on randomized complete block design with 4 replications. The first factor was planting space within row at three levels including 20, 30 and 40 cm and the second factor was harvesting method at two levels including multiple and one time on tomato variety hypeel 347. Measured traits included fruit number per plant, fruit weight per plant, yield, as quantitative also pH, brix as qualitative and labor consumption per each ton of harvested fruit were investigated. Each plot consisted of 5 rows with a length of 6 meters, the plant in the row bilaterally (a total of 10 lines per plot were planted. Drip irrigation method was performed using the T-tape with 1.6 liters per hour. Harvesting started in mid-September and ended in late October. Fully ripe and healthy fruits were harvested and rotten fruits were not collected. Results and Discussion Quantitative traits Analysis of variance showed that the effect of year and planting space on all quantitative traits was significant

  14. A quantitative association study of SLC25A12 and restricted repetitive behavior traits in autism spectrum disorders.

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    Kim, Soo-Jeong; Silva, Raquel M; Flores, Cindi G; Jacob, Suma; Guter, Stephen; Valcante, Gregory; Zaytoun, Annette M; Cook, Edwin H; Badner, Judith A

    2011-05-24

    SLC25A12 was previously identified by a linkage-directed association analysis in autism. In this study, we investigated the relationship between three SLC25A12 single nucleotide polymorphisms (SNPs) (rs2056202, rs908670 and rs2292813) and restricted repetitive behavior (RRB) traits in autism spectrum disorders (ASDs), based on a positive correlation between the G allele of rs2056202 and an RRB subdomain score on the Autism Diagnostic Interview-Revised (ADI-R). We used the Repetitive Behavior Scale-Revised (RBS-R) as a quantitative RRB measure, and conducted linear regression analyses for individual SNPs and a previously identified haplotype (rs2056202-rs2292813). We examined associations in our University of Illinois at Chicago-University of Florida (UIC-UF) sample (179 unrelated individuals with an ASD), and then attempted to replicate our findings in the Simons Simplex Collection (SSC) sample (720 ASD families). In the UIC-UF sample, three RBS-R scores (ritualistic, sameness, sum) had positive associations with the A allele of rs2292813 (p = 0.006-0.012) and with the rs2056202-rs2292813 haplotype (omnibus test, p = 0.025-0.040). The SSC sample had positive associations between the A allele of rs2056202 and four RBS-R scores (stereotyped, sameness, restricted, sum) (p = 0.006-0.010), between the A allele of rs908670 and three RBS-R scores (stereotyped, self-injurious, sum) (p = 0.003-0.015), and between the rs2056202-rs2292813 haplotype and six RBS-R scores (stereotyped, self-injurious, compulsive, sameness, restricted, sum)(omnibus test, p = 0.002-0.028). Taken together, the A alleles of rs2056202 and rs2292813 were consistently and positively associated with RRB traits in both the UIC-UF and SSC samples, but the most significant SNP with phenotype association varied in each dataset. This study confirmed an association between SLC25A12 and RRB traits in ASDs, but the direction of the association was different from that in the initial study. This could be due to

  15. A quantitative association study of SLC25A12 and restricted repetitive behavior traits in autism spectrum disorders

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    Kim Soo-Jeong

    2011-05-01

    Full Text Available Abstract Background SLC25A12 was previously identified by a linkage-directed association analysis in autism. In this study, we investigated the relationship between three SLC25A12 single nucleotide polymorphisms (SNPs (rs2056202, rs908670 and rs2292813 and restricted repetitive behavior (RRB traits in autism spectrum disorders (ASDs, based on a positive correlation between the G allele of rs2056202 and an RRB subdomain score on the Autism Diagnostic Interview-Revised (ADI-R. Methods We used the Repetitive Behavior Scale-Revised (RBS-R as a quantitative RRB measure, and conducted linear regression analyses for individual SNPs and a previously identified haplotype (rs2056202-rs2292813. We examined associations in our University of Illinois at Chicago-University of Florida (UIC-UF sample (179 unrelated individuals with an ASD, and then attempted to replicate our findings in the Simons Simplex Collection (SSC sample (720 ASD families. Results In the UIC-UF sample, three RBS-R scores (ritualistic, sameness, sum had positive associations with the A allele of rs2292813 (p = 0.006-0.012 and with the rs2056202-rs2292813 haplotype (omnibus test, p = 0.025-0.040. The SSC sample had positive associations between the A allele of rs2056202 and four RBS-R scores (stereotyped, sameness, restricted, sum (p = 0.006-0.010, between the A allele of rs908670 and three RBS-R scores (stereotyped, self-injurious, sum (p = 0.003-0.015, and between the rs2056202-rs2292813 haplotype and six RBS-R scores (stereotyped, self-injurious, compulsive, sameness, restricted, sum(omnibus test, p = 0.002-0.028. Taken together, the A alleles of rs2056202 and rs2292813 were consistently and positively associated with RRB traits in both the UIC-UF and SSC samples, but the most significant SNP with phenotype association varied in each dataset. Conclusions This study confirmed an association between SLC25A12 and RRB traits in ASDs, but the direction of the association was different from

  16. Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.

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    Noah Zaitlen

    2013-05-01

    Full Text Available Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability, the fraction of phenotypic variation in a population that is determined by genetic factors. Here, we make use of extensive phenotype data in Iceland, long-range phased genotypes, and a population-wide genealogical database to examine the heritability of 11 quantitative and 12 dichotomous phenotypes in a sample of 38,167 individuals. Most previous estimates of heritability are derived from family-based approaches such as twin studies, which may be biased upwards by epistatic interactions or shared environment. Our estimates of heritability, based on both closely and distantly related pairs of individuals, are significantly lower than those from previous studies. We examine phenotypic correlations across a range of relationships, from siblings to first cousins, and find that the excess phenotypic correlation in these related individuals is predominantly due to shared environment as opposed to dominance or epistasis. We also develop a new method to jointly estimate narrow-sense heritability and the heritability explained by genotyped SNPs. Unlike existing methods, this approach permits the use of information from both closely and distantly related pairs of individuals, thereby reducing the variance of estimates of heritability explained by genotyped SNPs while preventing upward bias. Our results show that common SNPs explain a larger proportion of the heritability than previously thought, with SNPs present on Illumina 300K genotyping arrays explaining more than half of the heritability for the 23 phenotypes examined in this study. Much of the remaining heritability is likely to be due to rare alleles that are not captured by standard genotyping arrays.

  17. Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.

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    Zaitlen, Noah; Kraft, Peter; Patterson, Nick; Pasaniuc, Bogdan; Bhatia, Gaurav; Pollack, Samuela; Price, Alkes L

    2013-05-01

    Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability, the fraction of phenotypic variation in a population that is determined by genetic factors. Here, we make use of extensive phenotype data in Iceland, long-range phased genotypes, and a population-wide genealogical database to examine the heritability of 11 quantitative and 12 dichotomous phenotypes in a sample of 38,167 individuals. Most previous estimates of heritability are derived from family-based approaches such as twin studies, which may be biased upwards by epistatic interactions or shared environment. Our estimates of heritability, based on both closely and distantly related pairs of individuals, are significantly lower than those from previous studies. We examine phenotypic correlations across a range of relationships, from siblings to first cousins, and find that the excess phenotypic correlation in these related individuals is predominantly due to shared environment as opposed to dominance or epistasis. We also develop a new method to jointly estimate narrow-sense heritability and the heritability explained by genotyped SNPs. Unlike existing methods, this approach permits the use of information from both closely and distantly related pairs of individuals, thereby reducing the variance of estimates of heritability explained by genotyped SNPs while preventing upward bias. Our results show that common SNPs explain a larger proportion of the heritability than previously thought, with SNPs present on Illumina 300K genotyping arrays explaining more than half of the heritability for the 23 phenotypes examined in this study. Much of the remaining heritability is likely to be due to rare alleles that are not captured by standard genotyping arrays.

