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Sample records for abundant quantitative trait

  1. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain.

    J Raphael Gibbs

    2010-05-01

    Full Text Available A fundamental challenge in the post-genome era is to understand and annotate the consequences of genetic variation, particularly within the context of human tissues. We present a set of integrated experiments that investigate the effects of common genetic variability on DNA methylation and mRNA expression in four human brain regions each from 150 individuals (600 samples total. We find an abundance of genetic cis regulation of mRNA expression and show for the first time abundant quantitative trait loci for DNA CpG methylation across the genome. We show peak enrichment for cis expression QTLs to be approximately 68,000 bp away from individual transcription start sites; however, the peak enrichment for cis CpG methylation QTLs is located much closer, only 45 bp from the CpG site in question. We observe that the largest magnitude quantitative trait loci occur across distinct brain tissues. Our analyses reveal that CpG methylation quantitative trait loci are more likely to occur for CpG sites outside of islands. Lastly, we show that while we can observe individual QTLs that appear to affect both the level of a transcript and a physically close CpG methylation site, these are quite rare. We believe these data, which we have made publicly available, will provide a critical step toward understanding the biological effects of genetic variation.

  2. Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato.

    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

    2015-03-01

    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

  3. Antagonistic coevolution between quantitative and Mendelian traits.

    Yamamichi, Masato; Ellner, Stephen P

    2016-03-30

    Coevolution is relentlessly creating and maintaining biodiversity and therefore has been a central topic in evolutionary biology. Previous theoretical studies have mostly considered coevolution between genetically symmetric traits (i.e. coevolution between two continuous quantitative traits or two discrete Mendelian traits). However, recent empirical evidence indicates that coevolution can occur between genetically asymmetric traits (e.g. between quantitative and Mendelian traits). We examine consequences of antagonistic coevolution mediated by a quantitative predator trait and a Mendelian prey trait, such that predation is more intense with decreased phenotypic distance between their traits (phenotype matching). This antagonistic coevolution produces a complex pattern of bifurcations with bistability (initial state dependence) in a two-dimensional model for trait coevolution. Furthermore, with eco-evolutionary dynamics (so that the trait evolution affects predator-prey population dynamics), we find that coevolution can cause rich dynamics including anti-phase cycles, in-phase cycles, chaotic dynamics and deterministic predator extinction. Predator extinction is more likely to occur when the prey trait exhibits complete dominance rather than semidominance and when the predator trait evolves very rapidly. Our study illustrates how recognizing the genetic architectures of interacting ecological traits can be essential for understanding the population and evolutionary dynamics of coevolving species. PMID:27009218

  4. Multiple Trait Analysis of Genetic Mapping for Quantitative Trait Loci

    Jiang, C.; Zeng, Z B

    1995-01-01

    We present in this paper models and statistical methods for performing multiple trait analysis on mapping quantitative trait loci (QTL) based on the composite interval mapping method. By taking into account the correlated structure of multiple traits, this joint analysis has several advantages, compared with separate analyses, for mapping QTL, including the expected improvement on the statistical power of the test for QTL and on the precision of parameter estimation. Also this joint analysis ...

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

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

    2008-01-01

    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...... effects were due to a pleiotropic QTL affecting fertility and milk yield traits or to linked QTL causing the effects. This distinction could only be made with confidence on BTA1 where a QTL affecting milk yield is linked to a pleiotropic QTL affecting days open and fertility treatments...

  6. Mapping Quantitative Trait Loci Controlling Endosperm Traits with Molecular Marker

    XU Chen-wu; LI Tao; SUN Chang-sen; GU Shi-liang

    2002-01-01

    Based on the genetic models for triploid endosperm traits and on the methods for mapping diploid quantitative traits loci (QTLs), the genetic constitutions, components of means and genetic variances of QTL controlling endosperm traits under flanking marker genotypes of different generations were presented. From these results, a multiple linear regression method for mapping QTL underlying endosperm traits in cereals was proposed, which used the means of endosperm traits under flanking marker genotypes as a dependent variable, the coefficient of additive effect ( d ) and dominance effect ( h 1 and/or h2 ) of a putative QTL in a given interval as independent variables. This method can work at any position in a genome covered by markers and increase the estimation precision of QTL location and their effects by eliminating the interference of other relative QTLs. This method can also be easily used in other uneven data such as markers and quantitative traits detected or measured in plants and tissues different either in generations or at chromosomal ploidy levels, and in endosperm traits controlled by complicated genetic models considering the effects produced by genotypes of both maternal plants and seeds on them.

  7. New methods for mapping quantitative trait loci

    Carlborg, Örjan

    2002-01-01

    This thesis presents and discusses the use of various genetic models, high performance computing, global optimization algorithms and statistical methods for mapping Quantitative Trait Loci (QTL). The aim of the work has been to develop statistically powerful and computationally efficient methods to detect genomic loci affecting multifactorial traits, and use the methods use to analyse experimental data. Imprinting is an epigenetic phenomena which causes differential expression of alleles base...

  8. #614411 GLYCEROL QUANTITATIVE TRAIT LOCUS; GLYCQTL [OMIM

    Full Text Available FIELD NO 614411 FIELD TI #614411 GLYCEROL QUANTITATIVE TRAIT LOCUS; GLYCQTL ;;GLYCEROL RELEASE D ... 07) screened 178 Spanish individuals, including 37 lean ... and 90 obese (see 606641) nondiabetics and 14 lean ... significant difference in its distribution between lean ... and obese individuals or between diabetics and non ...

  9. Quantitative trait loci pyramiding for fruit quality traits in tomato

    Sacco, Adriana; Di Matteo, Antonio; Lombardi, Nadia; Trotta, Nikita; Punzo, Biancavaleria; Mari, Angela; Barone, Amalia

    2012-01-01

    Fruit quality is a major focus for most conventional and innovative tomato breeding strategies, with particular attention being paid to fruit antioxidant compounds. Tomatoes represent a major contribution to dietary nutrition worldwide and a reservoir of diverse antioxidant molecules. In a previous study, we identified two Solanum pennellii introgression lines (IL7-3 and IL12-4) harbouring quantitative trait loci (QTL) that increase the content of ascorbic acid (AsA), phenols and soluble soli...

  10. Quantitative trait loci for male reproductive traits in beef cattle.

    Casas, E; Lunstra, D D; Stone, R T

    2004-12-01

    The objective of the present study was to detect quantitative trait loci (QTL) for male reproductive traits in a half-sib family from a Bos indicus (Brahman) x Bos taurus (Hereford) sire. The sire was mated with MARC III (1/4 Hereford, 1/4 Angus, 1/4 Red Poll and 1/4 Pinzgauer) cows. Testicular traits were measured from 126 male offspring born in 1996 and castrated at 8.5 months. Traits analysed were concentration of follicle stimulating hormone in peripheral blood at castration (FSH), paired testicular weight (PTW) and paired testicular volume (PTV) adjusted for age of dam, calculated age at puberty (AGE), and body weight at castration (BYW). A putative QTL was observed for FSH on chromosome 5. The maximum F-statistic was detected at 70 cM from the beginning of the linkage group. Animals inheriting the Hereford allele had a 2.47-ng/ml higher concentration of FSH than those inheriting the Brahman allele. Evidence also suggests the existence of a putative QTL on chromosome 29 for PTW, PTV, AGE and BYW. The maximum F-statistic was detected at cM 44 from the beginning of the linkage group for PTW, PTV and AGE, and at cM 52 for BYW. Animals that inherited the Brahman allele at this chromosomal region had a 45-g heavier PTW, a 42-cm(3) greater PTV, a 39-day younger AGE and a 22.8-kg heavier BYW, compared with those inheriting the Hereford allele. This is the first report of QTL for male reproductive traits in cattle. PMID:15566467

  11. Mapping Quantitative Trait Loci With Censored Observations

    Diao, Guoqing; Lin, D. Y.; Zou, Fei

    2004-01-01

    The existing statistical methods for mapping quantitative trait loci (QTL) assume that the phenotype follows a normal distribution and is fully observed. These assumptions may not be satisfied when the phenotype pertains to the survival time or failure time, which has a skewed distribution and is usually subject to censoring due to random loss of follow-up or limited duration of the experiment. In this article, we propose an interval-mapping approach for censored failure time phenotypes. We f...

  12. Precision Mapping of Quantitative Trait Loci

    Zeng, Z B

    1994-01-01

    Adequate separation of effects of possible multiple linked quantitative trait loci (QTLs) on mapping QTLs is the key to increasing the precision of QTL mapping. A new method of QTL mapping is proposed and analyzed in this paper by combining interval mapping with multiple regression. The basis of the proposed method is an interval test in which the test statistic on a marker interval is made to be unaffected by QTLs located outside a defined interval. This is achieved by fitting other genetic ...

  13. A Bayesian Nonparametric Approach for Mapping Dynamic Quantitative Traits

    Li, Zitong; Sillanpää, Mikko J.

    2013-01-01

    In biology, many quantitative traits are dynamic in nature. They can often be described by some smooth functions or curves. A joint analysis of all the repeated measurements of the dynamic traits by functional quantitative trait loci (QTL) mapping methods has the benefits to (1) understand the genetic control of the whole dynamic process of the quantitative traits and (2) improve the statistical power to detect QTL. One crucial issue in functional QTL mapping is how to correctly describe the ...

  14. Quantitative trait loci pyramiding for fruit quality traits in tomato.

    Sacco, Adriana; Di Matteo, Antonio; Lombardi, Nadia; Trotta, Nikita; Punzo, Biancavaleria; Mari, Angela; Barone, Amalia

    2013-01-01

    Fruit quality is a major focus for most conventional and innovative tomato breeding strategies, with particular attention being paid to fruit antioxidant compounds. Tomatoes represent a major contribution to dietary nutrition worldwide and a reservoir of diverse antioxidant molecules. In a previous study, we identified two Solanum pennellii introgression lines (IL7-3 and IL12-4) harbouring quantitative trait loci (QTL) that increase the content of ascorbic acid (AsA), phenols and soluble solids (degrees Brix; °Bx) in tomato fruit. The purpose of the present work was to pyramid into cultivated varieties the selected QTL for enhanced antioxidant and °Bx content. To better understand the genetic architecture of each QTL, the two ILs were crossed to the recurrent parent M82 (ILH7-3 and ILH12-4) and between them (ILH7-3+12-4). F1 hybrids (ILH7-3+12-4) were then selfed up to obtain F3 progenies in order to stabilize the favourable traits at the homozygous condition. Species-specific molecular markers were identified for each introgressed region and allowed us to select four F2 genotypes carrying both introgressions at the homozygous condition. The F3 double homozygous plants displayed AsA, total phenols and °Bx content significantly higher than M82. Therefore, they may represent suitable genetic material for breeding schemes aiming to increase antioxidant content in tomato fruit. PMID:23316114

  15. Joint association analysis of bivariate quantitative and qualitative traits.

    Yuan, Mengdie; Diao, Guoqing

    2011-01-01

    Univariate genome-wide association analysis of quantitative and qualitative traits has been investigated extensively in the literature. In the presence of correlated phenotypes, it is more intuitive to analyze all phenotypes simultaneously. We describe an efficient likelihood-based approach for the joint association analysis of quantitative and qualitative traits in unrelated individuals. We assume a probit model for the qualitative trait, under which an unobserved latent variable and a prespecified threshold determine the value of the qualitative trait. To jointly model the quantitative and qualitative traits, we assume that the quantitative trait and the latent variable follow a bivariate normal distribution. The latent variable is allowed to be correlated with the quantitative phenotype. Simultaneous modeling of the quantitative and qualitative traits allows us to make more precise inference on the pleiotropic genetic effects. We derive likelihood ratio tests for the testing of genetic effects. An application to the Genetic Analysis Workshop 17 data is provided. The new method yields reasonable power and meaningful results for the joint association analysis of the quantitative trait Q1 and the qualitative trait disease status at SNPs with not too small MAF. PMID:22373162

  16. Mapping quantitative trait loci in humans: achievements and limitations

    Majumder, Partha P.; Ghosh, Saurabh

    2005-01-01

    Recent advances in statistical methods and genomic technologies have ushered in a new era in mapping clinically important quantitative traits. However, many refinements and novel statistical approaches are required to enable greater successes in this mapping. The possible impact of recent findings pertaining to the structure of the human genome on efforts to map quantitative traits is yet unclear.

  17. Joint Mapping of Quantitative Trait Loci for Multiple Binary Characters

    Xu, Chenwu; Li, Zhikang; Xu, Shizhong

    2005-01-01

    Joint mapping for multiple quantitative traits has shed new light on genetic mapping by pinpointing pleiotropic effects and close linkage. Joint mapping also can improve statistical power of QTL detection. However, such a joint mapping procedure has not been available for discrete traits. Most disease resistance traits are measured as one or more discrete characters. These discrete characters are often correlated. Joint mapping for multiple binary disease traits may provide an opportunity to ...

  18. Joint association analysis of bivariate quantitative and qualitative traits

    2011-01-01

    Univariate genome-wide association analysis of quantitative and qualitative traits has been investigated extensively in the literature. In the presence of correlated phenotypes, it is more intuitive to analyze all phenotypes simultaneously. We describe an efficient likelihood-based approach for the joint association analysis of quantitative and qualitative traits in unrelated individuals. We assume a probit model for the qualitative trait, under which an unobserved latent variable and a presp...

  19. Quantitative trait loci analysis of osteocondrosis traits in the elbow joint of pigs

    Christensen, O F; Busch, M E; Gregersen, V R;

    2010-01-01

    Osteochondrosis is a growth disorder in the cartilage of young animals and is characterised by lesions found in the cartilage and bone. This study identified quantitative trait loci (QTLs) associated with six osteochondrosis lesion traits in the elbow joint of finishing pigs. The traits were...

  20. Plant Trait-Species Abundance Relationships Vary with Environmental Properties in Subtropical Forests in Eastern China

    En-Rong Yan; Xiao-Dong Yang; Chang, Scott X.; Xi-Hua Wang

    2013-01-01

    Understanding how plant trait-species abundance relationships change with a range of single and multivariate environmental properties is crucial for explaining species abundance and rarity. In this study, the abundance of 94 woody plant species was examined and related to 15 plant leaf and wood traits at both local and landscape scales involving 31 plots in subtropical forests in eastern China. Further, plant trait-species abundance relationships were related to a range of single and multivar...

  1. Mapping quantitative trait Loci using generalized estimating equations.

    Lange, C.; Whittaker, J C

    2001-01-01

    A number of statistical methods are now available to map quantitative trait loci (QTL) relative to markers. However, no existing methodology can simultaneously map QTL for multiple nonnormal traits. In this article we rectify this deficiency by developing a QTL-mapping approach based on generalized estimating equations (GEE). Simulation experiments are used to illustrate the application of the GEE-based approach.

  2. EM Algorithm for Mapping Quantitative Trait Loci in Multivalent Tetraploids

    Multivalent tetraploids that include many plant species, such as potato, sugarcane and rose, are of paramount importance to agricultural production and biological research. Quantitative trait locus (QTL) mapping in multivalent tetraploids is challenged by their unique cytogenetic properties, such ...

  3. Multiple Quantitative Trait Analysis Using Bayesian Networks

    Scutari, Marco; Howell, Phil; Balding, David J.; Mackay, Ian

    2014-01-01

    Models for genome-wide prediction and association studies usually target a single phenotypic trait. However, in animal and plant genetics it is common to record information on multiple phenotypes for each individual that will be genotyped. Modeling traits individually disregards the fact that they are most likely associated due to pleiotropy and shared biological basis, thus providing only a partial, confounded view of genetic effects and phenotypic interactions. In this article we use data f...

  4. Plant trait-species abundance relationships vary with environmental properties in subtropical forests in eastern china.

    En-Rong Yan

    Full Text Available Understanding how plant trait-species abundance relationships change with a range of single and multivariate environmental properties is crucial for explaining species abundance and rarity. In this study, the abundance of 94 woody plant species was examined and related to 15 plant leaf and wood traits at both local and landscape scales involving 31 plots in subtropical forests in eastern China. Further, plant trait-species abundance relationships were related to a range of single and multivariate (PCA axes environmental properties such as air humidity, soil moisture content, soil temperature, soil pH, and soil organic matter, nitrogen (N and phosphorus (P contents. At the landscape scale, plant maximum height, and twig and stem wood densities were positively correlated, whereas mean leaf area (MLA, leaf N concentration (LN, and total leaf area per twig size (TLA were negatively correlated with species abundance. At the plot scale, plant maximum height, leaf and twig dry matter contents, twig and stem wood densities were positively correlated, but MLA, specific leaf area, LN, leaf P concentration and TLA were negatively correlated with species abundance. Plant trait-species abundance relationships shifted over the range of seven single environmental properties and along multivariate environmental axes in a similar way. In conclusion, strong relationships between plant traits and species abundance existed among and within communities. Significant shifts in plant trait-species abundance relationships in a range of environmental properties suggest strong environmental filtering processes that influence species abundance and rarity in the studied subtropical forests.

  5. Plant Trait-Species Abundance Relationships Vary with Environmental Properties in Subtropical Forests in Eastern China

    Yan, En-Rong; Yang, Xiao-Dong; Chang, Scott X.; Wang, Xi-Hua

    2013-01-01

    Understanding how plant trait-species abundance relationships change with a range of single and multivariate environmental properties is crucial for explaining species abundance and rarity. In this study, the abundance of 94 woody plant species was examined and related to 15 plant leaf and wood traits at both local and landscape scales involving 31 plots in subtropical forests in eastern China. Further, plant trait-species abundance relationships were related to a range of single and multivariate (PCA axes) environmental properties such as air humidity, soil moisture content, soil temperature, soil pH, and soil organic matter, nitrogen (N) and phosphorus (P) contents. At the landscape scale, plant maximum height, and twig and stem wood densities were positively correlated, whereas mean leaf area (MLA), leaf N concentration (LN), and total leaf area per twig size (TLA) were negatively correlated with species abundance. At the plot scale, plant maximum height, leaf and twig dry matter contents, twig and stem wood densities were positively correlated, but MLA, specific leaf area, LN, leaf P concentration and TLA were negatively correlated with species abundance. Plant trait-species abundance relationships shifted over the range of seven single environmental properties and along multivariate environmental axes in a similar way. In conclusion, strong relationships between plant traits and species abundance existed among and within communities. Significant shifts in plant trait-species abundance relationships in a range of environmental properties suggest strong environmental filtering processes that influence species abundance and rarity in the studied subtropical forests. PMID:23560114

  6. Rank-based statistical methodologies for quantitative trait locus mapping.

    Zou, Fei; Yandell, Brian S.; Fine, Jason P.

    2003-01-01

    This article addresses the identification of genetic loci (QTL and elsewhere) that influence nonnormal quantitative traits with focus on experimental crosses. QTL mapping is typically based on the assumption that the traits follow normal distributions, which may not be true in practice. Model-free tests have been proposed. However, nonparametric estimation of genetic effects has not been studied. We propose an estimation procedure based on the linear rank test statistics. The properties of th...

  7. Quantitative trait analysis in sequencing studies under trait-dependent sampling.

    Lin, Dan-Yu; Zeng, Donglin; Tang, Zheng-Zheng

    2013-07-23

    It is not economically feasible to sequence all study subjects in a large cohort. A cost-effective strategy is to sequence only the subjects with the extreme values of a quantitative trait. In the National Heart, Lung, and Blood Institute Exome Sequencing Project, subjects with the highest or lowest values of body mass index, LDL, or blood pressure were selected for whole-exome sequencing. Failure to account for such trait-dependent sampling can cause severe inflation of type I error and substantial loss of power in quantitative trait analysis, especially when combining results from multiple studies with different selection criteria. We present valid and efficient statistical methods for association analysis of sequencing data under trait-dependent sampling. We pay special attention to gene-based analysis of rare variants. Our methods can be used to perform quantitative trait analysis not only for the trait that is used to select subjects for sequencing but for any other traits that are measured. For a particular trait of interest, our approach properly combines the association results from all studies with measurements of that trait. This meta-analysis is substantially more powerful than the analysis of any single study. By contrast, meta-analysis of standard linear regression results (ignoring trait-dependent sampling) can be less powerful than the analysis of a single study. The advantages of the proposed methods are demonstrated through simulation studies and the National Heart, Lung, and Blood Institute Exome Sequencing Project data. The methods are applicable to other types of genetic association studies and nongenetic studies. PMID:23847208

  8. Single nucleotide polymorphisms linked to quantitative trait loci for grain quality traits in wheat

    Chunlian Li; Guihua Bai; Shiaoman Chao; Brett Carver; Zhonghua Wang

    2016-01-01

    Wheat (Triticum aestivum L.) grain quality traits that are controlled by quantitative traits loci (QTL) define suitable growing areas and potential end-use products of a wheat cultivar. To dissect QTL for these traits including protein content (GPC);test weight (TW);single kernel characterization system (SKCS)-estimated kernel weight (SKW); kernel diameter (KD);kernel hardness measured by near-infrared reflectance spectroscopy (NIRS) hardness index (NHI); and SKCS-hardness index (SHI), a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers was developed using recombinant inbred lines (RILs) derived from Ning7840 × Clark. The RILs were evaluated for these quality traits in seven Oklahoma environments from 2001 to 2003. A total of 41 QTL with additive effects on different traits were mapped on most wheat chromosomes, excluding 1A, 2A, 3D, 4D, 6D, and 7B. Seven chromosome regions showed either tightly linked QTL or QTL with pleiotropic effects on two to four traits. Ten pairs of QTL showed additive × additive effects (AA), four QTL were involved in additive × environment (AE) effects, and one was involved in AAE effects. Two to eleven QTL for each of the six traits and 139 tightly linked markers to these QTL were identified. The findings shed light on the inheritance of wheat grain quality traits and provide DNA markers for manipulating these important traits to improve quality of new wheat cultivars.

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

    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.

  10. Quantitative trait loci for agronomic traits in an elite barley population for Mediterranean conditions

    Mansour, Elsayed; Casas Cendoya, Ana María; Gracia Gimeno, María Pilar; Molina-Cano, José Luis; Moralejo, Marian; Cattivelli, Luigi; William T.B. Thomas; Igartua Arregui, Ernesto

    2013-01-01

    Advances in plant breeding through marker-assisted selection (MAS) are only possible when genes or quantitative trait loci (QTLs) can contribute to the improvement of elite germplasm. A population of recombinant inbred lines (RILs) was developed for one of the best crosses of the Spanish National Barley Breeding Program, between two six-row winter barley cultivars Orria and Plaisant. The objective of this study was to identify favourable QTLs for agronomic traits in this population, which may...

  11. Estimating abundances of interacting species using morphological traits, foraging guilds, and habitat

    Dorazio, Robert M.; Connor, Edward F.

    2014-01-01

    We developed a statistical model to estimate the abundances of potentially interacting species encountered while conducting point-count surveys at a set of ecologically relevant locations - as in a metacommunity of species. In the model we assume that abundances of species with similar traits (e.g., body size) are potentially correlated and that these correlations, when present, may exist among all species or only among functionally related species (such as members of the same foraging guild). We also assume that species-specific abundances vary among locations owing to systematic and stochastic sources of heterogeneity. For example, if abundances differ among locations due to differences in habitat, then measures of habitat may be included in the model as covariates. Naturally, the quantitative effects of these covariates are assumed to differ among species. Our model also accounts for the effects of detectability on the observed counts of each species. This aspect of the model is especially important for rare or uncommon species that may be difficult to detect in community-level surveys. Estimating the detectability of each species requires sampling locations to be surveyed repeatedly using different observers or different visits of a single observer. As an illustration, we fitted models to species-specific counts of birds obtained while sampling an avian community during the breeding season. In the analysis we examined whether species abundances appeared to be correlated due to similarities in morphological measures (body mass, beak length, tarsus length, wing length, tail length) and whether these correlations existed among all species or only among species of the same foraging guild. We also used the model to estimate the effects of forested area on species abundances and the effects of sound power output (as measured by body size) on species detection probabilities.

  12. Quantitative trait loci for floral morphology in Arabidopsis thaliana.

    Juenger, T; Purugganan, M.; Mackay, T F

    2000-01-01

    A central question in biology is how genes control the expression of quantitative variation. We used statistical methods to estimate genetic variation in eight Arabidopsis thaliana floral characters (fresh flower mass, petal length, petal width, sepal length, sepal width, long stamen length, short stamen length, and pistil length) in a cosmopolitan sample of 15 ecotypes. In addition, we used genome-wide quantitative trait locus (QTL) mapping to evaluate the genetic basis of variation in these...

  13. Quantitative Trait Loci for Morphological Traits and their Association with Functional Genes in Raphanus sativus

    Yu, Xiaona; Choi, Su Ryun; Dhandapani, Vignesh; Rameneni, Jana Jeevan; Li, Xiaonan; Pang, Wenxing; Lee, Ji-Young; Lim, Yong Pyo

    2016-01-01

    Identification of quantitative trait loci (QTLs) governing morphologically important traits enables to comprehend their potential genetic mechanisms in the genetic breeding program. In this study, we used 210 F2 populations derived from a cross between two radish inbred lines (Raphanus sativus) “835” and “B2,” including 258 SSR markers were used to detect QTLs for 11 morphological traits that related to whole plant, leaf, and root yield in 3 years of replicated field test. Total 55 QTLs were ...

  14. Significance Thresholds for Quantitative Trait Locus Mapping Under Selective Genotyping

    Manichaikul, Ani; Palmer, Abraham A.; Sen, Śaunak; Broman, Karl W.

    2007-01-01

    In the case of selective genotyping, the usual permutation test to establish statistical significance for quantitative trait locus (QTL) mapping can give inappropriate significance thresholds, especially when the phenotype distribution is skewed. A stratified permutation test should be used, with phenotypes shuffled separately within the genotyped and ungenotyped individuals.

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

    Chengsong Zhu; Yuan-Ming Zhang; Zhigang Guo

    2008-12-01

    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 of biological interest and economic importance are seldom addressed. In this study, an attempt was made to map binary trait loci (BTL) in the F2:3 design. The fundamental idea was: the F2 plants were genotyped, all phenotypic values of each F2:3 progeny were measured for binary trait, and these binary trait values and the marker genotype informations were used to detect BTL under the penetrance and liability models. The proposed method was verified by a series of Monte–Carlo simulation experiments. These results showed that maximum likelihood approaches under the penetrance and liability models provide accurate estimates for the effects and the locations of BTL with high statistical power, even under of low heritability. Moreover, the penetrance model is as efficient as the liability model, and the F2:3 design is more efficient than classical F2 design, even though only a single progeny is collected from each F2:3 family. With the maximum likelihood approaches under the penetrance and the liability models developed in this study, we can map binary traits as we can do for quantitative trait in the F2:3 design.

  16. Variance Component Quantitative Trait Locus Analysis for Body Weight Traits in Purebred Korean Native Chicken.

    Cahyadi, Muhammad; Park, Hee-Bok; Seo, Dong-Won; Jin, Shil; Choi, Nuri; Heo, Kang-Nyeong; Kang, Bo-Seok; Jo, Cheorun; Lee, Jun-Heon

    2016-01-01

    Quantitative trait locus (QTL) is a particular region of the genome containing one or more genes associated with economically important quantitative traits. This study was conducted to identify QTL regions for body weight and growth traits in purebred Korean native chicken (KNC). F1 samples (n = 595) were genotyped using 127 microsatellite markers and 8 single nucleotide polymorphisms that covered 2,616.1 centi Morgan (cM) of map length for 26 autosomal linkage groups. Body weight traits were measured every 2 weeks from hatch to 20 weeks of age. Weight of half carcass was also collected together with growth rate. A multipoint variance component linkage approach was used to identify QTLs for the body weight traits. Two significant QTLs for growth were identified on chicken chromosome 3 (GGA3) for growth 16 to18 weeks (logarithm of the odds [LOD] = 3.24, Nominal p value = 0.0001) and GGA4 for growth 6 to 8 weeks (LOD = 2.88, Nominal p value = 0.0003). Additionally, one significant QTL and three suggestive QTLs were detected for body weight traits in KNC; significant QTL for body weight at 4 weeks (LOD = 2.52, nominal p value = 0.0007) and suggestive QTL for 8 weeks (LOD = 1.96, Nominal p value = 0.0027) were detected on GGA4; QTLs were also detected for two different body weight traits: body weight at 16 weeks on GGA3 and body weight at 18 weeks on GGA19. Additionally, two suggestive QTLs for carcass weight were detected at 0 and 70 cM on GGA19. In conclusion, the current study identified several significant and suggestive QTLs that affect growth related traits in a unique resource pedigree in purebred KNC. This information will contribute to improving the body weight traits in native chicken breeds, especially for the Asian native chicken breeds. PMID:26732327

  17. Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages

    Chaves, Cleber Juliano Neves; Dyonisio, Júlio César; Rossatto, Davi Rodrigo

    2016-01-01

    Epiphytes are strongly dependent on the conditions created by their host's traits and a certain degree of specificity is expected between them, even if these species are largely abundant in a series of tree hosts of a given environment, as in the case of atmospheric bromeliads. Despite their considerable abundance in these environments, we hypothesize that stochasticity alone cannot explain the presence and abundance of atmospheric bromeliads on host trees, since host traits could have a greater influence on the establishment of these bromeliads. We used secondary and reforested seasonal forests and three distinct silvicultures to test whether species richness, phylogenetic diversity and functional diversity of trees can predict the differential presence, abundance and distribution of atmospheric bromeliads on hosts. We compared the observed parameters of their assemblage with null models and performed successive variance hierarchic partitions of abundance and distribution of the assemblage to detect the influence of multiple traits of the tree hosts. Our results do not indicate direct relationships between the abundance of atmospheric bromeliads and phylogenetic or functional diversity of trees, but instead indicate that bromeliads occurred on fewer tree species than expected by chance. We distinguished functional tree patterns that can improve or reduce the abundance of atmospheric bromeliads, and change their distribution on branches and trunk. While individual tree traits are related to increased abundance, species traits are related to the canopy distribution of atmospheric bromeliad assemblages. A balance among these tree functional patterns drives the atmospheric bromeliad assemblage of the forest patches. PMID:26888951

  18. Functional mapping imprinted quantitative trait loci underlying developmental characteristics

    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. QTL analysis for some quantitative traits in bread wheat

    2007-01-01

    Quantitative trait loci (QTL) analysis was conducted in bread wheat for 14 important traits utilizing data from four different mapping populations involving different approaches of QTL analysis. Analysis for grain protein content (GPC) suggested that the major part of genetic variation for this trait is due to environmental interactions. In contrast, pre-harvest sprouting tolerance (PHST) was controlled mainly by main effect QTL (M-QTL) with very little genetic variation due to environmental interactions; a major QTL for PHST was detected on chromosome arm 3AL. For grain weight, one QTL each was detected on chromosome arms 1AS, 2BS and 7AS. QTL for 4 growth related traits taken together detected by different methods ranged from 37 to 40; nine QTL that were detected by single-locus as well as two-locus analyses were all M-QTL. Similarly, single-locus and two-locus QTL analyses for seven yield and yield contributing traits in two populations respectively allowed detection of 25 and 50 QTL by composite interval mapping (CIM), 16 and 25 QTL by multiple-trait composite interval mapping (MCIM) and 38 and 37 QTL by two-locus analyses. These studies should prove useful in QTL cloning and wheat improvement through marker aided selection.

  20. Genome-Wide Identification of Expression Quantitative Trait Loci (eQTLs) in Human Heart

    Moerland, Perry D.; Marsman, Roos F.; Westerveld, Margriet L.; Lal, Sean; Zhang, Taifang; Simmons, Christine Q.; Baczko, Istvan; dos Remedios, Cristobal; Bishopric, Nanette H.; Varro, Andras; George, Alfred L.; Lodder, Elisabeth M.; Bezzina, Connie R.

    2014-01-01

    In recent years genome-wide association studies (GWAS) have uncovered numerous chromosomal loci associated with various electrocardiographic traits and cardiac arrhythmia predisposition. A considerable fraction of these loci lie within inter-genic regions. The underlying trait-associated variants likely reside in regulatory regions and exert their effect by modulating gene expression. Hence, the key to unraveling the molecular mechanisms underlying these cardiac traits is to interrogate variants for association with differential transcript abundance by expression quantitative trait locus (eQTL) analysis. In this study we conducted an eQTL analysis of human heart. For a total of 129 left ventricular samples that were collected from non-diseased human donor hearts, genome-wide transcript abundance and genotyping was determined using microarrays. Each of the 18,402 transcripts and 897,683 SNP genotypes that remained after pre-processing and stringent quality control were tested for eQTL effects. We identified 771 eQTLs, regulating 429 unique transcripts. Overlaying these eQTLs with cardiac GWAS loci identified novel candidates for studies aimed at elucidating the functional and transcriptional impact of these loci. Thus, this work provides for the first time a comprehensive eQTL map of human heart: a powerful and unique resource that enables systems genetics approaches for the study of cardiac traits. PMID:24846176

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

    Abbott, Diana; Li, Yi-Ju; Guggenheim, Jeremy A; Metlapally, Ravikanth; Malecaze, Francois; Calvas, Patrick; Rosenberg, Thomas; Paget, Sandrine; Zayats, Tetyana; Mackey, David A; Feng, Sheng; Young, Terri L

    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....

  2. Haplotype-based quantitative trait mapping using a clustering algorithm

    Elston Robert C

    2006-05-01

    Full Text Available Abstract Background With the availability of large-scale, high-density single-nucleotide polymorphism (SNP markers, substantial effort has been made in identifying disease-causing genes using linkage disequilibrium (LD mapping by haplotype analysis of unrelated individuals. In addition to complex diseases, many continuously distributed quantitative traits are of primary clinical and health significance. However the development of association mapping methods using unrelated individuals for quantitative traits has received relatively less attention. Results We recently developed an association mapping method for complex diseases by mining the sharing of haplotype segments (i.e., phased genotype pairs in affected individuals that are rarely present in normal individuals. In this paper, we extend our previous work to address the problem of quantitative trait mapping from unrelated individuals. The method is non-parametric in nature, and statistical significance can be obtained by a permutation test. It can also be incorporated into the one-way ANCOVA (analysis of covariance framework so that other factors and covariates can be easily incorporated. The effectiveness of the approach is demonstrated by extensive experimental studies using both simulated and real data sets. The results show that our haplotype-based approach is more robust than two statistical methods based on single markers: a single SNP association test (SSA and the Mann-Whitney U-test (MWU. The algorithm has been incorporated into our existing software package called HapMiner, which is available from our website at http://www.eecs.case.edu/~jxl175/HapMiner.html. Conclusion For QTL (quantitative trait loci fine mapping, to identify QTNs (quantitative trait nucleotides with realistic effects (the contribution of each QTN less than 10% of total variance of the trait, large samples sizes (≥ 500 are needed for all the methods. The overall performance of HapMiner is better than that of

  3. Segregation Analysis on Genetic System of Quantitative Traits in Plants

    Gai Junyi

    2006-01-01

    Based on the traditional polygene inheritance model of quantitative traits,the author suggests the major gene and polygene mixed inheritance model.The model was considered as a general one,while the pure major gene and pure polygene inheritance model was a specific case of the general model.Based on the proposed theory,the author established the segregation analysis procedure to study the genetic system of quantitative traits of plants.At present,this procedure can be used to evaluate the genetic effect of individual major genes (up to two to three major genes),the collective genetic effect of polygene,and their heritability value.This paper introduces how to establish the procedure,its main achievements,and its applications.An example is given to illustrate the steps,methods,and effectiveness of the procedure.

  4. Multiparent intercross populations in analysis of quantitative traits

    Sujay Rakshit; Arunita Rakshit; J. V. Patil

    2011-04-01

    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 lines, backcross inbred lines and double haploids from biparental crosses are commonly used. Introgression lines and near isogenic lines are also being used for QTL analysis. However, such populations have major limitations like predominantly relying on the recombination events taking place in the F1 generation and mapping of only the allelic pairs present in the two parents. The second generation mapping resources like association mapping, nested association mapping and multiparent intercross populations potentially address the major limitations of available mapping resources. The potential of multiparent intercross populations in gene mapping has been discussed here. In such populations both linkage and association analysis can be conductted without encountering the limitations of structured populations. In such populations, larger genetic variation in the germplasm is accessed and various allelic and cytoplasmic interactions are assessed. For all practical purposes, across crop species, use of eight founders and a fixed population of 1000 individuals are most appropriate. Limitations with multiparent intercross populations are that they require longer time and more resource to be generated and they are likely to show extensive segregation for developmental traits, limiting their use in the analysis of complex traits. However, multiparent intercross population resources are likely to bring a paradigm shift towards QTL analysis in plant species.

  5. Mapping quantitative trait loci for kernel composition in almond

    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.

  6. EM Algorithm for Mapping Quantitative Trait Loci in Multivalent Tetraploids

    2010-01-01

    Multivalent tetraploids that include many plant species, such as potato, sugarcane, and rose, are of paramount importance to agricultural production and biological research. Quantitative trait locus (QTL) mapping in multivalent tetraploids is challenged by their unique cytogenetic properties, such as double reduction. We develop a statistical method for mapping multivalent tetraploid QTLs by considering these cytogenetic properties. This method is built in the mixture model-based framework an...

  7. Hnrnph1 Is A Quantitative Trait Gene for Methamphetamine Sensitivity

    Yazdani, Neema; Parker, Clarissa C.; Shen, Ying; Reed, Eric R.; Guido, Michael A.; Kole, Loren A.; Kirkpatrick, Stacey L.; Lim, Jackie E.; Sokoloff, Greta; Cheng, Riyan; Johnson, W. Evan; Palmer, Abraham A.; Bryant, Camron D.

    2015-01-01

    Psychostimulant addiction is a heritable substance use disorder; however its genetic basis is almost entirely unknown. Quantitative trait locus (QTL) mapping in mice offers a complementary approach to human genome-wide association studies and can facilitate environment control, statistical power, novel gene discovery, and neurobiological mechanisms. We used interval-specific congenic mouse lines carrying various segments of chromosome 11 from the DBA/2J strain on an isogenic C57BL/6J backgrou...

  8. On the genetic architecture of intelligence and other quantitative traits

    Hsu, Stephen D. H.

    2014-01-01

    How do genes affect cognitive ability or other human quantitative traits such as height or disease risk? Progress on this challenging question is likely to be significant in the near future. I begin with a brief review of psychometric measurements of intelligence, introducing the idea of a "general factor" or g score. The main results concern the stability, validity (predictive power), and heritability of adult g. The largest component of genetic variance for both height and intelligence is a...