  18. The Effect of Water Deficit Imposing Methods on Quantitative and Qualitative Traits of New Potato Cultivar

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    Kh Parvizi

    2016-02-01

    overlapping time for different irrigation regimes. The differences of flowering dateand its longevity between clones in different water treatments demonstrated that although flower longevity of potato is a qualitative trait related to cultivar inherit but it can be affected by environment condition like temperature, light intensity and soil moisture. In this research there have been remarkable changes in reducing sugar of tubers under different irrigation levels. Therefore we can conclude that by determining good strategy for water use management in potato, both water stresses and higher reduction of sugar can be avoided. This result was consistent with previous studies (12, 14 and 18 that evaluated the effect of water stress and water deficiency on qualitative characters of potato. Decreasing 20 percent water requirement of potato, resulted only 0.7 kg decrease of total yield per square meter. As a result, it can be save more than 40 million cubic meter of water only in Hamedan state every year. Moreover, if we apply some suitable cultivars same as Savalan and other promising clones that have more tolerance to water deficit, it can be more efficient. Conclusions Totally, the result of the this research showed that decreasing water requirement of potato until 20% not only did not impair the growth and performance of potato but also did not show adverse effects on qualify of harvested tuber. It is also found that Savalan and two clone had more advantage in comparison with others.

  19. Sex-specific regulation of mitochondrial DNA levels: genome-wide linkage analysis to identify quantitative trait loci.

    Science.gov (United States)

    López, Sonia; Buil, Alfonso; Souto, Juan Carlos; Casademont, Jordi; Blangero, John; Martinez-Perez, Angel; Fontcuberta, Jordi; Lathrop, Mark; Almasy, Laura; Soria, Jose Manuel

    2012-01-01

    Altered mitochondrial DNA (mtDNA) levels have been associated with common diseases in humans. We investigated the genetic mechanism that controls mtDNA levels using genome-wide linkage analyses in families from the Genetic Analysis of Idiopathic Thrombophilia Project (GAIT). We measure mtDNA levels by quantitative real-time PCR in 386 subjects from 21 extended Spanish families. A variance component linkage method using 485 microsatellites was conducted to evaluate linkage and to detect quantitative trait loci (QTLs) involved in the control of mtDNA levels. The heritalibility of mtDNA levels was 0.33 (p=1.82e-05). We identified a QTL on Chromosome 2 (LOD=2.21) using all of the subjects, independently on their sex. When females and males were analysed separately, three QTLs were identified. Females showed the same QTL on Chromosome 2 (LOD=3.09), indicating that the QTL identified in the analysis using all of the subjects was a strong female QTL, and another one on Chromosome 3 (LOD=2.67), whereas in males a QTL was identified on Chromosome 1 (LOD=2.81). These QTLs were fine-mapped to find associations with mtDNA levels. The most significant SNP association was for the rs10888838 on Chromosome 1 in males. This SNP mapped to the gene MRPL37, involved in mitochondrial protein translation. The rs2140855 on Chromosome 2 showed association in the analysis using all of the subjects. It was near the gene CMPK2, which encodes a mitochondrial enzyme of the salvage pathway of deoxyribonucleotide synthesis. Our results provide evidence of a sex-specific genetic mechanism for the control of mtDNA levels and provide a framework to identify new genes that influence mtDNA levels.

  20. Sex-specific regulation of mitochondrial DNA levels: genome-wide linkage analysis to identify quantitative trait loci.

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    Sonia López

    Full Text Available Altered mitochondrial DNA (mtDNA levels have been associated with common diseases in humans. We investigated the genetic mechanism that controls mtDNA levels using genome-wide linkage analyses in families from the Genetic Analysis of Idiopathic Thrombophilia Project (GAIT. We measure mtDNA levels by quantitative real-time PCR in 386 subjects from 21 extended Spanish families. A variance component linkage method using 485 microsatellites was conducted to evaluate linkage and to detect quantitative trait loci (QTLs involved in the control of mtDNA levels. The heritalibility of mtDNA levels was 0.33 (p=1.82e-05. We identified a QTL on Chromosome 2 (LOD=2.21 using all of the subjects, independently on their sex. When females and males were analysed separately, three QTLs were identified. Females showed the same QTL on Chromosome 2 (LOD=3.09, indicating that the QTL identified in the analysis using all of the subjects was a strong female QTL, and another one on Chromosome 3 (LOD=2.67, whereas in males a QTL was identified on Chromosome 1 (LOD=2.81. These QTLs were fine-mapped to find associations with mtDNA levels. The most significant SNP association was for the rs10888838 on Chromosome 1 in males. This SNP mapped to the gene MRPL37, involved in mitochondrial protein translation. The rs2140855 on Chromosome 2 showed association in the analysis using all of the subjects. It was near the gene CMPK2, which encodes a mitochondrial enzyme of the salvage pathway of deoxyribonucleotide synthesis. Our results provide evidence of a sex-specific genetic mechanism for the control of mtDNA levels and provide a framework to identify new genes that influence mtDNA levels.

  1. Identification of Cephalosporium stripe resistance quantitative trait loci in two recombinant inbred line populations of winter wheat.

    Science.gov (United States)

    Vazquez, M Dolores; Zemetra, Robert; Peterson, C James; Mundt, Christopher C

    2015-02-01

    Identification of genome regions linked to Cephalosporium stripe resistance across two populations on chromosome 3BS, 4BS, 5AL, C5BL. Results were compared to a similar previous study. Cephalosporium stripe is a vascular wilt disease of winter wheat (Triticum aestivum L.) caused by the soil-borne fungus Cephalosporium gramineum Nisikado & Ikata. In the USA it is known to be a recurring disease when susceptible cultivars are grown in the wheat-growing region of Midwest and Pacific Northwest. There is no complete resistance in commercial wheat cultivars, although the use of moderately resistant cultivars reduces the disease severity and the amount of inoculum in subsequent seasons. The goal of this study was to detect and to compare chromosomal regions for resistance to Cephalosporium stripe in two winter wheat populations. Field inoculation was performed and Cephalosporium stripe severity was visually scored as percent of prematurely ripening heads (whiteheads) per plot. 'Tubbs'/'NSA-98-0995' and 'Einstein'/'Tubbs', each comprising a cross of a resistant and a susceptible cultivar, with population sizes of 271 and 259 F (5:6) recombinant inbred lines, respectively, were genotyped and phenotyped across four environments. In the quantitative trait loci (QTL) analysis, six and nine QTL were found, explaining in total, around 30 and 50 % of the phenotypic variation in 'Tubbs'/'NSA-98-0995' and 'Einstein'/'Tubbs', respectively. The QTL with the largest effect from both 'NSA-98-0995' and 'Einstein' was on chromosome 5AL.1 and linked to marker gwm291. Several QTL with smaller effects were identified in both populations on chromosomes 5AL, 6BS, and 3BS, along with other QTL identified in just one population. These results indicate that resistance to Cephalosporium stripe in both mapping populations was of a quantitative nature.