  9. Quantitative trait loci linked to PRNP gene controlling health and production traits in INRA 401 sheep

    Brunel Jean-Claude

    2007-07-01

    Full Text Available Abstract In this study, the potential association of PrP genotypes with health and productive traits was investigated. Data were recorded on animals of the INRA 401 breed from the Bourges-La Sapinière INRA experimental farm. The population consisted of 30 rams and 852 ewes, which produced 1310 lambs. The animals were categorized into three PrP genotype classes: ARR homozygous, ARR heterozygous, and animals without any ARR allele. Two analyses differing in the approach considered were carried out. Firstly, the potential association of the PrP genotype with disease (Salmonella resistance and production (wool and carcass traits was studied. The data used included 1042, 1043 and 1013 genotyped animals for the Salmonella resistance, wool and carcass traits, respectively. The different traits were analyzed using an animal model, where the PrP genotype effect was included as a fixed effect. Association analyses do not indicate any evidence of an effect of PrP genotypes on traits studied in this breed. Secondly, a quantitative trait loci (QTL detection approach using the PRNP gene as a marker was applied on ovine chromosome 13. Interval mapping was used. Evidence for one QTL affecting mean fiber diameter was found at 25 cM from the PRNP gene. However, a linkage between PRNP and this QTL does not imply unfavorable linkage disequilibrium for PRNP selection purposes.

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

    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.

  11. A primary screen of the bovine genome for quantitative trait loci affecting carcass and growth traits.

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

    1999-06-01

    A primary genomic screen for quantitative trait loci (QTL) affecting carcass and growth traits was performed by genotyping 238 microsatellite markers on 185 out of 300 total progeny from a Bos indicus x Bos taurus sire mated to Bos taurus cows. The following traits were analyzed for QTL effects: birth weight (BWT), weaning weight (WW), yearling weight (YW), hot carcass weight (HCW), dressing percentage (DP), fat thickness (FT), marbling score (MAR), longissimus muscle area (LMA), rib bone (RibB), rib fat (RibF), and rib muscle (RibM), and the predicted whole carcass traits, retail product yield (RPYD), fat trim yield (FATYD), bone yield (BOYD), retail product weight (RPWT), fat weight (FATWT), and bone weight (BOWT). Data were analyzed by generating an F-statistic profile computed at 1-cM intervals for each chromosome by the regression of phenotype on the conditional probability of receiving the Brahman allele from the sire. There was compelling evidence for a QTL allele of Brahman origin affecting an increase in RibB and a decrease in DP on chromosome 5 (BTA5). Putative QTL at or just below the threshold for genome-wide significance were as follows: an increase in RPYD and component traits on BTA2 and BTA13, an increase in LMA on BTA14, and an increase in BWT on BTA1. Results provided represent a portion of our efforts to identify and characterize QTL affecting carcass and growth traits. PMID:10375215

  12. Understanding Genetic Diversity of Sorghum Using Quantitative Traits

    Sinha, Sweta; Kumaravadivel, N.

    2016-01-01

    Sorghum is the important cereal crop around the world and hence understanding and utilizing the genetic variation in sorghum accessions are essential for improving the crop. A good understanding of genetic variability among the accessions will enable precision breeding. So profiling the genetic diversity of sorghum is imminent. In the present investigation, forty sorghum accessions consisting of sweet sorghum, grain sorghum, forage sorghum, mutant lines, maintainer lines, and restorer lines were screened for genetic diversity using quantitative traits. Observations were recorded on 14 quantitative traits, out of which 9 diverse traits contributing to maximum variability were selected for genetic diversity analysis. The principle component analysis revealed that the panicle width, stem girth, and leaf breadth contributed maximum towards divergence. By using hierarchical cluster analysis, the 40 accessions were grouped under 6 clusters. Cluster I contained maximum number of accessions and cluster VI contained the minimum. The maximum intercluster distance was observed between cluster VI and cluster IV. Cluster III had the highest mean value for hundred-seed weight and yield. Hence the selection of parents must be based on the wider intercluster distance and superior mean performance for yield and yield components. Thus in the present investigation quantitative data were able to reveal the existence of a wide genetic diversity among the sorghum accessions used providing scope for further genetic improvement. PMID:27382499

  13. Quantitative Trait Loci (QTLs mapping for growth traits in the mouse: A review

    Medrano Juan F

    2001-03-01

    Full Text Available Abstract The attainment of a specific mature body size is one of the most fundamental differences among species of mammals. Moreover, body size seems to be the central factor underlying differences in traits such as growth rate, energy metabolism and body composition. An important proportion of this variability is of genetic origin. The goal of the genetic analysis of animal growth is to understand its "genetic architecture", that is the number and position of loci affecting the trait, the magnitude of their effects, allele frequencies and types of gene action. In this review, the different strategies developed to identify and characterize genes involved in the regulation of growth in the mouse are described, with emphasis on the methods developed to map loci contributing to the regulation of quantitative traits (QTLs.

  14. Mapping functional traits: comparing abundance and presence-absence estimates at large spatial scales.

    Tim Newbold

    Full Text Available Efforts to quantify the composition of biological communities increasingly focus on functional traits. The composition of communities in terms of traits can be summarized in several ways. Ecologists are beginning to map the geographic distribution of trait-based metrics from various sources of data, but the maps have not been tested against independent data. Using data for birds of the Western Hemisphere, we test for the first time the most commonly used method for mapping community trait composition - overlaying range maps, which assumes that the local abundance of a given species is unrelated to the traits in question - and three new methods that as well as the range maps include varying degrees of information about interspecific and geographic variation in abundance. For each method, and for four traits (body mass, generation length, migratory behaviour, diet we calculated community-weighted mean of trait values, functional richness and functional divergence. The maps based on species ranges and limited abundance data were compared with independent data on community species composition from the American Christmas Bird Count (CBC scheme coupled with data on traits. The correspondence with observed community composition at the CBC sites was mostly positive (62/73 correlations but varied widely depending on the metric of community composition and method used (R(2: 5.6 × 10(-7 to 0.82, with a median of 0.12. Importantly, the commonly-used range-overlap method resulted in the best fit (21/22 correlations positive; R(2: 0.004 to 0.8, with a median of 0.33. Given the paucity of data on the local abundance of species, overlaying range maps appears to be the best available method for estimating patterns of community composition, but the poor fit for some metrics suggests that local abundance data are urgently needed to allow more accurate estimates of the composition of communities.

  15. Quantitative Trait Loci for Morphological Traits and their Association with Functional Genes in Raphanus sativus.

    Yu, Xiaona; Choi, Su Ryun; Dhandapani, Vignesh; Rameneni, Jana Jeevan; Li, Xiaonan; Pang, Wenxing; Lee, Ji-Young; Lim, Yong Pyo

    2016-01-01

    Identification of quantitative trait loci (QTLs) governing morphologically important traits enables to comprehend their potential genetic mechanisms in the genetic breeding program. In this study, we used 210 F2 populations derived from a cross between two radish inbred lines (Raphanus sativus) "835" and "B2," including 258 SSR markers were used to detect QTLs for 11 morphological traits that related to whole plant, leaf, and root yield in 3 years of replicated field test. Total 55 QTLs were detected which were distributed on each linkage group of the Raphanus genome. Individual QTLs accounted for 2.69-12.6 of the LOD value, and 0.82-16.25% of phenotypic variation. Several genomic regions have multiple traits that clustered together, suggested the existence of pleiotropy linkage. Synteny analysis of the QTL regions with A. thaliana genome selected orthologous genes in radish. InDels and SNPs in the parental lines were detected in those regions by Illumina genome sequence. Five identified candidate gene-based markers were validated by co-mapping with underlying QTLs affecting different traits. Semi-quantitative reverse transcriptase PCR analysis showed the different expression levels of these five genes in parental lines. In addition, comparative QTL analysis with B. rapa revealed six common QTL regions and four key major evolutionarily conserved crucifer blocks (J, U, R, and W) harboring QTL for morphological traits. The QTL positions identified in this study will provide a valuable resource for identifying more functional genes when whole radish genome sequence is released. Candidate genes identified in this study that co-localized in QTL regions are expected to facilitate in radish breeding programs. PMID:26973691

  16. Correcting for bias in estimation of quantitative trait loci effects

    Ron Micha

    2005-09-01

    Full Text Available Abstract Estimates of quantitative trait loci (QTL effects derived from complete genome scans are biased, if no assumptions are made about the distribution of QTL effects. Bias should be reduced if estimates are derived by maximum likelihood, with the QTL effects sampled from a known distribution. The parameters of the distributions of QTL effects for nine economic traits in dairy cattle were estimated from a daughter design analysis of the Israeli Holstein population including 490 marker-by-sire contrasts. A separate gamma distribution was derived for each trait. Estimates for both the α and β parameters and their SE decreased as a function of heritability. The maximum likelihood estimates derived for the individual QTL effects using the gamma distributions for each trait were regressed relative to the least squares estimates, but the regression factor decreased as a function of the least squares estimate. On simulated data, the mean of least squares estimates for effects with nominal 1% significance was more than twice the simulated values, while the mean of the maximum likelihood estimates was slightly lower than the mean of the simulated values. The coefficient of determination for the maximum likelihood estimates was five-fold the corresponding value for the least squares estimates.

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

    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.

  18. Identifying genes associated with quantitative traits in pigs: integrating quantitative and molecular approaches for meat quality

    Karl Schellander

    2010-01-01

    Full Text Available Two major strategies are used to identify genes that are involved in complex traits, genome scanning and candidate gene approaches. While a quantitative trait locus (QTL strategy relies on a scan of the entire genome combined with phenotypic measurements, a candidate gene approach tries to identify genes based on their possible role in the physiology of the traits. Both strategies are based on the integration between quantitative and molecular approaches. Over the last decade, enormous effort has been applied to identify and localize QTL involved in most of the economically important traits in pigs and a number of candidate genes were suggested and further validated according to a concordant position to the detected QTL and related functions. However, lacking of information in regards to identified genes within the identified QTL, and false-positive QTL are major constraints that limit the successful of this approach. Additional approaches, including a gene expression analysis of the divergence of phenotype of interest was integrated into a candidate gene analysis, in which a putative candidate gene is the one that could be statistically detected from the genes controlling large components of inheritable gene expression variation. Furthermore, a remarkable progress of molecular approaches by newly developed technique, a study of an interaction between genes and a holistic study of biological regulation, system biology, is underway. These continuations will assist the researchers to identify direct candidate gene for quantitative traits in animal breeding.

  19. Stochastic search variable selection for identifying multiple quantitative trait loci.

    Yi, Nengjun; George, Varghese; Allison, David B

    2003-07-01

    In this article, we utilize stochastic search variable selection methodology to develop a Bayesian method for identifying multiple quantitative trait loci (QTL) for complex traits in experimental designs. The proposed procedure entails embedding multiple regression in a hierarchical normal mixture model, where latent indicators for all markers are used to identify the multiple markers. The markers with significant effects can be identified as those with higher posterior probability included in the model. A simple and easy-to-use Gibbs sampler is employed to generate samples from the joint posterior distribution of all unknowns including the latent indicators, genetic effects for all markers, and other model parameters. The proposed method was evaluated using simulated data and illustrated using a real data set. The results demonstrate that the proposed method works well under typical situations of most QTL studies in terms of number of markers and marker density. PMID:12871920

  20. Fine mapping of dental fluorosis quantitative trait loci in mice

    Everett, Eric T.; Yin, Zhaoyu; Yan, Dong; Zou, Fei

    2011-01-01

    Genetic factors underlie dental fluorosis (DF) susceptibility/resistance. The A/J (DF susceptible) and 129P3/J (DF resistant) strains have been previously used to detect quantitative trait loci (QTL) associated with DF on chromosomes (Chr) 2 and 11. In the present study increased marker density genotyping followed by interval mapping was performed to narrow the QTL intervals and improve the LOD scores. Narrower intervals on Chr 2 where LOD ≥ 6.0 (57–84 cM or ~51 Mb), LOD ≥ 7.0 (62–79 cM or ~3...

  1. Finding Quantitative Trait Loci Genes with Collaborative Targeted Maximum Likelihood Learning.

    Wang, Hui; Rose, Sherri; van der Laan, Mark J

    2011-07-01

    Quantitative trait loci mapping is focused on identifying the positions and effect of genes underlying an an observed trait. We present a collaborative targeted maximum likelihood estimator in a semi-parametric model using a newly proposed 2-part super learning algorithm to find quantitative trait loci genes in listeria data. Results are compared to the parametric composite interval mapping approach. PMID:21572586

  2. Finding Quantitative Trait Loci Genes with Collaborative Targeted Maximum Likelihood Learning

    Wang, Hui; Rose, Sherri; van der Laan, Mark J.

    2011-01-01

    Quantitative trait loci mapping is focused on identifying the positions and effect of genes underlying an an observed trait. We present a collaborative targeted maximum likelihood estimator in a semi-parametric model using a newly proposed 2-part super learning algorithm to find quantitative trait loci genes in listeria data. Results are compared to the parametric composite interval mapping approach.

  3. The nature and identification of quantitative trait loci : a community's view

    Abiola, O; Angel, JM; Avner, P; Bachmanov, AA; Belknap, JK; Bennett, B; Blankenhorn, EP; Blizard, DA; Bolivar, [No Value; Brockmann, GA; Buck, KJ; Bureau, JF; Casley, WL; Chesler, EJ; Cheverud, JM; Churchill, GA; Cook, M; Crabbe, JC; Crusio, WE; Darvasi, A; de Haan, G; Demant, P; Doerge, RW; Elliott, RW; Farber, CR; Flaherty, L; Flint, J; Gershenfeld, H; Gu, JPGJ; Gu, WK; Himmelbauer, H; Hitzemann, R; Hsu, HC; Hunter, K; Iraqi, FA; Jansen, RC; Johnson, TE; Jones, BC; Kempermann, G; Lammert, F; Lu, L; Manly, KF; Matthews, DB; Medrano, JF; Mehrabian, M; Mittleman, G; Mock, BA; Mogil, JS; Montagutelli, [No Value; Morahan, G; Mountz, JD; Nagase, H; Nowakowski, RS; O'Hara, BR; Osadchuk, AV; Paigen, B; Palmer, Abraham A.; Peirce, JL; Pomp, D; Rosemann, M; Rosen, GD; Schalkwyk, LC; Seltzer, Z; Settle, S; Shimomura, K; Shou, SM; Sikela, JM; Siracusa, LD; Spearow, JL; Teuscher, C; Threadgill, DW; Toth, LA; Toye, AA; Vadasz, C; Van Zant, G; Wakeland, E; Zhang, HG; Zou, F; Angel, Joe M.; Belknap, John K.; Blankenhorn, Elizabeth P.; Bolivar, Valerie; Brockmann, Gudrun A.; Buck, Kari J.; Bureau, Jean-Francois; Casley, William L.; Chesler, Elissa J.; Cheverud, James M.; Crabbe, John C.; Crusio, Wim E.; Elliott, Rosemary W.; Farber, Charles R.; Gibson, John P.; Gu, Jing; Gu, Weikuan; Hsu, Hui-Chen; Iraqi, Fuad A.; Johnson, Thomas E.; Jones, Byron C.; Manly, Kenneth F.; Matthews, Douglas B.; Medrano, Juan F.; Mock, Beverly A.; Mogil, Jeffrey S.; Montagutelli, Xavier; Mountz, John D.; Nowakowski, Richard S.; O’Hara, Bruce F.; Osadchuk, Alexander V.; Peirce, Jeremy L.; Rosen, Glenn D.; Shou, Siming; Siracusa, Linda D.; Spearow, Jimmy L.; Threadgill, David W.; Toth, Linda A.; Williams, Robert W.; Zhang, Huang-Ge; Williams, O.

    2003-01-01

    This white paper by eighty members of the Complex Trait Consortium presents a community’s view on the approaches and statistical analyses that are needed for the identification of genetic loci that determine quantitative traits. Quantitative trait loci (QTLs) can be identified in several ways, but i

  4. Detection of Quantitative Trait Loci Associated with Live Measurement Traits in Pigs

    ZHANG Jing-hu; XIONG Yuan-zhu; ZUO Bo; LEI Ming-gang; LI Feng-e; LI Jia-lian

    2007-01-01

    Live measurement growth traits are very important economic traits in pig production and breeding. In this research,quantitative trait loci (QTL) were detected for 11 live estimated growth and carcass traits, including birth weight (BWT),average daily gain over testing periods (ADG3), live backfat thickness at last 3-4th lumbar (LBFT3), live loin eye area (LLEA), and so on, in 214 pig resource family population, including 180 F2 individual, by 39 microsatellite marker loci on SSC4, SSC6, SSC7, SSC8, and SSC13. The results indicated that 4 chromosome significant level QTL and one suggestive QTL were detected for ADG3 (at position of 50 cM on SSC8), LBFT3 (at position of 147 cM on SSC4), LLEA (one highly significant at position of 48 cM on SSC7; another significant at position of 125 cM on SSC8) and BWT (suggestive significant at position of 0 cM, at marker sw489 on SSC4). The phenotypic variance of these QTL accounted for 0.95% to 16.91%. Most of them were mentioned in previous reports; except the QTL of LLEA at position of sw1953 on SSC8 which maybe a new QTL.

  5. Plastic traits of an exotic grass contribute to its abundance but are not always favourable.

    Jennifer Firn

    Full Text Available In herbaceous ecosystems worldwide, biodiversity has been negatively impacted by changed grazing regimes and nutrient enrichment. Altered disturbance regimes are thought to favour invasive species that have a high phenotypic plasticity, although most studies measure plasticity under controlled conditions in the greenhouse and then assume plasticity is an advantage in the field. Here, we compare trait plasticity between three co-occurring, C(4 perennial grass species, an invader Eragrostis curvula, and natives Eragrostis sororia and Aristida personata to grazing and fertilizer in a three-year field trial. We measured abundances and several leaf traits known to correlate with strategies used by plants to fix carbon and acquire resources, i.e. specific leaf area (SLA, leaf dry matter content (LDMC, leaf nutrient concentrations (N, C:N, P, assimilation rates (Amax and photosynthetic nitrogen use efficiency (PNUE. In the control treatment (grazed only, trait values for SLA, leaf C:N ratios, Amax and PNUE differed significantly between the three grass species. When trait values were compared across treatments, E. curvula showed higher trait plasticity than the native grasses, and this correlated with an increase in abundance across all but the grazed/fertilized treatment. The native grasses showed little trait plasticity in response to the treatments. Aristida personata decreased significantly in the treatments where E. curvula increased, and E. sororia abundance increased possibly due to increased rainfall and not in response to treatments or invader abundance. Overall, we found that plasticity did not favour an increase in abundance of E. curvula under the grazed/fertilized treatment likely because leaf nutrient contents increased and subsequently its' palatability to consumers. E. curvula also displayed a higher resource use efficiency than the native grasses. These findings suggest resource conditions and disturbance regimes can be manipulated to

  6. Plastic traits of an exotic grass contribute to its abundance but are not always favourable.

    Firn, Jennifer; Prober, Suzanne M; Buckley, Yvonne M

    2012-01-01

    In herbaceous ecosystems worldwide, biodiversity has been negatively impacted by changed grazing regimes and nutrient enrichment. Altered disturbance regimes are thought to favour invasive species that have a high phenotypic plasticity, although most studies measure plasticity under controlled conditions in the greenhouse and then assume plasticity is an advantage in the field. Here, we compare trait plasticity between three co-occurring, C(4) perennial grass species, an invader Eragrostis curvula, and natives Eragrostis sororia and Aristida personata to grazing and fertilizer in a three-year field trial. We measured abundances and several leaf traits known to correlate with strategies used by plants to fix carbon and acquire resources, i.e. specific leaf area (SLA), leaf dry matter content (LDMC), leaf nutrient concentrations (N, C:N, P), assimilation rates (Amax) and photosynthetic nitrogen use efficiency (PNUE). In the control treatment (grazed only), trait values for SLA, leaf C:N ratios, Amax and PNUE differed significantly between the three grass species. When trait values were compared across treatments, E. curvula showed higher trait plasticity than the native grasses, and this correlated with an increase in abundance across all but the grazed/fertilized treatment. The native grasses showed little trait plasticity in response to the treatments. Aristida personata decreased significantly in the treatments where E. curvula increased, and E. sororia abundance increased possibly due to increased rainfall and not in response to treatments or invader abundance. Overall, we found that plasticity did not favour an increase in abundance of E. curvula under the grazed/fertilized treatment likely because leaf nutrient contents increased and subsequently its' palatability to consumers. E. curvula also displayed a higher resource use efficiency than the native grasses. These findings suggest resource conditions and disturbance regimes can be manipulated to disadvantage

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

    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. PMID:23660834

  8. Quantitative Trait Loci Mapping of Leaf Morphological Traits and Chlorophyll Content in Cultivated Tetraploid Cotton

    Xian-Liang SONG; Wang-Zhen GUO; Zhi-Guo HAN; Tian-Zhen ZHANG

    2005-01-01

    Genetic mapping provides a powerful tool for quantitative trait loci (QTL) analysis at the molecular level. A simple sequence repeat (SSR) genetic map containing 590 markers and a BC1 population from two cultivated tetraploid cotton (Gossypium hirsutum L.) cultivars, namely TM-1 and Hai 7124 (G.barbadense L.), were used to map and analyze QTL using the composite interval mapping (CIM) method.Thirty one QTLs, 10 for lobe length, 13 for lobe width, six for lobe angle, and two for leaf chlorophyll content,were detected on 15 chromosomes or linkage groups at logarithm of odds (LOD) ≥ 2.0, of which 15 were found for leaf morphology at LOD ≥.3.0. The genetic effects of the QTL were estimated. These results are fundamental for marker-assisted selection (MAS) of these traits in tetraploid cotton breeding.

  9. Functional linear models for association analysis of quantitative traits.

    Fan, Ruzong; Wang, Yifan; Mills, James L; Wilson, Alexander F; Bailey-Wilson, Joan E; Xiong, Momiao

    2013-11-01

    Functional linear models are developed in this paper for testing associations between quantitative traits and genetic variants, which can be rare variants or common variants or the combination of the two. By treating multiple genetic variants of an individual in a human population as a realization of a stochastic process, the genome of an individual in a chromosome region is a continuum of sequence data rather than discrete observations. The genome of an individual is viewed as a stochastic function that contains both linkage and linkage disequilibrium (LD) information of the genetic markers. By using techniques of functional data analysis, both fixed and mixed effect functional linear models are built to test the association between quantitative traits and genetic variants adjusting for covariates. After extensive simulation analysis, it is shown that the F-distributed tests of the proposed fixed effect functional linear models have higher power than that of sequence kernel association test (SKAT) and its optimal unified test (SKAT-O) for three scenarios in most cases: (1) the causal variants are all rare, (2) the causal variants are both rare and common, and (3) the causal variants are common. The superior performance of the fixed effect functional linear models is most likely due to its optimal utilization of both genetic linkage and LD information of multiple genetic variants in a genome and similarity among different individuals, while SKAT and SKAT-O only model the similarities and pairwise LD but do not model linkage and higher order LD information sufficiently. In addition, the proposed fixed effect models generate accurate type I error rates in simulation studies. We also show that the functional kernel score tests of the proposed mixed effect functional linear models are preferable in candidate gene analysis and small sample problems. The methods are applied to analyze three biochemical traits in data from the Trinity Students Study. PMID:24130119

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

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

    2006-01-01

    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 ...

  11. Functional traits predict relationship between plant abundance dynamic and long-term climate warming.

    Soudzilovskaia, Nadejda A; Elumeeva, Tatiana G; Onipchenko, Vladimir G; Shidakov, Islam I; Salpagarova, Fatima S; Khubiev, Anzor B; Tekeev, Dzhamal K; Cornelissen, Johannes H C

    2013-11-01

    Predicting climate change impact on ecosystem structure and services is one of the most important challenges in ecology. Until now, plant species response to climate change has been described at the level of fixed plant functional types, an approach limited by its inflexibility as there is much interspecific functional variation within plant functional types. Considering a plant species as a set of functional traits greatly increases our possibilities for analysis of ecosystem functioning and carbon and nutrient fluxes associated therewith. Moreover, recently assembled large-scale databases hold comprehensive per-species data on plant functional traits, allowing a detailed functional description of many plant communities on Earth. Here, we show that plant functional traits can be used as predictors of vegetation response to climate warming, accounting in our test ecosystem (the species-rich alpine belt of Caucasus mountains, Russia) for 59% of variability in the per-species abundance relation to temperature. In this mountain belt, traits that promote conservative leaf water economy (higher leaf mass per area, thicker leaves) and large investments in belowground reserves to support next year's shoot buds (root carbon content) were the best predictors of the species increase in abundance along with temperature increase. This finding demonstrates that plant functional traits constitute a highly useful concept for forecasting changes in plant communities, and their associated ecosystem services, in response to climate change. PMID:24145400

  12. Detection of quantitative trait loci for meat quality traits in cattle.

    Gutiérrez-Gil, B; Wiener, P; Nute, G R; Burton, D; Gill, J L; Wood, J D; Williams, J L

    2008-02-01

    A whole-genome scan was carried out to detect quantitative trait loci (QTL) affecting sensory, organoleptic, physical and chemical properties of meat. The study used phenotypic data from 235 second-generation cross-bred bull calves of a Charolais x Holstein experimental population. Loin muscle samples were evaluated for yield force, intramuscular fat and nitrogen contents, myofibrillar fragmentation index, haem pigment concentration, moisture content and pH at 24 h postmortem. A sensory assessment was performed on grilled loin and roasted silverside joints by trained panellists. A linear regression analysis based on 165 markers revealed 35 QTL at the 5% chromosome-wide significance level (20 for sensory traits and 15 for physical and chemical traits), five of which were highly significant (F-value: > or =9). The most significant QTL was located on chromosome 6 (with the best likely position at 39 cM) and affected haem pigment concentration. The Holstein allele for this QTL was associated with an increase of 0.53 SD in the haem scores. A QTL for pH(24h) was identified on chromosome 14 (at 40 cM) and a QTL for moisture content was identified on chromosome 22 (at 21 cM). Two highly significant QTL were identified for sensory panel-assessed traits: beef odour intensity (grilled sample) on chromosome 10 (at 119 cM), and juiciness (roast sample) on chromosome 16 (at 70 cM). The proportion of phenotypic variance explained by the significant QTL ranged from 3.6% (for nitrogen content on chromosome 10) to 9.5% (for juiciness, roast sample on chromosome 16). PMID:18254735

  13. Quantitative Traits of Ion Beam Induced Mutagenesis in Triticum aestivum

    Huan FANG; Zhen JIAO

    2012-01-01

    [Objective] The aim of this study was to elucidate the quantitative traits of plants mutagenized by ion beam. [Method] The particular variation phenotypes, a- gronomic traits, and protein and wet gluten contents of progenies derived from the same ion beam induced mutant were investigated. [Result] Morphological polymor- phism existed in some individuals. Plant height, spike length and protein content were significantly influenced by ion beam, and effective tiller number and wet gluten content were moderately influenced. Multiple comparisons of all the indices within groups indicated genomic instability among these groups. Coefficient of variation im- plied the differences within group were very low. [Conclusion] Ion beam irradiation displayed characteristics of multi-directivity and non-directiveness. It aroused multiple variations in the same mutant. Instability among progeny indicates cells had different fate even in the same irradiated tissue. It may take several generations for mutants to stabilize particular phenotypes. The effects of ion beam irradiation may be the in- terrelated direct irradiation damage, indirect irradiation damage and late effect, such as bystander effect and adaptive response.

  14. Heterosis studies for quantitative traits in sesame (Sesamum indicum L.

    G.B.Chaudhari, M.R.Naik, S.A.Anarase and Y.G.Ban

    2015-03-01

    Full Text Available A study was conducted in sesame (Sesamum indicum L. at Department of Genetics and Plant Breeding, N.M. College of Agriculture, NAU, Navsari (Gujarat to assess the extent of heterosis for eleven quantitative traits. Five lines and ten testers were crossed in line x tester manner to develop 50 F1 hybrids. Analysis of variance revealed the significant differences among the crosses for all traits. Heterosis was worked out over better parent and standard varieties Gujarat Til-4 and TKG-22. Five hybrids viz., Gujarat Til-1 x JLS-116, Gujarat Til-2 x JLS-116, Gujarat Til-3 x AKT-64, Patan-64 x JLS-9707-2 and Patan-64 x JLT-408 showed desirable heterobeltiosis for seed yield per plant along with other six major yield contributing characters. The crosses Gujarat Til-3 x AKT-64, Gujarat Til-3 x PKV-NT-11, Gujarat Til-3 x JLS-9707-2 and Gujarat Til-3 x JLS-116 were the best heterotic combinations for seed yield, which recorded 85.81 and 98.08, 63.38 and 74.13, 63.38 and 74.13, 54.28 and 64.43 percent standard heterosis over Gujarat Til-4 and TKG-22, respectively. These crosses could be utilized for hybrid development after testing in large scale trials to confirm the superiority in heterosis.

  15. Gene action studies of different quantitative traits in maize

    The present study was carried out to determine the type of gene action, genetic parameters of yield and other quantitative traits by crossing 8 diverse maize inbred lines in complete diallel fashion. Seed of F/sub 1/ population along with their parents was planted in randomized complete block design replicated thrice. Analysis of variance showed that inbred lines differed significantly among each other for all traits. The estimates of components of genetic variation revealed that non additive genetic effects were more pronounced in the inheritance of plant height, days to 50% tasseling, days to 50% silking, ear height and grain yield per plant. Directional dominance was observed for all the characters under study. Asymmetrical gene distribution was observed for all the attributes except ear height for which parental lines contained equal number of dominant and recessive genes. The graphic analysis showed that all the characters were under the genetic control of over dominance type of gene action, therefore, the material can easily be exploited for heterotic effect. (author)

  16. Confirmation of quantitative trait loci affecting fatness in chickens

    Poel Jan

    2005-03-01

    Full Text Available Abstract In this report we describe the analysis of an advanced intercross line (AIL to confirm the quantitative trait locus (QTL regions found for fatness traits in a previous study. QTL analysis was performed on chromosomes 1, 3, 4, 15, 18, and 27. The AIL was created by random intercrossing in each generation from generation 2 (G2 onwards until generation 9 (G9 was reached. QTL for abdominal fat weight (AFW and/or percentage abdominal fat (AF% on chromosomes 1, 3 and 27 were confirmed in the G9 population. In addition, evidence for QTL for body weight at the age of 5 (BW5 and 7 (BW7 weeks and for the percentage of intramuscular fat (IF% were found on chromosomes 1, 3, 15, and 27. Significant evidence for QTL was detected on chromosome 1 for BW5 and BW7. Suggestive evidence was found on chromosome 1 for AFW, AF% and IF%, on chromosome 15 for BW5, and on chromosome 27 for AF% and IF%. Furthermore, evidence on the chromosome-wise level was found on chromosome 3 for AFW, AF%, and BW7 and on chromosome 27 for BW5. For chromosomes 4 and 18, test statistics did not exceed the significance threshold.

  17. Reliable Quantitative Mineral Abundances of the Martian Surface using THEMIS

    Smith, R. J.; Huang, J.; Ryan, A. J.; Christensen, P. R.

    2013-12-01

    The following presents a proof of concept that given quality data, Thermal Emission Imaging System (THEMIS) data can be used to derive reliable quantitative mineral abundances of the Martian surface using a limited mineral library. The THEMIS instrument aboard the Mars Odyssey spacecraft is a multispectral thermal infrared imager with a spatial resolution of 100 m/pixel. The relatively high spatial resolution along with global coverage makes THEMIS datasets powerful tools for comprehensive fine scale petrologic analyses. However, the spectral resolution of THEMIS is limited to 8 surface sensitive bands between 6.8 and 14.0 μm with an average bandwidth of ~ 1 μm, which complicates atmosphere-surface separation and spectral analysis. This study utilizes the atmospheric correction methods of both Bandfield et al. [2004] and Ryan et al. [2013] joined with the iterative linear deconvolution technique pioneered by Huang et al. [in review] in order to derive fine-scale quantitative mineral abundances of the Martian surface. In general, it can be assumed that surface emissivity combines in a linear fashion in the thermal infrared (TIR) wavelengths such that the emitted energy is proportional to the areal percentage of the minerals present. TIR spectra are unmixed using a set of linear equations involving an endmember library of lab measured mineral spectra. The number of endmembers allowed in a spectral library are restricted to a quantity of n-1 (where n = the number of spectral bands of an instrument), preserving one band for blackbody. Spectral analysis of THEMIS data is thus allowed only seven endmembers. This study attempts to prove that this limitation does not prohibit the derivation of meaningful spectral analyses from THEMIS data. Our study selects THEMIS stamps from a region of Mars that is well characterized in the TIR by the higher spectral resolution, lower spatial resolution Thermal Emission Spectrometer (TES) instrument (143 bands at 10 cm-1 sampling and 3

  18. Quantitative trait loci for growth trajectories in Populus.

    Wu, Rongling; Ma, Chang-Xing; Yang, Mark C K; Chang, Myron; Littell, Ramon C; Santra, Upasana; Wu, Samuel S; Yin, Tongming; Huang, Minren; Wang, Minxiu; Casella, George

    2003-02-01

    Growth trajectories are a biological process important to plant and animal breeding, and to evolutionary genetic studies. In this article, we report the detection of quantitative trait loci (QTLs) responsible for growth trajectories in poplars that are used as a model system for the study of forest biology. These QTLs were localized on a genetic linkage map of polymorphic markers using a statistical mapping method incorporating growth-curve models. The effects of the QTLs on growth are described as a function of age, so that age-specific changes in QTL effects can be readily projected throughout the entire growth process. The QTLs identified display increased effects on growth when trees age, yet the timing of QTL activation is earlier for stem height than diameter, which is consistent with the ecological viewpoint of canopy competition. The implications of the results for breeding and silviculture are discussed. PMID:12693683

  19. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation.

    Maria Májeková

    Full Text Available Functional diversity (FD is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively. We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package "traitor" to facilitate assessments of missing trait data.

  20. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation.

    Májeková, Maria; Paal, Taavi; Plowman, Nichola S; Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R; Luke, Sarah H; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package "traitor" to facilitate assessments of missing trait data. PMID:26881747

  1. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation

    Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R.; Luke, Sarah H.; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package “traitor” to facilitate assessments of missing trait data. PMID:26881747

  2. Mapping quantitative trait loci in noninbred mosquito crosses.

    Wang, Shuang; Huang, Song; Zheng, Liangbiao; Zhao, Hongyu

    2006-04-01

    The identification of genes that affect quantitative traits has been of great interest to geneticists for many decades, and many statistical methods have been developed to map quantitative trait loci (QTL). Most QTL mapping studies in experimental organisms use purely inbred lines, where the two homologous chromosomes in each individual are identical. As a result, many existing QTL mapping methods developed for experimental organisms are applicable only to genetic crosses between inbred lines. However, it may be difficult to obtain inbred lines for certain organisms, e.g., mosquitoes. Although statistical methods for QTL mapping in outbred populations, e.g., humans, can be applied for such crosses, these methods may not fully take advantage of the uniqueness of these crosses. For example, we can generally assume that the two grandparental lines are homozygous at the QTL of interest, but such information is not be utilized through methods developed for outbred populations. In addition, mating types and phases can be relatively easy to establish through the analysis of adjacent markers due to the large number of offspring that can be collected, substantially simplifying the computational need. In this article, motivated by a mosquito intercross experiment involving two selected lines that are not genetically homozygous across the genome, we develop statistical methods for QTL mapping for genetic crosses involving noninbred lines. In our procedure, we first infer parental mating types and use likelihood-based methods to infer phases in each parent on the basis of genotypes of offspring and one parent. A hidden Markov model is then employed to estimate the number of high-risk alleles at marker positions and putative QTL positions between markers in each offspring, and QTL mapping is finally conducted through the inferred QTL configuration across all offspring in all crosses. The performance of the proposed methods is assessed through simulation studies, and the

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

    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.

  4. Hnrnph1 Is A Quantitative Trait Gene for Methamphetamine Sensitivity.

    Neema Yazdani

    2015-12-01

    Full Text Available Psychostimulant addiction is a heritable substance use disorder; however its genetic basis is almost entirely unknown. Quantitative trait locus (QTL mapping in mice offers a complementary approach to human genome-wide association studies and can facilitate environment control, statistical power, novel gene discovery, and neurobiological mechanisms. We used interval-specific congenic mouse lines carrying various segments of chromosome 11 from the DBA/2J strain on an isogenic C57BL/6J background to positionally clone a 206 kb QTL (50,185,512-50,391,845 bp that was causally associated with a reduction in the locomotor stimulant response to methamphetamine (2 mg/kg, i.p.; DBA/2J < C57BL/6J-a non-contingent, drug-induced behavior that is associated with stimulation of the dopaminergic reward circuitry. This chromosomal region contained only two protein coding genes-heterogeneous nuclear ribonucleoprotein, H1 (Hnrnph1 and RUN and FYVE domain-containing 1 (Rufy1. Transcriptome analysis via mRNA sequencing in the striatum implicated a neurobiological mechanism involving a reduction in mesolimbic innervation and striatal neurotransmission. For instance, Nr4a2 (nuclear receptor subfamily 4, group A, member 2, a transcription factor crucial for midbrain dopaminergic neuron development, exhibited a 2.1-fold decrease in expression (DBA/2J < C57BL/6J; p 4.2 x 10-15. Transcription activator-like effector nucleases (TALENs-mediated introduction of frameshift deletions in the first coding exon of Hnrnph1, but not Rufy1, recapitulated the reduced methamphetamine behavioral response, thus identifying Hnrnph1 as a quantitative trait gene for methamphetamine sensitivity. These results define a novel contribution of Hnrnph1 to neurobehavioral dysfunction associated with dopaminergic neurotransmission. These findings could have implications for understanding the genetic basis of methamphetamine addiction in humans and the development of novel therapeutics for

  5. Local Abundance Patterns of Noctuid Moths in Olive Orchards: Life-History Traits, Distribution Type and Habitat Interactions

    Pérez-Guerrero, Sergio; Redondo, Alberto José; Yela, José Luis

    2011-01-01

    Local species abundance is related to range size, habitat characteristics, distribution type, body size, and life-history variables. In general, habitat generalists and polyphagous species are more abundant in broad geographical areas. Underlying this, local abundance may be explained from the interactions between life-history traits, chorological pattern, and the local habitat characteristics. The relationship within taxa between life-history traits, distribution area, habitat characteristic...

  6. Road Impacts on Abundance, Call Traits, and Body Size of Rainforest Frogs in Northeast Australia

    Miriam W. Goosem

    2010-09-01

    Full Text Available Frogs are potentially sensitive indicators of road impacts, with studies indicating particular susceptibility to road mortality. Calling, i.e., breeding, behavior could also be affected by traffic noise. We investigated effects on frog abundance and calling behavior where a busy highway crosses rainforest stream breeding habitat in northeast Australia. Frog abundance was repeatedly surveyed along five stream transects during a summer breeding season. Abundance of two species, Litoria rheocola and Austrochaperina pluvialis, increased significantly with perpendicular distance from the road along two transects. No trends in abundance were detected for A. pluvialis on two other transects where it was common, or for Litoria serrata on one transect where abundance was sufficient for analysis. Both species with lowered abundance near the road, L. rheocola and A. pluvialis, are rare in road kill statistics along this highway, suggesting road mortality is not the cause of reduced frog abundance near the road. We postulate that lowered abundance may reflect traffic noise effects. We analyzed calls of the International Union for Conservation of Nature endangered species L. rheocola along the one stream transect on which it was common. We found significant trends in two call traits over a very fine scale: both call rate and dominant frequency were significantly higher closer to the road. Furthermore, males were significantly smaller closer to the road. These call and body size trends most likely reflect road impacts, but resolving these is complicated by correlations between traits. Potential mechanisms, effects on fitness, and management recommendations to mitigate the impacts of roads on frogs are outlined.

  7. Hnrnph1 Is A Quantitative Trait Gene for Methamphetamine Sensitivity.

    Yazdani, Neema; Parker, Clarissa C; Shen, Ying; Reed, Eric R; Guido, Michael A; Kole, Loren A; Kirkpatrick, Stacey L; Lim, Jackie E; Sokoloff, Greta; Cheng, Riyan; Johnson, W Evan; Palmer, Abraham A; Bryant, Camron D

    2015-12-01

    Psychostimulant addiction is a heritable substance use disorder; however its genetic basis is almost entirely unknown. Quantitative trait locus (QTL) mapping in mice offers a complementary approach to human genome-wide association studies and can facilitate environment control, statistical power, novel gene discovery, and neurobiological mechanisms. We used interval-specific congenic mouse lines carrying various segments of chromosome 11 from the DBA/2J strain on an isogenic C57BL/6J background to positionally clone a 206 kb QTL (50,185,512-50,391,845 bp) that was causally associated with a reduction in the locomotor stimulant response to methamphetamine (2 mg/kg, i.p.; DBA/2J drug-induced behavior that is associated with stimulation of the dopaminergic reward circuitry. This chromosomal region contained only two protein coding genes-heterogeneous nuclear ribonucleoprotein, H1 (Hnrnph1) and RUN and FYVE domain-containing 1 (Rufy1). Transcriptome analysis via mRNA sequencing in the striatum implicated a neurobiological mechanism involving a reduction in mesolimbic innervation and striatal neurotransmission. For instance, Nr4a2 (nuclear receptor subfamily 4, group A, member 2), a transcription factor crucial for midbrain dopaminergic neuron development, exhibited a 2.1-fold decrease in expression (DBA/2J trait gene for methamphetamine sensitivity. These results define a novel contribution of Hnrnph1 to neurobehavioral dysfunction associated with dopaminergic neurotransmission. These findings could have implications for understanding the genetic basis of methamphetamine addiction in humans and the development of novel therapeutics for prevention and treatment of substance abuse and possibly other psychiatric disorders. PMID:26658939

  8. A Semiparametric Approach for Composite Functional Mapping of Dynamic Quantitative Traits

    Yang, Runqing; Gao, Huijiang; Wang, Xin; Zhang, Ji; Zeng, Zhao-Bang; Wu, Rongling

    2007-01-01

    Functional mapping has emerged as a powerful tool for mapping quantitative trait loci (QTL) that control developmental patterns of complex dynamic traits. Original functional mapping has been constructed within the context of simple interval mapping, without consideration of separate multiple linked QTL for a dynamic trait. In this article, we present a statistical framework for mapping QTL that affect dynamic traits by capitalizing on the strengths of functional mapping and composite interva...

  9. Semiparametric Quantitative-Trait-Locus Mapping: II. on Censored Age-at-Onset

    Ying Chen; Chengcheng Hu; Rongling Wu

    2004-01-01

    In genetic studies, the variation in genotypes may not only affect different inheritance patterns in qualitative traits, but may also affect the age-at-onset as quantitative trait. In this article, we use standard cross designs, such as backcross or F2, to propose some hazard regression models, namely, the additive hazards model in quantitative trait loci mapping for age-at-onset, although the developed method can be extended to more complex designs. With additive invariance of the additive h...

  10. Liver expression quantitative trait loci: a foundation for pharmacogenomic research

    Dylan eGlubb

    2012-08-01

    Full Text Available Expression quantitative trait loci (eQTL analysis can provide insights into the genetic regulation of gene expression at a genomic level and this information is proving extremely useful in many different areas of research. As a consequence of the role of the liver in drug metabolism and disposition, the study of eQTLs in primary human liver tissue could provide a foundation for pharmacogenomics. Thus far, four genome-wide eQTL studies have been performed using human livers. Many liver eQTLs have been found to be reproducible and a proportion of these may be specific to the liver. Already these data have been used to interpret and inform clinic genome-wide association studies, providing potential mechanistic evidence for clinical associations and identifying genes which may impact on clinical phenotypes. However, the utility of liver eQTL data has not yet been fully explored or realized in pharmacogenomics. As further liver eQTL research is undertaken, the genetic regulation of gene expression will become much better characterized and this knowledge will create a rational basis for the prospective pharmacogenomic study of many drugs.

  11. Quantitative trait locus mapping can benefit from segregation distortion.

    Xu, Shizhong

    2008-12-01

    Segregation distortion is a phenomenon that has been observed in many experimental systems. How segregation distortion among markers arises and its impact on mapping studies are the focus of this work. Segregation distortion of markers can be considered to arise from segregation distortion loci (SDL). I develop a theory of segregation distortion and show that the presence of only a few SDL can cause the entire chromosome to distort from Mendelian segregation. Segregation distortion is detrimental to the power of detecting quantitative trait loci (QTL) with dominance effects, but it is not always a detriment to QTL mapping for additive effects. When segregation distortion of a locus is a random event, the SDL is beneficial to QTL mapping approximately 44% of the time. If SDL are present and ignored, power loss can be substantial. A dense marker map can be used to ameliorate the situation, and if dense marker information is incorporated, power loss is minimal. However, other situations are less benign. A method that can simultaneously map QTL and SDL is discussed, maximizing both use of mapping resources and use by agricultural and evolutionary biologists. PMID:18957707

  12. Quantitative Trait Loci for Mercury Tolerance in Rice Seedlings

    WANG Chong-qing; WANG Tao; MU Ping; LI Zi-chao; YANG Ling

    2013-01-01

    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.

  13. Validation of commercial DNA tests for quantitative beef quality traits.

    Van Eenennaam, A L; Li, J; Thallman, R M; Quaas, R L; Dikeman, M E; Gill, C A; Franke, D E; Thomas, M G

    2007-04-01

    Associations between 3 commercially available genetic marker panels (GeneSTAR Quality Grade, GeneSTAR Tenderness, and Igenity Tender-GENE) and quantitative beef traits were validated by the US National Beef Cattle Evaluation Consortium. Validation was interpreted to be the independent confirmation of the associations between genetic tests and phenotypes, as claimed by the commercial genotyping companies. Validation of the quality grade test (GeneSTAR Quality Grade) was carried out on 400 Charolais x Angus crossbred cattle, and validation of the tenderness tests (GeneSTAR Tenderness and Igenity Tender-GENE) was carried out on over 1,000 Bos taurus and Bos indicus cattle. The GeneSTAR Quality Grade marker panel is composed of 2 markers (TG5, a SNP upstream from the start of the first exon of thyroglobulin, and QG2, an anonymous SNP) and is being marketed as a test associated with marbling and quality grade. In this validation study, the genotype results from this test were not associated with marbling score; however, the association of substituting favorable alleles of the marker panel with increased quality grade (percentage of cattle grading Choice or Prime) approached significance (P meat tenderness, as assessed by Warner-Bratzler shear force. These marker panels share 2 common mu-calpain SNP, but each has a different calpastatin SNP. In both panels, there were highly significant (P < 0.001) associations of the calpastatin marker and the mu-calpain haplotype with tenderness. The genotypic effects of the 2 tenderness panels were similar to each other, with a 1 kg difference in Warner-Bratzler shear force being observed between the most and least tender genotypes. Unbiased and independent validation studies are important to help build confidence in marker technology and also as a potential source of data required to enable the integration of marker data into genetic evaluations. As DNA tests associated with more beef production traits enter the marketplace, it will

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

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

    2015-01-01

    Background 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 i...

  15. Habitat traits and species interactions differentially affect abundance and body size in pond-breeding amphibians.

    Ousterhout, Brittany H; Anderson, Thomas L; Drake, Dana L; Peterman, William E; Semlitsch, Raymond D

    2015-07-01

    In recent studies, habitat traits have emerged as stronger predictors of species occupancy, abundance, richness and diversity than competition. However, in many cases, it remains unclear whether habitat also mediates processes more subtle than competitive exclusion, such as growth, or whether intra- and interspecific interactions among individuals of different species may be better predictors of size. To test whether habitat traits are a stronger predictor of abundance and body size than intra- and interspecific interactions, we measured the density and body size of three species of larval salamanders in 192 ponds across a landscape. We found that the density of larvae was best predicted by models that included habitat features, while models incorporating interactions among individuals of different species best explained the body size of larvae. Additionally, we found a positive relationship between focal species density and congener density, while focal species body size was negatively related to congener density. We posit that salamander larvae may not experience competitive exclusion and thus reduced densities, but instead compensate for increased competition behaviourally (e.g. reduced foraging), resulting in decreased growth. The discrepancy between larval density and body size, a strong predictor of fitness in this system, also highlights a potential shortcoming in using density or abundance as a metric of habitat quality or population health. PMID:25643605

  16. Two-part zero-inflated negative binomial regression model for quantitative trait loci mapping with count trait.

    Moghimbeigi, Abbas

    2015-05-01

    Poisson regression models provide a standard framework for quantitative trait locus (QTL) mapping of count traits. In practice, however, count traits are often over-dispersed relative to the Poisson distribution. In these situations, the zero-inflated Poisson (ZIP), zero-inflated generalized Poisson (ZIGP) and zero-inflated negative binomial (ZINB) regression may be useful for QTL mapping of count traits. Added genetic variables to the negative binomial part equation, may also affect extra zero data. In this study, to overcome these challenges, I apply two-part ZINB model. The EM algorithm with Newton-Raphson method in the M-step uses for estimating parameters. An application of the two-part ZINB model for QTL mapping is considered to detect associations between the formation of gallstone and the genotype of markers. PMID:25728790

  17. Quantitative autistic traits ascertained in a national survey of 22 529 Japanese schoolchildren

    Kamio, Y; Inada, N.; Moriwaki, A; Kuroda, M; Koyama, T; Tsujii, H.; Kawakubo, Y; Kuwabara, H.; Tsuchiya, K J; Uno, Y; Constantino, J N

    2012-01-01

    Objective Recent epidemiologic studies worldwide have documented a rise in prevalence rates for autism spectrum disorders (ASD). Broadening of diagnostic criteria for ASD may be a major contributor to the rise in prevalence, particularly if superimposed on an underlying continuous distribution of autistic traits. This study sought to determine the nature of the population distribution of autistic traits using a quantitative trait measure in a large national population sample of children. Meth...

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

    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. PMID:21667037

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

    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. Genetic mapping of quantitative trait loci in plants - a novel statistical approach.

    Jansen, R.C.

    1995-01-01

    Quantitative variation is a feature of many important traits such as yield, quality and disease resistance in crop plants and farm animals, and diseases in humans. The genetic mapping, understanding and manipulation of quantitative trait loci (QTLs) are therefore of prime importance. Only by using genetically marked chromosomes is it possible to detect and map these QTLs. The recent advent of complete genetic maps of molecular markers for many plant and animal species therefore heralds a new ...

  1. Life history traits and exploitation affect the spatial mean-variance relationship in fish abundance.

    Kuo, Ting-chun; Mandal, Sandip; Yamauchi, Atsushi; Hsieh, Chih-hao

    2016-05-01

    Fishing is expected to alter the spatial heterogeneity of fishes. As an effective index to quantify spatial heterogeneity, the exponent b in Taylor's power law (V = aMb) measures how spatial variance (V) varies with changes in mean abundance (M) of a population, with larger b indicating higher spatial aggregation potential (i.e., more heterogeneity). Theory predicts b is related with life history traits, but empirical evidence is lacking. Using 50-yr spatiotemporal data from the California Current Ecosystem, we examined fishing and life history effects on Taylor's exponent by comparing spatial distributions of exploited and unexploited fishes living in the same environment. We found that unexploited species with smaller size and generation time exhibit larger b, supporting theoretical prediction. In contrast, this relationship in exploited species is much weaker, as the exponents of large exploited species were higher than unexploited species with similar traits. Our results suggest that fishing may increase spatial aggregation potential of a species, likely through degrading their size/age structure. Results of moving-window cross-correlation analyses on b vs. age structure indices (mean age and age evenness) for some exploited species corroborate our findings. Furthermore, through linking our findings to other fundamental ecological patterns (occupancy-abundance and size-abundance relationships), we provide theoretical arguments for the usefulness of monitoring the exponent b for management purposes. We propose that age/size-truncated species might have lower recovery rate in spatial occupancy, and the spatial variance-mass relationship of a species might be non-linear. Our findings provide theoretical basis explaining why fishery management strategy should be concerned with changes to the age and spatial structure of exploited fishes. PMID:27349101

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

    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

  3. [Spontaneous mutation variation (quantitative manifestation) of some traits of the garden rose].

    Zykov, K I

    2002-01-01

    Quantitative variability of four traits (anthocyan coloration, flower aroma, double-flowering capacity, and a flower size) in spontaneous gemmacous mutants (sports) of garden rose may be not accidental but preferably orientated to the increase or decrease in the trait manifestation in the case of transaggressive inheritance by initial hybrid forms of the increased or decreased level of these traits in parents. Revealing this regularity enabled us to evolve a hypothesis explaining the decrease or increase in trait quantitative manifestation in sports by inactivation or elimination resulting from mutations in dominant alleles of the polymer genes responsible either for increasing or decreasing in phenotypic expression. Thus, if the parents of an initial form are known, it is possible to forecast in what way the quantitative characters in somatic mutants of the initial form will change, accidentally or getting preferably higher or lower. PMID:12379016

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

    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 key...... pigs has been used for a QTL analysis of meat quality traits. Results: In total, we analyzed 39 meat quality traits and identified eight genome-wide significant QTL peaks in four regions: one on chromosome 3, two on chromosome 6 and one on chromosome 16. At least two of the QTLs do not appear to have...... respectively. Conclusion: We identified at least two new meat quality trait QTLs at the genome-wide significance level. We detected two QTLs on chromosome 6 that possibly coincide with QTLs detected in other studies. We were also able to exclude the C1843T mutation in the ryanodine receptor (RYRI) as a...

  5. Analysis of quantitative trait loci underlying the traits related to chlorophyll content of the flag leaf in rice

    Guohua YANG; Sansi TU; Shaoqing LI; Lingling FENG; Jin KONG; Hui LI; Yangsheng LI

    2008-01-01

    A population of 117 doubled haploid (DH) lines derived from the cross of Zhaiyeqing 8 (indica) x Jingxi 17 (japonica) was employed to map quantitative trait loci (QTL) underlying four physiological traits related to chlorophyll contents of the flag leaf. There were significantly positive correlations among chlorophyll a, chlorophyll b and chlorophyll a+ b content. Chlorophyll a/b ratio was significantly negatively correlated with chlorophyll b content. These four traits were normally distributed with transgressive segregation, suggesting that they were controlled by multiple minor genes. A total of 11 QTLs were detected for the four traits and they lay on six chromosomes. Each of them explained 9.2%-19.6% of the phenotypic variations, respectively. Of these, two QTLs controlling chlorophyll a content were mapped on chromosomes 2 and 5; four QTLs underlying chlorophyll b content were mapped on chromosomes 2, 3, 5 and 9; three QTLs underlying chlorophyll a+b amount were mapped on chromosomes 3, 5 and 9; two QTLs under-lying chlorophyll a/b ratio were mapped on chromosomes 6 and 1 1. The intrinsic relationship among the four traits and the practical implication in rice breeding are discussed.

  6. Quantitative trait loci associated with murine central corneal thickness

    Lively, Geoffrey D.; Koehn, Demelza; Hedberg-Buenz, Adam; Wang, Kai; Anderson, Michael G.

    2010-01-01

    The cornea is a specialized transparent tissue responsible for refracting light, serving as a protective barrier, and lending structural support to eye shape. Given its importance, the cornea exhibits a surprising amount of phenotypic variability in some traits, including central corneal thickness (CCT). More than a mere anatomic curiosity, differences in CCT have recently been associated with risk for glaucoma. Although multiple lines of evidence support a strong role for heredity in regulat...

  7. Multienvironment Quantitative Trait Loci Analysis for Photosynthate Acquisition, Accumulation, and Remobilization Traits in Common Bean Under Drought Stress

    Asfaw, A.; Blair, M. W.; Struik, P.C.

    2012-01-01

    Many of the world’s common bean (Phaseolus vulgaris L.) growing regions are prone to either intermittent or terminal drought stress, making drought the primary cause of yield loss under farmers’ field conditions. Improved photosynthate acquisition, accumulation, and then remobilization have been observed as important mechanisms for adaptation to drought stress. The objective of this study was to tag quantitative trait loci (QTL) for photosynthate acquisition, accumulation, and remobilization ...

  8. Pleiotropy analysis of quantitative traits at gene level by multivariate functional linear models.

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

    2015-05-01

    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 tests based on Pillai-Bartlett trace, Hotelling-Lawley trace, and Wilks's Lambda are introduced to test for association between multiple quantitative traits and multiple genetic variants in one genetic region. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and optimal sequence kernel association test (SKAT-O). Extensive simulations were performed to evaluate the false positive rates and power performance of the proposed models and tests. We show that the approximate F-distribution tests control the type I error rates very well. Overall, simultaneous analysis of multiple traits can increase power performance compared to an individual test of each trait. The proposed methods were applied to analyze (1) four lipid traits in eight European cohorts, and (2) three biochemical traits in the Trinity Students Study. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and SKAT-O for the three biochemical traits. The approximate F-distribution tests of the proposed functional linear models are more sensitive than those of the traditional multivariate linear models that in turn are more sensitive than SKAT-O in the univariate case. The analysis of the four lipid traits and the three biochemical traits detects more association than SKAT-O in the univariate case. PMID:25809955

  9. An improved procedure of mapping a quantitative trait locus via the EM algorithm using posterior probabilities

    Saurabh Ghosh; Partha P. Majumder

    2000-08-01

    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 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 complications in estimating for a quantitative trait in humans is the lack of haplotype information on members of families. We have devised a computationally simple two-stage method of estimation of in the absence of haplotypic information using the expectation-maximization (EM) algorithm. In the first stage, parameters of the quantitative trait locus (QTL) are estimated on the basis of 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 EM algorithm for obtaining the maximum-likelihood estimate of based on data of informative families (which are identified upon inferring parental QTL genotypes performed in the first stage). The purpose of this paper is to investigate whether, instead of using genotypically `classified' data of parents, the use of posterior probabilities of QT genotypes of parents at the second stage yields better estimators. We show, using simulated data, that the proposed procedure using posterior probabilities is statistically more efficient than our earlier classification procedure, although it is computationally heavier.

  10. Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken.

    Johnsson, Martin; Jonsson, Kenneth B; Andersson, Leif; Jensen, Per; Wright, Dominic

    2015-01-01

    Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. Overlaps between egg loci and expression loci, and trait-gene expression correlations identify 29 candidates from bone and five from hypothalamus. The candidate quantitative trait genes include fibroblast growth factor 1, and mitochondrial ribosomal proteins L42 and L32. In summary, we found putative quantitative trait genes for egg traits in the chicken that may have been affected by regulatory variants under chicken domestication. These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species. PMID:26637433

  11. Quantitative trait loci analysis for rice seed vigor during the germination stage*

    Wang, Zhou-fei; Wang, Jian-Fei; Bao, Yong-Mei; Wang, Fu-hua; Zhang, Hong-Sheng

    2010-01-01

    Seed vigor is an important characteristic of seed quality, and rice cultivars with strong seed vigor are desirable in direct-sowing rice production for optimum stand establishment. In the present study, the quantitative trait loci (QTLs) of three traits for rice seed vigor during the germination stage, including germination rate, final germination percentage, and germination index, were investigated using one recombinant inbred line (RIL) population derived from a cross between japonica Dagua...

  12. A Statistical Variance Components Framework for Mapping Imprinted Quantitative Trait Locus in Experimental Crosses

    Yuehua Cui; Gengxin Li

    2009-01-01

    Current methods for mapping imprinted quantitative trait locus (iQTL) with inbred line crosses assume fixed QTL effects. When an iQTL segregates in experimental line crosses, combining different line crosses with similar genetic background can improve the accuracy of iQTLs inference. In this article, we develop a general interval-based statistical variance components framework to map iQTLs underlying complex traits by combining different backcross line crosses. We propose a new iQTL variance ...

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

    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 w...

  14. Mapping of Imprinted Quantitative Trait Loci Using Immortalized F2 Populations

    Wen, Yongxian; Wu, Weiren

    2014-01-01

    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 map...

  15. Extended multipoint identity-by-descent analysis of human quantitative traits: efficiency, power, and modeling considerations.

    Schork, N J

    1993-01-01

    Goldgar introduced a novel marker-based method for partitioning the variation of a quantitative trait into specific chromosomal regions. Unlike traditional linkage mapping methods, Goldgar's method does not require the estimation of statistical quantities characterizing each locus thought to influence the trait under scrutiny (e.g., allele frequencies, penetrances, etc.). Goldgar's method is thus more flexible and less model dependent than many traditional marker-based genetic analysis techni...

  16. Quantitation of Vacuolar Sugar Transporter Abundance Changes Using QconCAT Synthtetic Peptides

    Pertl-Obermeyer, Heidi; Trentmann, Oliver; Duscha, Kerstin; Neuhaus, H. Ekkehard; Schulze, Waltraud X.

    2016-01-01

    Measurements of protein abundance changes are important for biological conclusions on protein-related processes such as activity or complex formation. Proteomic analyses in general are almost routine tasks in many laboratories, but a precise and quantitative description of (absolute) protein abundance changes require careful experimental design and precise data quality. Today, a vast choice of metabolic labeling and label-free quantitation protocols are available, but the trade-off between quantitative precision and proteome coverage of quantified proteins including missing value problems remain. Here, we provide an example of a targeted proteomic approach using artificial standard proteins consisting of concatenated peptides of interest (QconCAT) to specifically quantify abiotic stress-induced abundance changes in low abundant vacuolar transporters. An advantage of this approach is the reliable quantitation of alimited set of low-abundant target proteins throughout different conditions. We show that vacuolar ATPase AVP1 and sugar transporters of the ERDL (early responsive to dehydration-like) family and TMT2 (tonoplast monosaccharide transporter 2) showed increased abundance upon salt stress. PMID:27148277

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

    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...... linked QTL, each affecting one trait; or one QTL affecting a single trait. A QTL affecting CM was fine-mapped. In FA, a haplotype having a strong association with a high negative effect on mastitis resistance was identified. The mapping precision of an earlier detected SCS-QTL was not improved by the...

  18. Study on mapping Quantitative Trait Loci for animal complex binary traits using Bayesian-Markov chain Monte Carlo approach

    LIU; Jianfeng; ZHANG; Yuan; ZHANG; Qin; WANG; Lixian; ZHANG; Jigang

    2006-01-01

    It is a challenging issue to map Quantitative Trait Loci (QTL) underlying complex discrete traits, which usually show discontinuous distribution and less information, using conventional statistical methods. Bayesian-Markov chain Monte Carlo (Bayesian-MCMC) approach is the key procedure in mapping QTL for complex binary traits, which provides a complete posterior distribution for QTL parameters using all prior information. As a consequence, Bayesian estimates of all interested variables can be obtained straightforwardly basing on their posterior samples simulated by the MCMC algorithm. In our study, utilities of Bayesian-MCMC are demonstrated using simulated several animal outbred full-sib families with different family structures for a complex binary trait underlied by both a QTL and polygene. Under the Identity-by-Descent-Based variance component random model, three samplers basing on MCMC, including Gibbs sampling, Metropolis algorithm and reversible jump MCMC, were implemented to generate the joint posterior distribution of all unknowns so that the QTL parameters were obtained by Bayesian statistical inferring. The results showed that Bayesian-MCMC approach could work well and robust under different family structures and QTL effects. As family size increases and the number of family decreases, the accuracy of the parameter estimates will be improved. When the true QTL has a small effect, using outbred population experiment design with large family size is the optimal mapping strategy.

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

    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.

  20. Ecological effects of cell-level processes: genome size, functional traits and regional abundance of herbaceous plant species

    Herben, Tomáš; Suda, Jan; Klimešová, Jitka; Mihulka, Stanislav; Říha, Pavel; Šímová, Irena

    2012-01-01

    Background and Aims Genome size is known to be correlated with a number of phenotypic traits associated with cell sizes and cell-division rates. Genome size was therefore used as a proxy for them in order to assess how common plant traits such as height, specific leaf area and seed size/number predict species regional abundance. In this study it is hypothesized that if there is residual correlation between genome size and abundance after these traits are partialled out, there must be additional ecological effects of cell size and/or cell-division rate. Methods Variation in genome size, plant traits and regional abundance were examined in 436 herbaceous species of central European flora, and relationships were sought for among these variables by correlation and path analysis. Key Results Species regional abundance was weakly but significantly correlated with genome size; the relationship was stronger for annuals (R2 = 0·145) than for perennials (R2 = 0·027). In annuals, genome size was linked to abundance via its effect on seed size, which constrains seed number and hence population growth rate. In perennials, it weakly affected (via height and specific leaf area) competitive ability. These relationships did not change qualitatively after phylogenetic correction. In both annuals and perennials there was an unresolved effect of genome size on abundance. Conclusions The findings indicate that additional predictors of regional abundance should be sought among variables that are linked to cell size and cell-division rate. Signals of these cell-level processes remain identifiable even at the landscape scale, and show deep differences between perennials and annuals. Plant population biology could thus possibly benefit from more systematic use of indicators of cell-level processes. PMID:22628380

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

    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.

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

    Thomson, Peter C

    2003-01-01

    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. PMID:12729549

  3. Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken

    Martin Johnsson

    2016-02-01

    Full Text Available Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. Overlaps between egg loci and expression loci, and trait–gene expression correlations identify 29 candidates from bone and five from hypothalamus. The candidate quantitative trait genes include fibroblast growth factor 1, and mitochondrial ribosomal proteins L42 and L32. In summary, we found putative quantitative trait genes for egg traits in the chicken that may have been affected by regulatory variants under chicken domestication. These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species.

  4. Major Gene Identiifcation and Quantitative Trait Locus Mapping for Yield-Related Traits in Upland Cotton (Gossypium hirsutum L.)

    XIA Zhe; ZHANG Xin; LIU Yang-yang; JIA Zi-fang; ZHAO Hai-hong; LI Cheng-qi; WANG Qing-lian

    2014-01-01

    Segregation analysis of the mixed genetic model of major gene plus polygene was used to identify the major genesfor cotton yield-related traits using six generations P1, P2, F1, B1, B2, and F2 generated from the cross of Baimian 1×TM-1. In addition to boll size and seed index, the major genes for the other ifve traits were detected:one each for seed yield, lint percentage, boll number, lint index; and two for lint yield. Quantitative trait locus/loci (QTL) mapping was performed in the F2 and F2:3 populations of above cross through molecular marker technology, and a total of 50 QTL (26 suggestive and 24 signiifcant) for yield-related traits were detected. Four common QTL were discovered: qLP-3b(F2)/qLP-3(F2:3)andqLP-19b (F2)/qLP-19(F2:3) for lint percentage, qBN-17(F2)/qBN-17(F2:3)for boll number, and qBS-26b(F2)/qBS-26(F2:3) for boll size. Especially, qLP-3b(F2)/qLP-3(F2:3), not only had LOD scores>3 but also exceeded the permutation threshold (5.13 and 5.29, respectively), correspondingly explaining 23.47 and 29.55% of phenotypic variation. This QTL should be considered preferentially in marker assisted selection (MAS). Segregation analysis and QTL mapping could mutually complement and verify, which provides a theoretical basis for genetic improvement of cotton yield-related traits by using major genes (QTL).

  5. Quantitative trait loci associated with constitutive traits control water use in pearl millet [Pennisetum glaucum (L.) R. Br].

    Aparna, K; Nepolean, T; Srivastsava, R K; Kholová, J; Rajaram, V; Kumar, S; Rekha, B; Senthilvel, S; Hash, C T; Vadez, V

    2015-09-01

    There is substantial genetic variation for drought adaption in pearl millet in terms of traits controlling plant water use. It is important to understand genomic regions responsible for these traits. Here, F7 recombinant inbred lines were used to identify quantitative trait loci (QTL) and allelic interactions for traits affecting plant water use, and their relevance is discussed for crop productivity in water-limited environments. Four QTL contributed to increased transpiration rate under high vapour pressure deficit (VPD) conditions, all with alleles from drought-sensitive parent ICMB 841. Of these four QTL, a major QTL (35.7%) was mapped on linkage group (LG) 6. The alleles for 863B at this QTL decreased transpiration rate and this QTL co-mapped to a previously detected LG 6 QTL, with alleles from 863B for grain weight and panicle harvest index across severe terminal drought stress environments. This provided additional support for a link between water saving from a lower transpiration rate under high VPD and drought tolerance. 863B alleles in this same genomic region also increased shoot weight, leaf area and total transpiration under well-watered conditions. One unexpected outcome was reduced transpiration under high VPD (15%) from the interaction of two alleles for high VPD transpiration (LG 6 (B), 40.7) and specific leaf mass and biomass (LG 7 (A), 35.3), (A, allele from ICMB 841, B, allele from 863B, marker position). The LG 6 QTL appears to combine alleles for growth potential, beneficial for non-stress conditions, and for saving water under high evaporative demand, beneficial under stressful conditions. Mapping QTL for water-use traits, and assessing their interactions offers considerable potential for improving pearl millet adaptation to specific stress conditions through physiology-informed marker-assisted selection. PMID:25946470

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

    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.

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

    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.

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

    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...

  9. Novel Statistical Methods in Quantitative Genetics : Modeling Genetic Variance for Quantitative Trait Loci Mapping and Genomic Evaluation

    Shen, Xia

    2012-01-01

    This thesis develops and evaluates statistical methods for different types of genetic analyses, including quantitative trait loci (QTL) analysis, genome-wide association study (GWAS), and genomic evaluation. The main contribution of the thesis is to provide novel insights in modeling genetic variance, especially via random effects models. In variance component QTL analysis, a full likelihood model accounting for uncertainty in the identity-by-descent (IBD) matrix was developed. It was found t...

  10. Validation and Estimation of Additive Genetic Variation Associated with DNA Tests for Quantitative Beef Cattle Traits

    The U.S. National Beef Cattle Evaluation Consortium (NBCEC) has been involved in the validation of commercial DNA tests for quantitative beef quality traits since their first appearance on the U.S. market in the early 2000s. The NBCEC Advisory Council initially requested that the NBCEC set up a syst...

  11. #602025 BODY MASS INDEX QUANTITATIVE TRAIT LOCUS 9; BMIQ9 [OMIM

    Full Text Available FIELD NO 602025 FIELD TI #602025 BODY MASS INDEX QUANTITATIVE TRAIT LOCUS 9; BMIQ9 ;;OBESITY, SU ... North American adults (889 severely obese and 932 lean ... controls) from 2 cohorts, and did not find an asso ... of MC3R in 839 severely obese individuals and 967 lean ... controls of French or Italian origin and performed ...

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

    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…

  13. Association of single nucleotide polymorphisms in candidate genes residing under quantitative trait loci in beef cattle

    The objective was to assess the association of single nucleotide polymorphisms (SNP) developed on candidate genes residing under previously identified quantitative trait loci for marbling score and meat tenderness. Two hundred five SNP were identified on twenty candidate genes. Genes selected under ...

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

    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.

    2013-01-01

    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 CBS6

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

    Lam Mary K; Hobbs Matthew; McGill David; Jonas Elisabeth; Raadsma Herman W; Thomson Peter C

    2009-01-01

    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 ...

  16. Quantitative and In-Depth Survey of the Isotopic Abundance Distribution Errors in Shotgun Proteomics.

    Chang, Cheng; Zhang, Jiyang; Xu, Changming; Zhao, Yan; Ma, Jie; Chen, Tao; He, Fuchu; Xie, Hongwei; Zhu, Yunping

    2016-07-01

    Accuracy is an important metric when mass spectrometry (MS) is used in large-scale quantitative proteomics research. For MS-based quantification by extracting ion chromatogram (XIC), both the mass and intensity dimensions must be accurate. Although much research has focused on mass accuracy in recent years, less attention has been paid to intensity errors. Here, we investigated signal intensity measurement errors systematically and quantitatively using the natural properties of isotopic distributions. First, we defined a normalized isotopic abundance error model and presented its merits and demerits. Second, a comprehensive survey of the isotopic abundance errors using data sets with increasing sample complexities and concentrations was performed. We examined parameters such as error distribution, relationships between signal intensities within one isotopic cluster, and correlations between different peak errors in isotopic profiles. Our data demonstrated that the high resolution MS platforms might also generate large isotopic intensity measurement errors (approximately 20%). Meanwhile, this error can be reduced to less than 5% using a novel correction algorithm, which is based on the theoretical isotopic abundance distribution. Finally, a nonlinear relationship was observed as the abundance error decreased in isotopic profiles with higher intensity. Our findings are expected to provide insight into isotopic abundance recalibration in quantitative proteomics. PMID:27266261

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

    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

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

    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.

  19. 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

    2011-08-01

    The thousand-grain weight and spikelets per panicle directly contribute to rice yield. Heading date and plant height also greatly influence the yield. Dissection of genetic bases of yield-related traits would provide tools for yield improvement. In this study, quantitative trait loci (QTL) mapping for spikelets per panicle, thousand-grain weight, heading date and plant height was performed using recombinant inbred lines derived from a cross between two diverse cultivars, Nanyangzhan and Chuan7. In total, 20 QTLs were identified for four traits. They were located to 11 chromosomes except on chromosome 4. Seven and five QTLs were detected for thousand-grain weight and spikelets per panicle, respectively. Four QTLs were identified for both heading date and plant height. About half the QTLs were commonly detected in both years, 2006 and 2007. Six QTLs are being reported for the first time. Two QTL clusters were identified in regions flanked by RM22065 and RM5720 on chromosome 7 and by RM502 and RM264 on chromosome 8, respectively. The parent, Nanyangzhan with heavy thousand-grain weight, carried alleles with increased effects on all seven thousand-grain weight QTL, which explained why there was no transgressive segregation for thousand-grain weight in the population. In contrast, Chuan7 with more spikelets per panicle carried positive alleles at all five spikelets per panicle QTL except qspp5. Further work on distinction between pleiotropic QTL and linked QTL is needed in two yield-related QTL clusters.

  20. Quantitative trait locus mapping and functional genomics of an organophosphate resistance trait in the western corn rootworm, Diabrotica virgifera virgifera.

    Coates, B S; Alves, A P; Wang, H; Zhou, X; Nowatzki, T; Chen, H; Rangasamy, M; Robertson, H M; Whitfield, C W; Walden, K K; Kachman, S D; French, B W; Meinke, L J; Hawthorne, D; Abel, C A; Sappington, T W; Siegfried, B D; Miller, N J

    2016-02-01

    The western corn rootworm, Diabrotica virgifera virgifera, is an insect pest of corn and population suppression with chemical insecticides is an important management tool. Traits conferring organophosphate insecticide resistance have increased in frequency amongst D. v. virgifera populations, resulting in the reduced efficacy in many corn-growing regions of the USA. We used comparative functional genomic and quantitative trait locus (QTL) mapping approaches to investigate the genetic basis of D. v. virgifera resistance to the organophosphate methyl-parathion. RNA from adult methyl-parathion resistant and susceptible adults was hybridized to 8331 microarray probes. The results predicted that 11 transcripts were significantly up-regulated in resistant phenotypes, with the most significant (fold increases ≥ 2.43) being an α-esterase-like transcript. Differential expression was validated only for the α-esterase (ST020027A20C03), with 11- to 13-fold greater expression in methyl-parathion resistant adults (P resistance trait were obtained from a reciprocal backcross design. QTL analyses of high-throughput single nucleotide polymorphism genotype data predicted involvement of a single genome interval. These data suggest that a specific carboyxesterase may function in field-evolved corn rootworm resistance to organophosphates, even though direct linkage between the QTL and this locus could not be established. PMID:26566705

  1. Restricted maximum likelihood analysis of linkage between genetic markers and quantitative trait loci for a granddaughter design.

    Arendonk, van J.A.M.; Tier, B.; Bink, M.C.A.M.; Bovenhuis, H.

    1998-01-01

    REML for the estimation of location and variance of a single quantitative trait locus, together with polygenic and residual variance, is described for the analysis of a granddaughter design. The method is based on a mixed linear model that includes the allelic effects of the quantitative trait locus

  2. Mapping Quantitative Trait Loci From a Single-Tail Sample of the Phenotype Distribution Including Survival Data

    Sillanpää, Mikko J.; Hoti, Fabian

    2007-01-01

    A new effective Bayesian quantitative trait locus (QTL) mapping approach for the analysis of single-tail selected samples of the phenotype distribution is presented. The approach extends the affected-only tests to single-tail sampling with quantitative traits such as the log-normal survival time or censored/selected traits. A great benefit of the approach is that it enables the utilization of multiple-QTL models, is easy to incorporate into different data designs (experimental and outbred pop...