  2. Survivorship: Sleep Disorders, Version 1.2014

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    Denlinger, Crystal S.; Ligibel, Jennifer A.; Are, Madhuri; Baker, K. Scott; Demark-Wahnefried, Wendy; Friedman, Debra L.; Goldman, Mindy; Jones, Lee; King, Allison; Ku, Grace H.; Kvale, Elizabeth; Langbaum, Terry S.; Leonardi-Warren, Kristin; McCabe, Mary S.; Melisko, Michelle; Montoya, Jose G.; Mooney, Kathi; Morgan, Mary Ann; Moslehi, Javid J.; O’Connor, Tracey; Overholser, Linda; Paskett, Electra D.; Raza, Muhammad; Syrjala, Karen L.; Urba, Susan G; Wakabayashi, Mark T.; Zee, Phyllis; McMillian, Nicole; Freedman-Cass, Deborah

    2015-01-01

    Sleep disorders, including insomnia and excessive sleepiness, affect a significant proportion of patients with cancer and survivors, often in combination with fatigue, anxiety, and depression. Improvements in sleep lead to improvements in fatigue, mood, and quality of life. This section of the NCCN Guidelines for Survivorship provides screening, diagnosis, and management recommendations for sleep disorders in survivors. Management includes combinations of sleep hygiene education, physical activity, psychosocial interventions, and pharmacologic treatments. PMID:24812132

  3. Congenic strains of mice for verification and genetic decomposition of quantitative trait loci for femoral bone mineral density.

    Science.gov (United States)

    Shultz, Kathryn L; Donahue, Leah Rae; Bouxsein, Mary L; Baylink, David J; Rosen, Clifford J; Beamer, Wesley G

    2003-02-01

    Peak femoral volumetric bone mineral density (femoral bone mineral density) in C57BL/6J (B6) 4-month-old female mice is 50% lower than in C3H/HeJ (C3H) and 34% lower than in CAST/EiJ (CAST) females. Genome-wide analyses of (B6 x C3H)F2 and (B6 x CAST)F2 4-month-old female progeny demonstrated that peak femoral bone mineral density is a complex quantitative trait associated with genetic loci (QTL) on numerous chromosomes (Chrs) and with trait heritabilities of 83% (C3H) and 57% (CAST). To test the effect of each QTL on femoral bone mineral density, two sets of loci (six each from C3H and CAST) were selected to make congenic strains by repeated backcrossing of donor mice carrying a given QTL-containing chromosomal region to recipient mice of the B6 progenitor strain. At the N6F1 generation, each B6.C3H and B6.CAST congenic strain (statistically 98% B6-like in genomic composition) was intercrossed to obtain N6F2 progeny for testing the effect of each QTL on femoral bone mineral density. In addition, the femoral bone mineral density QTL region on Chr 1 of C3H was selected for congenic subline development to facilitate fine mapping of this strong femoral bone mineral density locus. In 11 of 12 congenic strains, 6 B6.C3H and 5 B6.CAST, femoral bone mineral density in mice carrying c3h or cast alleles in the QTL regions was significantly different from that of littermates carrying b6 alleles. Differences also were observed in body weight, femoral length, and mid-diaphyseal periosteal circumference among these 11 congenic strains when compared with control littermates; however, these latter three phenotypes were not consistently correlated with femoral bone mineral density. Analyses of eight sublines derived from the B6.C3H-1T congenic region revealed two QTLs: one located between 36.9 and 49.7 centiMorgans (cM) and the other located between 73.2 and 100.0 cM distal to the centromere. In conclusion, these congenic strains provide proof of principle that many QTLs

  4. Identification and validation of quantitative trait loci (QTL for canine hip dysplasia (CHD in German Shepherd Dogs.

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    Lena Fels

    Full Text Available Canine hip dysplasia (CHD is the most common hereditary skeletal disorder in dogs. To identify common alleles associated with CHD, we genotyped 96 German Shepherd Dogs affected by mild, moderate and severe CHD and 96 breed, sex, age and birth year matched controls using the Affymetrix canine high density SNP chip. A mixed linear model analysis identified five SNPs associated with CHD scores on dog chromosomes (CFA 19, 24, 26 and 34. These five SNPs were validated in a by sex, age, birth year and coancestry stratified sample of 843 German Shepherd Dogs including 277 unaffected dogs and 566 CHD-affected dogs. Mean coancestry coefficients among and within cases and controls were <0.1%. Genotype effects of these SNPs explained 20-32% of the phenotypic variance of CHD in German Shepherd Dogs employed for validation. Genome-wide significance in the validation data set could be shown for each one CHD-associated SNP on CFA24, 26 and 34. These SNPs are located within or in close proximity of genes involved in bone formation and related through a joint network. The present study validated positional candidate genes within two previously known quantitative trait loci (QTL and a novel QTL for CHD in German Shepherd Dogs.

  5. Detection of quantitative trait loci for agronomic, yield, grain and disease characters in spring barley (Hordeum vulgare L.).

    Science.gov (United States)

    Thomas, W T; Powell, W; Waugh, R; Chalmers, K J; Barua, U M; Jack, P; Lea, V; Forster, B P; Swanston, J S; Ellis, R P; Hanson, P R; Lance, R C

    1995-11-01

    Quantitative trait loci (QTLs) have been revealed for characters in a segregating population from a spring barley cross between genotypes adapted to North-West Europe. Transgressive segregation was found for all the characters, which was confirmed by the regular detection of positive and negative QTLs from both parents. A QTL for all the agronomic, yield and grain characters measured except thousand grain weight was found in the region of the denso dwarfing gene locus. There were considerable differences between the location of QTLs found in the present study and those found in previous studies of North American germ plasm, revealing the diversity between the two gene pools. Thirty-one QTLs were detected in more than one environment for the 13 characters studied, although many more were detected in just one environment. Whilst biometrical analyses suggested the presence of epistasis in the genetic control of some characters, there was little evidence of interactions between the QTLs apart from those associated with yield. QTLs of large effect sometimes masked the presence of QTLs of smaller effect.

  6. Quantitative Trait Loci Associated with Pollen Fertility under High Temperature Stress at Flowering Stage in Rice (Oryza sativa

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    Ying-hui XIAO

    2011-09-01

    Full Text Available High temperature stress (HTS, an increasingly important problem in rice production, significantly reduces rice yield by reducing pollen fertility and seed setting rate. Breeding rice varieties with tolerance to HTS at the flowering stage is therefore essential for maintaining rice production as the climate continues to become warm. In this study, two quantitative trait loci (QTLs underlying tolerance to HTS were identified using recombinant inbred lines derived from a cross between an HTS-tolerant rice cultivar 996 and a sensitive cultivar 4628. Pollen fertility was used as a heat-tolerance indicator for the lines subjected to HTS at the flowering stage in field experiments. Two QTLs that affected pollen fertility, qPF4 and qPF6, were detected between RM5687 and RM471 on chromosome 4, and between RM190 and RM225 on chromosome 6, by using the composite interval mapping (CIM analysis. The two QTLs explained 15.1% and 9.31% of the total phenotypic variation in pollen fertility, and increased the pollen fertility of the plants subjected to HTS by 7.15% and 5.25%, respectively. The positive additive effects of the two QTLs were derived from the 996 alleles. The two major QTLs identified would be useful for further fine mapping and cloning of these genes and for molecular marker-assistant breeding of heat-tolerant rice varieties.

  7. Mapping multiple linked quantitative trait loci in non-obese diabetic mice using a stepwise regression strategy.

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    Cordell, H J; Todd, J A; Lathrop, G M

    1998-02-01

    A simple regression strategy for mapping multiple linked quantitative trait loci (QTLs) in inbred populations is proposed and applied to data from a non-obese diabetic (NOD) mouse backcross. The method involves adding and deleting markers from a linear model in a stepwise manner, allowing the association with a particular marker to be examined once associations with other (in particular neighbouring) markers have been taken into account. This approach has the advantage of using programs available in standard statistical packages while still allowing adequate separation of possible multiple linked effects. For the mouse backcross, using these methods, at least two and possibly three diabetogenic loci are detected on each of chromosomes 1 and 3. Some evidence for epistasis is seen between the loci on chromosome 1, with a possible additional epistatic interaction between the loci on chromosome 3. Congenic strain analysis of the chromosome regions in NOD diabetes suggests that although the true type I error rate may be larger than that suggested by the nominal P values, our results nevertheless correspond well with those disease loci and interactions detected using a congenic approach, indicating that the regression method may be a powerful strategy for the detection and characterization of QTLs in inbred populations.