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

    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.

  4. Quantitative trait locus analysis of lateral branch-related traits in cucumber (Cucumis sativus L.) using recombinant inbred lines

    2008-01-01

    A group of 224 recombinant inbred lines (RILs) was derived from a narrow cross between 2 cucumber (Cucumis sativus L.) lines, namely, S94 (Northern China type with weak lateral branch growth potential and early lateral branch sprouting time) and S06 (Northern European type with strong lateral branch growth potential and late lateral branch sprouting time). These lines were then used for investigating lateral branch-related traits. A total of 36 quantitative trait loci (QTLs) were detected for the following 4 lateral branch-related traits: lateral branch average length (LBAL), lateral branch total length (LBTL), lateral branch number (LBN), and first lateral branch node (FLBN). Further, each QTL explained 3.1% (lbtl2.1, spring) to 32.3% (lbn2.3, spring) of the observed phenotypic variance. Eleven QTLs (lbal1.1, lbtl1.1, lbn1.2, flbn1.2, etc.) for different traits were found to be clustered on the e23m18d-ME23EM6c section (7.4 cM) of linkage group (LG) 1; further, 15 QTLs (lbal2.1, lbtl2.1, lbn2.1, flbn2.1, etc.) were found to be clustered on the S94A1-ME4SA4a section (13.9 cM) of LG2. Twenty-one QTLs explained more than 10% of the phenotypic variance. Moreover, lbtl1.3 (autumn, 26.2%, logarithm of odds (LOD) = 17.4; spring, 26.9%, LOD = 17.9) had stable position and contribution in both seasons. Several se-quence-anchor markers (CMBR40, F, CS30, S94A1, CSWTA11B, etc.) were closely linked with some QTLs for LBAL, LBTL, LBN, and FLBN, which can be used for the marker-assisted selection to improve the plant architecture in cucumber breeding.

  5. Quantitative trait locus analysis of lateral branchrelated traits in cucumber (Cucumis sativus L.) using recombinant inbred lines

    JIANG Su; YUAN XiaoJun; PAN JunSong; HE HuanLe; CAI Run

    2008-01-01

    A group of 224 recombinant inbred lines (RILs) was derived from a narrow cross between 2 cucumber (Cucumis sativus L.) lines, namely, S94 (Northern China type with weak lateral branch growth potential and early lateral branch sprouting time) and S06 (Northern European type with strong lateral branch growth potential and late lateral branch sprouting time). These lines were then used for investigating lateral branch-related traits. A total of 36 quantitative trait loci (QTLs) were detected for the following 4 lateral branch-related traits: lateral branch average length (LBAL), lateral branch total length (LBTL), lateral branch number (LBN), and first lateral branch node (FLBN). Further, each QTL explained 3.1% (Ibtl 2.1, spring) to 32.3% (Ibn2.3, spring) of the observed phenotypic variance. Eleven QTLs (Ibal1.1, Ibtl 1.1, Ibn1.2, fIbn1.2, etc.) for different traits were found to be clustered on the e23m18d-ME23EM6c section (7.4 cM) of linkage group (LG) 1; further, 15 QTLs (Ibal 2.1, Ibtl 2.1, Ibn 2.1, flbn 2.1, etc.)were found to be clustered on the S94A1-ME4SA4a section (13.9 cM) of LG2. Twenty-one QTLs explained more than 10% of the phenotypic variance. Moreover, Ibtl 1.3 (autumn, 26.2%, logarithm of odds (LOD)= 17.4; spring, 26,9%, LOD=17.9) had stable position and contribution in both seasons. Several se-quence-anchor markers (CMBR40, F, CS30, S94A1, CSWTA11B, etc.) were closely linked with some QTLs for LBAL, LBTL, LBN, and FLBN, which can be used for the marker-assisted selection to improve the plant architecture in cucumber breeding.

  6. Investigations on abundance and activity of microbial sponge symbionts using quantitative real - time PCR

    Kumala, Lars; Hentschel, Ute; Bayer, Kristina

    the host. Of particular interest is determining the community structure and function of microbial symbionts in order to gain deeper insight into host-symbiont interactions. We investigated the abundance and activity of microbial symbionts in two Mediterranean sponge species using quantitative real-time PCR...... aerophoba. Absolute quantification of archaeal amoA-genes provided evidence of highly abundant ammonia-oxidizing archaea (AOA) in both HMA and LMA sponge species. Interestingly, detected amoA-transcripts indicated the activity of AOA only in the HMA representative. The variable abundance of AOA in chimneys......Marine sponges are hosts to dense and diverse microbial consortia that are likely to play a key role in the metabolic processes of the host sponge due to their enormous abundance. Common symbioses between nitrogen transforming microorganisms and sponges indicate complex nitrogen cycling within...

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

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

    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 parental-asymmetry tests Q-PAT() with any constant 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 parental-asymmetry tests Q-PPAT() with any constant 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() 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() are robust to population stratification. In addition, the power comparison demonstrates that Q-PPAT() and Q-MCPPAT() for pedigree data are much more powerful than Q-PAT() only using two-generation nuclear families selected from extended pedigrees.

  8. Ecophysiological Traits May Explain the Abundance of Climbing Plant Species across the Light Gradient in a Temperate Rainforest

    Gianoli, Ernesto; Saldaña, Alfredo; Jiménez-Castillo, Mylthon

    2012-01-01

    Climbing plants are a key component of rainforests, but mechanistic approaches to their distribution and abundance are scarce. In a southern temperate rainforest, we addressed whether the dominance of climbing plants across light environments is associated with the expression of ecophysiological traits. In mature forest and canopy gaps, we measured leaf size, specific leaf area, photosynthetic rate, and dark respiration in six of the most abundant woody vines. Mean values of traits and their phenotypic change (%) between mature forest and canopy gaps were predictor variables. Leaf size and specific leaf area were not significantly associated with climbing plant dominance. Variation in gas-exchange traits between mature forest and canopy gaps explained, at least partly, the dominance of climbers in this forest. A greater increase in photosynthetic rate and a lower increase in dark respiration rate when canopy openings occur were related to the success of climbing plant species. Dominant climbers showed a strategy of maximizing exploitation of resource availability but minimizing metabolic costs. Results may reflect phenotypic plasticity or genetic differentiation in ecophysiological traits between light environments. It is suggested that the dominant climbers in this temperate rainforest would be able to cope with forest clearings due to human activities. PMID:22685611

  9. Quantitative trait gene Slit2 positively regulates murine hematopoietic stem cell numbers

    Waterstrat, Amanda; Rector, Kyle; Geiger, Hartmut; Liang, Ying

    2016-01-01

    Hematopoietic stem cells (HSC) demonstrate natural variation in number and function. The genetic factors responsible for the variations (or quantitative traits) are largely unknown. We previously identified a gene whose differential expression underlies the natural variation of HSC numbers in C57BL/6 (B6) and DBA/2 (D2) mice. We now report the finding of another gene, Slit2, on chromosome 5 that also accounts for variation in HSC number. In reciprocal chromosome 5 congenic mice, introgressed D2 alleles increased HSC numbers, whereas B6 alleles had the opposite effect. Using gene array and quantitative polymerase chain reaction, we identified Slit2 as a quantitative trait gene whose expression was positively correlated with the number of HSCs. Ectopic expression of Slit2 not only increased the number of the long-term colony forming HSCs, but also enhanced their repopulation capacity upon transplantation. Therefore, Slit2 is a novel quantitative trait gene and a positive regulator of the number and function of murine HSCs. This finding suggests that Slit2 may be a potential therapeutic target for the effective in vitro and in vivo expansion of HSCs without compromising normal hematopoiesis. PMID:27503415

  10. Quantitative trait gene Slit2 positively regulates murine hematopoietic stem cell numbers.

    Waterstrat, Amanda; Rector, Kyle; Geiger, Hartmut; Liang, Ying

    2016-01-01

    Hematopoietic stem cells (HSC) demonstrate natural variation in number and function. The genetic factors responsible for the variations (or quantitative traits) are largely unknown. We previously identified a gene whose differential expression underlies the natural variation of HSC numbers in C57BL/6 (B6) and DBA/2 (D2) mice. We now report the finding of another gene, Slit2, on chromosome 5 that also accounts for variation in HSC number. In reciprocal chromosome 5 congenic mice, introgressed D2 alleles increased HSC numbers, whereas B6 alleles had the opposite effect. Using gene array and quantitative polymerase chain reaction, we identified Slit2 as a quantitative trait gene whose expression was positively correlated with the number of HSCs. Ectopic expression of Slit2 not only increased the number of the long-term colony forming HSCs, but also enhanced their repopulation capacity upon transplantation. Therefore, Slit2 is a novel quantitative trait gene and a positive regulator of the number and function of murine HSCs. This finding suggests that Slit2 may be a potential therapeutic target for the effective in vitro and in vivo expansion of HSCs without compromising normal hematopoiesis. PMID:27503415

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

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

    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 high-yielding 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.

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

    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.

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

    Quampah Alfred; Hai Ying Liu; Hai Ming Xu; Jin Rong Li; Jian Guo Wu; Shui Jin Zhu; Chun Hai Shi

    2012-12-01

    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 knowledge of quantitative trait loci (QTLs) and the genetic effects related to oil content in both genomes could facilitate the improvement in its quality and quantity. 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 parents, HS46 and MARCABUCAG8US-1-88, were used to simultaneously locate QTLs for oil content in the embryo and maternal plant genomes. The four QTLs found to be associated with oil content in cottonseed were: qOC-18-1 on chromosome 18; qOC-LG-11 on linkage group 11; qOC-18-2 on chromosome 18; and qOC-22 on chromosome 22. At a high selection threshold of 0.05, there was strong evidence linking the QTLs above the oil content in cottonseed. Embryo additive and dominant effects from the tetraploid embryo genome, as well as maternal additive effects from the tetraploid maternal plant genome were found to be significant contributors to genetic variation in cottonseed oil content.

  14. Analysis of heterosis and quantitative trait loci for kernel shape related traits using triple testcross population in maize.

    Lu Jiang

    Full Text Available Kernel shape related traits (KSRTs have been shown to have important influences on grain yield. The previous studies that emphasize kernel length (KL and kernel width (KW lack a comprehensive evaluation of characters affecting kernel shape. In this study, materials of the basic generations (B73, Mo17, and B73 × Mo17, 82 intermated B73 × Mo17 (IBM individuals, and the corresponding triple testcross (TTC populations were used to evaluate heterosis, investigate correlations, and characterize the quantitative trait loci (QTL for six KSRTs: KL, KW, length to width ratio (LWR, perimeter length (PL, kernel area (KA, and circularity (CS. The results showed that the mid-parent heterosis (MPH for most of the KSRTs was moderate. The performance of KL, KW, PL, and KA exhibited significant positive correlation with heterozygosity but their Pearson's R values were low. Among KSRTs, the strongest significant correlation was found between PL and KA with R values was up to 0.964. In addition, KW, PL, KA, and CS were shown to be significant positive correlation with 100-kernel weight (HKW. 28 QTLs were detected for KSRTs in which nine were augmented additive, 13 were augmented dominant, and six were dominance × additive epistatic. The contribution of a single QTL to total phenotypic variation ranged from 2.1% to 32.9%. Furthermore, 19 additive × additive digenic epistatic interactions were detected for all KSRTs with the highest total R2 for KW (78.8%, and nine dominance × dominance digenic epistatic interactions detected for KL, LWR, and CS with the highest total R2 (55.3%. Among significant digenic interactions, most occurred between genomic regions not mapped with main-effect QTLs. These findings display the complexity of the genetic basis for KSRTs and enhance our understanding on heterosis of KSRTs from the quantitative genetic perspective.

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

    Geroldinger, Ludwig; Bürger, Reinhard

    2014-01-01

    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 c...

  16. Dynamic Quantitative Trait Locus Analysis of Seed Vigor at Three Maturity Stages in Rice

    Liu, Liangfeng; Lai, Yanyan; Cheng, Jinping; Wang, Ling; Du, Wenli; Wang, ZhouFei; Zhang, Hongsheng

    2014-01-01

    Seed vigor is an important characteristic of seed quality. In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of seed vigor, including the germination potential, germination rate, germination index and time for 50% of germination, at 4 (early), 5 (middle) and 6 weeks (late) after heading in two years. A total of 24 additive and 9 epistatic quantitative trait loci (QTL) for seed vigor were identified using QTL Cartographer an...

  17. Strategy for Mapping Quantitative Trait Loci (QTL) by Using Human Metapopulations

    Rudan, I; Campbell, H.; Biloglav, Z.; Carothers, A D; Wright, A F

    2006-01-01

    AIM:To present a novel strategy for mapping quantitative trait loci (QTL), using human metapopulations. The strategy is based on the expectation that in geographic clusters of small and distinct human isolates, a combination of founder effect and genetic drift can dramatically increase population frequency of rare QTL variants with large effect. In such cases, the distribution of QT measurements in an (affected) isolate is expected to deviate from that observed in neighboring isolates.METHODS...

  18. %612729 LEAN BODY MASS QUANTITATIVE TRAIT LOCUS 1; LBMQTL1 [OMIM

    Full Text Available FIELD NO 612729 FIELD TI %612729 LEAN ... BODY MASS QUANTITATIVE TRAIT LOCUS 1; LBMQTL1 FIELD TX MAP ... bSNP rs7832552, were significantly associated with lean ... body mass (LBM; corrected p = 7.55 x 10(-8) and 7. ... n studies identified TRHR as an important gene for lean ... body mass. Am. J. Hum. Genet. 84: 418-423, 2009. F ...

  19. Multi-QTL Mapping for Quantitative Traits Using Epistatic Distorted Markers

    Xie, Shang-Qian; Wen, Jia; Zhang, Yuan-Ming

    2013-01-01

    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 ...

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

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

    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 ...

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

    Laura eToppino; Lorenzo eBarchi; Roberto eLo Scalzo; Eristanna ePalazzolo; Gianluca eFrancese; Marta eFibiani; Antonietta eD'Alessandro; Vincenza ePapa; Vito Armando Laudicina; Leo eSabatino; Laura ePulcini; Nazzareno eAcciarri; Ezio ePortis; Sergio eLanteri; Giuseppe eMennella

    2016-01-01

    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 th...

  2. Mapping Quantitative Trait Loci Affecting Biochemical and Morphological Fruit Properties in Eggplant (Solanum melongena L.)

    Toppino, Laura; Barchi, Lorenzo; Lo Scalzo, Roberto; Palazzolo, Eristanna; Francese, Gianluca; Fibiani, Marta; D'Alessandro, Antonietta; Papa, Vincenza; Laudicina, Vito A.; Leo SABATINO; Pulcini, Laura; Sala, Tea; Acciarri, Nazzareno; Portis, Ezio; Lanteri, Sergio

    2016-01-01

    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 th...

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

    Feenstra, Bjarke; Skovgaard, Ib M

    2004-01-01

    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 fro...

  4. Haplotype-sharing analysis for alcohol dependence based on quantitative traits and the Mantel statistic

    König Inke R; Franke Daniel; Kleensang Andre; Ziegler Andreas

    2005-01-01

    Abstract Haplotype-based methods have become increasingly popular in the last decade because shared lengths in haplotypes can be used for disease localization. In this contribution, we propose a novel linkage-based haplotype-sharing approach for quantitative traits based on the class of Mantel statistics which is closely related to the weighted pair-wise correlation statistic. Because these statistics are known to be liberal, we propose a permutation test to evaluate significance. We applied ...

  5. Advances in Statistical Methods to Map Quantitative Trait Loci in Outbred Populations

    Hoeschele, I.; Uimari, P; Grignola, F. E.; Q. Zhang; Gage, K. M.

    1997-01-01

    Statistical methods to map quantitative trait loci (QTL) in outbred populations are reviewed, extensions and applications to human and plant genetic data are indicated, and areas for further research are identified. Simple and computationally inexpensive methods include (multiple) linear regression of phenotype on marker genotypes and regression of squared phenotypic differences among relative pairs on estimated proportions of identity-by-descent at a locus. These methods are less suited for ...

  6. Quantitative candidate gene association studies of metabolic traits in Han Chinese type 2 diabetes patients.

    Wei, F J; Cai, C Y; Yu, P; Lv, J; Ling, C; Shi, W T; Jiao, H X; Chang, B C; Yang, F H; Tian, Y; Li, M S; Wang, Y H; Zou, L; Shi, J M; Chen, L M; Li, W D

    2015-01-01

    Recent genome-wide association studies have identified many loci associated with type 2 diabetes mellitus (T2DM), hyperuricemia, and obesity in various ethnic populations. However, quantitative traits have been less well investigated in Han Chinese T2DM populations. We investigated the association between candidate gene single nucleotide polymorphisms (SNPs) and metabolic syndrome-related quantitative traits in Han Chinese T2DM subjects. Unrelated Han Chinese T2DM patients (1975) were recruited. Eighty-six SNPs were genotyped and tested for association with quantitative traits including lipid profiles, blood pressure, body mass index (BMI), serum uric acid (SUA), glycated hemoglobin (HbA1c), plasma glucose [fasting plasma glucose (FPG)], plasma glucose 120 min post-OGTT (P2PG; OGTT = oral glucose tolerance test), and insulin resistance-related traits. We found that CAMTA1, ABI2, VHL, KAT2B, PKHD1, ESR1, TOX, SLC30A8, SFI1, and MYH9 polymorphisms were associated with HbA1c, FPG, and/or P2PG; GCK, HHEX, TCF7L2, KCNQ1, and TBX5 polymorphisms were associated with insulin resistance-related traits; ABCG2, SLC2A9, and PKHD1 polymorphisms were associated with SUA; CAMTA1, VHL, KAT2B, PON1, NUB1, SLITRK5, SMAD3, FTO, FANCA, and PCSK2 polymorphisms were associated with blood lipid traits; CAMTA1, SPAG16, TOX, KCNQ1, ACACB, and MYH9 polymorphisms were associated with blood pressure; and UBE2E3, SPAG16, SLC2A9, CDKAL1, CDKN2A/B, TCF7L2, SMAD3, and PNPLA3 polymorphisms were associated with BMI (all P values <0.05). Some of the candidate genes were associated with metabolic and anthropometric traits in T2DM in Han Chinese. Although none of these associations reached genome-wide significance (P < 5 x 10(-8)), genes and loci identified in this study are worthy of further replication and investigation. PMID:26634513

  7. Butterfly abundance is determined by food availability and is mediated by species traits

    Curtis, Robin J.; Brereton, Tom M.; Roger L H Dennis; Carbone, Chris; Isaac, Nick J. B.

    2015-01-01

    1. Understanding the drivers of population abundance across species and sites is crucial for effective conservation management. At present, we lack a framework for predicting which sites are likely to support abundant butterfly communities. 2. We address this problem by exploring the determinants of abundance among 1111 populations of butterflies in the UK, spanning 27 species on 54 sites. Our general hypothesis is that the availability of food resources is a strong predictor of population...

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

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

    2005-12-01

    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

  9. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations.

    Santure, Anna W; Poissant, Jocelyn; De Cauwer, Isabelle; van Oers, Kees; Robinson, Matthew R; Quinn, John L; Groenen, Martien A M; Visser, Marcel E; Sheldon, Ben C; Slate, Jon

    2015-12-01

    Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long-term studies across Europe and consequently are considered an ecological 'model organism'. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long-term study populations of great tits-one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population-specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population-specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free-living populations. PMID:26661500

  10. A genome scan for quantitative trait loci affecting growth-related traits in an F1 family of Asian seabass (Lates calcarifer)

    Yue Gen; Zhu Ze; Lo Loong; Wang Chun

    2006-01-01

    Abstract Background Body weight and length are economically important traits in foodfish species influenced by quantitative trait loci (QTL) and environmental factors. It is usually difficult to dissect the genetic and environmental effects. Asian seabass (Lates calcarifer) is an important marine foodfish species with a compact genome (~700 Mb). The recent construction of a first generation linkage map of Asian seabass with 240 microsatellites provides a good opportunity to determine the numb...

  11. Detection of quantitative trait loci on chromosomes 1,2,3,12,14,15, X in pigs: performance characteristics

    Paixao, D.M.; Carneiro, P.L.S.; Paiva, S.R.; Sousa, K.R.S.; Verardo, L.L.; Braccini Neto, J.; Pinto, A.P.G.; Marubayashi Hidalgo, A.; Nascimento, C.; Périssé, I.V.; Lopes, P.S.; Guimaraes, S.E.F.

    2013-01-01

    The accomplishment of the present study had the objective of mapping Quantitative Trait Loci (QTL) related to performance traits in a F2 pig population developed by mating two Brazilian Piau breed sires with 18 dams from a commercial line (Landrace × Large White × Pietrain). The linkage map for this

  12. Joint Analysis Method for Major Genes Controlling Multiple Correlated Quantitative Traits

    2006-01-01

    Based on the major gene and polygene mixed inheritance model for multiple correlated quantitative traits, the authors proposed a new joint segregation analysis method of major gene controlling multiple correlated quantitative traits, which include major gene detection and its effect and variation estimation. The effect and variation of major gene are estimated by the maximum likelihood method implemented via expectation-maximization (EM) algorithm. Major gene is tested with the likelihood ratio (LR) test statistic. Extensive simulation studies showed that joint analysis not only increases the statistical power of major gene detection but also improves the precision and accuracy of major gene effect estimates. An example of the plant height and the number of tiller of F2 population in rice cross Duonieai × Zhonghua 11 was used in the illustration. The results indicated that the genetic difference of these two traits in this cross refers to only one pleiotropic major gene. The additive effect and dominance effect of the major gene are estimated as -21.3 and 40.6 cm on plant height, and 22.7 and -25.3 on number of tiller, respectively. The major gene shows overdominance for plant height and close to complete dominance for number of tillers.

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

    Pengyuan Liu

    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.

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

    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 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. PMID:14731222

  15. Identification of quantitative trait loci associated with salt tolerance at seedling stage from Oryza rufipogon

    Lei Tian; Lubin Tan; Fengxia Liu; Hongwei Cai; Chuanqing Sun

    2011-01-01

    Soil salinity is one of the major abiotic stresses affecting plant growth and crop production.In the present study,salt tolerance at rice seedling stage was evaluated using 87 introgression lines (ILs),which were derived from a cross between an elite indica cultivar Teqing and an accession of common wild rice (Oryza rufipogon Griff.).Substantial variation was observed for four traits including salt tolerance score (STS),relative root dry weight (RRW),relative shoot dry weight (RSW) and relative total dry weight (RTW).STS was significantly positively correlated with all other three traits.A total of 15 putative quantitative trait loci (QTLs) associated with these four traits were detected using single-point analysis,which were located on chromosomes 1,2,3,6,7,9 and 10 with 8%-26% explaining the phenotypic variance.The O.rufipogon-derived alleles at 13 QTLs (86.7%) could improve the salt tolerance in the Teqing background.Four QTL clusters affecting RRW,RSW and RTW were found on chromosomes 6,7,9 and 10,respectively.Among these four QTL clusters,a major cluster including three QTLs (qRRW10,qRSW10 and qRTW10) was found near the maker RM271 on the long arm of chromosome 10,and the O.rufipogon-derived alleles at these three loci increased RRW,RSW and RTW with additive effects of 22.7%,17.3% and 18.5%,respectively,while the phenotypic variance explained by these three individual QTLs for the three traits varied from 19% to 26%.In addition,several salt tolerant ILs were selected and could be used for identifying and utilizing favorable salt tolerant genes from common wild rice and used in the salt tolerant rice breeding program.

  16. Mapping quantitative trait loci for T lymphocyte subpopulations in peripheral blood in swine

    Wang Zhi-Peng

    2011-09-01

    Full Text Available Abstract Background Increased disease resistance through improved general immune capacity would be beneficial for the welfare and productivity of farm animals. T lymphocyte subpopulations in peripheral blood play an important role in immune capacity and disease resistance in animals. However, very little research to date has focused on quantitative trait loci (QTL for T lymphocyte subpopulations in peripheral blood in swine. Results In the study, experimental animals consist of 446 piglets from three different breed populations. To identify QTL for T lymphocyte subpopulations in peripheral blood in swine, the proportions of CD4+, CD8+, CD4+CD8+, CD4+CD8-, CD4-CD8+, and CD4-CD8- T cells and the ratio of CD4+:CD8+ T cells were measured for all individuals before and after challenge with modified live CSF (classical swine fever vaccine. Based on the combined data of individuals from three breed populations, genome-wide scanning of QTL for these traits was performed based on a variance component model, and the genome wide significance level for declaring QTL was determined via permutation tests as well as FDR (false discovery rate correction. A total of 27 QTL (two for CD4+CD8+, one for CD4+CD8-, three for CD4-CD8+, two for CD4-CD8-, nine for CD4+, two for CD8+, and eight for CD4+:CD8+ ratio were identified with significance level of FDR FDR FDR Conclusions Within these QTL regions, a number of known genes having potential relationships with the studied traits may serve as candidate genes for these traits. Our findings herein are helpful for identification of the causal genes underlying these immune-related trait and selection for immune capacity of individuals in swine breeding in the future.

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

    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

  18. Application of an Effective Statistical Technique for an Accurate and Powerful Mining of Quantitative Trait Loci for Rice Aroma Trait.

    Farahnaz Sadat Golestan Hashemi

    Full Text Available When a phenotype of interest is associated with an external/internal covariate, covariate inclusion in quantitative trait loci (QTL analyses can diminish residual variation and subsequently enhance the ability of QTL detection. In the in vitro synthesis of 2-acetyl-1-pyrroline (2AP, the main fragrance compound in rice, the thermal processing during the Maillard-type reaction between proline and carbohydrate reduction produces a roasted, popcorn-like aroma. Hence, for the first time, we included the proline amino acid, an important precursor of 2AP, as a covariate in our QTL mapping analyses to precisely explore the genetic factors affecting natural variation for rice scent. Consequently, two QTLs were traced on chromosomes 4 and 8. They explained from 20% to 49% of the total aroma phenotypic variance. Additionally, by saturating the interval harboring the major QTL using gene-based primers, a putative allele of fgr (major genetic determinant of fragrance was mapped in the QTL on the 8th chromosome in the interval RM223-SCU015RM (1.63 cM. These loci supported previous studies of different accessions. Such QTLs can be widely used by breeders in crop improvement programs and for further fine mapping. Moreover, no previous studies and findings were found on simultaneous assessment of the relationship among 2AP, proline and fragrance QTLs. Therefore, our findings can help further our understanding of the metabolomic and genetic basis of 2AP biosynthesis in aromatic rice.

  19. Plastic Traits of an Exotic Grass Contribute to Its Abundance but Are Not Always Favourable

    Firn, Jennifer; Prober, Suzanne M.; Buckley, Yvonne M.

    2012-01-01

    In herbaceous ecosystems worldwide, biodiversity has been negatively impacted by changed grazing regimes and nutrient enrichment. Altered disturbance regimes are thought to favour invasive species that have a high phenotypic plasticity, although most studies measure plasticity under controlled conditions in the greenhouse and then assume plasticity is an advantage in the field. Here, we compare trait plasticity between three co-occurring, C4 perennial grass species, an invader Eragrostis curv...

  20. Detection and parameter estimation for quantitative trait loci using regression models and multiple markers

    Da, Yang; VanRaden, Paul; Schook, Lawrence

    2000-01-01

    International audience A strategy of multi-step minimal conditional regression analysis has been developed to determine the existence of statistical testing and parameter estimation for a quantitative trait locus (QTL) that are unaffected by linked QTLs. The estimation of marker-QTL recombination frequency needs to consider only three cases: 1) the chromosome has only one QTL, 2) one side of the target QTL has one or more QTLs, and 3) either side of the target QTL has one or more QTLs. Ana...

  1. Gamma ray and ems induced genetic variability for quantitative traits in urdbean (Vigna mungo l. Hepper)

    Range, mean and coefficient of variation for different characters in two cultivars, namely, PDUI and T9 of urdbean suggested that the mutagenic treatments had wider values than control. Positive and negative shifts in mean were observed for all the quantitative traits in both the cultivars. All the mutagenic treatments influenced the mean, range and CV values independently in both the varieties. However, the combination of varying doses of gamma rays with EMS (0.02 M) was found effective for causing induced genetic variability in urdbean cultivars

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

    Akiko Watanabe; Tomoko Toyota; Yuji Owada; Takeshi Hayashi; Yoshimi Iwayama; Miho Matsumata; Yuichi Ishitsuka; Akihiro Nakaya; Motoko Maekawa; Tetsuo Ohnishi; Ryoichi Arai; Katsuyasu Sakurai; Kazuo Yamada; Hisatake Kondo; Kenji Hashimoto

    2007-01-01

    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 ...

  3. A Genome Scan to Detect Quantitative Trait Loci for Economically Important Traits in Holstein Cattle Using Two Methods and a Dense Single Nucleotide Polymorphism Map

    Daetwyler, H.D.; Schenkel, F.S.; Sargolzaei, M.; Robinson, J.A.B.

    2008-01-01

    Genome scans for detection of bovine quantitative trait loci (QTL) were performed via variance component linkage analysis and linkage disequilibrium single-locus regression (LDRM). Four hundred eighty-four Holstein sires, of which 427 were from 10 grandsire families, were genotyped for 9,919 single

  4. Alternative models for detection of quantitative trait loci (QTL) for growth and carcass traits in pigs chromosomes 4, 5 and 7

    Moraes Gonçalves, de T.; Nunes de Oliveira, H.; Bovenhuis, H.; Bink, M.C.A.M.; Arendonk, van J.A.M.

    2005-01-01

    Genome scans can be used to identify chromosomal regions and eventually genes that control quantitative traits (QTL) of economic importance. In an experimental cross between Meishan (male) and Dutch Large White and Landrace lines (female), 298 F1 and 831 F2 animals were evaluated for intramuscular f

  5. Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

    Jin, Minliang; Liu, Haijun; He, Cheng; Fu, Junjie; Xiao, Yingjie; Wang, Yuebin; Xie, Weibo; Wang, Guoying; Yan, Jianbing

    2016-01-01

    Gene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. The ePAV was directly used as “genotype” to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes, and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding. PMID:26729541

  6. Genetic mapping of quantitative trait loci affecting susceptibility in chicken to develop pulmonary hypertension syndrome.

    Rabie, T S K M; Crooijmans, R P M A; Bovenhuis, H; Vereijken, A L J; Veenendaal, T; van der Poel, J J; Van Arendonk, J A M; Pakdel, A; Groenen, M A M

    2005-12-01

    Pulmonary hypertension syndrome (PHS), also referred to as ascites syndrome, is a growth-related disorder of chickens frequently observed in fast-growing broilers with insufficient pulmonary vascular capacity at low temperature and/or at high altitude. A cross between two genetically different broiler dam lines that originated from the White Plymouth Rock breed was used to produce a three-generation population. This population was used for the detection and localization of quantitative trait loci (QTL) affecting PHS-related traits. Ten full-sib families consisting of 456 G2 birds were typed with 420 microsatellite markers covering 24 autosomal chromosomes. Phenotypic observations were collected on 4202 G3 birds and a full-sib across family regression interval mapping approach was used to identify QTL. There was statistical evidence for QTL on chicken chromosome 2 (GGA2), GGA4 and GGA6. Suggestive QTL were found on chromosomes 5, 8, 10, 27 and 28. The most significant QTL were located on GGA2 for right and total ventricular weight as percentage of body weight (%RV and %TV respectively). A related trait, the ratio of right ventricular weight as percentage to total ventricular weight (RATIO), reached the suggestive threshold on this chromosome. All three QTL effects identified on GGA2 had their maximum test statistic in the region flanked by markers MCW0185 and MCW0245 (335-421 cM). PMID:16293119

  7. Quantitative trait loci analysis of individual and total isoflavone contents in soybean seeds

    Hai Jun Zhang; Jing Wen Li; Ya Jing Liu; Wen Zhu Jiang; Xing Lin Du; Lin Li; Xiao Wei Li; Lian Tai Su; Qing Yu Wang; Ying Wang

    2014-08-01

    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 contents (TIC) in soybean seeds. A population of 184 F2:10 recombinant inbred lines derived from a ‘Xiaoheidou’ × ‘GR8836’ cross was planted in pot and field conditions to evaluate soybean isoflavones. Twenty-one QTL were detected by composite interval mapping. Several QTL were associated with the traits for DC, GeC, GlC and TIC only. QDGeGlTIC4_1 and QDGlTIC12_1 are reported first in this study and were associated with the DC, GeC, GlC and TIC traits simultaneously. The QTL identified have potential value for marker-assisted selection to develop soybean varieties with desirable isoflavone content.

  8. The effect of habitat conditions on the abundance of populations and selected individual and floral traits of Impatiens glandulifera Royle

    Kostrakiewicz-Gierałt Kinga

    2015-03-01

    Full Text Available The effect of site conditions on the abundance of populations of I. glandulifera, selected individual features (height and width of stems, number of whorls and side branches, flower production, and floral traits (total length of flowers, length and width of lower sepal, spur length were investigated in years 2013-14. Observations were conducted on fallow land, at roadsides, along riverbanks and edges of a riparian forest as well as in a willow thicket and a riparian forest inside located in the Vistula River valley in southern Poland. In these stands, taken successively, light availability gradually diminished, while plant canopy height and soil moisture increased. The low abundance of the population on the fallow land may have been caused by low soil humidity triggering seedling mortality, whereas the low abundance in the interior of the riparian forest may have been due to seasonal water stagnation hampering the development of offspring. The increasing values of individual traits from the fallow land to riparian forest edge might be linked to growing lateral shade, whereas the much lower values in the willow thicket and forest interior might be caused by full shade. Individuals growing on the fallow land, at roadsides, and along riverbanksproduced flowers with small total lengths and large lower sepals and spurs, whereas individuals occurring in willow thickets and riparian forests showed opposite tendency. The considerable stem dimensions and substantial production of large flowers may augment chances for successful resource capture and pollinator visits in open sites, while the reduced size of individuals and moderate production of small flowers may be sufficient for the maintenance of populations in closed habitats

  9. Variation in Plant Traits Explains Global Biogeographic Variation in the Abundance of Major Forest Functional Types

    Wang, Y.

    2015-12-01

    Contrasting leaf types (needle vs. broadleaf) with different lifespans (annual vs. perennial) represent different adaptive strategies of plants under different environmental conditions. Previous studies explained adaptive advantages of different strategies using empirical models but cannot adequately explain the co-dominance of multiple plant functional types (PFTs) as observed in many parts of the world. Here we used a process-based model to explore whether observed inter- and intra-PFT variation in key plant traits can explain global biogeographic variation in co-dominance of major forest functional types. Using a parameter screening method, we identified the four most important plant traits for simulating annual net primary production (NPP) using the Australian Community Atmosphere-Biosphere-Land Exchange model (CABLE). Using ensemble CABLE simulations, we estimated the fraction of global land cover attributed to each PFT by comparing the simulated NPP for all three PFTs at each land point, globally. Our results were consistent with land area cover fractions of major forest types estimated from remote sensing data products; i.e., evergreen needle-leaf forests dominate in boreal regions, evergreen broadleaf forests dominate in tropical regions, and deciduous broadleaf forests are distributed widely across a broad range of environmental conditions. More importantly our approach successfully explained a paradox that has puzzled ecologists for over a century: why evergreen leaf types dominate in both boreal and tropical regions. We conclude that variation in and co-variation between key plant traits can explain significant fractions of global biogeographic variation of three major forest types, and should be taken into account when simulating global vegetation dynamics.

  10. Functional traits predict relationship between plant abundance dynamic and long-term climate warming

    Soudzilovskaia, Nadejda A; Elumeeva, Tatiana G.; Onipchenko, Vladimir G.; Shidakov, Islam I.; Salpagarova, Fatima S.; Khubiev, Anzor B.; Tekeev, Dzhamal K.; Cornelissen, Johannes H. C.

    2013-01-01

    Although the response of the Plant Kingdom to climate change is acknowledged as one of the fundamental feedback mechanisms of environmental changes on the Earth, until now, the response of plant species to in situ climate warming has been described at the level of a few fixed plant functional types (i.e. grasses, forbs, shrubs etc.). This approach is very coarse and inflexible. Here, we show that plant functional traits (i.e., plant features) can be used as predictors of vegetation response t...

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

    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

  12. Quantitative Trait Loci for Resistance to Stripe Disease in Rice (Oryza sativa)

    2007-01-01

    In order to map the quantitative trait loci for rice stripe resistance, a molecular linkage map was constructed based on the lines to rice stripe were investigated by both artificial inoculation at laboratory and natural infection in the field, and the ratios of ranged from 0 to 134.08 and from 6.25 to 133.6 under artificial inoculation at laboratory and natural infection in the field, respectively,and showed a marked bias towards resistant parent (Zhaiyeqing 8), indicating that the resistance to rice stripe was controlled by quantitative trait loci (QTL). QTL analysis showed that the QTLs detected by the two inoculation methods were completely different.Only one QTL, qSTV7, was detected under artificial inoculation, at which the Zhaiyeqing 8 allele increased the resistance to rice stripe, while two QTLs, qSTV5 and qSTV1, were detected under natural infection, in which resistant alleles came from Zhaiyeqing 8and Wuyujing 3, respectively. These results showed that resistant parent Zhaiyeqing 8 carried the alleles associated with the resistance to rice stripe virus and the small brown planthopper, and susceptible parent Wuyujing 3 also carried the resistant allele to rice stripe virus. In comparison with the results previously reported, QTLs detected in the study were new resistant genes to rice stripe disease. This will provide a new resistant resource for avoiding genetic vulnerability for single utilization of the resistant gene Stvb-i.

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

    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.

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

    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.

  15. Mapping Quantitative Trait Loci Affecting Biochemical and Morphological Fruit Properties in Eggplant (Solanum melongena L.).

    Toppino, Laura; Barchi, Lorenzo; Lo Scalzo, Roberto; Palazzolo, Eristanna; Francese, Gianluca; Fibiani, Marta; D'Alessandro, Antonietta; Papa, Vincenza; Laudicina, Vito A; Sabatino, Leo; Pulcini, Laura; Sala, Tea; Acciarri, Nazzareno; Portis, Ezio; Lanteri, Sergio; Mennella, Giuseppe; Rotino, Giuseppe L

    2016-01-01

    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" × "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. PMID:26973692

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

    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

  17. Impact of abundance weighting on the response of seed traits to climate and land use

    Pakeman, R. J.; Garnier, E.; Lavorel, S.; Ansquer, P.; Castro, H.; Cruz, P.; Doležal, Jiří; Eriksson, O.; Freitas, H.; Golodets, C.; Kigel, J.; Kleyer, M.; Lepš, Jan; Meier, T.; Papanastasis, V. P.; Quested, H.; Quétier, F.; Rusch, G.; Sternberg, M.; Theau, J.-P.; Thébault, A.; Vile, D.

    2008-01-01

    Roč. 96, č. 2 (2008), s. 355-366. ISSN 0022-0477 Grant ostatní: EU(XE) EVK2–CT-2001-00123; EU(XE) ENV4-CT95-0002 Institutional research plan: CEZ:AV0Z60050516; CEZ:AV0Z50070508 Keywords : seed mass * dispersal vector * abundance weighting Subject RIV: EF - Botanics Impact factor: 4.262, year: 2008

  18. Quantitative relationship between flagellate abundance and suspended particle density in Huanghai Sea and East China Sea in summer

    HUANG Lingfeng; PAN Ke; GUO Feng

    2006-01-01

    An investigation was carried out in the Huanghai Sea and the East China Sea to study the quantitative relationship between the abundance of flagellates and the density of suspended particles in the summer of 2001. The results show that the abundance of flagellates varies from 44~12 600 cell/cm3, and flagellates sometimes constitutes a significant part of suspended particles. The size-spectra of suspended particles can be divided into four categories: flat spectrum, humped spectrum, plankton spectrum and mixed spectrum. In general, the abundance of flagellates varies in proportion to the density of suspended particles. However, their quantitative relations reveal different characteristics in the seawater samples of different types of particle-size spectrum. This is only a preliminary study of the quantitative relationship between flagellates and suspended particles, which might lead to a potential convenient approach to the estimation of flagellate abundance in the sea.

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

    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. Identification and Validation of a Major Quantitative Trait Locus for Slow-rusting Resistance to Stripe Rust in Wheat

    Xiaohua Cao; Jianghong Zhou; Xiaoping Gong; Guangyao Zhao; Jizeng Jia; Xiaoquan Qi

    2012-01-01

    Stripe (yellow) rust,caused by Puccinia striiformis Westend.f.sp.tritici Eriks (Pst),is one of the most important wheat (Triticum aestivum L.) diseases and causes significant yield losses.A recombinant inbred (RI) population derived from a cross between Yanzhan 1 and Xichang 76-9 cultivars was evaluated for resistance to wheat stripe rust strain CYR32 at both the seedling and adult plant stages.Four resistance quantitative trait loci (QTLs) were detected in this population,in which the major one,designated as Yrq1,was mapped on chromosome 2DS.The strategy of using the Brachypodium distachyon genome,wheat expressed sequence tags and a draft DNA sequences (scaffolds) of the D-genome (Aegilops tauschii Coss.) for the development of simple sequence repeat (SSR) markers was successfully used to identify 147 SSRs in hexaploid wheat.Of the 19 polymorphic SSRs in the RI population,17 SSRs were mapped in the homeologous group 2 chromosomes near Yrq1 region and eight SSRs were genetically mapped in the 2.7 cM region of Yrq1,providing abundant DNA markers for fine-mapping of Yrq1 and marker-assisted selection in wheat breeding program.The effectiveness of Yrq1 was validated in an independent population,indicating that this resistance QTL can be successfully transferred into a susceptible cultivar for improvement of stripe rust resistance.

  1. Mapping Quantitative Trait Loci Using Naturally Occurring Genetic Variance Among Commercial Inbred Lines of Maize (Zea mays L.)

    Zhang, Yuan-Ming; Mao, Yongcai; Xie, Chongqing; Smith, Howie; Luo, Lang; Xu, Shizhong

    2005-01-01

    Many commercial inbred lines are available in crops. A large amount of genetic variation is preserved among these lines. The genealogical history of the inbred lines is usually well documented. However, quantitative trait loci (QTL) responsible for the genetic variances among the lines are largely unexplored due to lack of statistical methods. In this study, we show that the pedigree information of the lines along with the trait values and marker information can be used to map QTL without the...

  2. Evaluating functional diversity: Missing trait data and the importance of species abundance structure and data transformation

    Májeková, M.; Paal, T.; Plowman, Nichola S.; Bryndová, Michala; Kasari, L.; Norberg, A.; Weiss, Matthias; Bishop, T. R.; Luke, S. H.; Sam, Kateřina; Le Bagousse-Pinguet, Y.; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Roč. 11, č. 2 (2016), e0149270. E-ISSN 1932-6203 R&D Projects: GA ČR GB14-36098G; GA ČR(CZ) GP14-32024P; GA ČR GAP505/12/1296 Grant ostatní: GA JU(CZ) 156/2013/P Institutional support: RVO:60077344 ; RVO:67985939 Keywords : data incompleteness * functional diversity * species abundance Subject RIV: EH - Ecology, Behaviour Impact factor: 3.234, year: 2014 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149270

  3. A comprehensive collection of experimentally validated primers for Polymerase Chain Reaction quantitation of murine transcript abundance

    Wang Xiaowei

    2008-12-01

    Full Text Available Abstract Background Quantitative polymerase chain reaction (QPCR is a widely applied analytical method for the accurate determination of transcript abundance. Primers for QPCR have been designed on a genomic scale but non-specific amplification of non-target genes has frequently been a problem. Although several online databases have been created for the storage and retrieval of experimentally validated primers, only a few thousand primer pairs are currently present in existing databases and the primers are not designed for use under a common PCR thermal profile. Results We previously reported the implementation of an algorithm to predict PCR primers for most known human and mouse genes. We now report the use of that resource to identify 17483 pairs of primers that have been experimentally verified to amplify unique sequences corresponding to distinct murine transcripts. The primer pairs have been validated by gel electrophoresis, DNA sequence analysis and thermal denaturation profile. In addition to the validation studies, we have determined the uniformity of amplification using the primers and the technical reproducibility of the QPCR reaction using the popular and inexpensive SYBR Green I detection method. Conclusion We have identified an experimentally validated collection of murine primer pairs for PCR and QPCR which can be used under a common PCR thermal profile, allowing the evaluation of transcript abundance of a large number of genes in parallel. This feature is increasingly attractive for confirming and/or making more precise data trends observed from experiments performed with DNA microarrays.

  4. Effect of the scale of quantitative trait data on the representativeness of a cotton germplasm sub-core collection

    Jian-cheng WANG; Jin HU; Ya-jing GUAN; Yan-fang ZHU

    2013-01-01

    A cotton germplasm collection with data for 20 quantitative traits was used to investigate the effect of the scale of quantitative trait data on the representativeness of plant sub-core collections.The relationship between the representativeness of a sub-core collection and two influencing factors,the number of traits and the sampling percentage,was studied.A mixed linear model approach was used to eliminate environmental errors and predict genotypic values of accessions.Sub-core collections were constructed using a least distance stepwise sampling(LDSS)method combining standardized Euclidean distance and an unweighted pair-group method with arithmetic means (UPGMA)cluster method.The mean difference percentage(MD),variance difference percentage(VD),coincidence rate of range(CR),and variable rate of coefficient of variation(VR)served as evaluation parameters.Monte Carlo simulation was conducted to study the relationship among the number of traits,the sampling percentage,and the four evaluation parameters.The results showed that the representativeness of a sub-core collection was affected greatly by the number of traits and the sampling percentage,and that these two influencing factors were closely connected.Increasing the number of traits improved the representativeness of a sub-core collection when the data of genotypic values were used.The change in the genetic diversity of sub-core collections with different sampling percentages showed a linear tendency when the number of traits was small,and a logarithmic tendency when the number of traits was large.However,the change in the genetic diversity of sub-core collections with different numbers of traits always showed a strong logarithmic tendency when the sampling percentage was changing.A CR threshold method based on Monte Carlo simulation is proposed to determine the rational number of traits for a relevant sampling percentage of a sub-core collection.

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

    Camilla Noelle Rathcke

    Full Text Available BACKGROUND: 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. METHODS/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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.

  6. Identification of quantitative trait loci for four morphologic traits under water stress in rice(Oryza sativa L.)

    2008-01-01

    Late season drought coinciding with the rice booting to heading stage affects the development of plant height,panicle exsertion,and flag leaf size,and causes significant yield loss.In this study,a recombinant inbred line population derived from a cross between paddy and upland cultivars was used for data collection of the morphologic traits under well water and drought stress conditions.bought stress was applied at the stage of panicle initiation in the field in 2002 and at the booting stage in PVC pipes in 2003.The data from stress con ditions and their ratios(tait measured under stress condition/trait measured under well water condition)or differences(trait measured under stress condition minus trait measured under well water condition)were used for OTL analysis.Totally,17 and 36 QTLs for these traits were identified in 2002 and 2003,respectively,which explained a range of 2.58%-29.82%Of the phenotypic variation.Among them,six QTLs were commonly identified in the two years,suggesting that the drought stress in the two years was different.The genetic basis of these traits will provide useful information for improving rice late season drought resistance,and their application as indirect indices in rice late season drought resistance screening was also discussed.

  7. Mapping of hepatic expression quantitative trait loci (eQTLs) in a Han Chinese population

    Wang, Xiaoliang; Tang, Huamei; Teng, Mujian; Li, Zhiqiang; Li, Jianguo; Fan, Junwei; Zhong, Lin; Sun, Xing; Xu, Junming; Chen, Guoqing; Chen, Dawei; Wang, Zhaowen; Xing, Tonghai; Zhang, Jinyan; Huang, Li; Wang, Shuyun; Peng, Xiao; Qin, Shengying; Shi, Yongyong; Peng, Zhihai

    2014-01-01

    Background Elucidating the genetic basis underlying hepatic gene expression variability is of importance to understand the aetiology of the disease and variation in drug metabolism. To date, no genome-wide expression quantitative trait loci (eQTLs) analysis has been conducted in the Han Chinese population, the largest ethnic group in the world. Methods We performed a genome-wide eQTL mapping in a set of Han Chinese liver tissue samples (n=64). The data were then compared with published eQTL data from a Caucasian population. We then performed correlations between these eQTLs with important pharmacogenes, and genome-wide association study (GWAS) identified single nucleotide polymorphisms (SNPs), in particular those identified in the Asian population. Results Our analyses identified 1669 significant eQTLs (false discovery rate (FDR) < 0.05). We found that 41% of Asian eQTLs were also eQTLs in Caucasians at the genome-wide significance level (p=10−8). Both cis- and trans-eQTLs in the Asian population were also more likely to be eQTLs in Caucasians (p<10−4). Enrichment analyses revealed that trait-associated GWAS-SNPs were enriched within the eQTLs identified in our data, so were the GWAS-SNPs specifically identified in Asian populations in a separate analysis (p<0.001 for both). We also found that hepatic expression of very important pharmacogenetic (VIP) genes (n=44) and a manually curated list of major genes involved in pharmacokinetics (n=341) were both more likely to be controlled by eQTLs (p<0.002 for both). Conclusions Our study provided, for the first time, a comprehensive hepatic eQTL analysis in a non-European population, further generating valuable data for characterising the genetic basis of human diseases and pharmacogenetic traits. PMID:24665059

  8. Use of Major Quantitative Trait Loci to Improve Grain Yield of Rice

    GUO Long-biao; YE Guo-you

    2014-01-01

    Further improvement of rice productivity remains a challenge. Breeding is perceived as an important option to increase rice yield. However, the genetic progress of grain yield in most rice breeding programs was slow in the last decades. Although great progress in rice genomics and molecular biology has been achieved, the effect of such technological innovations on rice breeding is far small. Marker-assisted selection (MAS) for a few target quantitative trait loci (QTLs) has significant effects in improving qualitative traits, such as disease resistance. The success of MAS has therefore motivated breeders to identify and use major QTLs for yield and yield component traits. In this review, we summarized the recent methods in QTL identification, including novel statistical methods for linkage and association mapping, special population types, and whole-genome sequencing. We reviewed the successful application of marker-assisted gene introgression and gene pyramiding to improve grain yield and discussed the design of efficient MAS schemes to further increase the success rate of breeding programs. The use of well-characterized major QTLs through introgression and gene pyramiding is proven effective in improving grain yield, particularly yield under abiotic stress. Major QTLs that are stable across genetic background and growing environments are often found in less adapted germplasms, such as landraces and wild relatives. Advanced backcross QTL analysis and introgression lines, which integrate QTL discovery and utilization, are important methods for exploiting major QTLs contained in such germplasms. Next-generation sequencing substantially increases mapping resolution and accelerates the identification of casual genes underlying major QTLs. Practical guidelines derived from theoretical and empirical studies are given to guide the design of efficient marker-assisted gene introgression and pyramiding schemes.

  9. Detection of quantitative trait loci for growth and carcass composition in cattle.

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

    2003-12-01

    The objective of the present study was to detect quantitative trait loci for economically important traits in a family from a Bos indicus x Bos taurus sire. A Brahman x Hereford sire was used to develop a half-sib family (n = 547). The sire was mated to Bos taurus cows. Traits analyzed were birth (kg) and weaning weights (kg); hot carcass weight (kg); marbling score; longissimus area (cm2); USDA yield grade; estimated kidney, pelvic, and heart fat (%); fat thickness (cm); fat yield (%); and retail product yield (%). Meat tenderness was measured as Warner-Bratzler shear force (kg) at 3 and 14 d postmortem. Two hundred and thirty-eight markers were genotyped in 185 offspring. One hundred and thirty markers were used to genotype the remaining 362 offspring. A total of 312 markers were used in the final analysis. Seventy-four markers were common to both groups. Significant QTL (expected number of false-positives yield on chromosome 9, for birth weight on chromosome 21, and for marbling score on chromosome 23. Evidence suggesting (expected number of false-positives yield grade were identified on chromosomes 2, 11, 14, and 19. Three QTL for fat thickness were detected on chromosomes 2, 3, 7, and 14. For marbling score, QTL were identified on chromosomes 3, 10, 14, and 27. Four QTL were identified for retail product yield on chromosomes 12, 18, 19, and 29. A QTL for estimated kidney, pelvic, and heart fat was detected on chromosome 15, and a QTL for meat tenderness measured as Warner-Bratzler shear force at 3 d postmortem was identified on chromosome 20. Two QTL were detected for meat tenderness measured as Warner-Bratzler shear force at 14 d postmortem on chromosomes 20 and 29. These results present a complete scan in all available progeny in this family. Regions underlying QTL need to be assessed in other populations. PMID:14677852

  10. Targeted introgression of cotton fibre quality quantitative trait loci using molecular markers

    Within the framework of a cotton breeding programme, molecular markers are used to improve the efficiency of the introgression of fibre quality traits of Gossypium barbadense into G. hirsutum. A saturated genetic map was developed based on genotyping data obtained from the BC1 (75 plants) and BC2 (200 plants) generations. Phenotypic measurements conducted over three generations (BC1, BC2 and BC2S1) allowed 80 quantitative trait loci (QTL) to be detected for fibre length, uniformity, strength, elongation, fineness and colour. Positive QTL, i.e. those for which favourable alleles came from the G. barbadense parent, were harboured by 19 QTL-rich regions on 15 'carrier' chromosomes. In subsequent generations (BC3 and BC4), markers framing the QTL-rich regions were used to select about 10 percent of over 400 plants analysed in each generation. Although BC plants selected through the marker-assisted selection (MAS) process show promising fibre quality, only their full field evaluation will allow validation of the procedure. (author)

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

    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.

  12. Global genetic architecture of an erythroid quantitative trait locus, HMIP-2.

    Menzel, Stephan; Rooks, Helen; Zelenika, Diana; Mtatiro, Siana N; Gnanakulasekaran, Akshala; Drasar, Emma; Cox, Sharon; Liu, Li; Masood, Mariam; Silver, Nicholas; Garner, Chad; Vasavda, Nisha; Howard, Jo; Makani, Julie; Adekile, Adekunle; Pace, Betty; Spector, Tim; Farrall, Martin; Lathrop, Mark; Thein, Swee Lay

    2014-11-01

    HMIP-2 is a human quantitative trait locus affecting peripheral numbers, size and hemoglobin composition of red blood cells, with a marked effect on the persistence of the fetal form of hemoglobin, HbF, in adults. The locus consists of multiple common variants in an enhancer region for MYB (chr 6q23.3), which encodes the hematopoietic transcription factor cMYB. Studying a European population cohort and four African-descended groups of patients with sickle cell anemia, we found that all share a set of two spatially separate HbF-promoting alleles at HMIP-2, termed "A" and "B." These typically occurred together ("A-B") on European chromosomes, but existed on separate homologous chromosomes in Africans. Using haplotype signatures for "A" and "B," we interrogated public population datasets. Haplotypes carrying only "A" or "B" were typical for populations in Sub-Saharan Africa. The "A-B" combination was frequent in European, Asian, and Amerindian populations. Both alleles were infrequent in tropical regions, possibly undergoing negative selection by geographical factors, as has been reported for malaria with other hematological traits. We propose that the ascertainment of worldwide distribution patterns for common, HbF-promoting alleles can aid their further genetic characterization, including the investigation of gene-environment interaction during human migration and adaptation. PMID:25069958

  13. QTug.sau-3B Is a Major Quantitative Trait Locus for Wheat Hexaploidization

    Hao, Ming; Luo, Jiangtao; Zeng, Deying; Zhang, Li; Ning, Shunzong; Yuan, Zhongwei; Yan, Zehong; Zhang, Huaigang; Zheng, Youliang; Feuillet, Catherine; Choulet, Frédéric; Yen, Yang; Zhang, Lianquan; Liu, Dengcai

    2014-01-01

    Meiotic nonreduction resulting in unreduced gametes is thought to be the predominant mechanism underlying allopolyploid formation in plants. Until now, however, its genetic base was largely unknown. The allohexaploid crop common wheat (Triticum aestivum L.), which originated from hybrids of T. turgidum L. with Aegilops tauschii Cosson, provides a model to address this issue. Our observations of meiosis in pollen mother cells from T. turgidum×Ae. tauschii hybrids indicated that first division restitution, which exhibited prolonged cell division during meiosis I, was responsible for unreduced gamete formation. A major quantitative trait locus (QTL) for this trait, named QTug.sau-3B, was detected on chromosome 3B in two T. turgidum×Ae. tauschii haploid populations. This QTL is situated between markers Xgwm285 and Xcfp1012 and covered a genetic distance of 1 cM in one population. QTug.sau-3B is a haploid-dependent QTL because it was not detected in doubled haploid populations. Comparative genome analysis indicated that this QTL was close to Ttam-3B, a collinear homolog of tam in wheat. Although the relationship between QTug.sau-3B and Ttam requires further study, high frequencies of unreduced gametes may be related to reduced expression of Ttam in wheat. PMID:25128436

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

    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. PMID:20298472

  15. Variability Assessment of Aromatic and Fine Rice Germplasm in Bangladesh Based on Quantitative Traits.

    Islam, M Z; Khalequzzaman, M; Bashar, M K; Ivy, N A; Haque, M M; Mian, M A K

    2016-01-01

    The study was conducted to investigate genetic variability among 113 aromatic and fine local rice genotypes of which five were exotic in origin. The test genotypes were evaluated for 19 growth traits, yield components, and yield. All the quantitative traits varied significantly among the test genotypes. High heritability along with high genetic advance was observed for flag leaf area, secondary branches per panicle, filled grains per panicle, grain length, grain breadth, grain length breadth ratio, and 1000 grain weight. Such findings suggested preponderance of additive gene action in gene expression for these characters. Grain yield was significantly and positively correlated with days to flowering, days to maturity, panicle length, filled grains per panicle, and 1000 grain weight. According to D (2) cluster analysis, 113 test genotypes formed 10 clusters. Selection of parents from the clusters V and X followed by hybridization would possibly result in desirable heterosis for the development of heterotic rice hybrids. Finally, molecular characterizations of the studied germplasm are required for high resolution QTL mapping and validating the presence of candidate genes responsible for valuable characters. PMID:27127800

  16. Feasibility of the grandprogeny design for quantitative trait loci (QTL) detection in purebred beef cattle.

    Moody, D E; Pomp, D; Buchanan, D S

    1997-04-01

    The grandprogeny design (GPD) was developed for dairy cattle to use existing pedigreed populations for quantitative trait locus (QTL) detection. Marker genotypes of grandsires and sons are determined, and trait phenotypic data from grandprogeny are analyzed. The objective of this study was to investigate the potential application of GPD in purebred beef cattle populations. Pedigree structures of Angus (n = 123,319), Hereford (n = 107,778), Brangus (n = 14,449), and Gelbvieh (n = 8,114) sire evaluation reports were analyzed to identify potentially useful families. Power of QTL detection was calculated for a range of QTL effects (.1 to .5 SD) and two Type I error rates (.01 and .001). Reasonable power (> .75) could be achieved using GPD in Angus and Hereford for QTL having moderate effects (.3 SD) on weaning weight and large effects (.4 to .5 SD) on birth, yearling, and maternal weaning weights by genotyping 500 animals. Existing Gelbvieh and Brangus families useful for GPD were limited, and reasonable power could be expected only for QTL having large effects on weaning or birth weights. Although family structures suitable for GPD exist in purebred beef populations, large amounts of genotyping would be required to achieve reasonable power, and only QTL having moderate to large effects could be expected to be identified. PMID:9110205

  17. Identification of quantitative trait loci affecting gastrointestinal parasite resistance in an experimental Angus population.

    Kim, Eui-Soo; Sonstegard, Tad S; Silva, Marcos Vinicius G B; Gasbarre, Louis C; Van Tassell, Curtis P

    2014-02-01

    DNA markers associated with quantitative trait loci (QTL) affecting host tolerance to gastrointestinal (GI) parasite infection are ideal targets for marker-assisted selection. However, few studies in cattle have attempted to identify this type of QTL due to the difficulty of generating accurate phenotypic data from a resource population with adequate statistical power for detection. For this effort, we amassed fecal egg count (FEC) measures from annual natural field challenges with GI nematodes that spanned 12 different contemporary groups of Angus calves (1992-2000) derived from a closed breeding population. FEC and blood pepsinogen measures were taken weekly over a 26-week period post-weaning, and the FEC data were Box-Cox transformed to normalize the distribution of phenotypes. These 305 test animals and more than 100 founding animals from the extended pedigree were genotyped across 190 microsatellites markers. The genome-wide analyses identified a suggestive genome-wide QTL on bovine chromosome (Chr) 8 (P cattle, and some corresponded to previously identified QTL locations for parasite-related traits in sheep to provide genome locations for further fine mapping of parasite resistance/susceptibility in Angus cattle. PMID:24303892

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

    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.

  19. Quantitative Genetics and Functional-Structural Plant Growth Models: Simulation of Quantitative Trait Loci Detection for Model Parameters and Application to Potential Yield Optimization

    Letort, Veronique; Cournède, Paul-Henry; De Reffye, Philippe; Courtois, Brigitte; 10.1093/aob/mcm197

    2010-01-01

    Background and Aims: Prediction of phenotypic traits from new genotypes under untested environmental conditions is crucial to build simulations of breeding strategies to improve target traits. Although the plant response to environmental stresses is characterized by both architectural and functional plasticity, recent attempts to integrate biological knowledge into genetics models have mainly concerned specific physiological processes or crop models without architecture, and thus may prove limited when studying genotype x environment interactions. Consequently, this paper presents a simulation study introducing genetics into a functional-structural growth model, which gives access to more fundamental traits for quantitative trait loci (QTL) detection and thus to promising tools for yield optimization. Methods: The GreenLab model was selected as a reasonable choice to link growth model parameters to QTL. Virtual genes and virtual chromosomes were defined to build a simple genetic model that drove the settings ...

  20. Role of ATG10 expression quantitative trait loci in non-small cell lung cancer survival.

    Xie, Kaipeng; Liang, Cheng; Li, Qin; Yan, Caiwang; Wang, Cheng; Gu, Yayun; Zhu, Meng; Du, Fangzhi; Wang, Hui; Dai, Juncheng; Liu, Xiao'an; Jin, Guangfu; Shen, Hongbing; Ma, Hongxia; Hu, Zhibin

    2016-10-01

    The aim of this article was to evaluate whether genetic variants in autophagy-related genes affect the overall survival (OS) of non-small cell lung cancer (NSCLC) patients. We analyzed 14 single nucleotide polymorphisms (SNPs) in core autophagy-related genes for OS in 1,001 NSCLC patients. Three promising SNPs in ATG10 were subsequently annotated by the expression quantitative trait loci (eQTL) and methylation quantitative trait loci (meQTL) analyses based on Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) datasets. We observed that the variants of rs10514231, rs1864182 and rs1864183 were associated with poor lung cancer survival (HR = 1.33, 95% CI = 1.07-1.65; HR = 1.43, 95% CI = 1.13-1.81; HR = 1.38, 95% CI = 1.14-1.68, respectively) and positively correlated with ATG10 expression (all p lung cancer patients in TCGA dataset (HR = 2.10, 95% CI = 1.33-3.29). Moreover, the variants of rs10514231 and rs1864182 were associated with the increased methylation levels of cg17942617 (meQTL), which in turn contributed to the elevated ATG10 expression and decreased survival time. Further functional assays revealed that ATG10 facilitated lung cancer cell proliferation and migration. Our findings suggest that eQTL/meQTL variations of ATG10 could influence lung cancer survival through regulating ATG10 expression. PMID:27225307

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

    Jung, JaeHwang; Matemba, Lucas E.; 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...

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

    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.

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

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

    2012-01-01

    per sire was 38 and ranged between 16 and 59. Wool traits (14) were analyzed and phenotypes were corrected for fixed effects of birth year, sex, flock, litter size and shearing date (year and season). The QTL analyses were performed using regression-based interval mapping. The results revealed 4 QTL...

  4. Confirmatory Factor Analytic Structure and Measurement Invariance of Quantitative Autistic Traits Measured by the Social Responsiveness Scale-2

    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…

  5. Pathogen-specific effects of quantitative trait loci affecting clinical mastitis and somatic cell count in danish holstein cattle

    Sørensen, Lars Peter; Guldbrandtsen, Bernt; Thomasen, J.R.;

    2008-01-01

    The aim of this study was to investigate whether quantitative trait loci (QTL) affecting the risk of clinical mastitis (CM) and QTL affecting somatic cell score (SCS) exhibit pathogen-specific effects on the incidence of mastitis. Bacteriological data on mastitis pathogens were used to investigate...

  6. Quantitative trait loci for resistance to Haemonchus contortus under artificial challenge in Red Maasai and Dorper sheep of East Africa

    A genome-wide scan was performed to detect quantitative trait loci (QTL) for resistance to the gastro-intestinal nematode Haemonchus contortus in a double backcross population of Red Maasai and Dorper sheep. The mapping population comprised six sire families, with 1026 lambs in total. The lambs we...

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

    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.

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

    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.

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

    Covarrubias-Pazaran, Giovanny

    2016-01-01

    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. PMID:27271781

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

    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.

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

    2016-01-01

    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. PMID:27271781

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

    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

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

    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

  14. Fine mapping of quantitative trait loci underlying sensory meat quality traits in three French beef cattle breeds.

    Allais, S; Levéziel, H; Hocquette, J F; Rousset, S; Denoyelle, C; Journaux, L; Renand, G

    2014-10-01

    Improving the traits that underlie meat quality is a major challenge in the beef industry. The objective of this paper was to detect QTL linked to sensory meat quality traits in 3 French beef cattle breeds. We genotyped 1,059, 1,219, and 947 young bulls and their sires belonging to the Charolais, Limousin, and Blonde d'Aquitaine breeds, respectively, using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). After estimating relevant genetic parameters using VCE software, we performed a linkage disequilibrium and linkage analysis on 4 meat traits: intramuscular fat content, muscle lightness, shear force, and tenderness score. Heritability coefficients largely ranged between 0.10 and 0.24; however, they reached a maximum of 0.44 and 0.50 for intramuscular fat content and tenderness score, respectively, in the Charolais breed. The 2 meat texture traits, shear force and tenderness score, were strongly genetically correlated (-0.91 in the Charolais and Limousin breed and -0.86 in the Blonde d'Aquitaine breed), indicating that they are 2 different measures of approximately the same trait. The genetic correlation between tenderness and intramuscular fat content differed across breeds. Using a significance threshold of 5 × 10(-4) for QTL detection, we found more than 200 significant positions across the 29 autosomal chromosomes for the 4 traits in the Charolais and Blonde d'Aquitaine breeds; in contrast, there were only 78 significant positions in the Limousin breed. Few QTL were common across breeds. We detected QTL for intramuscular fat content located near the myostatin gene in the Charolais and Blonde d'Aquitaine breeds. No mutation in this gene has been reported for the Blonde d'Aquitaine breed; therefore, it suggests that an unknown mutation could be segregating in this breed. We confirmed that, in certain breeds, markers in the calpastatin and calpain 1 gene regions affect tenderness. We also found new QTL as several QTL on chromosome 3 that are

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

    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.

  16. The genetic basis of a domestication trait in the chicken: mapping quantitative trait loci for plumage colour

    Huq, Md. Nazmul

    2012-01-01

    Domestication is the process by which animals become adapted to the environment provided by humans. The process of domestication has let to a number of correlated behavioural, morphological and physiological changes among many domesticated animal species. An example is the changes of plumage colour in the chicken. Plumage colour is one of the most readily observable traits that make distinction between breeds as well as between strains within a breed. Understanding the genetic architecture of...

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

    Iqbal, Asif; Kim, You-Sam; Kang, Jun-Mo; Lee, Yun-Mi; Rai, Rajani; Jung, Jong-Hyun; Oh, Dong-Yup; Nam, Ki-Chang; Lee, Hak-Kyo; Kim, Jong-Joo

    2015-01-01

    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...

  18. Impact of the D genome and quantitative trait loci on quantitative traits in a spring durum by spring bread wheat cross

    Desirable agronomic traits are similar for common hexaploid (6X) bread wheat (Triticum aestivum, 2n = 6x = 42, genome, AABBDD) and tetraploid (4X) durum wheat (Triticum turgidum durum, 2n = 4x = 28, genome, AABB). However, they are genetically isolated from each other due to an unequal number of ge...

  19. Quantitative trait loci for resistance to Haemonchus contortus artificial challenge in Red Maasai and Dorper sheep of East Africa.

    Marshall, K; Mugambi, J M; Nagda, S; Sonstegard, T S; Van Tassell, C P; Baker, R L; Gibson, J P

    2013-06-01

    A genome-wide scan was performed to detect quantitative trait loci (QTL) for resistance to the gastrointestinal nematode Haemonchus contortus in a double backcross population of Red Maasai and Dorper sheep. The mapping population comprised six sire families, with 1026 lambs in total. The lambs were artificially challenged with H. contortus at about 6.5 months of age, and nine phenotypes were measured: fecal egg count, packed cell volume decline, two weight traits and five worm traits. A subset of the population (342 lambs) was selectively genotyped for 172 microsatellite loci covering 25 of the 26 autosomes. QTL mapping was performed for models which assumed that the QTL alleles were either fixed or segregating within each breed, combined with models with only an additive QTL effect fitted or both additive and dominance QTL effects fitted. Overall, QTL significant at the 1% chromosome-wide level were identified for 22 combinations of trait and chromosome. Of particular interest are a region of chromosome 26 with putative QTL for all nine traits and a region of chromosome 2 with putative QTL for three traits. Favorable QTL alleles for disease resistance originated in both the Red Maasai and Dorper breeds, were not always fixed within breed and had significant dominance effects in some cases. We anticipate that this study, in combination with follow-up work and other relevant studies, will help elucidate the biology of disease resistance. PMID:23051556

  20. Quantitative Trait Locus Analysis of Mating Behavior and Male Sex Pheromones in Nasonia Wasps

    Wenwen Diao

    2016-06-01

    Full Text Available A major focus in speciation genetics is to identify the chromosomal regions and genes that reduce hybridization and gene flow. We investigated the genetic architecture of mating behavior in the parasitoid wasp species pair Nasonia giraulti and Nasonia oneida that exhibit strong prezygotic isolation. Behavioral analysis showed that N. oneida females had consistently higher latency times, and broke off the mating sequence more often in the mounting stage when confronted with N. giraulti males compared with males of their own species. N. oneida males produce a lower quantity of the long-range male sex pheromone (4R,5S-5-hydroxy-4-decanolide (RS-HDL. Crosses between the two species yielded hybrid males with various pheromone quantities, and these males were used in mating trials with females of either species to measure female mate discrimination rates. A quantitative trait locus (QTL analysis involving 475 recombinant hybrid males (F2, 2148 reciprocally backcrossed females (F3, and a linkage map of 52 equally spaced neutral single nucleotide polymorphism (SNP markers plus SNPs in 40 candidate mating behavior genes revealed four QTL for male pheromone amount, depending on partner species. Our results demonstrate that the RS-HDL pheromone plays a role in the mating system of N. giraulti and N. oneida, but also that additional communication cues are involved in mate choice. No QTL were found for female mate discrimination, which points at a polygenic architecture of female choice with strong environmental influences.

  1. Confirmation of Novel Quantitative Trait Loci for Seed Dormancy at Different Ripening Stages in Rice

    Kazuhiro SASAKI; Yuri KAZAMA; Youn CHAE; Tadashi SATO

    2013-01-01

    Seed dormancy contributes resistance to pre-harvest sprouting.Effects on respective quantitative trait loci (QTLs) for dormancy should be assessed by using fresh seeds before germinability altered through storage.We investigated QTLs related to seed dormancy using backcross inbred lines derived from a cross between Nipponbare and Kasalath.Four putative QTLs for seed dormancy were detected immediately after harvest using composite interval mapping.These putative QTLs were mapped near C1488 on chromosome 3 (qSD-3.1),R2171 on chromosome 6 (qSD-6.1),R1245 on chromosome 7 (qSD-7.1) and C488 on chromosome 10 (qSD-10.1).Kasalath alleles promoted dormancy for qSD-3.1,qSD-6.1 and qSD-7.1,and the respective proportions of phenotypic variation explained by each QTL were 12.9%,9.3% and 8.1%.We evaluated the seed dormancy harvested at different ripening stages during seed development using chromosome segment substitution lines (CSSLs) to confirm gene effects.The germination rates of CSSL27 and CSSL28 substituted with the region including qSD-6.1 were significantly lower than those of Nipponbare and other CSSLs at the late ripening stage.Therefore,qSD-6.1 is considered the most effective novel QTL for pre-harvest sprouting resistance among the QTLs detected in this study.

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

    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.

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

    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.

  4. Quantitative trait loci for a neurocranium deformity, lack of operculum, in gilthead seabream (Sparus aurata L.).

    Negrín-Báez, D; Navarro, A; Afonso, J M; Toro, M A; Zamorano, M J

    2016-04-01

    Lack of operculum, a neurocranial deformity, is the most common external abnormality to be found among industrially produced gilthead seabream (Sparus aurata L.), and this entails significant financial losses. This study conducts, for the first time in this species, a quantitative trait loci (QTL) analysis of the lack of operculum. A total of 142 individuals from a paternal half-sibling family (six full-sibling families) were selected for QTL mapping. They had previously shown a highly significant association with the prevalence of lack of operculum in a segregation analysis. All the fish were genotyped for 106 microsatellite markers using a set of multiplex PCRs (ReMsa1-ReMsa13). A linear regression methodology was used for the QTL analysis. Four QTL were detected for this deformity, two of which (QTLOP1 and QTLOP2) were significant. They were located at LG (linkage group) nine and LG10 respectively. Both QTL showed a large effect (about 27%), and furthermore, the association between lack of operculum and sire allelic segregation observed was statistically significant in the QTLOP1 analysis. These results represent a significant step towards including marker-assisted selection for this deformity in genetic breeding programmes to reduce the incidence of the deformity in the species. PMID:26995565

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

    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. PMID:25086652

  6. Two Quantitative Trait Loci Influence Whipworm (Trichuris trichiura) Infection in a Nepalese Population

    Williams-Blangero, Sarah; VandeBerg, John L.; Subedi, Janardan; Jha, Bharat; Dyer, T.D.; Blangero, John

    2014-01-01

    Background Whipworm (Trichuris trichiura) is a soil-transmitted helminth which infects over a billion people. It is a serious public health problem in many developing countries and can result in deficits in growth and cognitive development. In a follow-up study of a significant heritability for whipworm infection, we conducted the first genome scan for susceptibility to this important parasitic disease. Methods We assessed whipworm eggs per gram of feces in 1253 members of the Jirel population of eastern Nepal. All sampled individuals belonged to a single pedigree containing over 26,000 relative pairs that are informative for genetic analysis. Results Linkage analysis of genome scan data generated for the pedigree provided unambiguous evidence for two quantitative trait loci influencing susceptibility to whipworm infection, one located on chromosome 9 (LOD = 3.35, genome-wide p = 0.0138) and the other located on chromosome 18 (LOD = 3.29, genome-wide p = 0.0159). There was also suggestive evidence for two loci located on chromosomes 12 and 13 influencing whipworm infection. Conclusion The results of this first genome scan for susceptibility to whipworm infection may ultimately lead to the identification of novel targets for vaccine and drug development efforts. PMID:18462166

  7. Quantitative trait loci for mercury accumulation in maize (Zea mays L. identified using a RIL population.

    Zhongjun Fu

    Full Text Available 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 (QTLs for mercury accumulation at two locations. The results showed that the average Hg concentration in the different tissues of maize followed the order: leaves > bracts > stems > axis > kernels. Twenty-three QTLs for mercury accumulation in five tissues were detected on chromosomes 1, 4, 7, 8, 9 and 10, which explained 6.44% to 26.60% of the phenotype variance. The QTLs included five QTLs for Hg concentration in kernels, three QTLs for Hg concentration in the axis, six QTLs for Hg concentration in stems, four QTLs for Hg concentration in bracts and five QTLs for Hg concentration in leaves. Interestingly, three QTLs, qKHC9a, qKHC9b, and qBHC9 were in linkage with two QTLs for drought tolerance. In addition, qLHC1 was in linkage with two QTLs for arsenic accumulation. The study demonstrated the concentration of Hg in Hg-contaminated paddy soil could be reduced, and maize production maintained simultaneously by selecting and breeding maize Hg pollution-safe cultivars (PSCs.