  8. Quantitative Trait Loci and Inter-Organ Partitioning for Essential Metal and Toxic Analogue Accumulation in Barley.

    Science.gov (United States)

    Reuscher, Stefan; Kolter, Andreas; Hoffmann, Astrid; Pillen, Klaus; Krämer, Ute

    2016-01-01

    The concentrations of both essential nutrients and chemically similar toxic analogues accumulated in cereal grains have a major impact on the nutritional quality and safety of crops. Naturally occurring genetic diversity can be exploited for the breeding of improved varieties through introgression lines (ILs). In this study, multi-element analysis was conducted on vegetative leaves, senesced flag leaves and mature grains of a set of 54 ILs of the wild ancestral Hordeum vulgare ssp. spontaneum in the cultivated variety Hordeum vulgare ssp. vulgare cv. Scarlett. Plants were cultivated on an anthropogenically heavy metal-contaminated soil collected in an agricultural field, thus allowing simultaneous localization of quantitative trait loci (QTL) for the accumulation of both essential nutrients and toxic trace elements in barley as a model cereal crop. For accumulation of the micronutrients Fe and Zn and the interfering toxin Cd, we identified 25, 16 and 5 QTL, respectively. By examining the gene content of the introgressions, we associated QTL with candidate genes based on homology to known metal homeostasis genes of Arabidopsis and rice. Global comparative analyses suggested the preferential remobilization of Cu and Fe, over Cd, from the flag leaf to developing grains. Our data identifies grain micronutrient filling as a regulated and nutrient-specific process, which operates differently from vegetative micronutrient homoeostasis. In summary, this study provides novel QTL for micronutrient accumulation in the presence of toxic analogues and supports a higher degree of metal specificity of trace element partitioning during grain filling in barley than previously reported for other cereals.

  9. Quantitative trait loci that control body weight in DDD/Sgn and C57BL/6J inbred mice.

    Science.gov (United States)

    Suto, Jun-Ichi; Kojima, Misaki

    2017-02-01

    Inbred DDD/Sgn mice are heavier than inbred C57BL/6J mice. In the present study, we performed quantitative trait loci (QTL) mapping for body weight using R/qtl in reciprocal F2 male populations between the two strains. We identified four significant QTL on Chrs 1, 2, 5, and 17 (proximal region). The DDD/Sgn allele was associated with increased body weight at QTL on Chrs 1 and 5, and the DDD/Sgn allele was associated with decreased body weight at QTL on Chrs 2 and 17. A multiple regression analysis indicated that the detected QTL explain 30.94 % of the body weight variation. Because DDD/Sgn male mice have extremely high levels of circulating testosterone relative to other inbred mouse strains, we performed QTL mapping for plasma testosterone level to examine the effect of testosterone levels on body weight. We identified one suggestive QTL on Chr 5, which overlapped with body weight QTL. The DDD/Sgn allele was associated with increased testosterone level. Thus, we confirmed that there was a genetic basis for the changes in body weight and testosterone levels in male mice. These findings provide insights into the genetic mechanism by which body weight is controlled in male mice.

  10. Systems genetics of liver fibrosis: identification of fibrogenic and expression quantitative trait loci in the BXD murine reference population.

    Directory of Open Access Journals (Sweden)

    Rabea A Hall

    Full Text Available The progression of liver fibrosis in response to chronic injury varies considerably among individual patients. The underlying genetics is highly complex due to large numbers of potential genes, environmental factors and cell types involved. Here, we provide the first toxicogenomic analysis of liver fibrosis induced by carbon tetrachloride in the murine 'genetic reference panel' of recombinant inbred BXD lines. Our aim was to define the core of risk genes and gene interaction networks that control fibrosis progression. Liver fibrosis phenotypes and gene expression profiles were determined in 35 BXD lines. Quantitative trait locus (QTL analysis identified seven genomic loci influencing fibrosis phenotypes (pQTLs with genome-wide significance on chromosomes 4, 5, 7, 12, and 17. Stepwise refinement was based on expression QTL mapping with stringent selection criteria, reducing the number of 1,351 candidate genes located in the pQTLs to a final list of 11 cis-regulated genes. Our findings demonstrate that the BXD reference population represents a powerful experimental resource for shortlisting the genes within a regulatory network that determine the liver's vulnerability to chronic injury.

  11. Segregation and mapping in the root-knot nematode Meloidogyne hapla of quantitatively inherited traits affecting parasitism.

    Science.gov (United States)

    Thomas, Varghese P; Williamson, Valerie M

    2013-09-01

    The root-knot nematode Meloidogyne hapla can reproduce on a wide range of crop species but there is variability in host range and pathogenicity both within and between isolates. The inbred strain VW9 causes galling but does not reproduce on Solanum bulbocastanum clone SB22 whereas strain VW8 causes little galling and reproduces poorly on this host. Comparison of reproduction on SB22 of nematode F2 lines generated from hybrids between strains VW8 and VW9 revealed that, whereas over half the lines produced no progeny, some lines reproduced to higher levels than did either parental strain. Using a genetic map previously generated using the same set of F2 lines, three quantitative trait loci (QTLs) were identified and positioned on linkage groups. A combination of two QTL alleles from one parent and one from the other was highly represented in F2 lines that exhibited higher reproduction than either parental strain but was absent from lines that failed to reproduce on SB22. This result suggests that sexual hybridization and assortment of opposing alleles leads to segregation of individuals with improved reproductive ability on a particular host. The genome sequence and integrated genetic and physical linkage map of M. hapla provide resources for identification of genes responsible for the identified QTL.

  12. Genetics of local adaptation in the laboratory: flowering time quantitative trait loci under geographic and seasonal conditions in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Yan Li

    Full Text Available Flowering time in Arabidopsis thaliana is controlled by a large number of genes and various environmental factors, such as light and temperature. The objective of this study was to identify flowering time quantitative trait loci (QTL under growth conditions simulating seasonal conditions from native geographic locations. Our growth chambers were set to simulate the spring conditions in Spain and Sweden, with appropriate changes in light color, intensity and day length, as well as temperature and relative humidity. Thus the Sweden-like spring conditions changed more dramatically compared to Spain-like spring conditions across the duration of our experiment. We have used these conditions to map QTL responsible for flowering time in the Kas-1/Col-gl1 recombinant inbred lines (RILs across two replicate blocks. A linkage map from 96 RILs was established using 119 markers including 64 new SNPs markers. One major QTL, mapping to the FRIGIDA (FRI locus, was detected on the top of chromosome 4 that showed significant gene x seasonal environment interactions. Three other minor QTL also were detected. One QTL mapping near FLOWERING LOCUS M (FLM showed an epistatic interaction with the QTL at FRI. These QTLxenvironment and QTL x QTL interactions suggest that subtle ecologically relevant changes in light, temperature, and relative humidity are differentially felt by alleles controlling flowering time and may be responsible for adaptation to regional environments.

  13. Resistance to powdery mildew in Spanish barley landraces is controlled by different sets of quantitative trait loci.

    Science.gov (United States)

    Silvar, C; Casas, A M; Igartua, E; Ponce-Molina, L J; Gracia, M P; Schweizer, G; Herz, M; Flath, K; Waugh, R; Kopahnke, D; Ordon, F

    2011-10-01

    Twenty-two landrace-derived inbred lines from the Spanish Barley Core Collection (SBCC) were found to display high levels of resistance to a panel of 27 isolates of the fungus Blumeria graminis that exhibit a wide variety of virulences. Among these lines, SBCC145 showed high overall resistance and a distinctive spectrum of resistance compared with the other lines. Against this background, the main goal of the present work was to investigate the genetic basis underlying such resistance using a doubled haploid population derived from a cross between SBCC145 and the elite spring cultivar Beatrix. The population was genotyped with the 1,536-SNP Illumina GoldenGate Oligonucleotide Pool Assay (Barley OPA-1 or BOPA1 for short), whereas phenotypic analysis was performed using two B. graminis isolates. A major quantitative trait locus (QTL) for resistance to both isolates was identified on the long arm of chromosome 6H (6HL) and accounted for ca. 60% of the phenotypic variance. Depending on the B. graminis isolate tested, three other minor QTLs were detected on chromosomes 2H and 7H, which explained less than 5% of the phenotypic variation each. In all cases, the alleles for resistance derived from the Spanish parent SBCC145. The position, the magnitude of the effect observed and the proportion of phenotypic variation accounted for by the QTL on 6HL suggest this is a newly identified locus for broad-based resistance to powdery mildew.