  8. Expression quantitative trait analysis reveals fine germline transcript regulation in mouse lung tumors.

    Cotroneo, Chiara E; Dassano, Alice; Colombo, Francesca; Pettinicchio, Angela; Lecis, Daniele; Dugo, Matteo; De Cecco, Loris; Dragani, Tommaso A; Manenti, Giacomo

    2016-06-01

    Gene expression modulates cellular functions in both physiologic and pathologic conditions. Herein, we carried out a genetic linkage study on the transcriptome of lung tumors induced by urethane in an (A/J x C57BL/6)F4 intercross population, whose individual lung tumor multiplicity (Nlung) is linked to the genotype at the Pulmonary adenoma susceptibility 1 (Pas1) locus. We found that expression levels of 1179 and 1579 genes are modulated by an expression quantitative trait locus (eQTL) in cis and in trans, respectively (LOD score > 5). Of note, the genomic area surrounding and including the Pas1 locus regulated 14 genes in cis and 857 genes in trans. In lung tumors of the same (A/J x C57BL/6)F4 mice, we found 1124 genes whose transcript levels associated with Nlung (FDR cancer: they highlight the importance of Pas1 as a tumor-modifier locus, attribute to it a novel role as a major regulator of transcription in lung tumor nodules and strengthen the candidacy of the Kras gene as the effector of this locus. PMID:26966001

  9. A genome-wide search for quantitative trait loci influencing substance dependence vulnerability in adolescence.

    Stallings, Michael C; Corley, Robin P; Hewitt, John K; Krauter, Kenneth S; Lessem, Jeffrey M; Mikulich, Susan K; Rhee, Soo Hyun; Smolen, Andrew; Young, Susan E; Crowley, Thomas J

    2003-06-01

    This study describes results from a genome-wide search for quantitative trait loci (QTL) influencing substance dependence vulnerability in adolescence. We utilized regression-based multipoint (and single-point) QTL mapping procedures designed for selected sibpair samples. Selected sibling pairs included 250 proband-sibling pairs from 192 families. Clinical probands (13-19 years of age) were drawn from consecutive admissions to substance abuse treatment facilities in the Denver metropolitan area; siblings of probands ranged in age from 12 to 25 years. In addition to the selected sample, a community-based sample of 3676 adolescents and young adults were utilized to define a clinically-significant, heritable, age- and sex-normed index of substance dependence vulnerability-a priori and independent of our linkage results. Siblings and their parents were genotyped for 374 STR micro-satellite markers distributed across the 22 autosomes (average inter-marker distance=9.2 cM). Non-parametric single-point linkage results indicated 17 markers on 11 chromosomes with nominally significant tests of linkage; six markers with LOD scores greater than 1.0 and one marker (D3S1614) with a LOD score of 2.2. Multipoint mapping corroborated two locations and provided preliminary evidence for linkage to regions on chromosome 3q24-25 (near markers D3S1279 and D3S1614) and chromosome 9q34 (near markers D9S1826 and D9S1838). PMID:12757967

  10. Identification of quantitative trait loci affecting tolerance to low phosphorus in rice (Oryza Sativa L.)

    2000-01-01

    Phosphorus (P)-deficiency in rice (Oryza.Sativa.L) may cause yield reductions.This research has been conducted to map quantitative trait loci (QTLs) for tolerance to low phosphorus stress in a doubled haploid (DH) population.By using the linkage map of this population,the QTLs for relative dry weight,relative P content and relative P utilization efficiency have been located.The results indicate that one RFLP marker located on chromosome 6 is closely associated with relative root dry weight,relative shoot dry weight and relative total dry weight,which explain 24.9%,20.5% and 25.2% of the total phenotypic variations,respectively.Two QTLs affect relative P uptake content,which account for 20.7% of the total phenotypic variations.One micro-effect QTL has been found to be associated with relative P utilization efficiency.It is suggested that the P uptake efficiency is more associated with P efficiency.Among the secondary physiological indices of P uptake efficiency,the root dry weight is more important than others.

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

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

    2009-01-01

    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 disequil......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...... 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...... for phenotyping to extract maximum power and precision in a QTL fine mapping experiment were developed and assessed. Linkage analyses for the mapping was performed for individuals sampled on LAC within families and combined linkage disequilibrium and linkage analyses was performed for individuals...

  12. Using advanced intercross lines for high-resolution mapping of HDL cholesterol quantitative trait loci.

    Wang, Xiaosong; Le Roy, Isabelle; Nicodeme, Edwige; Li, Renhua; Wagner, Richard; Petros, Christina; Churchill, Gary A; Harris, Stephen; Darvasi, Ariel; Kirilovsky, Jorge; Roubertoux, Pierre L; Paigen, Beverly

    2003-07-01

    Mapping quantitative trait loci (QTLs) with high resolution facilitates identification and positional cloning of the underlying genes. The novel approach of advanced intercross lines (AILs) generates many more recombination events and thus can potentially narrow QTLs significantly more than do conventional backcrosses and F2 intercrosses. In this study, we carried out QTL analyses in (C57BL/6J x NZB/BlNJ) x C57BL/6J backcross progeny fed either chow or an atherogenic diet to detect QTLs that regulate high-density lipoprotein cholesterol (HDL)concentrations, and in (C57BL/6J x NZB/BlNJ) F11 AIL progeny to confirm and narrow those QTLs. QTLs for HDL concentrations were found on chromosomes 1, 5, and 16. AIL not only narrowed the QTLs significantly more than did a conventional backcross but also resolved a chromosome 5 QTL identified in the backcross into two QTLs, the peaks of both being outside the backcross QTL region. We tested 27 candidate genes and found significant mRNA expression differences for 12 (Nr1i3, Apoa2, Sap, Tgfb2, Fgfbp1, Prom, Ppargc1, Tcf1, Ncor2, Srb1, App, and Ifnar). Some of these underlay the same QTL, indicating that expression differences are common and not sufficient to identify QTL genes. All the major HDL QTLs in our study had homologous counterparts in humans, implying that their underlying genes regulate HDL in humans. PMID:12805272

  13. Identification of Chromosome Segment Substitution Lines of Gossypium barbadense Introgressed in G. hirsutum and Quantitative Trait Locus Mapping for Fiber Quality and Yield Traits.

    Zhai, Huanchen; Gong, Wankui; Tan, Yunna; Liu, Aiying; Song, Weiwu; Li, Junwen; Deng, Zhuying; Kong, Linglei; Gong, Juwu; Shang, Haihong; Chen, Tingting; Ge, Qun; Shi, Yuzhen; Yuan, Youlu

    2016-01-01

    Chromosome segment substitution lines MBI9804, MBI9855, MBI9752, and MBI9134, which were obtained by advanced backcrossing and continuously inbreeding from an interspecific cross between CCRI36, a cultivar of upland cotton (Gossypium hirsutum) as the recurrent parent, and Hai1, a cultivar of sea island cotton (G. barbadense) as the donor parent, were used to construct a multiple parent population of (MBI9804×MBI9855)×(MBI9752×MBI9134). The segregating generations of double-crossed F1 and F2 and F2:3 were used to map the quantitative trait locus (QTL) for fiber quality and yield-related traits. The recovery rate of the recurrent parent CCRI36 in the four parental lines was from 94.3%-96.9%. Each of the parental lines harbored 12-20 introgressed segments from Hai1across 21 chromosomes. The number of introgressed segments ranged from 1 to 27 for the individuals in the three generations, mostly from 9 to 18, which represented a genetic length of between 126 cM and 246 cM. A total of 24 QTLs controlling fiber quality and 11 QTLs controlling yield traits were detected using the three segregating generations. These QTLs were distributed across 11 chromosomes and could collectively explain 1.78%-20.27% of the observed phenotypic variations. Sixteen QTLs were consistently detected in two or more generations, four of them were for fiber yield traits and 12 were for fiber quality traits. One introgressed segment could significantly reduce both lint percentage and fiber micronaire. This study provides useful information for gene cloning and marker-assisted breeding for excellent fiber quality. PMID:27603312

  14. Construction of a genetic linkage map and analysis of quantitative trait loci associated with the agronomically important traits of Pleurotus eryngii.

    Im, Chak Han; Park, Young-Hoon; Hammel, Kenneth E; Park, Bokyung; Kwon, Soon Wook; Ryu, Hojin; Ryu, Jae-San

    2016-07-01

    Breeding new strains with improved traits is a long-standing goal of mushroom breeders that can be expedited by marker-assisted selection (MAS). We constructed a genetic linkage map of Pleurotus eryngii based on segregation analysis of markers in postmeiotic monokaryons from KNR2312. In total, 256 loci comprising 226 simple sequence-repeat (SSR) markers, 2 mating-type factors, and 28 insertion/deletion (InDel) markers were mapped. The map consisted of 12 linkage groups (LGs) spanning 1047.8cM, with an average interval length of 4.09cM. Four independent populations (Pd3, Pd8, Pd14, and Pd15) derived from crossing between four monokaryons from KNR2532 as a tester strain and 98 monokaryons from KNR2312 were used to characterize quantitative trait loci (QTL) for nine traits such as yield, quality, cap color, and earliness. Using composite interval mapping (CIM), 71 QTLs explaining between 5.82% and 33.17% of the phenotypic variations were identified. Clusters of more than five QTLs for various traits were identified in three genomic regions, on LGs 1, 7 and 9. Regardless of the population, 6 of the 9 traits studied and 18 of the 71 QTLs found in this study were identified in the largest cluster, LG1, in the range from 65.4 to 110.4cM. The candidate genes for yield encoding transcription factor, signal transduction, mycelial growth and hydrolase are suggested by using manual and computational analysis of genome sequence corresponding to QTL region with the highest likelihood odds (LOD) for yield. The genetic map and the QTLs established in this study will help breeders and geneticists to develop selection markers for agronomically important characteristics of mushrooms and to identify the corresponding genes. PMID:27166667

  15. Comparative quantitative trait locus mapping of maize flowering-related traits in an F2:3 and recombinant inbred line population.

    Liu, Y H; Yi, Q; Hou, X B; Zhang, X G; Zhang, J J; Liu, H M; Hu, Y F; Huang, Y B

    2016-01-01

    Flowering-related traits in maize are affected by complex factors and are important for the improvement of cropping systems in the maize zone. Quantitative trait loci (QTLs) detected using different materials and methods usually vary. In the present study, 266 maize (Zea mays) F2:3 families and 301 recombinant inbred lines (RIL) derived from a cross between 08-641 (founding parent from southeast China) and Ye478 (founding parent from China) were evaluated for four flowering-related traits, including days to tasseling (DTT), days to pollen shedding (DPS), days to silking (DTS), and anthesis-silking interval. Sixty-six QTLs controlling the target traits were detected in the F2:3 and RIL populations via single environment analysis and joint analysis across all environments (JAAE). The QTLs explained 0.8-13.47% of the phenotypic variation, with 12 QTLs explaining more than 10%. The results of meta-QTL (MQTL) analysis indicated that 41 QTLs could be integrated into 14 MQTLs. One MQTL included 2.9 QTLs, ranging from two to ten QTLs for one to three traits. QTLs, including MQTL1-1 and MQTL9-1, were detected across the F2:3 and RIL populations via SAE and JAAE. Among the MQTLs, nine QTLs were integrated into MQTL9-1 and affected DTT, DPS, and DTS, with the favored allele being derived from 08-641. MQTL3-2 showed high phenotypic variation and was suitable for fine mapping to determine the genetic mechanisms of flowering. MQTL3-2 could be applied to improve inbred lines using marker-assisted selection. PMID:27420987

  16. Quantitative trait locus mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower.

    Whitney, Kenneth D; Broman, Karl W; Kane, Nolan C; Hovick, Stephen M; Randell, Rebecca A; Rieseberg, Loren H

    2015-05-01

    The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H. annuus to form the natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping populations were grown in central Texas, genotyped for 384 single nucleotide polymorphism (SNP) markers and then phenotyped in the field for two fitness and 22 herbivore resistance, ecophysiological, phenological and architectural traits. We identified a total of 110 QTL, including at least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at least one H. debilis QTL allele that would shift the trait in the direction of the wild hybrid H. a. texanus. We identified three chromosomal regions where H. debilis alleles increased both female and male components of fitness; these regions are expected to be strongly favoured in the wild. QTL for a number of other ecophysiological, phenological and architectural traits colocalized with these three regions and are candidates for the actual traits driving adaptive shifts. G × E interactions played a modest role, with 17% of the QTL showing potentially divergent phenotypic effects between the two field sites. The candidate adaptive chromosomal regions identified here serve as explicit hypotheses for how the genetic architecture of the hybrid lineage came into existence. PMID:25522096

  17. Quantitative trait locus analysis and construction of consensus genetic map for drought tolerance traits based on three recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.)

    Gautami, B.; M.K. Pandey; Vadez, V.; Nigam, S. N.; Ratnakumar, P.; L. Krishnamurthy; T. Radhakrishnan; M. V. C. Gowda; Narasu, M. L.; Hoisington, D. A.; Knapp, S. J.; Varshney, R.K.

    2011-01-01

    Groundnut (Arachis hypogaea L.) is an important food and cash crop grown mainly in semi-arid tropics (SAT) regions of the world where drought is the major constraint on productivity. With the aim of understanding the genetic basis and identification of quantitative trait loci (QTL) for drought tolerance, two new recombinant inbred line (RIL) mapping populations, namely ICGS 76 × CSMG 84-1 (RIL-2) and ICGS 44 × ICGS 76 (RIL-3), were used. After screening of 3,215 simple sequence repeat (SSR) m...

  18. Genetic variability components of some quantitative traits of winter oilseed rape - Brassica napus L.

    Marinković Radovan

    2003-01-01

    Full Text Available Analysis of genetic variance components for number of leaves and branches per plant and stem diameter was done according to the method of HAYMAN (1954. Heritability in narrow (h2a and broad (h2b sense was determined for the same traits, using the method of Mather and Jinks (1971. Non-additive component of genetic variance was greater than additive component in all three studied traits. Dominant and recessive genes were not equally distributed in parent genotypes, with dominant genes prevailing. Ratio (H1/D1/2 was higher than 1 in all three tested traits. Calculated values for heritability in narrow sense showed that stem diameter and number of branches per plant are traits with low heritability, and number of leaves per plant a trait with the high heritability. Heritability in a broad sense Was high for all three tested traits.

  19. Mapping quantitative trait loci for nitrogen uptake and utilization efficiency in rice (Oryza sativa L.) at different nitrogen fertilizer levels.

    Dai, G J; Cheng, S H; Hua, Z T; Zhang, M L; Jiang, H B; Feng, Y; Shen, X H; Su, Y A; He, N; Ma, Z B; Ma, X Q; Hou, S G; Wang, Y R

    2015-01-01

    Genetic improvement is the fundamental basis for improving nitrogen-use efficiency. A better understanding of genetic factors controlling nitrogen uptake and utilization is required for crop genetic improvement. In this study, we identified the quantitative trait loci (QTLs) associated with traits of nitrogen uptake and utilization by using the single-sequence repeat marker method and a recombinant inbred line (RIL) population derived from a super hybrid Xieyou9308. All the traits investigated were inherited quantitatively by continuous variation and showed normal distribution in phenotype with transgressive segregation in the RIL population. Most of the traits were significantly correlated with each other except for nitrogen absorption ability (NAA) with nitrogen harvest index (NHI) and NHI with agricultural nitrogen-absorption efficiency (ANAE). At logarithmic odds value of 2.3, total 13 candidate QTLs, including 4 for NAA, 2 for NHI, 2 for physiological nitrogen-use efficiency, 1 for agricultural nitrogen-use efficiency (ANUE), and 4 for ANAE, were detected and mapped on chromosomes 2, 3, 4, 5, 8, 9, 10, and 12. Significant pleiotropic effect or neighboring expression of QTLs was observed among traits. At position 64.8 cM on chromosome 4 near the marker RM5757, there was a QTL cluster of NAA, ANUE, and ANAE, and at chromosome 5 near the marker RM5968, there was a QTL cluster of NAA and ANUE. The QTL clusters might provide partial explanation and genetic mechanism for the observed correlations between nitrogen uptake and utilization efficiency traits and might form a basis for future breeding programs. PMID:26400271

  20. 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

    Li, Xiaonan; Ramchiary, Nirala; Dhandapani, Vignesh; Choi, Su Ryun; Hur, Yoonkang; Nou, Ill-Sup; Yoon, Moo Kyoung; Lim, Yong Pyo

    2012-01-01

    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 t...

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

    LI Xiao-ling; LU Yong-gen; LI Jin-quan; Xu Hai-ming; Muhammad Qasim SHAHID

    2011-01-01

    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.

  2. Quantitative Trait Loci and Trait Correlations for Maize Stover Cell Wall Composition and Glucose Release for Cellulosic Ethanol

    In cellulosic ethanol production, the efficiency of converting maize (Zea mays L.) stover into fermentable sugars partly depends on the stover cell wall structure. Breeding for improved stover quality for cellulosic ethanol may benefit from the use of molecular markers. However, limited quantitative...

  3. Characterization of Expression Quantitative Trait Loci in Pedigrees from Colombia and Costa Rica Ascertained for Bipolar Disorder

    Peterson, Christine B.; Service, Susan K.; Jasinska, Anna J.; Gao, Fuying; Zelaya, Ivette; Teshiba, Terri M.; Bearden, Carrie E.; Cantor, Rita M.; Reus, Victor I.; Macaya, Gabriel; López-Jaramillo, Carlos; Bogomolov, Marina; Benjamini, Yoav; Eskin, Eleazar; Coppola, Giovanni; Freimer, Nelson B.; Sabatti, Chiara

    2016-01-01

    The observation that variants regulating gene expression (expression quantitative trait loci, eQTL) are at a high frequency among SNPs associated with complex traits has made the genome-wide characterization of gene expression an important tool in genetic mapping studies of such traits. As part of a study to identify genetic loci contributing to bipolar disorder and other quantitative traits in members of 26 pedigrees from Costa Rica and Colombia, we measured gene expression in lymphoblastoid cell lines derived from 786 pedigree members. The study design enabled us to comprehensively reconstruct the genetic regulatory network in these families, provide estimates of heritability, identify eQTL, evaluate missing heritability for the eQTL, and quantify the number of different alleles contributing to any given locus. In the eQTL analysis, we utilize a recently proposed hierarchical multiple testing strategy which controls error rates regarding the discovery of functional variants. Our results elucidate the heritability and regulation of gene expression in this unique Latin American study population and identify a set of regulatory SNPs which may be relevant in future investigations of complex disease in this population. Since our subjects belong to extended families, we are able to compare traditional kinship-based estimates with those from more recent methods that depend only on genotype information. PMID:27176483

  4. Characterization of Expression Quantitative Trait Loci in Pedigrees from Colombia and Costa Rica Ascertained for Bipolar Disorder.

    Peterson, Christine B; Service, Susan K; Jasinska, Anna J; Gao, Fuying; Zelaya, Ivette; Teshiba, Terri M; Bearden, Carrie E; Cantor, Rita M; Reus, Victor I; Macaya, Gabriel; López-Jaramillo, Carlos; Bogomolov, Marina; Benjamini, Yoav; Eskin, Eleazar; Coppola, Giovanni; Freimer, Nelson B; Sabatti, Chiara

    2016-05-01

    The observation that variants regulating gene expression (expression quantitative trait loci, eQTL) are at a high frequency among SNPs associated with complex traits has made the genome-wide characterization of gene expression an important tool in genetic mapping studies of such traits. As part of a study to identify genetic loci contributing to bipolar disorder and other quantitative traits in members of 26 pedigrees from Costa Rica and Colombia, we measured gene expression in lymphoblastoid cell lines derived from 786 pedigree members. The study design enabled us to comprehensively reconstruct the genetic regulatory network in these families, provide estimates of heritability, identify eQTL, evaluate missing heritability for the eQTL, and quantify the number of different alleles contributing to any given locus. In the eQTL analysis, we utilize a recently proposed hierarchical multiple testing strategy which controls error rates regarding the discovery of functional variants. Our results elucidate the heritability and regulation of gene expression in this unique Latin American study population and identify a set of regulatory SNPs which may be relevant in future investigations of complex disease in this population. Since our subjects belong to extended families, we are able to compare traditional kinship-based estimates with those from more recent methods that depend only on genotype information. PMID:27176483

  5. Mapping Quantitative Trait Loci From a Single-Tail Sample of the Phenotype Distribution Including Survival Data

    Sillanpää, Mikko J.; Hoti, Fabian

    2007-01-01

    A new effective Bayesian quantitative trait locus (QTL) mapping approach for the analysis of single-tail selected samples of the phenotype distribution is presented. The approach extends the affected-only tests to single-tail sampling with quantitative traits such as the log-normal survival time or censored/selected traits. A great benefit of the approach is that it enables the utilization of multiple-QTL models, is easy to incorporate into different data designs (experimental and outbred populations), and can potentially be extended to epistatic models. In inbred lines, the method exploits the fact that the parental mating type and the linkage phases (haplotypes) are known by definition. In outbred populations, two-generation data are needed, for example, selected offspring and one of the parents (the sires) in breeding material. The idea is to statistically (computationally) generate a fully complementary, maximally dissimilar, observation for each offspring in the sample. Bayesian data augmentation is then used to sample the space of possible trait values for the pseudoobservations. The benefits of the approach are illustrated using simulated data sets and a real data set on the survival of F2 mice following infection with Listeria monocytogenes. PMID:18073434

  6. Structural and functional correlates of a quantitative autistic trait measured using the social responsive scale in neurotypical male adolescents.

    Tu, Pei-Chi; Hsu, Ju-Wei; Lan, Chen-Chia; Liu, Chia-Chien; Su, Tung-Ping; Chen, Ying-Sheue

    2016-05-01

    Behaviors associated with autism spectrum disorder (ASD) have been suggested to be considered as quantitative traits. This study investigated the structural and functional correlates of autistic traits measured using the Social Responsiveness Scale (SRS) in neurotypical adolescents. Twenty-six neurotypical male adolescents (12-18 years old) were recruited for this study and underwent structural and resting functional magnetic resonance image scanning, and intelligence quotient and SRS evaluations. We used the automated surface-based method (FreeSurfer) to measure cortical thickness and seed-based functional connectivity (FC) analysis to derive the FC map of the dorsal anterior cingulate (dACC). Brain-wise regression analyses of cortical thickness and FC maps on SRS scores were performed using a general linear model. The results indicated that higher autistic trait ratings of total SRS scores were associated with a thinner cortex in the left insula, right insula, and right superior temporal gyrus. Furthermore, we observed that only higher scores of social awareness were correlated with increased FC between the dACC and right superior temporal gyrus and decreased FC between the dACC and right putamen and thalamus. These results indicated that a quantitative trait in social cognition is associated with structural and connectivity variations linked to ASD patients. Autism Res 2016, 9: 570-578. © 2015 International Society for Autism Research, Wiley Periodicals, Inc. PMID:26284955

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

    Mikołajczak, Krzysztof; Ogrodowicz, Piotr; Gudyś, Kornelia; Krystkowiak, Karolina; Sawikowska, Aneta; Frohmberg, Wojciech; Górny, Andrzej; Kędziora, Andrzej; Jankowiak, Janusz; Józefczyk, Damian; Karg, Grzegorz; Andrusiak, Joanna; Krajewski, Paweł; Szarejko, Iwona; Surma, Maria; Adamski, Tadeusz; Guzy-Wróbelska, Justyna; Kuczyńska, Anetta

    2016-01-01

    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). PMID:27227880

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

    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.

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

    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.

  10. Quantitative trait loci associated with tipburn, heat stress-induced physiological disorders, and maturity traits in crisphead lettuce.

    Jenni, Sylvie; Truco, Maria José; Michelmore, Richard W

    2013-09-28

    Crisphead lettuce (Lactuca sativa L.) crops exhibit several economically important, physiological disorders when grown in high temperature conditions. These include tipburn, rib discoloration, premature bolting, ribbiness, and internal rib cracking. We evaluated seven physiological disorders and three agronomic traits segregating in a recombinant inbred line (RIL) population consisting of 152 F7 RILs derived from an intra-specific cross between two crisphead cultivars, L. sativa cv. Emperor x L. sativa cv. El Dorado; evaluations were carried out at each of two parental maturities in one planting and at one intermediate maturity in a second planting in each of 2 years for a total of six evaluations. A genetic map was developed using 449 polymorphic SNP markers; it comprises 807 cM in 20 linkage groups that covered 51 % of the nine lettuce chromosomes. Composite interval mapping revealed a total of 36 significant QTLs for eight out of the ten traits evaluated. Significant QTLs were distributed in 11 linkage groups on seven of the chromosomes and accounted for up to 83 % of the phenotypic variation observed. The three largest QTLs for rib discoloration, which accounted individually for 7-21 % of the variation, were clustered with stem length, two with ribbiness and one with head firmness. Three major clusters of QTLs revealed pleiotropic effects or tight linkage between tipburn incidence and severity, head type, stem length, head firmness and ribbiness. One QTL, qTPB5.2, was detected in multiple trials and described 38-70 % of the variation in tipburn incidence. qTPB5.2 is, therefore, a useful candidate gene for breeding for tipburn resistance using marker-assisted selection. PMID:24078012

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

    Iqbal, Asif; Kim, You-Sam; Kang, Jun-Mo; Lee, Yun-Mi; Rai, Rajani; Jung, Jong-Hyun; Oh, Dong-Yup; Nam, Ki-Chang; Lee, Hak-Kyo; Kim, Jong-Joo

    2015-11-01

    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 (peffect 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. PMID:26580276

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

    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. PMID:20028471

  13. Detection of associations with rare and common SNPs for quantitative traits: a nonparametric Bayes-based approach

    Ding Lili; Baye Tesfaye M; He Hua; Zhang Xue; Kurowski Brad G; Martin Lisa J

    2011-01-01

    Abstract We propose a nonparametric Bayes-based clustering algorithm to detect associations with rare and common single-nucleotide polymorphisms (SNPs) for quantitative traits. Unlike current methods, our approach identifies associations with rare genetic variants at the variant level, not the gene level. In this method, we use a Dirichlet process prior for the distribution of SNP-specific regression coefficients, conduct hierarchical clustering with a distance measure derived from posterior ...

  14. ASSOCIATION OF GENETIC DIVERGENCE WITH HETEROSIS, COMBINING ABILITY AND MEAN VALUE FOR QUANTITATIVE TRAITS IN POPCORN (ZEA MAYS VAR. EVERTA)

    N V SONI; S M KHANORKAR

    2013-01-01

    The study was aimed to analyze the genetic diversity among popcorn inbred lines using Random Amplified Polymorphic DNA profiling and to associate it with heterosis, specific combining ability and mean values of hybrids for quantitative traits viz., days to 50% tasseling, days to 50% silking, days to maturity, plant height, ear height, seed index, grain yield per plant, dry fodder yield per plant and popping expansion obtained in diallel study. The highest heterosis was observed fo...

  15. Functional impact of a recently identified quantitative trait locus for hippocampal volume with genome-wide support

    Erk, S.; Meyer-Lindenberg, A; Nöthen, M M; Heinz, A.; Walter, H.; Schmierer, P; Grimm, O.; H. Tost; Mühleisen, T; Mattheisen, M; Seiferth, N.; Cichon, S; Rietschel, M

    2013-01-01

    In a large brain-imaging study, a multinational consortium has recently identified a common genetic variation in rs7294919 being associated with hippocampal volume. Here, we explored whether this quantitative trait locus also affects hippocampal function using a previously established reliable neuroimaging paradigm. We observed a significant effect of rs7294919 variation in the right hippocampus showing that hippocampal activation increased with the number of risk alleles. Furthermore, the ri...

  16. Expression quantitative trait loci infer the regulation of isoflavone accumulation in soybean (Glycine max L. Merr.) seed

    Wang, Yan; Han, Yingpeng; Teng, Weili; Zhao, Xue; Li, Yongguang; Wu, Lin; Li, Dongmei; Li, Wenbin

    2014-01-01

    Background Mapping expression quantitative trait loci (eQTL) of targeted genes represents a powerful and widely adopted approach to identify putative regulatory variants. Linking regulation differences to specific genes might assist in the identification of networks and interactions. The objective of this study is to identify eQTL underlying expression of four gene families encoding isoflavone synthetic enzymes involved in the phenylpropanoid pathway, which are phenylalanine ammonia-lyase (PA...

  17. Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance

    Huang, Yadong; Li, Lin; Smith, Kevin P.; Muehlbauer, Gary J.

    2016-01-01

    Background Fusarium graminearum causes Fusarium head blight (FHB), a major disease problem worldwide. Resistance to FHB is controlled by quantitative trait loci (QTL) of which two are located on barley chromosomes 2H bin8 and 6H bin7. The mechanisms of resistance mediated by FHB QTL are poorly defined. Results Near-isogenic lines (NILs) carrying Chevron-derived resistant alleles for the two QTL were developed and exhibited FHB resistance in field trials. To understand the molecular responses ...

  18. Sex-specific quantitative trait loci contribute to normal variation in bone structure at the proximal femur in men

    Peacock, Munro; Koller, Daniel L; Lai, Dongbing; Hui, Siu; Foroud, Tatiana; Econs, Michael J.

    2005-01-01

    Bone structure is an important determinant of osteoporotic fracture. In women bone structure is highly heritable and several quantitative trait loci (QTL) have been reported. There are few comparable data in men. This study in men aimed at establishing the heritability of bone structure at the proximal femur, identifying QTL contributing to normal variation in bone structure, and determining which QTL might be sex-specific. Bone structure at the proximal femur was measured in 205 pairs of bro...

  19. Dynamic quantitative trait locus analysis of seed vigor at three maturity stages in rice.

    Liangfeng Liu

    Full Text Available Seed vigor is an important characteristic of seed quality. In this study, one rice population of recombinant inbred lines (RILs was used to determine the genetic characteristics of seed vigor, including the germination potential, germination rate, germination index and time for 50% of germination, at 4 (early, 5 (middle and 6 weeks (late after heading in two years. A total of 24 additive and 9 epistatic quantitative trait loci (QTL for seed vigor were identified using QTL Cartographer and QTLNetwork program respectively in 2012; while 32 simple sequence repeat (SSR markers associated with seed vigor were detected using bulked segregant analysis (BSA in 2013. The additive, epistatic and QTL × development interaction effects regulated the dry maturity developmental process to improve seed vigor in rice. The phenotypic variation explained by each additive, epistatic QTL and QTL × development interaction ranged from 5.86 to 40.67%, 4.64 to 11.28% and 0.01 to 1.17%, respectively. The QTLs were rarely co-localized among the different maturity stages; more QTLs were expressed at the early maturity stage followed by the late and middle stages. Twenty additive QTLs were stably expressed in two years which might play important roles in establishment of seed vigor in different environments. By comparing chromosomal positions of these stably expressed additive QTLs with those previously identified, the regions of QTL for seed vigor are likely to coincide with QTL for grain size, low temperature germinability and seed dormancy; while 5 additive QTL might represent novel genes. Using four selected RILs, three cross combinations of seed vigor for the development of RIL populations were predicted; 19 elite alleles could be pyramided by each combination.

  20. Quantitative trait loci mapping and genetic dissection for lint percentage in upland cotton (Gossypium hirsutum)

    Min Wang; Chengqi Li; Qinglian Wang

    2014-08-01

    Lint percentage is an important character of cotton yield components and it is also correlated with cotton fibre development. In this study, we used a high lint percentage variety, Baimian1, and a low lint percentage, TM-1 genetic standard for Gossypium hirsutum, as parents to construct a mapping populations in upland cotton (G. hirsutum). A quantitative trait locus/loci (QTL) analysis of lint percentage was performed by using two mapping procedures; composite interval mapping (CIM), inclusive composite interval mapping (ICIM) and the F2:3 populations in 2 years. Six main-effect QTL (M-QTL) for lint percentage (four significant and two suggestive) were detected in both years by CIM, and were located on chr. 3, chr. 19, chr. 26 and chr. 5 /chr. 19. Of the six QTL, marker intervals and favourable gene sources of the significant M-QTL, qLP-3(2010) and qLP-3(2011) were consistent. These QTL were also detected by ICIM, and therefore, should preferentially be used for marker-assisted selection (MAS) of lint percentage. Another M-QTL, qLP-19(2010), was detected by two mapping procedures, and it could also be a candidate for MAS. We detected the interaction between two M-QTL and environment, and 11 epistatic QTL (E-QTL) and their interaction with environment by using ICIM. The study also found two EST-SSRs, NAU1187 and NAU1255, linked to M-QTL for lint percentage that could be candidate markers affecting cotton fibre development.

  1. Estimating effects of a single gene and polygenes on quantitative traits from a diallel design.

    Lou, Xiang-Yang; Yang, Mark C K

    2006-01-01

    A genetic model is developed with additive and dominance effects of a single gene and polygenes as well as general and specific reciprocal effects for the progeny from a diallel mating design. The methods of ANOVA, minimum norm quadratic unbiased estimation (MINQUE), restricted maximum likelihood estimation (REML), and maximum likelihood estimation (ML) are suggested for estimating variance components, and the methods of generalized least squares (GLS) and ordinary least squares (OLS) for fixed effects, while best linear unbiased prediction, linear unbiased prediction (LUP), and adjusted unbiased prediction are suggested for analyzing random effects. Monte Carlo simulations were conducted to evaluate the unbiasedness and efficiency of statistical methods involving two diallel designs with commonly used sample sizes, 6 and 8 parents, with no and missing crosses, respectively. Simulation results show that GLS and OLS are almost equally efficient for estimation of fixed effects, while MINQUE (1) and REML are better estimators of the variance components and LUP is most practical method for prediction of random effects. Data from a Drosophila melanogaster experiment (Gilbert 1985a, Theor appl Genet 69:625-629) were used as a working example to demonstrate the statistical analysis. The new methodology is also applicable to screening candidate gene(s) and to other mating designs with multiple parents, such as nested (NC Design I) and factorial (NC Design II) designs. Moreover, this methodology can serve as a guide to develop new methods for detecting indiscernible major genes and mapping quantitative trait loci based on mixture distribution theory. The computer program for the methods suggested in this article is freely available from the authors. PMID:17028974

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

    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.

  3. A genome scan for quantitative trait loci affecting growth-related traits in an F1 family of Asian seabass (Lates calcarifer

    Yue Gen

    2006-10-01

    Full Text Available Abstract Background Body weight and length are economically important traits in foodfish species influenced by quantitative trait loci (QTL and environmental factors. It is usually difficult to dissect the genetic and environmental effects. Asian seabass (Lates calcarifer is an important marine foodfish species with a compact genome (~700 Mb. The recent construction of a first generation linkage map of Asian seabass with 240 microsatellites provides a good opportunity to determine the number and position of QTL, and the magnitude of QTL effects with a genome scan. Results We conducted a genome scan for QTL affecting body weight, standard length and condition factors in an F1 family containing 380 full-sib individuals from a breeding stock by using 97 microsatellites evenly covering 24 chromosomes. Interval mapping and multiple QTL model mapping detected five significant and 27 suggestive QTL on ten linkage groups (LGs. Among the five significant QTL detected, three (qBW2-a, qTL2-a and qSL2-a controlling body weight, total and standard length respectively, were mapped on the same region near Lca287 on LG2, and explained 28.8, 58.9 and 59.7% of the phenotypic variance. The other two QTL affecting body weight, qBW2-b and qBW3, were located on LG2 and 3, and accounted for 6.4 and 8.8% of the phenotypic variance. Suggestive QTL associated with condition factors are located on six different LGs. Conclusion This study presents the first example of QTL detection for growth-related traits in an F1 family of a marine foodfish species. The results presented here will enable further fine-mapping of these QTL for marker-assisted selection of the Asian seabass, eventually identifying individual genes responsible for growth-related traits.

  4. Quantitative plant ecology:statistical and ecological modelling of plant abundance

    Damgaard, Christian

    2014-01-01

    This e-book is written in the Wolfram' CDF format (download free CDF player from Wolfram.com)The objective of this e-book is to introduce the population ecological concepts for measuring and predicting the ecological success of plant species. This will be done by focusing on the measurement and statistical modelling of plant species abundance and the relevant ecological processes that control species abundance. The focus on statistical modelling and likelihood function based methods also mean...

  5. Quantitative Trait Loci for Grain Chalkiness and Endosperm Transparency Detected in Three Recombinant Inbred Line Populations of Indica Rice

    MEI De-yong; ZHU Yu-jun; YU Yong-hong; FAN Ye-yang; HUANG De-run; ZHUANG Jie-yun

    2013-01-01

    Quantitative trait loci (QTL) for percentage of chalky grain, degree of chalkiness, and endosperm transparency were detected using 3 recombinant inbred line populations derived from crosses between parental lines of commercial three-line hybrids of indica rice. Two of the populations showed great variations on heading date, and the other had a short range of heading date variation. A total of 40 QTLs were detected and fell into 15 regions of 10 chromosomes, of which 5 regions were detected for 1 or more same traits over different populations, 2 were detected for different traits in different populations, 3 were detected for 2 or all the 3 traits in a single population, and 5 were detected for a single trait in a single population. Most of these QTLs have been reported previously, but a region located on the long arm of chromosome 10 showing significant effects in all the 3 populations has not been reported before. It was shown that a number of gene cloned, including the Wx and Alk for the physiochemical property of rice grain, and GW2, GS3 and GW5 for grain weight and grain size, could have played important roles for the genetic control of grain chalkiness in rice, but there are many more QTLs exerting stable effects for rice chalkiness over different genetic backgrounds. It is worth paying more attentions to these regions which harbor QTL such as the qPCG5.2/qDC5.2/qET5.2 and qPCG10/qDC10/qET10 detected in our study. Our results also showed that the use of segregating populations having high-uniform heading date could greatly increase the efficiency of the identification of QTL responsible for traits that are subjected to great environmental influence.

  6. Quantitative inheritance for fruit traits in inter varietal crosses of okra (Abelmoschus esculentus L. Moench

    Deepak Arora, Salesh Kumar Jindal and T. R. Ghai

    2010-12-01

    Full Text Available Gene effects for important fruit traits of four inter-varietal crosses of okra were estimated by partitioning the means and variances of means of sixbasic generations from each cross into their genetic components to assess the gene action governing the inheritance of fruit yield and earlinessrelated traits in spring and rainy season. The additive, dominance and digenic non-allelic gene interactions were observed to govern most of thefruit traits. The non-additive gene effects were more pronounced than additive ones for most of the traits in both the environments. The evidenceof duplicate type of epistasis has been obtained for all the characters in different crosses in both the seasons. Thus for developing high yieldingokra cultivars, recurrent selection in biparental progenies would help in exploiting the duplicate type of non-allelic interactions and allowrecombination and concentration of genes having cumulative effects in population.