  14. Hepatitis B virus mutations, expression quantitative trait loci for PTPN12, and their interactions in hepatocellular carcinoma.

    Science.gov (United States)

    Song, Ci; Liu, Yao; Xu, Lu; Wen, Juan; Jiang, Deke; Chen, Jianguo; Zhai, Xiangjun; Hu, Zhibin; Liu, Li; Liu, Jibin

    2016-07-01

    Previously we identified that HBV(Hepatitis B virus) sequence variation, which may interact with host human leukocyte antigen (HLA) genetic variation, could influence host risk of hepatocellular carcinoma (HCC). More HBV-host interactions need to be identified. Protein tyrosine phosphatase nonreceptor type 12 (PTPN12), serves as an antagonist to tyrosine kinase signaling, may play integral roles in immune response against HBV infection and the development of HCC. Rs11485985 was an expression quantitative trait loci (eQTL) for PTPN12 by bioinformatics analyses. In this study, we genotyped the PTPN12 eQTL and sequenced the HBV region EnhII/BCP/PC in a case-control cohort including 1507 HBV-related HCC cases and 1560 HBV persistent carriers as controls. The variant genotype GG of rs11489585 increased HCC risk compared to the HBV persistent carriers (adjusted OR = 2.03, 95% confidence interval [CIs] = 1.30-3.18). We also detected borderline significant associations of PTPN12 eQTL rs11489585 with HBV mutations (P = 0.05 for G1799C). Taken together, PTPN12 may influence HCC risk accompanied by HBV mutations. © 2016 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

  15. Identification and validation of quantitative trait loci (QTL) for canine hip dysplasia (CHD) in German Shepherd Dogs.

    Science.gov (United States)

    Fels, Lena; Distl, Ottmar

    2014-01-01

    Canine hip dysplasia (CHD) is the most common hereditary skeletal disorder in dogs. To identify common alleles associated with CHD, we genotyped 96 German Shepherd Dogs affected by mild, moderate and severe CHD and 96 breed, sex, age and birth year matched controls using the Affymetrix canine high density SNP chip. A mixed linear model analysis identified five SNPs associated with CHD scores on dog chromosomes (CFA) 19, 24, 26 and 34. These five SNPs were validated in a by sex, age, birth year and coancestry stratified sample of 843 German Shepherd Dogs including 277 unaffected dogs and 566 CHD-affected dogs. Mean coancestry coefficients among and within cases and controls were Dogs employed for validation. Genome-wide significance in the validation data set could be shown for each one CHD-associated SNP on CFA24, 26 and 34. These SNPs are located within or in close proximity of genes involved in bone formation and related through a joint network. The present study validated positional candidate genes within two previously known quantitative trait loci (QTL) and a novel QTL for CHD in German Shepherd Dogs.

  16. Fine mapping of a quantitative trait locus for bovine milk fat composition on Bos taurus autosome 19.

    Science.gov (United States)

    Bouwman, Aniek C; Visker, Marleen H P W; van Arendonk, Johana M; Bovenhuis, Henk

    2014-02-01

    A major quantitative trait locus (QTL) for milk fat content and fatty acids in both milk and adipose tissue has been detected on Bos taurus autosome 19 (BTA19) in several cattle breeds. The objective of this study was to refine the location of the QTL on BTA19 for bovine milk fat composition using a denser set of markers. Opportunities for fine mapping were provided by imputation from 50,000 genotyped single nucleotide polymorphisms (SNP) toward a high-density SNP panel with up to 777,000 SNP. The QTL region was narrowed down to a linkage disequilibrium block formed by 22 SNP covering 85,007 bp, from 51,303,322 to 51,388,329 bp on BTA19. This linkage disequilibrium block contained 2 genes: coiled-coil domain containing 57 (CCDC57) and fatty acid synthase (FASN). The gene CCDC57 is minimally characterized and has not been associated with bovine milk fat previously, but is expressed in the mammary gland. The gene FASN has been associated with bovine milk fat and fat in adipose tissue before. This gene is a likely candidate for the QTL on BTA19 because of its involvement in de novo fat synthesis. Future studies using sequence data of both CCDC57 and FASN, and eventually functional studies, will have to be pursued to assign the causal variant(s). Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  17. Comparison of multipoint linkage analyses for quantitative traits in the CEPH data: parametric LOD scores, variance components LOD scores, and Bayes factors.

    Science.gov (United States)

    Sung, Yun Ju; Di, Yanming; Fu, Audrey Q; Rothstein, Joseph H; Sieh, Weiva; Tong, Liping; Thompson, Elizabeth A; Wijsman, Ellen M

    2007-01-01

    We performed multipoint linkage analyses with multiple programs and models for several gene expression traits in the Centre d'Etude du Polymorphisme Humain families. All analyses provided consistent results for both peak location and shape. Variance-components (VC) analysis gave wider peaks and Bayes factors gave fewer peaks. Among programs from the MORGAN package, lm_multiple performed better than lm_markers, resulting in less Markov-chain Monte Carlo (MCMC) variability between runs, and the program lm_twoqtl provided higher LOD scores by also including either a polygenic component or an additional quantitative trait locus.

  18. Quantitative Trait Loci Mapping in Brassica rapa Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of Brassica Species

    Science.gov (United States)

    Li, Xiaonan; Ramchiary, Nirala; Dhandapani, Vignesh; Choi, Su Ryun; Hur, Yoonkang; Nou, Ill-Sup; Yoon, Moo Kyoung; Lim, Yong Pyo

    2013-01-01

    Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species. PMID:23223793

  19. Quantitative trait loci mapping in Brassica rapa revealed the structural and functional conservation of genetic loci governing morphological and yield component traits in the A, B, and C subgenomes of Brassica species.

    Science.gov (United States)

    Li, Xiaonan; Ramchiary, Nirala; Dhandapani, Vignesh; Choi, Su Ryun; Hur, Yoonkang; Nou, Ill-Sup; Yoon, Moo Kyoung; Lim, Yong Pyo

    2013-02-01

    Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species.

  20. Dissemination and Translation: A Frontier for Cancer Survivorship Research

    OpenAIRE

    Pollack, Lori A; Hawkins, Nikki A; Peaker, Brandy L.; Buchanan, Natasha; Risendal, Betsy C.

    2011-01-01

    As the field of survivorship research grows, the need for translation is imperative to expand new knowledge into arenas that directly impact survivors. This commentary seeks to encourage research focused on dissemination and translation of survivorship interventions and programs, including practice-based research. We overview diffusion, dissemination and translation in the context of cancer survivorship and present the RE-AIM and Knowledge to Action frameworks as approaches that can be used t...

  1. Mapping Quantitative Trait Loci (QTL in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL

    Directory of Open Access Journals (Sweden)

    Thomson Peter C

    2010-09-01

    Full Text Available Abstract An (Awassi × Merino × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1 and 3.5 (cohort 2 years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3, 15 significant (LOD ≥ 2, and 11 suggestive QTL (1.7 ≤ LOD P P A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.