  7. Abundance and distribution of ultramafic microbreccia in Moses Rock dike - Quantitative application of mapping spectroscopy

    Mustard, John F.; Pieters, Carle M.

    1987-01-01

    Data from the Airborne Imaging Spectrometer were used to map the distribution and abundance of the serpentized ultramafic microbreccia (SUM) component in the Moses Rock dike, which is a Tertiary diatreme located on the Colorado Plateau in Utah. The geologic setting and composition of Moses Rock dike are discussed together with its texture and the relationship to the bedrock of surface materials. These observations along with laboratory spectroscopic data are used to interpret surface mineralogy of the dike and the surrounding regions from the imaging spectometer data. The spatial distribution and the abundance of the primary surface components were calculated using a nonlinear model for the mixing of spectra from multicomponent surfaces. The derived SUM distribution and abundance data support McGetchin's (1968) model for the emplacement of Moses Rock dike as a fluidized system.

  8. Selection for quantitative trait loci associated with resistance to Stewart's wilt in sweet corn.

    Pataky, J K; Bohn, M O; Lutz, J D; Richter, P M

    2008-04-01

    The objectives of this research were to identify quantitative trait loci (QTL) for Stewart's wilt resistance from a mapping population derived from a sweet corn hybrid that is highly resistant to Pantoea stewartii and to determine if marker-based selection for those QTL could substantially improve Stewart's wilt resistance in a population derived from a cross of resistant lines and a highly susceptible sweet corn inbred. Three significant QTL for Stewart's wilt resistance on chromosomes 2 (bin 2.03), 5 (bin 5.03), and 6 (bin 6.06/6.07) explained 31% of the genetic variance in a population of 110 F(3:4) families derived from the sweet corn hybrid Bonus. The three QTL appeared to be additive in their effects on Stewart's wilt ratings. Based on means of families that were either homozygous or heterozygous for marker alleles associated with the resistance QTL, the QTL on chromosomes 2 and 6 appeared to have dominant or partially dominant gene action, while the QTL on chromosome 5 appeared to be recessive. A population of 422 BC(2)S(2) families was derived from crosses of a sweet corn inbred highly susceptible to Stewart's wilt, Green Giant Code 88 (GG88), and plants from two F(3:4) families (12465 and 12467) from the Bonus mapping population that were homozygous for marker alleles associated with Stewart's wilt resistance at the three QTL. Mean Stewart's wilt ratings for BC(2)S(2) families were significantly (P < 0.05) lower for families that were homozygous for the bnlg1902 marker allele (bin 5.03) from resistant lines 12465 or 12467 than for families that were heterozygous at this marker locus or homozygous for the bnlg1902 marker allele from GG88. Resistance associated with this QTL was expressed only if F(3:5) or BC(2)S(2) families were homozygous for marker alleles associated with the resistant inbred parent (P(1)). Marker alleles identified in the F(3:5) mapping population that were in proximity to the resistance QTL on chromosomes 2 and 6 were not polymorphic in

  9. Identifying quantitative trait loci affecting resistance to congenital hypothyroidism in 129/SvJcl strain mice.

    Yayoi Hosoda

    Full Text Available Tyrosylprotein sulfotransferase 2 (TPST2 is one of the enzymes responsible for tyrosine O-sulfation and catalyzes the sulfation of the specific tyrosine residue of thyroid stimulating hormone receptor (TSHR. Since this modification is indispensable for the activation of TSH signaling, a non-functional TPST2 mutation (Tpst2(grt in DW/J-grt mice leads to congenital hypothyroidism (CH characterized by severe thyroid hypoplasia and dwarfism related to TSH hyporesponsiveness. Previous studies indicated that the genetic background of the 129(+Ter/SvJcl (129 mouse strain ameliorates Tpst2(grt-induced CH. To identify loci responsible for CH resistance in 129 mice, we performed quantitative trait locus (QTL analysis using backcross progenies from susceptible DW/J and resistant 129 mice. We used the first principal component calculated from body weights at 5, 8 and 10 weeks as an indicator of CH, and QTL analysis mapped a major QTL showing a highly significant linkage to the distal portion of chromosome (Chr 2; between D2Mit62 and D2Mit304, particularly close to D2Mit255. In addition, two male-specific QTLs showing statistically suggestive linkage were also detected on Chrs 4 and 18, respectively. All QTL alleles derived from the 129 strain increased resistance to growth retardation. There was also a positive correlation between recovery from thyroid hypoplasia and the presence of the 129 allele at D2Mit255 in male progenies. These results suggested that the major QTL on Chr 2 is involved in thyroid development. Moreover, since DW/J congenic strain mice carrying both a Tpst2(grt mutation and 129 alleles in the major QTL show resistance to dwarfism and thyroid hypoplasia, we confirmed the presence of the resistant gene in this region, and that it is involved in thyroid development. Further genetical analysis should lead to identification of genes for CH tolerance and, from a better understanding of thyroid organogenesis and function, the subsequent

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

    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

  11. Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

    Frank M. You

    2016-04-01

    Full Text Available The type 2 modified augmented design (MAD2 is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters. Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline (http://probes.pw.usda.gov/bioinformatics_ tools/MADPipeline/index.html.

  12. Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

    Frank M. You; Qijian Song; Gaofeng Jia; Yanzhao Cheng; Scott Duguid; Helen Booker; Sylvie Cloutier

    2016-01-01

    The type 2 modified augmented design (MAD2) is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters. Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline (http://probes.pw.usda.gov/bioinformatics_ tools/MADPipeline/index.html).

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

    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.

  14. Quantitative trait locus analysis and construction of consensus genetic map for drought tolerance traits based on three recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.).

    Gautami, B; Pandey, M K; Vadez, V; Nigam, S N; Ratnakumar, P; Krishnamurthy, L; Radhakrishnan, T; Gowda, M V C; Narasu, M L; Hoisington, D A; Knapp, S J; Varshney, R K

    2012-08-01

    Groundnut (Arachis hypogaea L.) is an important food and cash crop grown mainly in semi-arid tropics (SAT) regions of the world where drought is the major constraint on productivity. With the aim of understanding the genetic basis and identification of quantitative trait loci (QTL) for drought tolerance, two new recombinant inbred line (RIL) mapping populations, namely ICGS 76 × CSMG 84-1 (RIL-2) and ICGS 44 × ICGS 76 (RIL-3), were used. After screening of 3,215 simple sequence repeat (SSR) markers on the parental genotypes of these populations, two new genetic maps were developed with 119 (RIL-2) and 82 (RIL-3) SSR loci. Together with these maps and the reference map with 191 SSR loci based on TAG 24 × ICGV 86031 (RIL-1), a consensus map was constructed with 293 SSR loci distributed over 20 linkage groups, spanning 2,840.8 cM. As all these three populations segregate for drought-tolerance-related traits, a comprehensive QTL analysis identified 153 main effect QTL (M-QTL) and 25 epistatic QTL (E-QTL) for drought-tolerance-related traits. Localization of these QTL on the consensus map provided 16 genomic regions that contained 125 QTL. A few key genomic regions were selected on the basis of the QTL identified in each region, and their expected role in drought adaptation is also discussed. Given that no major QTL for drought adaptation were identified, novel breeding approaches such as marker-assisted recurrent selection (MARS) and genomic selection (GS) approaches are likely to be the preferred approaches for introgression of a larger number of QTL in order to breed drought-tolerant groundnut genotypes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9660-0) contains supplementary material, which is available to authorized users. PMID:22924017

  15. Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog Ranitomeya imitator

    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...

  16. Sex chromosome linked genetic variance and the evolution of sexual dimorphism of quantitative traits.

    Husby, Arild; Schielzeth, Holger; Forstmeier, Wolfgang; Gustafsson, Lars; Qvarnström, Anna

    2013-03-01

    Theory predicts that sex chromsome linkage should reduce intersexual genetic correlations thereby allowing the evolution of sexual dimorphism. Empirical evidence for sex linkage has come largely from crosses and few studies have examined how sexual dimorphism and sex linkage are related within outbred populations. Here, we use data on an array of different traits measured on over 10,000 individuals from two pedigreed populations of birds (collared flycatcher and zebra finch) to estimate the amount of sex-linked genetic variance (h(2)z ). Of 17 traits examined, eight showed a nonzero h(2)Z estimate but only four were significantly different from zero (wing patch size and tarsus length in collared flycatchers, wing length and beak color in zebra finches). We further tested how sexual dimorphism and the mode of selection operating on the trait relate to the proportion of sex-linked genetic variance. Sexually selected traits did not show higher h(2)Z than morphological traits and there was only a weak positive relationship between h(2)Z and sexual dimorphism. However, given the relative scarcity of empirical studies, it is premature to make conclusions about the role of sex chromosome linkage in the evolution of sexual dimorphism. PMID:23461313

  17. Laboratory reflectance spectra of clay minerals mixed with Mars analog materials: Toward enabling quantitative clay abundances from Mars spectra

    Roush, Ted L.; Bishop, Janice L.; Brown, Adrian J.; Blake, David F.; Bristow, Thomas F.

    2015-09-01

    Quantitative estimates of clay minerals on the martian surface, via remote sensing observations, provide constraints on activity, timing, duration, and extent of aqueous processes and the geochemical environment in martian history. We describe an analytical study to begin enabling quantitative estimates of phyllosilicates when mixed with martian analog materials. We characterize the chemistry, mineralogy, particle size distribution, and reflectance spectra of the end-member materials: saponite, montmorillonite, pyroxene, and palagonitic soil. Reflectance spectra were obtained for physical mixtures of saponite and montmorillonite with pyroxene, and saponite with palagonitic soil. We analyzed the diagnostic phyllosilicate spectral signatures in the 2.2-2.4 μm wavelength region in detail for the mixtures. This involved fitting the observed ∼2.3 or ∼2.2 μm band depth, associated with the presence of saponite and montmorillonite, respectively, as a function of the abundance of these materials in the mixtures. Based upon the band depth of the spectral features we find that 3-5 wt.% of the clay minerals in the mixture with pyroxene can be recognized and at 25 wt.% their presence is indisputable in the mixtures. When the saponite is mixed with the lower albedo palagonitic soil, its presence is clearly distinguishable via the 1.4 and 2.3 μm features at 25 wt.% abundance. These relationships, between abundance and band depth, provide an ability to quantitatively address the amount of these materials in mixtures. The trends described here provide guidance for estimating the presence of phyllosilicates in matrices on the martian surface.

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

    Ci, Dunwei; Jiang, Dong; Li, Sishen;

    2012-01-01

    tolerance indexes (TI) were calculated for plants under Cd stress relative to control conditions. Cd concentrations in both root and shoot were determined and the amount of Cd accumulation and translocation calculated. The phenotypic variation of the above traits showed a continuous distribution pattern...... 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...

  19. Mapping quantitative trait loci in F2 incorporating phenotypes of F3 progeny.

    Zhang, Yuan-Ming; Xu, Shizhong

    2004-01-01

    In plants and laboratory animals, QTL mapping is commonly performed using F(2) or BC individuals derived from the cross of two inbred lines. Typical QTL mapping statistics assume that each F(2) individual is genotyped for the markers and phenotyped for the trait. For plant traits with low heritability, it has been suggested to use the average phenotypic values of F(3) progeny derived from selfing F(2) plants in place of the F(2) phenotype itself. All F(3) progeny derived from the same F(2) pl...

  20. Discovery of quantitative trait loci for resistance to parasitic nematode infection in sheep: I. Analysis of outcross pedigrees

    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

  1. Genetic and Physiological Characterization of Two Clusters of Quantitative Trait Loci Associated With Seed Dormancy and Plant Height in Rice

    Ye, Heng; Beighley, Donn H.; Feng, Jiuhuan; Gu, Xing-You

    2013-01-01

    Seed dormancy and plant height have been well-studied in plant genetics, but their relatedness and shared regulatory mechanisms in natural variants remain unclear. The introgression of chromosomal segments from weedy into cultivated rice (Oryza sativa) prompted the detection of two clusters (qSD1-2/qPH1 and qSD7-2/qPH7) of quantitative trait loci both associated with seed dormancy and plant height. Together, these two clusters accounted for >96% of the variances for plant height and ~71% of t...

  2. Identification of elite pure-lines from local lentil germplasm using diversity index based on quantitative traits

    Three hundred and seventeen accessions of lentil collected from all over the country were evaluated for six quantitative traits to investigate inter and intra-accession diversity in association with geographic pattern. Variation indicated that areas with high geographic diversity that is supposed to present high biological diversity are yet to be explored. Classification of germplasm gave rise to some elite lines for specific characters and the accessions for days to flowering (45), days to maturity (7), plant height (12), pods per cluster (17) and seed weight (27) have been selected and suggested for exploitation in breeding programme. Twelve clusters were observed with varying degrees of intercluster dissimilarity that suggested the selection of diverse superior parents for hybridization. Some of the characters associated with origin as high seed weight of germplasm collected from Baluchistan is needed to exploit for specific trait/s. Germplasm distribution revealed that Punjab and Sindh represented a high collections along with high diversity, whereas other areas are yet to be explored. Similarly zone 3a, 6, 7, 9 and 10 along with high mountains lack complete representation that indicated the importance for future collection mission to these areas. (author)

  3. Identification of a major quantitative trait locus for ear size induced by space flight in sweet corn.

    Yu, Y T; Li, G K; Yang, Z L; Hu, J G; Zheng, J R; Qi, X T

    2014-01-01

    The development of molecular markers has contributed to progress in identifying the gene(s) responsible for favorable variations in maize studies. In this study, quantitative trait locus (QTL) mapping was conducted using simple sequence repeat markers in an F2 sweet corn population from a cross between parental line 1132 and space flight-induced mutant line 751 to identify the loci contributing to an increase in some yield traits. A primary mutated genomic region was located on chromosome 9. In total, 26 QTL were detected for eight yield-related traits and assembled into three clusters on chromosome 9. The largest QTL cluster at bin 9.02/03, primarily contributing to >10% of the phenotypic variation in ear and cob diameters, was likely due to a major QTL. Desired alleles of these QTL were provided by the mutant line 751. The primary action of the major mutant allele was an additive effect. Another mutant locus, which was induced in bin 9.01, increased cob and ear diameters by dominant genetic action. PMID:24782164

  4. Habitat traits and patterns of abundance of the purple sea urchin, Paracentrotus lividus (Lamarck, 1816), at multiple scales along the north Portuguese coast

    Domínguez, Rula; Domínguez Godino, Jorge; Freitas, Cristiano; Machado, Inês; Bertocci, Iacopo

    2015-03-01

    Spatial and temporal patterns of abundance and distribution of sea urchins (Paracentrotus lividus) from intertidal rockpools of the north Portuguese coast were examined in relation to physical (surface, altitude, depth, topographic complexity and exposure) and biological (substrate cover by dominant organisms) habitat traits. The methodology was based on a multi-factorial design where the total number and the abundance of urchins in each of six size classes were sampled over a range of spatial scales, from 10s of cm to kms, and a temporal scale of five months. The results highlighted three main features of the studied system: (1) the largest proportion of variability of sea urchins occurred at the smallest scale examined; (2) urchins from different size classes showed different patterns of abundance in relation to habitat traits; (3) variables normally invoked as potential drivers of distribution of urchins at a range of scales, such as hydrodynamics and shore height, were relatively less important than other abiotic (i.e. pool area, pool mean depth calculated over five replicate measures and sand cover) and biological (i.e. space occupancy by the reef-forming polychaete Sabellaria alveolata and mussels vs. availability of bare rock) variables to provide a considerable contribution to the variability of sea urchins. Intertidal populations of sea urchins are abundant on many rocky shores, where they are socially and economically important as food resource and ecologically key as habitat modelers. This study provides new clues on relatively unstudied populations, with relevant implications for possible management decisions, including the implementation of protection schemes able to preserve the main recruitment, settlement and development areas of P. lividus.

  5. Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method.

    Lee, S. Y.; Bollinger, J; Bezdicek, D; Ogram, A

    1996-01-01

    Strain EA25 was identified in a clone library of bacterial 16S rRNA gene sequences that had been amplified from DNA extracted from soil collected in eastern Washington State. EA25 was subsequently shown to be related to members of the genera Planctomyces and Chlamydia and most closely related (93% similarity) to strain MC18, a strain identified in an Australian soil sample (W. Liesack and E. Stackebrandt, J. Bacteriol. 174:5072-5078, 1992). A competitive quantitative PCR method developed by Z...

  6. Using a Label Free Quantitative Proteomics Approach to Identify Changes in Protein Abundance in Multidrug-Resistant Mycobacterium tuberculosis.

    Phong, Truong Quoc; Ha, Do Thi Thu; Volker, Uwe; Hammer, Elke

    2015-06-01

    Reports in recent years indicate that the increasing emergence of resistance to drugs be using to TB treatment. The resistance to them severely affects to options for effective treatment. The emergence of multidrug-resistant tuberculosis has increased interest in understanding the mechanism of drug resistance in M. tuberculosis and the development of new therapeutics, diagnostics and vaccines. In this study, a label-free quantitative proteomics approach has been used to analyze proteome of multidrug-resistant and susceptible clinical isolates of M. tuberculosis and identify differences in protein abundance between the two groups. With this approach, we were able to identify a total of 1,583 proteins. The majority of identified proteins have predicted roles in lipid metabolism, intermediary metabolism, cell wall and cell processes. Comparative analysis revealed that 68 proteins identified by at least two peptides showed significant differences of at least twofolds in relative abundance between two groups. In all protein differences, the increase of some considering proteins such as NADH dehydrogenase, probable aldehyde dehydrogenase, cyclopropane mycolic acid synthase 3, probable arabinosyltransferase A, putative lipoprotein, uncharacterized oxidoreductase and six membrane proteins in resistant isolates might be involved in the drug resistance and to be potential diagnostic protein targets. The decrease in abundance of proteins related to secretion system and immunogenicity (ESAT-6-like proteins, ESX-1 secretion system associated proteins, O-antigen export system and MPT63) in the multidrug-resistant strains can be a defensive mechanism undertaken by the resistant cell. PMID:25805910

  7. Detection of quantitative trait loci for growth and beef carcass fatness traits in a cross between Bos taurus (Angus) and Bos indicus (Brahman) cattle.

    Kim, J J; Farnir, F; Savell, J; Taylor, J F

    2003-08-01

    This study was conducted to detect quantitative trait loci (QTL) affecting growth and beef carcass fatness traits in an experimental population of Angus and Brahman crossbreds. The three-generation mapping population was generated with 602 progeny from 29 reciprocal backcross and three F2 full-sib families, and 417 genetic markers were used to produce a sex-averaged map of the 29 autosomes spanning 2,642.5 Kosambi cM. Alternative interval-mapping approaches were applied under line-cross (LC) and random infinite alleles (RA) models to detect QTL segregating between and within breeds. A total of 35 QTL (five with genomewide significant and 30 with suggestive evidence for linkage) were found on 19 chromosomes. One QTL affecting yearling weight was found with genomewide significant evidence for linkage in the interstitial region of bovine autosome (BTA) 1, and an additional 19 QTL were detected with suggestive evidence for linkage under the LC model. Many of these QTL had a dominant (complete or overdominant) mode of gene action, and only a few of the QTL were primarily additive, which reflects the fact that heterosis for growth is known to be appreciable in crosses among Brahman and British breeds. Four QTL affecting growth were detected with genomewide significant evidence for linkage under the RA model on BTA 2 and BTA 6 for birth weight, BTA 5 for yearling weight, and BTA 23 for hot carcass weight. An additional 11 QTL were detected with suggestive evidence for linkage under the RA model. None of the QTL (except for yearling weight on BTA 5) detected under the RA model were found by the LC analyses, suggesting the segregation of alternate alleles within one or both of the parental breeds. Our results reveal the utility of implementing both the LC and RA models to detect dominant QTL and also QTL with similar allele frequency distributions within parental breeds. PMID:12926775

  8. Quadrature conductivity: A quantitative indicator of bacterial abundance in porous media

    Chi Zhang; Andre Revil; Yoshiko Fujita; Junko Munakata-Marr; George Redden

    2014-09-01

    ABSTRACT The abundance and growth stages of bacteria in subsurface porous media affect the concentrations and distributions of charged species within the solid-solution interfaces. Therefore, spectral induced polarization (SIP) measurements can be used to monitor changes in bacterial biomass and growth stage. Our goal was to gain a better understanding of the SIP response of bacteria present in a porous material. Bacterial cell surfaces possess an electric double layer and therefore become polarized in an electric field. We performed SIP measurements over the frequency range of 0.1–1 kHz on cell suspensions alone and cell suspensions mixed with sand at four pore water conductivities. We used Zymomonas mobilis at four different cell densities (in- cluding the background). The quadrature conductivity spectra exhibited two peaks, one around 0.05–0.10 Hz and the other around 1–10 Hz. Because SIP measurements on bacterial suspensions are typically made at frequencies greater than 1 Hz, these peaks have not been previously reported. In the bac-terial suspensions in growth medium, the quadrature conduc-tivity at peak I was linearly proportional to the density of the bacteria. For the case of the suspensions mixed with sands, we observed that peak II presented a smaller increase in the quadrature conductivity with the cell density. A comparison of the experiments with and without sand grains illustrated the effect of the porous medium on the overall quadrature con- ductivity response (decrease in the amplitude and shift of the peaks to the lower frequencies). Our results indicate that for a given porous medium, time-lapse SIP has potential for mon- itoring changes in bacterial abundance within porous media.

  9. ASSOCIATION OF GENETIC DIVERGENCE WITH HETEROSIS, COMBINING ABILITY AND MEAN VALUE FOR QUANTITATIVE TRAITS IN POPCORN (ZEA MAYS VAR. EVERTA

    N V SONI

    2013-12-01

    Full Text Available The study was aimed to analyze the genetic diversity among popcorn inbred lines using Random Amplified Polymorphic DNA profiling and to associate it with heterosis, specific combining ability and mean values of hybrids for quantitative traits viz., days to 50% tasseling, days to 50% silking, days to maturity, plant height, ear height, seed index, grain yield per plant, dry fodder yield per plant and popping expansion obtained in diallel study. The highest heterosis was observed for grain yield (99.16% followed by dry fodder yield (96.57%. Fifteen polymorphic RAPD primers were used for polymerase chain reaction amplification. In dendrogram, most of the genotypes were clustered in a single cluster except I-07-35-7-3 which grouped in another cluster. The estimate of genetic diversity varies from 0.49 to 0.86. Correlation coefficients (r ranged from -0.472 to 0.295. These correlations were extremely low or non-significant for all the quantitative traits. The results depicted that RAPD technique was efficient in detecting polymorphism in popcorn populations. Genetic diversity showed no significant association with all parameters of hybrid performance for days to maturity, plant height and seed index.

  10. Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice

    Lixia Xie; Zhengwei Tan; Yuan Zhou; Rongbao Xu; Laibao Feng; Yongzhong Xing; Xiaoquan Qi

    2014-01-01

    Seed vigor is an index of seed quality that is used to describe the rapid and uniform germination and the establish-ment of strong seedlings in any environmental conditions. Strong seed vigor in low-temperature germination conditions is particularly important in direct-sowing rice production systems. However, seed vigor has not been selected as an important breeding trait in traditional breeding programs due to its quantitative inherence. In this study, we identified and mapped eight quantitative trait loci (QTLs) for seed vigor by using a recombinant inbred population from a cross between rice (Oryza sativa L. ssp. indica) cultivars ZS97 and MH63. Conditional QTL analysis identified qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-11 influenced seedling establishment and that qSV-5a, qSV-5c, and qSV-8 influenced only germination. Of these, qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-8 were low-tempera-ture-specific QTLs. Two major-effective QTLs, qSV-1, and qSV-5c were narrowed down to 1.13-Mbp and 400-kbp genomic regions, respectively. The results provide tightly linked DNA markers for the marker-assistant pyramiding of multiple positive al eles for increased seed vigor in both normal and low-temperature germination environments.

  11. Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue.

    Federico Innocenti

    2011-05-01

    Full Text Available The discovery of expression quantitative trait loci ("eQTLs" can help to unravel genetic contributions to complex traits. We identified genetic determinants of human liver gene expression variation using two independent collections of primary tissue profiled with Agilent (n = 206 and Illumina (n = 60 expression arrays and Illumina SNP genotyping (550K, and we also incorporated data from a published study (n = 266. We found that ∼30% of SNP-expression correlations in one study failed to replicate in either of the others, even at thresholds yielding high reproducibility in simulations, and we quantified numerous factors affecting reproducibility. Our data suggest that drug exposure, clinical descriptors, and unknown factors associated with tissue ascertainment and analysis have substantial effects on gene expression and that controlling for hidden confounding variables significantly increases replication rate. Furthermore, we found that reproducible eQTL SNPs were heavily enriched near gene starts and ends, and subsequently resequenced the promoters and 3'UTRs for 14 genes and tested the identified haplotypes using luciferase assays. For three genes, significant haplotype-specific in vitro functional differences correlated directly with expression levels, suggesting that many bona fide eQTLs result from functional variants that can be mechanistically isolated in a high-throughput fashion. Finally, given our study design, we were able to discover and validate hundreds of liver eQTLs. Many of these relate directly to complex traits for which liver-specific analyses are likely to be relevant, and we identified dozens of potential connections with disease-associated loci. These included previously characterized eQTL contributors to diabetes, drug response, and lipid levels, and they suggest novel candidates such as a role for NOD2 expression in leprosy risk and C2orf43 in prostate cancer. In general, the work presented here will be

  12. Linkage Map Construction and Quantitative Trait Loci Analysis for Bolting Based on a Double Haploid Population of Brassica rapa

    Xu Yang; Yang-Jun Yu; Feng-Lan Zhang; Zhi-Rong Zou; Xiu-Yun Zhao; De-Shuang Zhang; Jia-Bing Xu

    2007-01-01

    Early bolting of Chinese cabbage (Brassica rapa L.) during spring cultivation often has detrimental effects on the yield and quality of the harvested products. Breeding late bolting varieties is a major objective of Chinese cabbage breeding programs. in order to analyze the genetic basis of bolting traits, a genetic map of B. rapa was constructed based on amplified fragment-length polymorphism (AFLP), sequence-related amplified polymorphism (SRAP), simple sequence repeat (SSR), random amplification of polymorphic DNA (RAPD), and isozyme markers. Marker analysis was carried out on 81 double haploid (DH) lines obtained by mlcrospore culture from F1 progeny of two homozygous parents: B. rapa L. ssp. pekinensis (BY) (an extra-early bolting Chinese cabbage line) and B. rapa L. ssp. rapifera (MM) (an extra-late bolting European turnip line). A total of 326 markers including 130 AFLPs, 123 SRAPs, 16 SSRs, 43RAPDs and 14 isozymes were used to construct a linkage map with 10 linkage groups covering 882 cM with an average distance of 2.71 cM between loci. The bolting trait of each DH line was evaluated by the bolting index under controlled conditions. Quantitative trait loci (QTL) analysis was conducted using multiple QTL model mapping with MapQTL5.0 software. Eight QTLs controlling bolting resistance were identified. These QTLs, accounting for 14.1% to 25.2% of the phenotyplc variation with positive additive effects, were distributed into three linkage groups. These results provide useful information for molecular marker-assisted selection of late bolting traits in Chinese cabbage breeding programs.

  13. Impact of type 2 diabetes susceptibility variants on quantitative glycemic traits reveals mechanistic heterogeneity

    Dimas, Antigone S; Lagou, Vasiliki; Barker, Adam;

    2013-01-01

    Patients with established type 2 diabetes display both beta-cell dysfunction and insulin resistance. To define fundamental processes leading to the diabetic state, we examined the relationship between type 2 diabetes risk variants at 37 established susceptibility loci and indices of proinsulin...... processing, insulin secretion and insulin sensitivity. We included data from up to 58,614 non-diabetic subjects with basal measures, and 17,327 with dynamic measures. We employed additive genetic models with adjustment for sex, age and BMI, followed by fixed-effects inverse variance meta-analyses. Cluster....... The final group contained twenty risk loci with no clear-cut associations to continuous glycemic traits. By assembling extensive data on continuous glycemic traits, we have exposed the diverse mechanisms whereby type 2 diabetes risk variants impact disease predisposition....

  14. Genetic Parameters and Combining Ability Effects of Parents for Seed Yield and other Quantitative Traits in Black Gram [Vigna mungo (L. Hepper

    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.

  15. Quantitative trait loci analysis of chlorophyll content for flag leaf in rice

    2000-01-01

    @@Chlorophyll contents are one of important physiological traits, which affect photosynthesis in plants. There were significant differences in chlorophyll contents between Zhaiyeqing 8(ZYQ 8), an indica variety and Jingxi 17(JX 17), a japonica variety (Table 1). In 117 DH lines of the cross of ZYQ 8/ JX 17, these parameters distributed conTwo neutral alleles of improving male gamete abortion in indica-japonica hybrid rice LU Chuangen and ZOU Jiangshi, Jiangsu Acad of Agri Sci, Nanjing 210014, China

  16. Association mapping, a method to detect quantitative trait loci: statistical bases

    2012-01-01

    Traditionally, QTL mapping has been used as methodology to understand the genetic control of polygenic traits and has been useful for identifying QTL in different species, however QTL mapping presents limitations, such as the difficulty to build segregating populations in some species, the presence of only one meiotic generation and the reduced genetically diversity derived of just two parental. Recently, association genetics studies are becoming an important methodology to identify quantitat...

  17. Unilateral and Bilateral Expression of a Quantitative Trait: Asymmetry and Symmetry in Coronal Craniosynostosis

    Heuzé, Yann; Martínez-Abadías, Neus; STELLA, JENNIFER M.; Senders, Craig W.; Simeon A Boyadjiev; Lo, Lun-Jou; Richtsmeier, Joan T.

    2012-01-01

    Bilateral symmetry in vertebrates is imperfect and mild asymmetries are found in normal growth and development. However, abnormal development is often characterized by strong asymmetries. Coronal craniosynostosis, defined here as consisting of premature suture closure and a characteristic skull shape, is a complex trait. The premature fusion of the coronal suture can occur unilaterally associated with skull asymmetry (anterior plagiocephaly) or bilaterally associated with a symmetric but brac...

  18. A Haplotype Block Model for Fine Mapping of Quantitative Trait Loci Regulating HIV-1 Pathogenesis

    Zhu, Yun; Hou, Wei; Wu, Rongling

    2003-01-01

    The dynamic change of human immunodeficiency virus type-1 (HIV-1) particles that cause AIDS displays considerable variation from patients to patients. It is likely that such variation in HIV-1 pathogenesis is correlated with the genetic architecture of hosts. Traditional genetic analysis of HIV-1 infection is based on various biochemical approaches, but it has been little successful because HIV-1 dynamics, as a complex trait, is under polygenic control and sensitive to environmental changes. ...

  19. Evaluation of Qualitative and Quantitative Traits of Maize (cv. 604 Under Drought Stress and Plant Density

    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.

  20. Abundance and distribution of ultramafic microbreccia in Moses Rock Dike: Quantitative application of AIS data

    Mustard, John F.; Pieters, Carle M.

    1987-01-01

    Moses Rock dike is a Tertiary diatreme containing serpentinized ultramafic microbreccia (SUM). Field evidence indicates the SUM was emplaced first followed by breccias derived from the Permian strata exposed in the walls of the diatreme and finally by complex breccias containing basement and mantle derived rocks. SUM is found primarily dispersed throughout the matrix of the diatreme. Moses Rock dike was examined with Airborne Imaging Spectrometer (AIS) to map the distribution and excess of SUM in the matrix and to better understand the nature of the eruption which formed this explosive volcanic feature. AIS data was calibrated by dividing the suite of AIS data by data from an internal standard area and then multiplying this relative reflectance data by the absolute bidirectional reflectance of a selected sample from the standard area which was measured in the lab. From the calibrated AIS data the minerals serpentine, gypsum, and illite as well as desert varnish and the lithologies SUM and other sandstones were identified. SUM distribution and abundance in the matrix of the diatreme were examined in detail and two distinct styles of SUM dispersion were observed. The two styles are discussed in detail.

  1. Identification of quantitative trait locus for abscisic acid responsiveness on chromosome 5A and association with dehydration tolerance in common wheat seedlings.

    Iehisa, Julio C M; Matsuura, Takakazu; Mori, Izumi C; Takumi, Shigeo

    2014-01-15

    The phytohormone abscisic acid (ABA) plays important roles in response to environmental stress as well as in seed maturation and dormancy. In common wheat, quantitative trait loci (QTLs) for ABA responsiveness at the seedling stage have been reported on chromosomes 1B, 2A, 3A, 6D and 7B. In this study, we identified a novel QTL for ABA responsiveness on chromosome 5A using an F2 population derived from a cross between the common wheat cultivar Chinese Spring (CS) and a chromosome substitution line of CS with chromosome 5A of cultivar Hope (Hope5A). This QTL was found in a similar chromosomal region to previously reported QTLs for drought tolerance and seed dormancy. Physiological characterization of the QTL revealed a small effect on dehydration tolerance and seed dormancy. The rate of water loss from leaves during dehydration was lower, and transcript accumulation of the cold responsive (COR)/late embryogenesis abundant (LEA) genes Wrab18 and Wdhn13 tended to be higher under dehydration stress in F2 individuals carrying the Hope allele of the QTL, which also showed higher ABA responsiveness than the CS allele-carrying individuals. Seed dormancy of individuals carrying the Hope allele also tended to be lower than those carrying the CS allele. Our results suggest that variation in ABA responsiveness among common wheat cultivars is at least partly determined by the 5A QTL, and that this QTL contributes to development of dehydration and preharvest sprouting tolerance. PMID:24331416

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

    Brøndum, Rasmus Froberg; Su, Guosheng; Janss, Luc;

    2015-01-01

    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...... 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...

  3. Molecular identification of a major quantitative trait locus, qLTG3–1, controlling low-temperature germinability in rice

    Fujino, Kenji; Sekiguchi, Hiroshi; Matsuda, Yasuyuki; Sugimoto, Kazuhiko; Ono, Kazuko; Yano, Masahiro

    2008-01-01

    Tolerance to abiotic stress is an important agronomic trait in crops and is controlled by many genes, which are called quantitative trait loci (QTLs). Identification of these QTLs will contribute not only to the understanding of plant biology but also for plant breeding, to achieve stable crop production around the world. Previously, we mapped three QTLs controlling low-temperature tolerance at the germination stage (called low-temperature germinability). To understand the molecular basis of ...

  4. Quantitative Trait Loci Mapping of Maize Yield and Its Components Under Different Water Treatments at Flowering Time

    Gui-He Lu; Yi-Rong Zhang; Jing-Rui Dai; Ji-Hua Tang; Jian-Bing Yan; Xi-Qing Ma; Jian-Sheng Li; Shao-Jiang Chen; Jian-Cang Ma; Zhan-Xian Liu; Li-Zhu E

    2006-01-01

    Drought or water stress is a serious agronomic problem resulting in maize (Zea mays L.) yield loss throughout the world. Breeding hybrids with drought tolerance is one important approach for solving this problem. However, lower efficiency and a longer period of breeding hybrids are disadvantages of traditional breeding programs. It is generally recognized that applying molecular marker techniques to traditional breeding programs could improve the efficiency of the breeding of drought-tolerant maize. To provide useful information for use in studies of maize drought tolerance,the mapping and tagging of quantitative trait loci (QTL) for yield and its components were performed in the present study on the basis of the principle of a mixed linear model. Two hundred and twenty-one recombinant inbred lines (RIL) of Yuyu 22 were grown under both well-watered and water-stressed conditions. In the former treatment group, plants were well irrigated, whereas those in the latter treatment group were stressed at flowering time.Ten plants of each genotype were grown in a row that was 3.00 m×0.67 m (length×width). The results show that a few of the QTL were the same (one additive QTL for ear length, two additive QTL and one pair of epistatic QTL for kernel number per row, one additive QTL for kernel weight per plant), whereas most of other QTL were different between the two different water treatment groups. It may be that genetic expression differs under the two different water conditions. Furthermore, differences in the additive and epistatic QTL among the traits under water-stressed conditions indicate that genetic expression also differs from trait to trait.Major and minor QTL were detected for the traits,except for kernel number per row, under water-stressed conditions. Thus, the genetic mechanism of drought tolerance in maize is complex because the additive and epistatic QTL exist at the same time and the major and minor QTL all contribute to phenotype under water

  5. Power to detect trends in abundance of secretive marsh birds: effects of species traits and sampling effort

    Steidl, Robert J.; Conway, Courtney J.; Litt, Andrea R.

    2013-01-01

    Standardized protocols for surveying secretive marsh birds have been implemented across North America, but the efficacy of surveys to detect population trends has not been evaluated. We used survey data collected from populations of marsh birds across North America and simulations to explore how characteristics of bird populations (proportion of survey stations occupied, abundance at occupied stations, and detection probability) and aspects of sampling effort (numbers of survey routes, stations/route, and surveys/station/year) affect statistical power to detect trends in abundance of marsh bird populations. In general, the proportion of survey stations along a route occupied by a species had a greater relative effect on power to detect trends than did the number of birds detected per survey at occupied stations. Uncertainty introduced by imperfect detection during surveys reduced power to detect trends considerably, but across the range of detection probabilities for most species of marsh birds, variation in detection probability had only a minor influence on power. For species that occupy a relatively high proportion of survey stations (0.20), have relatively high abundances at occupied stations (2.0 birds/station), and have high detection probability (0.50), ≥40 routes with 10 survey stations per route surveyed 3 times per year would provide an 80% chance of detecting a 3% annual decrease in abundance after 20 years of surveys. Under the same assumptions but for species that are less common, ≥100 routes would be needed to achieve the same power. Our results can help inform the design of programs to monitor trends in abundance of marsh bird populations, especially with regards to the amount of sampling effort necessary to meet programmatic goals.