  2. Genetic Mapping of Quantitative Trait Loci for Yield-Affecting Traits in a Barley Doubled Haploid Population Derived from Clipper × Sahara 3771.

    Science.gov (United States)

    Vafadar Shamasbi, Fatemeh; Jamali, Seyed Hossein; Sadeghzadeh, Behzad; Abdollahi Mandoulakani, Babak

    2017-01-01

    Many traits play essential roles in determining crop yield. Wide variation for morphological traits exists in Hordeum vulgare L., but the genetic basis of this morphological variation is largely unknown. To understand genetic basis controlling morphological traits affecting yield, a barley doubled haploid population (146 individuals) derived from Clipper × Sahara 3771 was used to map chromosome regions underlying days to awn appearance, plant height, fertile spike number, flag leaf length, spike length, harvest index, seed number per plant, thousands kernel weight, and grain yield. Twenty-seven QTLs for nine traits were mapped to the barley genome that described 3-69% of phenotypic variations; and some genomic regions harbor a given QTL for more than one trait. Out of 27 QTLs identified, 19 QTLs were novel. Chromosomal regions on 1H, 2H, 4H, and 6H associated with seed grain yield, and chromosome regions on 2H and 6H had major effects on grain yield (GY). One major QTL for seed number per plant was flanked by marker VRS1-KSUF15 on chromosome 2H. This QTL was also associated with GY. Some loci controlling thousands kernel weight (TKW), fertile spike number (FSN), and GY were the same. The major grain yield QTL detected on linkage PSR167 co-localized with TAM10. Two major QTLs controlling TKW and FSN were also mapped at this locus. Eight QTLs on chromosomes 1H, 2H, 3H, 4H, 5H, 6H, and 7H consistently affected spike characteristics. One major QTL (ANIONT1A-TACMD) on 4H affected both spike length (SL) and spike number explained 9 and 5% of the variation of SL and FSN, respectively. In conclusion, this study could cast some light on the genetic basis of the studied pivotal traits. Moreover, fine mapping of the identified major effect markers may facilitate the application of molecular markers in barley breeding programs.

  3. Inheritance of quantitative traits in crosses between two Pisum sativum subspecies with particular reference to their breeding value.

    Science.gov (United States)

    Kosev, V; Pachev, I; Angelova, S; Mikić, A

    2012-01-01

    The experimental study was conducted during the period of 2008-2010 at the experimental field of the Institute of Forage Crops in Pleven. The hybridization scheme included direct and back crosses covering four varieties of forage pea (Pisum sativum L.), namely two spring ones, Usatii 90 and Kamerton from Ukraine, and a winter one from Bulgaria, Pleven 10. There was analyzed the inheritance of quantitative traits such as plant height, height to first pod, pod number per plant, seed number per plant, seed number per pod, seed weight per plant and number of fertile nodes per plant of parental components (P1 and P2) and both first (F1) and second (F2) hybrid generations. The cross Usatii 90 x Pleven 10 showed the highest real heterosis effect for plant height (8.26%), pods per plant (158.79%), seeds per plant (272.16%), seeds per pod (42.09%), seed weight per plant (432.43%) and number of fertile nodes per plant (117.14%). The cross Pleven 10 x Usatii 90 had the highest real heterosis effect height to first pod (11.06%). In F2 plants, the strongest depression for plant height (5.88%), seeds per plant (57.88%), seeds per pod (55.93%) and seed weight per plant (55.99%) was in the cross Usatii 90 x Pleven 10, for height to first pod (1.47%) in the cross Kamerton x Pleven 10 and for number of fertile nodes per plant (15.91%) in the cross Pleven 10 x Usatii 90. The highest positive degree of transgression for number of fertile nodes per plant (165.64%) and seed weight per plant (162.10%) was in the cross Pleven 10 x Kamerton and for pod number per plant (102.54%) and seeds per plant (99.13%) in Kamerton x Pleven 10. The stability of the characters was determined. Low variability in F1 and F2 was found in plant height (3.97-6.85%). Variability of number seeds per plant in F1 was highest (11.86-33.23%). For all other traits, the variability varied from average to high. A lower narrow-sense heritability coefficient was observed for plant height, height to first pod, pods per

  4. Male breast cancer: risk factors, biology, diagnosis, treatment, and survivorship

    National Research Council Canada - National Science Library

    Ruddy, K J; Winer, E P

    2013-01-01

    ...'. Relevant published data regarding risk factors, biological characteristics, presentation and prognosis, appropriate evaluation and treatment, and survivorship issues in male breast cancer patients are presented...

  5. ReCAP: ASCO Core Curriculum for Cancer Survivorship Education

    National Research Council Canada - National Science Library

    Shapiro, Charles L; Jacobsen, Paul B; Henderson, Tara; Hurria, Arti; Nekhlyudov, Larissa; Ng, Andrea; Surbone, Antonella; Mayer, Deborah K; Rowland, Julia H

    2016-01-01

    ..., training programs, and policymaking organizations. Adapted from Institute of Medicine recommendations for survivorship care, the core curriculum and competencies include the following subheadings...

  6. No consistent effect of ADRB2 haplotypes on obesity, hypertension and quantitative traits of body fatness and blood pressure among 6,514 adult Danes

    DEFF Research Database (Denmark)

    Gjesing, Anette P; Sparsø, Thomas; Borch-Johnsen, Knut

    2009-01-01

    prevalence of obesity and hypertension among adults. METHODOLOGY/PRINCIPAL FINDINGS: We genotyped five variants required to capture common variation in a region including the ADRB2 locus in a population-based study of 6,514 unrelated, middle-aged Danes. Phases of the genotypes were estimated in silico....... The variations were then investigated for their combined association with obesity, hypertension and related quantitative traits. The present study did not find consistent evidence for an association of ADRB2 variants with either obesity or hypertension when variations were analysed in a case-control study....... The same lack of impact was also seen in the quantitative trait analyses, apart from nominal differences on waist-to-hip ratio and systolic blood pressure between specific haplotype combinations. CONCLUSIONS/SIGNIFICANCE: In a population-based sample of 6,514 Danes we found no consistent associations...

  7. Relationships between the functional PPARalpha Leu162Val polymorphism and obesity, type 2 diabetes, dyslipidaemia, and related quantitative traits in studies of 5799 middle-aged white people

    DEFF Research Database (Denmark)

    Sparsø, Thomas; Hussain, Meena S; Andersen, Gitte

    2007-01-01

    polymorphism was not associated with WHO-defined obesity or dyslipidaemia in case-control settings involving 961 obese and 2563 lean subjects and 1399 dyslipidaemic and 4399 normolipidaemic subjects, respectively. Quantitative trait studies of metabolic variables were carried out in 5799 middle-aged, treatment.......01). In conclusion, in a relative large-scale study of middle-aged whites we found no evidence of association between the PPARalpha Leu162Val polymorphism and obesity or type 2 diabetes. If replicated, the Val162Val variant may, however, confer an increase in fasting levels of serum lipids....... with quantitative traits related to obesity, type 2 diabetes, and dyslipidaemia. We genotyped the Leu162Val polymorphism in 1383 patients with type 2 diabetes and 4401 control subjects with normal glucose tolerance (NGT) without showing any association between diabetes and genotype. In addition, the Leu162Val...

  8. Towards positional isolation of three quantitative trait loci conferring resistance to powdery mildew in two Spanish barley landraces.

    Directory of Open Access Journals (Sweden)

    Cristina Silvar

    Full Text Available Three quantitative trait loci (QTL conferring broad spectrum resistance to powdery mildew, caused by the fungus Blumeria graminis f. sp. hordei, were previously identified on chromosomes 7HS, 7HL and 6HL in the Spanish barley landrace-derived lines SBCC097 and SBCC145. In the present work, a genome-wide putative linear gene index of barley (Genome Zipper and the first draft of the physical, genetic and functional sequence of the barley genome were used to go one step further in the shortening and explicit demarcation on the barley genome of these regions conferring resistance to powdery mildew as well as in the identification of candidate genes. First, a comparative analysis of the target regions to the barley Genome Zippers of chromosomes 7H and 6H allowed the development of 25 new gene-based molecular markers, which slightly better delimit the QTL intervals. These new markers provided the framework for anchoring of genetic and physical maps, figuring out the outline of the barley genome at the target regions in SBCC097 and SBCC145. The outermost flanking markers of QTLs on 7HS, 7HL and 6HL defined a physical area of 4 Mb, 3.7 Mb and 3.2 Mb, respectively. In total, 21, 10 and 16 genes on 7HS, 7HL and 6HL, respectively, could be interpreted as potential candidates to explain the resistance to powdery mildew, as they encode proteins of related functions with respect to the known pathogen defense-related processes. The majority of these were annotated as belonging to the NBS-LRR class or protein kinase family.

  9. Towards positional isolation of three quantitative trait loci conferring resistance to powdery mildew in two Spanish barley landraces.

    Science.gov (United States)

    Silvar, Cristina; Perovic, Dragan; Nussbaumer, Thomas; Spannagl, Manuel; Usadel, Björn; Casas, Ana; Igartua, Ernesto; Ordon, Frank

    2013-01-01

    Three quantitative trait loci (QTL) conferring broad spectrum resistance to powdery mildew, caused by the fungus Blumeria graminis f. sp. hordei, were previously identified on chromosomes 7HS, 7HL and 6HL in the Spanish barley landrace-derived lines SBCC097 and SBCC145. In the present work, a genome-wide putative linear gene index of barley (Genome Zipper) and the first draft of the physical, genetic and functional sequence of the barley genome were used to go one step further in the shortening and explicit demarcation on the barley genome of these regions conferring resistance to powdery mildew as well as in the identification of candidate genes. First, a comparative analysis of the target regions to the barley Genome Zippers of chromosomes 7H and 6H allowed the development of 25 new gene-based molecular markers, which slightly better delimit the QTL intervals. These new markers provided the framework for anchoring of genetic and physical maps, figuring out the outline of the barley genome at the target regions in SBCC097 and SBCC145. The outermost flanking markers of QTLs on 7HS, 7HL and 6HL defined a physical area of 4 Mb, 3.7 Mb and 3.2 Mb, respectively. In total, 21, 10 and 16 genes on 7HS, 7HL and 6HL, respectively, could be interpreted as potential candidates to explain the resistance to powdery mildew, as they encode proteins of related functions with respect to the known pathogen defense-related processes. The majority of these were annotated as belonging to the NBS-LRR class or protein kinase family.

  10. 'MN1606SP' by 'Spencer' filial soybean population reveals novel quantitative trait loci and interactions among loci conditioning SDS resistance.

    Science.gov (United States)

    Luckew, Alexander S; Swaminathan, Sivakumar; Leandro, Leonor F; Orf, James H; Cianzio, Silvia R

    2017-10-01

    Four novel QTL and interactions among QTL were identified in this research, using as a parent line the most SDS-resistant genotype within soybean cultivars of the US early maturity groups. Soybean sudden death syndrome (SDS) reduces soybean yield in most of the growing areas of the world. The causal agent of SDS, soilborne fungus Fusarium virguliforme (Fv), releases phytotoxins taken up by the plant to produce chlorosis and necrosis in the leaves. Planting resistant cultivars is the most successful management practice to control the disease. The objective of this study was to identify quantitative trait loci (QTL) associated with the resistance response of MN1606SP to SDS. A mapping population of F 2:3 lines created by crossing the highly resistant cultivar 'MN1606SP' and the susceptible cultivar 'Spencer' was phenotyped in the greenhouse at three different planting times, each with three replications. Plants were artificially inoculated using SDS infested sorghum homogeneously mixed with the soil. Data were collected on three disease criteria, foliar disease incidence (DI), foliar leaf scorch disease severity (DS), and root rot severity. Disease index (DX) was calculated as DI × DS. Ten QTL were identified for the different disease assessment criteria, three for DI, four for DX, and three for root rot severity. Three QTL identified for root rot severity and one QTL for disease incidence are considered novel, since no previous reports related to these QTL are available. Among QTL, two interactions were detected between four different QTL. The interactions suggest that resistance to SDS is not only dependent on additive gene effects. The novel QTL and the interactions observed in this study will be useful to soybean breeders for improvement of SDS resistance in soybean germplasm.

  11. Five quantitative trait loci control radiation-induced adenoma multiplicity in Mom1R Apc Min/+ mice.

    Directory of Open Access Journals (Sweden)

    Eiram Elahi

    Full Text Available Ionising radiation is a carcinogen capable of inducing tumours, including colorectal cancer, in both humans and animals. By backcrossing a recombinant line of Apc(Min/+ mice to the inbred BALB/c mouse strain, which is unusually sensitive to radiation-induced tumour development, we obtained panels of 2Gy-irradiated and sham-irradiated N2 Apc(Min/+ mice for genotyping with a genome-wide panel of microsatellites at approximately 15 cM density and phenotyping by counting adenomas in the small intestine. Interval and composite interval mapping along with permutation testing identified five significant susceptibility quantitative trait loci (QTLs responsible for radiation induced tumour multiplicity in the small intestine. These were defined as Mom (Modifier of Min radiation-induced polyposis (Mrip1-5 on chromosome 2 (log of odds, LOD 2.8, p = 0.0003, two regions within chromosome 5 (LOD 5.2, p<0.00001, 6.2, p<0.00001 and two regions within chromosome 16 respectively (LOD 4.1, p = 4x10(-5, 4.8, p<0.00001. Suggestive QTLs were found for sham-irradiated mice on chromosomes 3, 6 and 13 (LOD 1.7, 1.5 and 2.0 respectively; p<0.005. Genes containing BALB/c specific non-synonymous polymorphisms were identified within Mrip regions and prediction programming used to locate potentially functional polymorphisms. Our study locates the QTL regions responsible for increased radiation-induced intestinal tumorigenesis in Apc(Min/+ mice and identifies candidate genes with predicted functional polymorphisms that are involved in spindle checkpoint and chromosomal stability (Bub1b, Casc5, and Bub1, DNA repair (Recc1 and Prkdc or inflammation (Duox2, Itgb2l and Cxcl5. Our study demonstrates use of in silico analysis in candidate gene identification as a way of reducing large-scale backcross breeding programmes.

  12. Quantitative Trait Loci and Inter-Organ Partitioning for Essential Metal and Toxic Analogue Accumulation in Barley.

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    Stefan Reuscher

    Full Text Available The concentrations of both essential nutrients and chemically similar toxic analogues accumulated in cereal grains have a major impact on the nutritional quality and safety of crops. Naturally occurring genetic diversity can be exploited for the breeding of improved varieties through introgression lines (ILs. In this study, multi-element analysis was conducted on vegetative leaves, senesced flag leaves and mature grains of a set of 54 ILs of the wild ancestral Hordeum vulgare ssp. spontaneum in the cultivated variety Hordeum vulgare ssp. vulgare cv. Scarlett. Plants were cultivated on an anthropogenically heavy metal-contaminated soil collected in an agricultural field, thus allowing simultaneous localization of quantitative trait loci (QTL for the accumulation of both essential nutrients and toxic trace elements in barley as a model cereal crop. For accumulation of the micronutrients Fe and Zn and the interfering toxin Cd, we identified 25, 16 and 5 QTL, respectively. By examining the gene content of the introgressions, we associated QTL with candidate genes based on homology to known metal homeostasis genes of Arabidopsis and rice. Global comparative analyses suggested the preferential remobilization of Cu and Fe, over Cd, from the flag leaf to developing grains. Our data identifies grain micronutrient filling as a regulated and nutrient-specific process, which operates differently from vegetative micronutrient homoeostasis. In summary, this study provides novel QTL for micronutrient accumulation in the presence of toxic analogues and supports a higher degree of metal specificity of trace element partitioning during grain filling in barley than previously reported for other cereals.

  13. Coexpression and expression quantitative trait loci analyses of the angiogenesis gene-gene interaction network in prostate cancer.

    Science.gov (United States)

    Lin, Hui-Yi; Cheng, Chia-Ho; Chen, Dung-Tsa; Chen, Y Ann; Park, Jong Y

    2016-10-01

    Prostate cancer (PCa) shows a substantial clinical heterogeneity. The existing risk classification for PCa prognosis based on clinical factors is not sufficient. Although some biomarkers for PCa aggressiveness have been identified, their underlying functional mechanisms are still unclear. We previously reported a gene-gene interaction network associated with PCa aggressiveness based on single nucleotide polymorphism (SNP)-SNP interactions in the angiogenesis pathway. The goal of this study is to investigate potential functional evidence of the involvement of the genes in this gene-gene interaction network. A total of 11 angiogenesis genes were evaluated. The crosstalks among genes were examined through coexpression and expression quantitative trait loci (eQTL) analyses. The study population is 352 Caucasian PCa patients in the Cancer Genome Atlas (TCGA) study. The pairwise coexpressions among the genes of interest were evaluated using the Spearman coefficient. The eQTL analyses were tested using the Kruskal-Wallis test. Among all within gene and 55 possible pairwise gene evaluations, 12 gene pairs and one gene (MMP16) showed strong coexpression or significant eQTL evidence. There are nine gene pairs with a strong correlation (Spearman correlation ≥0.6, PROBO1 (r=0.62), CSF1-HSPG2 (r=0.61), CSF1-FBLN5 (r=0.6), and CSF1-ROBO1 (r=0.60). One cis-eQTL in MMP16 and five trans-eQTLs (MMP16-ESR1, ESR1-ROBO1, CSF1-ROBO1, HSPG2-ROBO1, and FBLN5-CSF1) are significant with a false discovery rate q value less than 0.2. These findings provide potential biological evidence for the gene-gene interactions in this angiogenesis network. These identified interactions between the angiogenesis genes not only provide information for PCa etiology mechanism but also may serve as integrated biomarkers for building a risk prediction model for PCa aggressiveness.

  14. Metabolomic Quantitative Trait Loci (mQTL Mapping Implicates the Ubiquitin Proteasome System in Cardiovascular Disease Pathogenesis.

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    William E Kraus

    2015-11-01

    Full Text Available Levels of certain circulating short-chain dicarboxylacylcarnitine (SCDA, long-chain dicarboxylacylcarnitine (LCDA and medium chain acylcarnitine (MCA metabolites are heritable and predict cardiovascular disease (CVD events. Little is known about the biological pathways that influence levels of most of these metabolites. Here, we analyzed genetics, epigenetics, and transcriptomics with metabolomics in samples from a large CVD cohort to identify novel genetic markers for CVD and to better understand the role of metabolites in CVD pathogenesis. Using genomewide association in the CATHGEN cohort (N = 1490, we observed associations of several metabolites with genetic loci. Our strongest findings were for SCDA metabolite levels with variants in genes that regulate components of endoplasmic reticulum (ER stress (USP3, HERC1, STIM1, SEL1L, FBXO25, SUGT1 These findings were validated in a second cohort of CATHGEN subjects (N = 2022, combined p = 8.4x10-6-2.3x10-10. Importantly, variants in these genes independently predicted CVD events. Association of genomewide methylation profiles with SCDA metabolites identified two ER stress genes as differentially methylated (BRSK2 and HOOK2. Expression quantitative trait loci (eQTL pathway analyses driven by gene variants and SCDA metabolites corroborated perturbations in ER stress and highlighted the ubiquitin proteasome system (UPS arm. Moreover, culture of human kidney cells in the presence of levels of fatty acids found in individuals with cardiometabolic disease, induced accumulation of SCDA metabolites in parallel with increases in the ER stress marker BiP. Thus, our integrative strategy implicates the UPS arm of the ER stress pathway in CVD pathogenesis, and identifies novel genetic loci associated with CVD event risk.

  15. Susceptibility quantitative trait loci for pathogenic leucocytosis in SCG/Kj mice, a spontaneously occurring crescentic glomerulonephritis and vasculitis model

    Science.gov (United States)

    Hamano, Y; Abe, M; Matsuoka, S; Zhang, D; Kondo, Y; Kagami, Y; Ishigami, A; Maruyama, N; Tsuruta, Y; Yumura, W; Suzuki, K

    2014-01-01

    The spontaneous crescentic glomerulonephritis-forming/Kinjoh (SCG/Kj) mouse, a model of human crescentic glomerulonephritis (CrGN) and systemic vasculitis, is characterized by the production of myeloperoxidase-specific anti-neutrophil cytoplasmic autoantibody (MPO-ANCA) and marked leucocytosis. This study was performed to identify the specific populations of leucocytes associated with CrGN and susceptibility loci for pathogenic leucocytosis. Four hundred and twenty female (C57BL/6 × SCG/Kj) F2 intercross mice were subjected to serial flow cytometry examination of the peripheral blood (PB). Kidney granulocytes and monocytes were examined histopathologically. Linkage analyses were performed with 109 polymorphic microsatellite markers. Correlation studies revealed that increase of the granulocytes, F4/80+ cells, CD3+CD4−CD8− T cells and dendritic cells (DCs) in peripheral blood (PB) were associated significantly with glomerulonephritis, crescent formation and vasculitis. In kidney sections, F4/80low cells were observed in crescent, while F4/80high cells were around the Bowman's capsules and in the interstitium. Numbers of F4/80+ cells in crescents correlated significantly with F4/80+ cell numbers in PB, but not with numbers of F4/80+ cells in the interstitium. Genome-wide quantitative trait locus (QTL) mapping revealed three SCG/Kj-derived non-Fas QTLs for leucocytosis, two on chromosome 1 and one on chromosome 17. QTLs on chromosome 1 affected DCs, granulocytes and F4/80+ cells, but QTL on chromosome 17 affected DCs and granulocytes. We found CrGN-associated leucocytes and susceptibility QTLs with their positional candidate genes. F4/80+ cells in crescents are considered as recruited inflammatory macrophages. The results provide information for leucocytes to be targeted and genetic elements in CrGN and vasculitis. PMID:24654803

  16. PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies.

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    Wenchao Zhang

    2016-05-01

    Full Text Available The term epistasis refers to interactions between multiple genetic loci. Genetic epistasis is important in regulating biological function and is considered to explain part of the 'missing heritability,' which involves marginal genetic effects that cannot be accounted for in genome-wide association studies. Thus, the study of epistasis is of great interest to geneticists. However, estimating epistatic effects for quantitative traits is challenging due to the large number of interaction effects that must be estimated, thus significantly increasing computing demands. Here, we present a new web server-based tool, the Pipeline for estimating EPIStatic genetic effects (PEPIS, for analyzing polygenic epistatic effects. The PEPIS software package is based on a new linear mixed model that has been used to predict the performance of hybrid rice. The PEPIS includes two main sub-pipelines: the first for kinship matrix calculation, and the second for polygenic component analyses and genome scanning for main and epistatic effects. To accommodate the demand for high-performance computation, the PEPIS utilizes C/C++ for mathematical matrix computing. In addition, the modules for kinship matrix calculations and main and epistatic-effect genome scanning employ parallel computing technology that effectively utilizes multiple computer nodes across our networked cluster, thus significantly improving the computational speed. For example, when analyzing the same immortalized F2 rice population genotypic data examined in a previous study, the PEPIS returned identical results at each analysis step with