  6. Evaluation of genetic variance components for some quantitative traits in rapeseed (Brassica napus L.

    Marjanović-Jeromela Ana

    2014-01-01

    Full Text Available Three hybrid combinations obtained by crossing six winter rapeseed cultivars were analyzed for the impact of genes with additive and dominant effects and their interactions with inheritance of plant height and first lateral branch height. The linkage among the expected progeny means was checked using the scaling test method (Mather, 1949, while the estimates of genetic effects and mode of inheritance was made by the Generation Mean Analysis (Mather and Jinks, 1982. The additive dominant model did not prove adequate for plant height in all three crosses, and for first lateral branch height in the second and third cross. The inadequacy of the model showed epistatic gene effects were also of large importance in the inheritance of these traits. Duplicate epistasis for plant height inheritance was found in all three cross combinations and for inheritance of height of the first lateral branch in second and third cross combination. However, it should be emphasized that duplicate epistasis among dominant positive genes occurred on plant height inheritance in C1 and C3, and on inheritance of first lateral branch height in C3. Duplicate epistasis among dominant negative genes occurred in C2 on the mode of inheritance of both traits. [Projekat Ministarstva nauke Republike Srbije, br. TR-31025

  7. Impact of type 2 diabetes susceptibility variants on quantitative glycemic traits reveals mechanistic heterogeneity.

    Dimas, Antigone S; Lagou, Vasiliki; Barker, Adam; Knowles, Joshua W; Mägi, Reedik; Hivert, Marie-France; Benazzo, Andrea; Rybin, Denis; Jackson, Anne U; Stringham, Heather M; Song, Ci; Fischer-Rosinsky, Antje; Boesgaard, Trine Welløv; Grarup, Niels; Abbasi, Fahim A; Assimes, Themistocles L; Hao, Ke; Yang, Xia; Lecoeur, Cécile; Barroso, Inês; Bonnycastle, Lori L; Böttcher, Yvonne; Bumpstead, Suzannah; Chines, Peter S; Erdos, Michael R; Graessler, Jurgen; Kovacs, Peter; Morken, Mario A; Narisu, Narisu; Payne, Felicity; Stancakova, Alena; Swift, Amy J; Tönjes, Anke; Bornstein, Stefan R; Cauchi, Stéphane; Froguel, Philippe; Meyre, David; Schwarz, Peter E H; Häring, Hans-Ulrich; Smith, Ulf; Boehnke, Michael; Bergman, Richard N; Collins, Francis S; Mohlke, Karen L; Tuomilehto, Jaakko; Quertemous, Thomas; Lind, Lars; Hansen, Torben; Pedersen, Oluf; Walker, Mark; Pfeiffer, Andreas F H; Spranger, Joachim; Stumvoll, Michael; Meigs, James B; Wareham, Nicholas J; Kuusisto, Johanna; Laakso, Markku; Langenberg, Claudia; Dupuis, Josée; Watanabe, Richard M; Florez, Jose C; Ingelsson, Erik; McCarthy, Mark I; Prokopenko, Inga

    2014-06-01

    Patients with established type 2 diabetes display both β-cell dysfunction and insulin resistance. To define fundamental processes leading to the diabetic state, we examined the relationship between type 2 diabetes risk variants at 37 established susceptibility loci, and indices of proinsulin processing, insulin secretion, and insulin sensitivity. We included data from up to 58,614 nondiabetic subjects with basal measures and 17,327 with dynamic measures. We used additive genetic models with adjustment for sex, age, and BMI, followed by fixed-effects, inverse-variance meta-analyses. Cluster analyses grouped risk loci into five major categories based on their relationship to these continuous glycemic phenotypes. The first cluster (PPARG, KLF14, IRS1, GCKR) was characterized by primary effects on insulin sensitivity. The second cluster (MTNR1B, GCK) featured risk alleles associated with reduced insulin secretion and fasting hyperglycemia. ARAP1 constituted a third cluster characterized by defects in insulin processing. A fourth cluster (TCF7L2, SLC30A8, HHEX/IDE, CDKAL1, CDKN2A/2B) was defined by loci influencing insulin processing and secretion without a detectable change in fasting glucose levels. The final group contained 20 risk loci with no clear-cut associations to continuous glycemic traits. By assembling extensive data on continuous glycemic traits, we have exposed the diverse mechanisms whereby type 2 diabetes risk variants impact disease predisposition. PMID:24296717

  8. Impact of Type 2 Diabetes Susceptibility Variants on Quantitative Glycemic Traits Reveals Mechanistic Heterogeneity

    Dimas, Antigone S.; Lagou, Vasiliki; Barker, Adam; Knowles, Joshua W.; Mägi, Reedik; Hivert, Marie-France; Benazzo, Andrea; Rybin, Denis; Jackson, Anne U.; Stringham, Heather M.; Song, Ci; Fischer-Rosinsky, Antje; Boesgaard, Trine Welløv; Grarup, Niels; Abbasi, Fahim A.; Assimes, Themistocles L.; Hao, Ke; Yang, Xia; Lecoeur, Cécile; Barroso, Inês; Bonnycastle, Lori L.; Böttcher, Yvonne; Bumpstead, Suzannah; Chines, Peter S.; Erdos, Michael R.; Graessler, Jurgen; Kovacs, Peter; Morken, Mario A.; Narisu, Narisu; Payne, Felicity; Stancakova, Alena; Swift, Amy J.; Tönjes, Anke; Bornstein, Stefan R.; Cauchi, Stéphane; Froguel, Philippe; Meyre, David; Schwarz, Peter E.H.; Häring, Hans-Ulrich; Smith, Ulf; Boehnke, Michael; Bergman, Richard N.; Collins, Francis S.; Mohlke, Karen L.; Tuomilehto, Jaakko; Quertemous, Thomas; Lind, Lars; Hansen, Torben; Pedersen, Oluf; Walker, Mark; Pfeiffer, Andreas F.H.; Spranger, Joachim; Stumvoll, Michael; Meigs, James B.; Wareham, Nicholas J.; Kuusisto, Johanna; Laakso, Markku; Langenberg, Claudia; Dupuis, Josée; Watanabe, Richard M.; Florez, Jose C.; Ingelsson, Erik; McCarthy, Mark I.; Prokopenko, Inga

    2014-01-01

    Patients with established type 2 diabetes display both β-cell dysfunction and insulin resistance. To define fundamental processes leading to the diabetic state, we examined the relationship between type 2 diabetes risk variants at 37 established susceptibility loci, and indices of proinsulin processing, insulin secretion, and insulin sensitivity. We included data from up to 58,614 nondiabetic subjects with basal measures and 17,327 with dynamic measures. We used additive genetic models with adjustment for sex, age, and BMI, followed by fixed-effects, inverse-variance meta-analyses. Cluster analyses grouped risk loci into five major categories based on their relationship to these continuous glycemic phenotypes. The first cluster (PPARG, KLF14, IRS1, GCKR) was characterized by primary effects on insulin sensitivity. The second cluster (MTNR1B, GCK) featured risk alleles associated with reduced insulin secretion and fasting hyperglycemia. ARAP1 constituted a third cluster characterized by defects in insulin processing. A fourth cluster (TCF7L2, SLC30A8, HHEX/IDE, CDKAL1, CDKN2A/2B) was defined by loci influencing insulin processing and secretion without a detectable change in fasting glucose levels. The final group contained 20 risk loci with no clear-cut associations to continuous glycemic traits. By assembling extensive data on continuous glycemic traits, we have exposed the diverse mechanisms whereby type 2 diabetes risk variants impact disease predisposition. PMID:24296717

  9. Identification of quantitative trait loci for the dead leaf rate and the seedling dead rate under alkaline stress in rice

    Dongling Qi; Guizhen Guo; Myung-chul Lee; Junguo Zhang; Guilan Cao; Sanyuan Zhang; Seok-cheol Suh; Qingyang Zhou; Longzhi Han

    2008-01-01

    The quantitative trait loci (QTLs) for the dead leaf rate (DLR) and the dead seedling rate (DSR) at the different rice growing periods after transplanting under alkaline stress were identified using an F2:3 population, which included 200 individuals and lines derived from a cross betweea two japonica rice cultivars Gaochan 106 and Changbai 9 with microsatellite markers. The DLR detected at 20 days to 62 days after transplanting under alkaline stress showed continuous normal or near normal distributions in F3 lines, which was the quantita-tive trait controlled by multiple genes. The DSR showed a continuous distribution with 3 or 4 peaks and was the quantitative trait con-trolled by main and multiple genes when rice was grown for 62 days after transplanting under alkaline stress. Thirteen QTLs associated with DLR were detected at 20 days to 62 days after transplanting under alkaline stress. Among these, qDLR9-2 located in RM5786-RMI60 on chromosome 9 was detected at 34 days, 41 days, 48 days, 55 days, and 62 days, respectively; qDLR4 located in RM3524-RM3866 on chromosome 4 was detected at 34 days, 41 days, and 48 days, respectively; qDLR7-1 located in RM3859-RM320 on chromosome 7 was detected at 20 days and 27 days; and qDLR6-2 in RM1340-RM5957 on chromosome 6 was detected at 55 days and 62 days, respectively. The alleles of both qDLR9-2 and qDLR4 were derived from alkaline sensitive parent "Gaochan 106". The alleles of both qDLR7-1 and qDLR6-2 were from alkaline tolerant parent Changbai 9. These geue actions showed dominance and over dominance primarily. Six QTLs associated with DSR were detected at 62 days after transplanting under alkaline stress. Among these, qDSR6-2 and qDSR8 were located in RM1340-RM5957 on chromosome 6 and in RM3752-RM404 on chromosome 8, respectively, which were asso-ciated with DSR and accounted for 20.32% and 18.86% of the observed phenotypic variation, respectively; qDSR11-2 and qDSR11-3 were located in RM536-RM479 and RM2596-RM286 on

  10. Quantitative trait loci for thermal time to flowering and photoperiod responsiveness discovered in summer annual-type Brassica napus L.

    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.

  11. Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping.

    Shinada, Hiroshi; Yamamoto, Toshio; Sato, Hirokazu; Yamamoto, Eiji; Hori, Kiyosumi; Yonemaru, Junichi; Sato, Takashi; Fujino, Kenji

    2015-12-01

    Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits. Here, we attempted to detect quantitative trait loci (QTL) for rice blast resistance (BR) using a local breeding rice population from Hokkaido, Japan. Using genotyping data on single nucleotide polymorphisms and simple sequence repeat markers distributed throughout the whole genomic region, we detected genetic regions associated with phenotypic variation in BR by a genome-wide association mapping study (GWAS). An additional association analysis using other breeding cultivars verified the effect and inheritance of the associated region. Furthermore, the existence of a gene for BR in the associated region was confirmed by QTL mapping. The results from these studies enabled us to estimate potential of the Hokkaido rice population as a gene pool for improving BR. The results of this study could be useful for developing novel cultivars with vigorous BR in rice breeding programs. PMID:26719741

  12. Molecular genetic and quantitative trait divergence associated with recent homoploid hybrid speciation: a study of Senecio squalidus (Asteraceae).

    Brennan, A C; Barker, D; Hiscock, S J; Abbott, R J

    2012-02-01

    Hybridization is increasingly seen as a trigger for rapid evolution and speciation. To quantify and qualify divergence associated with recent homoploid hybrid speciation, we compared quantitative trait (QT) and molecular genetic variation between the homoploid hybrid species Senecio squalidus and its parental species, S. aethnensis and S. chrysanthemifolius, and also their naturally occurring Sicilian hybrids. S. squalidus originated and became invasive in the United Kingdom following the introduction of hybrid plants from Mount Etna, Sicily, about 300 years ago. We recorded considerable molecular genetic differentiation between S. squalidus and its parents and their Sicilian hybrids in terms of both reduced genetic diversity and altered allele frequencies, potentially due to the genetic bottleneck associated with introduction to the United Kingdom. S. squalidus is also distinct from its parents and Sicilian hybrids for QTs, but less so than for molecular genetic markers. We suggest that this is due to resilience of polygenic QTs to changes in allele frequency or lack of selection for hybrid niche divergence in geographic isolation. While S. squalidus is intermediate or parental-like for most QTs, some trangressively distinct traits were observed, which might indicate emerging local adaptation in its invasive range. This study emphasizes the important contribution of founder events and geographic isolation to successful homoploid hybrid speciation. PMID:21829224

  13. Quantitative trait loci detection of Edwardsiella tarda resistance in Japanese flounder Paralichthys olivaceus using bulked segregant analysis

    Wang, Xiaoxia; Xu, Wenteng; Liu, Yang; Wang, Lei; Sun, Hejun; Wang, Lei; Chen, Songlin

    2016-03-01

    In recent years, Edwardsiella tarda has become one of the most deadly pathogens of Japanese flounder (Paralichthys olivaceus), causing serious annual losses in commercial production. In contrast to the rapid advances in the aquaculture of P. olivaceus, the study of E. tarda resistance-related markers has lagged behind, hindering the development of a disease-resistant strain. Thus, a marker-trait association analysis was initiated, combining bulked segregant analysis (BSA) and quantitative trait loci (QTL) mapping. Based on 180 microsatellite loci across all chromosomes, 106 individuals from the F1333 (♀: F0768 ×♂: F0915) (Nomenclature rule: F+year+family number) were used to detect simple sequence repeats (SSRs) and QTLs associated with E. tarda resistance. After a genomic scan, three markers (Scaffold 404-21589, Scaffold 404-21594 and Scaffold 270-13812) from the same linkage group (LG)-1 exhibited a significant difference between DNA, pooled/bulked from the resistant and susceptible groups (P disease-resistant Japanese flounder in the future.

  14. Quantitative-Trait Homozygosity and Association Mapping and Empirical Genomewide Significance in Large, Complex Pedigrees: Fasting Serum-Insulin Level in the Hutterites

    Abney, Mark; Ober, Carole; McPeek, Mary Sara

    2002-01-01

    We present methods for linkage and association mapping of quantitative traits for a founder population with a large, known genealogy. We detect linkage to quantitative-trait loci (QTLs) through a multipoint homozygosity-mapping method. We propose two association methods, one of which is single point and uses a general two-allele model and the other of which is multipoint and uses homozygosity by descent for a particular allele. In all three methods, we make extensive use of the pedigree and g...

  15. 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

    Sparsø, Thomas; Hussain, Meena S; Andersen, Gitte; Hainerova, Irena; Borch-Johnsen, Knut; Jørgensen, Torben; Hansen, Torben; Pedersen, Oluf

    2007-01-01

    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 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...

  16. Molecular Tagging and Mapping of Quantitative Trait Loci for Lint Percentage and Morphological Marker Genes in Upland Cotton

    2006-01-01

    Using 219 F2 individuals developed by crossing the genetic standard line TM-1 and the multiple dominant marker line T586 in Gossypium hirsutum L., a genetic linkage map with 19 linkage groups was constructed based on simple sequence repeat (SSR) markers. Compared with our tetraploid backboned molecular genetic map from a (TM-1xHai 7124)xTM-1 BC1 population, 17 of the 19 linkage groups were combined and anchored to 12 chromosomes (sub-genomes). Of these groups, four morphological marker genes in T586 had been mapped into the molecular linkage map. Meanwhile, three quantitative trait loci for lint percentage were tagged and mapped separately on the A03 linkage group and chromosome 6.

  17. Combined use of phenotypic and genotypic information in sampling animalsfor genotyping in detection of quantitative trait loci

    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...

  18. Detecting case-control expression quantitative trait loci using locally most powerful or maximin robust rank tests.

    Yuan, Ao; Xu, Jinfeng; Yue, Qingqi; Zheng, Gang

    2012-04-30

    In testing genome-wide gene expression quantitative trait loci, efficiency robust statistical methods and their computational convenience are most relevant. For this purpose, we propose to use a modified locally most powerful rank test for the analysis of case-control expression data. This modified rank test statistic is computationally simple, robust for non-normally distributed expression data, and asymptotically locally most powerful. It depends on the specification of a location distribution form for data but is not sensitive to misspecifications. When such a location distribution form cannot be specified, we apply Gastwirth's maximin efficiency robust rank test to gene expression data to maximize the worst Pitman asymptotic relative efficiency among a family of location distributions. We conduct simulation studies to assess their performance and use an application to real data for illustration. PMID:22173706

  19. Four quantitative trait loci associated with low Nosema ceranae (Microsporidia) spore load in the honeybee Apis mellifera

    Huang, Qiang; Kryger, Per; Le Conte, Yves;

    2014-01-01

    Nosema ceranae has been recently introduced into the honeybee Apis mellifera as a novel microsporidian gut parasite. To locate the genetic region involved in N. ceranae infection tolerance, we fed N. ceranae spores to haploid drones of a F1 hybrid queen produced from a cross between a queen...... of a Nosema-resistant bred strain and drones of susceptible colonies. The spore loads of the infected F1 drones were used as the phenotype to identify quantitative trait loci (QTLs) associated with N. ceranae spore load. One hundred forty-eight infected drones were individually genotyped with microsatellite...... markers at an average marker distance of 20 cM along the genome. Four QTLs were significantly associated with low spore load, explaining 20.4 % of total spore load variance. Moreover, a candidate gene Aubergine (Aub) within the major QTL region was significantly overexpressed in drones with low spore...

  20. Quantitative Variation in Water-Use Efficiency across Water Regimes and Its Relationship with Circadian, Vegetative, Reproductive, and Leaf Gas-Exchange Traits

    Christine E. Edwards; Brent E. Ewers; C. Robertson McClung; Ping Lou; Cynthia Weinig

    2012-01-01

    Drought limits light harvesting,resulting in lower plant growth and reproduction.One trait important for plant drought response is water-use efficiency (WUE).We investigated (1) how the joint genetic architecture of WUE,reproductive characters,and vegetative traits changed across drought and well-watered conditions,(2) whether traits with distinct developmental bases (e.g.leaf gas exchange versus reproduction) differed in the environmental sensitivity of their genetic architecture,and (3) whether quantitative variation in circadian period was related to drought response in Brassica rapa.Overall,WUE increased in drought,primarily because stomatal conductance,and thus water loss,declined more than carbon fixation.Genotypes with the highest WUE in drought expressed the lowest WUE in well-watered conditions,and had the largest vegetative and floral organs in both treatments.Thus,large changes in WUE enabled some genotypes to approach vegetative and reproductive trait optima across environments.The genetic architecture differed for gas-exchange and vegetative traits across drought and well-watered conditions,but not for floral traits.Correlations between circadian and leaf gas-exchange traits were significant but did not vary across treatments,indicating that circadian period affects physiological function regardless of water availability.These results suggest that WUE is important for drought tolerance in Brassica rapa and that artificial selection for increased WUE in drought will not result in maladaptive expression of other traits that are correlated with WUE.

  1. Multilocus association testing of quantitative traits based on partial least-squares analysis.

    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.

  2. Identification of Quantitative Trait Loci (QTL) and Candidate Genes for Cadmium Tolerance in Populus

    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.

  3. A Simulation Study of Truncation Selection for a Quantitative Trait Opposed by Natural Selection

    Minvielle, Francis

    1980-01-01

    A quantitative character controlled at one locus with two alleles was submitted to artificial (mass) selection and to three modes of opposing natural selection (directional selection, overdominance and underdominance) in a large random-mating population. The selection response and the limits of the selective process were studied by deterministic simulation. The lifetime of the process was generally between 20 and 100 generations and did not appear to depend on the mode of natural selection. H...

  4. Correlações entre caracteres quantitativos em milho pipoca Correlation among quantitative traits in popcorn maize

    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

  5. Quantitative trait loci for resistance to trichostrongylid infection in Spanish Churra sheep

    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

  6. CCRaVAT and QuTie - enabling analysis of rare variants in large-scale case control and quantitative trait association studies

    Elliott Katherine S

    2010-10-01

    Full Text Available Abstract Background Genome-wide association studies have been successful in finding common variants influencing common traits. However, these associations only account for a fraction of trait heritability. There has been a shift in the field towards studying low frequency and rare variants, which are now widely recognised as putative complex trait determinants. Despite this increasing focus on examining the role of low frequency and rare variants in complex disease susceptibility, there is a lack of user-friendly analytical packages implementing powerful association tests for the analysis of rare variants. Results We have developed two software tools, CCRaVAT (Case-Control Rare Variant Analysis Tool and QuTie (Quantitative Trait, which enable efficient large-scale analysis of low frequency and rare variants. Both programs implement a collapsing method examining the accumulation of low frequency and rare variants across a locus of interest that has more power than single variant analysis. CCRaVAT carries out case-control analyses whereas QuTie has been developed for continuous trait analysis. Conclusions CCRaVAT and QuTie are easy to use software tools that allow users to perform genome-wide association analysis on low frequency and rare variants for both binary and quantitative traits. The software is freely available and provides the genetics community with a resource to perform association analysis on rarer genetic variants.

  7. A Generalization of the Mixture Model in the Mapping of Quantitative Trait Loci for Progeny from a Biparental Cross of Inbred Lines

    Fisch, R. D.; Ragot, M.; Gay, G.

    1996-01-01

    The recent advent of molecular markers has created a great potential for the understanding of quantitative inheritance. In parallel to rapid developments and improvements in molecular marker technologies, biometrical models have been constructed, refined and generalized for the mapping of quantitative trait loci (QTL). However, current models present restricitions in terms of breeding designs to which they apply. In this paper, we develop an approach for the generalization of the mixture mode...

  8. Optical constants using two particle size distributions: On-going laboratory efforts to quantitatively address clay abundance on Mars

    Roush, T. L.; Bishop, J. L.; Brown, A. J.; Blake, D.; Bristow, T.

    2013-12-01

    Data obtained at visible and near-infrared wavelengths by OMEGA on MarsExpress and CRISM on MRO provide definitive evidence for the presence of phyllosilicates and other hydrated phases on Mars. A diverse range of both Fe/Mg-OH and Al-OH-bearing phyllosilicates were identified including the smectites, nontronite, saponite, and montmorillonite. In order to constrain the abundances of these phyllosilicates spectral analyses of mixtures of pure end-members are needed. We report on the final stages of our on-going effort to enable the quantitative evaluation of the abundance of hydrated-hydroxylated silicates when they are contained in mixtures. We include several two component mixtures of hydrated/hydroxylated silicates with each other and with two analogs for other martian materials: pyroxene (enstatite) and palagonitic soil (an alteration product of basaltic glass). For the hydrated-hydroxylated silicates we include saponite and montmorillonite (Mg- and Al- rich smectites). We prepared three size separates of each end-member for study: 20-45, 63-90, and 125-150 μm. We used scanning electron microscope images to characterize the grain size distribution, of each sample. Using the grain size distribution, we have derived initial estimates of the optical constants of these materials and compare them to values estimated for the same samples, but using the mean particle size of the sieve fraction. We discuss the results of our calculations for these materials and their implications for modeling the physical mixtures and eventual comparison to Martian spectra.

  9. Dynamic quantitative trait loci analysis of seed reserve utilization during three germination stages in rice.

    Xinxin Cheng

    Full Text Available In this study, one rice population of recombinant inbred lines (RILs was used to determine the genetic characteristics of seed reserve utilization during the early (day 6, middle (day 10 and late (day 14 germination stages. The seedling dry weight (SDW and weight of the mobilized seed reserve (WMSR were increased, while the seed reserve utilization efficiency (SRUE decreased, during the process of seed germination. The SDW and WMSR were affected by the seed weight, while the SRUE was not affected by the seed weight. A total of twenty unconditional and twenty-one conditional additive QTLs and eight epistatic QTLs were identified at three germination stages, and the more QTLs were expressed at the late germination stage. Among them, twelve additive and three epistatic QTLs for SDW, eight additive and three epistatic QTLs for WMSR and thirteen additive and two epistatic QTLs for SRUE were identified, respectively. The phenotypic variation explained by each additive QTL, epistatic QTL and QTL × development interaction ranged from 6.10 to 23.91%, 1.79 to 6.88% and 0.22 to 2.86%, respectively. Two major additive QTLs qWMSR7.1 and qSRUE4.3 were identified, and each QTL could explain more than 20% of the total phenotypic variance. By comparing the chromosomal positions of these additive QTLs with those previously identified, eleven QTLs might represent novel genes. The best four cross combinations of each trait for the development of RIL populations were selected. The selected RILs and the identified QTLs might be applicable to improve rice seed reserve utilization by the marker-assisted selection approach.

  10. Genetic variability for different quantitative traits in M2 generations of opium poppy (Papaver somniferum L.)

    An experiment on induced mutation in two varieties of opium poppy was laid out to create new genetic variability for isolation of high yielding genotypes. Varieties NBRI-1 and NBRI-5 were subjected to irradiation for five doses of gamma rays and NBRI-5 was also treated with four doses of EMS and 20 mixed doses of EMS plus gamma rays. The data were recorded on 15 plants/treatment for 10 polygenic characters as pooled in M1 and M2 generations separately as well as in each dose-wise in M2 population. The results indicated that GCV, heritability and genetic advance were higher in M1 than M2 in both the varieties for all the traits except for opium and seed yield. The genetic advance was consistently high for opium yield, seed yield and capsule weight in all the doses for both the varieties with some exception. The dose level of kR10 and kR30 in NBRI-1 revealed high GCV, heritability and genetic advance for seed weight. These treatment levels also had high values of all these three genetic parameters for capsules per plant, capsule size and capsule weight. The values of these three parameters were also high for all the doses in M2 generations of both the varieties for opium yield, seed weight, capsule weight and capsule size in comparison to control. The GCV, heritability and genetic advance were consistently high for all the mixed doses in NBRI-5 for opium yield, seed weight and capsule weight, with some exception

  11. Dissecting quantitative trait loci for boron efficiency across multiple environments in Brassica napus.

    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.

  12. A putative quantitative trait locus on chromosome 20 associated with bovine pathogenic disease incidence.

    Casas, E; Snowder, G D

    2008-10-01

    The objective of this study was to detect QTL associated with the incidence of multiple pathogenic diseases in offspring from half-sib bovine families. Four F(1) sires were used to produce offspring: Brahman x Hereford (BH; n = 547), Piedmontese x Angus (PA; n = 209), Brahman x Angus (n = 176), and Belgian Blue x MARC III (n = 246). Treatment records for bovine respiratory disease, infectious keratoconjunctivitis (pinkeye), and infectious pododermatitis (footrot) were available for all of the offspring from birth to slaughter. The incidences of these 3 microbial pathogenic diseases were combined into a single binary trait to represent an overall pathogenic disease incidence. Offspring diagnosed and treated for 1 or more of the previously mentioned pathogenic diseases were coded as a 1 for affected. Cattle with no treatment record were coded as 0 for healthy. A putative QTL for pathogenic disease incidence was detected in the family derived from the BH sire at the genome-wise suggestive level. This was supported by evidence, in the same chromosomal region, of a similar QTL in the family derived from the PA sire. The maximum F-statistic (F = 13.52; P = 0.0003) was located at cM 18. The support interval of the QTL spanned from cM 9 to 28. Further studies should explore this QTL by using other bovine populations to further confirm the QTL and refine the QTL support interval. Offspring inheriting the Hereford allele, in the family from the BH sire, and the Angus allele, in the family from the PA sire, were less susceptible to incidence of pathogenic diseases, when compared with those inheriting the Brahman allele and Piedmontese allele, from the BH and PA sires, respectively. PMID:18502878

  13. Detection of novel quantitative trait loci for cutaneous melanoma by genome-wide scan in the MeLiM swine model

    Du, Z. Q.; Vincent-Naulleau, S.; Gilbert, H.; Vignoles, F.; Créchet, F.; Shimogiri, T.; Yasue, H.; Leplat, J. J.; Bouet, S.; Gruand, J.; Horák, Vratislav; Milan, D.; Le Roy, P.; Geffrotin, C.

    2006-01-01

    Roč. 120, - (2006), s. 303-320. ISSN 0020-7136 Institutional research plan: CEZ:AV0Z50450515 Keywords : swine melanoma * quantitative trait loci * MC1R Subject RIV: FD - Oncology ; Hematology Impact factor: 4.693, year: 2006

  14. Implications of central obesity-related variants in LYPLAL1, NRXN3, MSRA, and TFAP2B on quantitative metabolic traits in adult Danes

    Bille, Dorthe Sadowa; Banasik, Karina; Justesen, Johanne Marie; Sandholt, Camilla H; Sandbæk, Annelli; Lauritzen, Torsten; Jørgensen, Torben; Witte, Daniel Rinse; Holm, Jens-Christian; Hansen, Torben; Pedersen, Oluf

    2011-01-01

    -binding protein 2 beta (TFAP2B) associate with measures of central obesity. To elucidate potential underlying phenotypes we aimed to investigate whether these variants associated with: 1) quantitative metabolic traits, 2) anthropometric measures (waist circumference (WC), waist-hip ratio, and BMI), or 3) type 2...

  15. Identification of quantitative trait loci affecting resistance to gastro-intestinal parasites in a double backcross population of Red Maasai and Dorper sheep

    A genome-wide scan for quantitative trait loci (QTL) affecting gastrointestinal (GI) nematode resistance was completed using a double backcross sheep population derived from Red Maasai and Dorper ewes bred to F1 rams. These breeds were chosen, because Red Maasai sheep are known to be more tolerant ...

  16. Genes and quantitative trait loci (QTL) controlling trace element concentrations in perennial grasses grown on phytotoxic soil contaminated with heavy metals

    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...

  17. Genetic analysis and hybrid vigor study of grain yield and other quantitative traits in auto tetraploid rice

    Genetic analysis and genotype-by-environment interaction for important traits of auto tetraploid rice were evaluated by additive, dominance and additive X additive model. It was show n that genetic effects had more influence on grain yield and other quantitative traits of auto tetraploid rice than genotypic environment interaction. Plant height, panicle length, seed set , grain yield, dry matter production and 1000-grain weight we re mainly regulated by dominance variance. Additive and additive X additive gene action constructed the main proportion of genetic variance for heading date (flowering), number of panicles, grains per panicle, grain length, however grain width was supposed to be affected by additive X additive and dominance variance. Flag leaf length and width, fresh weight, peduncle length, unfilled grains and awn length were greatly influenced by genotypic environment interaction. Heading date produced highly negative heterosis over mid parent (H pm) and better parent ( H pb), whereas H pm and H pb were detected to be highly positive and significant for grain yield, seed set, peduncle length, filled grains and 1000-grain weight in F/sub 1/ and F/sub 2/ generations. The results indicated that auto tetraploid hybrids 96025 X Jackson (indica/japonica), 96025 X Linglun (indica/indica) and Linglun X Jackson (indica/japonica) showed highly significant hybrid vigor with improved seed set percentage and grain yield. These results suggest that intra-specific auto tetraploid rice hybrids have more hybrid vigor as compared to intra-sub specific auto tetraploid rice hybrids and auto tetraploid rice has the potential to be used for further studies and commercial application. (author)

  18. Development of Oryza rufipogon and O. sativa Introgression Lines and Assessment for Yield-related Quantitative Trait Loci

    Lubin Tan; Fengxia Liu; Wei Xue; Guijuan Wang; Sheng Ye; Zuofeng Zhu; Yongcai Fu; Xiangkun Wang; Chuanqing Sun

    2007-01-01

    Introgression lines population was effectively used in mapping quantitative trait loci (QTLs), identifying favorable genes, discovering hidden genetic variation, evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research. In this study, an advanced backcross and consecutive selfing strategy was used to develop introgression lines (ILs), which derived from an accession of Oryza rufipogon Griff, collected from Yuanjiang County, Yunnan Province of China, as the donor, and an elite indica cultivar Teqing (O. sativa L.), as the recipient. Introgression segments from O. rufipogon were screened using 179 polymorphic simple sequence repeats (SSR) markers in the genome of each IL. Introgressed segments carried by the introgression lines population contained 120 ILs covering the whole O. rufipogon genome. The mean number of homozygous O. rufipogon segments per introgression line was about 3.88. The average length of introgressed segments was approximate 25.5 cM, and about 20.8% of these segments had sizes less than 10 cM. The genome of each IL harbored the chromosomal fragments of O. rufipogon ranging from 0.54% to 23.7%, with an overall average of 5.79%. At each locus, the ratio of substitution of O. rufipogon alleles had a range of 1.67-9.33, with an average of 5.50. A wide range of alterations in morphological and yield-related traits were also found in the introgression lines population. Using single-point analysis, a total of 37 putative QTLs for yield and yield components were detected at two sites with 7%-20% explaining the phenotypic variance. Nineteen QTLs (51.4%) were detected at both sites, and the alleles from O. rufipogon at fifteen loci (40.5%) improved the yield and yield components in the Teqing background. These O. rufipogon-O. sativa introgression lines will serve as genetic materials for identifying and using favorable genes from common wild rice.

  19. The Finland–United States Investigation of Non–Insulin-Dependent Diabetes Mellitus Genetics (FUSION) Study. II. An Autosomal Genome Scan for Diabetes-Related Quantitative-Trait Loci

    Watanabe, Richard M; Ghosh, Soumitra; Langefeld, Carl D.; Valle, Timo T.; Hauser, Elizabeth R; Magnuson, Victoria L.; Mohlke, Karen L.; Silander, Kaisa; Ally, Delphine S.; Chines, Peter; Blaschak-Harvan, Jillian; Douglas, Julie A.; Duren, William L.; Epstein, Michael P.; Fingerlin, Tasha E.

    2000-01-01

    Type 2 diabetes mellitus is a complex disorder encompassing multiple metabolic defects. We report results from an autosomal genome scan for type 2 diabetes–related quantitative traits in 580 Finnish families ascertained for an affected sibling pair and analyzed by the variance components-based quantitative-trait locus (QTL) linkage approach. We analyzed diabetic and nondiabetic subjects separately, because of the possible impact of disease on the traits of interest. In diabetic individuals, o...

  20. Genome-wide gene-environment interactions on quantitative traits using family data.

    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. PMID:26626313

  1. Public Availability of a Genotyped Segregating Population May Foster Marker Assisted Breeding (MAB) and Quantitative Trait Loci (QTL) Discovery: An Example Using Strawberry

    Hancock, James F.; Sooriyapathirana, Suneth S.; Bassil, Nahla V.; Stegmeir, Travis; Cai, Lichun; Finn, Chad E.; Van de Weg, Eric; Weebadde, Cholani K.

    2016-01-01

    Much of the cost associated with marker discovery for marker assisted breeding (MAB) can be eliminated if a diverse, segregating population is generated, genotyped, and made available to the global breeding community. Herein, we present an example of a hybrid, wild-derived family of the octoploid strawberry that can be used by other breeding programs to economically find and tag useful genes for MAB. A pseudo test cross population between two wild species of Fragaria virginiana and F. chiloensis (FVC 11) was generated and evaluated for a set of phenotypic traits. A total of 106 individuals in the FVC 11 were genotyped for 29,251 single nucleotide polymorphisms (SNPs) utilizing a commercially available, genome-wide scanning platform (Affymetrix Axiom IStraw90TW). The marker trait associations were deduced using TASSEL software. The FVC 11 population segregating for daughters per mother, inflorescence number, inflorescence height, crown production, flower number, fruit size, yield, internal color, soluble solids, fruit firmness, and plant vigor. Coefficients of variations ranged from 10% for fruit firmness to 68% for daughters per mother, indicating an underlying quantitative inheritance for each trait. A total of 2,474 SNPs were found to be polymorphic in FVC 11 and strong marker trait associations were observed for vigor, daughters per mother, yield and fruit weight. These data indicate that FVC 11 can be used as a reference population for quantitative trait loci detection and subsequent MAB across different breeding programs and geographical locations.

  2. Public Availability of a Genotyped Segregating Population May Foster Marker Assisted Breeding (MAB) and Quantitative Trait Loci (QTL) Discovery: An Example Using Strawberry.

    Hancock, James F; Sooriyapathirana, Suneth S; Bassil, Nahla V; Stegmeir, Travis; Cai, Lichun; Finn, Chad E; Van de Weg, Eric; Weebadde, Cholani K

    2016-01-01

    Much of the cost associated with marker discovery for marker assisted breeding (MAB) can be eliminated if a diverse, segregating population is generated, genotyped, and made available to the global breeding community. Herein, we present an example of a hybrid, wild-derived family of the octoploid strawberry that can be used by other breeding programs to economically find and tag useful genes for MAB. A pseudo test cross population between two wild species of Fragaria virginiana and F. chiloensis (FVC 11) was generated and evaluated for a set of phenotypic traits. A total of 106 individuals in the FVC 11 were genotyped for 29,251 single nucleotide polymorphisms (SNPs) utilizing a commercially available, genome-wide scanning platform (Affymetrix Axiom IStraw90(TW)). The marker trait associations were deduced using TASSEL software. The FVC 11 population segregating for daughters per mother, inflorescence number, inflorescence height, crown production, flower number, fruit size, yield, internal color, soluble solids, fruit firmness, and plant vigor. Coefficients of variations ranged from 10% for fruit firmness to 68% for daughters per mother, indicating an underlying quantitative inheritance for each trait. A total of 2,474 SNPs were found to be polymorphic in FVC 11 and strong marker trait associations were observed for vigor, daughters per mother, yield and fruit weight. These data indicate that FVC 11 can be used as a reference population for quantitative trait loci detection and subsequent MAB across different breeding programs and geographical locations. PMID:27242825

  3. Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.

    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.

  4. Analysis of Natural Allelic Variation Controlling Arabiciopsis thaliana Seed Germinability in Response to Cold and Dark: Identification of Three Major Quantitative Trait Loci

    Ping-Hong Meng; Audrey Macquet; Olivier Loudet; Annie Marion-Poll; Helen M.North

    2008-01-01

    Light and temperature are key external factors in the control of Arabidopsis thaliana seed germination and dormancy mechanisms. Perception and response to these stimuli have to ensure that seedling emergence and growth occur at the most advantageous time for correct establishment. Analysis of over 300 Arabidopsis accessions identified 14, from 12 different geographical locations, that were able to germinate to greater than 20% at 6℃ in the dark. This natural variation was exploited to identify genetic loci responsible for cold-tolerant, dark germination. A quantitative trait loci approach was used on recombinant inbred line progeny of a cross between Bay-0 and Shahdara. Six distinct quantitative trait loci were identified, three of which were major loci, each responsible for 17-25% of the phenotypic variability in this trait. Parental phenotypes indicated that the majority of the cold-tolerant, dark-germination characteristics are related to light responses. Validation of the three major loci using heterogeneous inbred families confirmed the feasibility of fine mapping and cloning the genes at the quantitative trait loci responsible for cold-tolerant, dark germination.

  5. Whole Genome Re-Sequencing Identifies a Quantitative Trait Locus Repressing Carbon Reserve Accumulation during Optimal Growth in Chlamydomonas reinhardtii.

    Goold, Hugh Douglas; Nguyen, Hoa Mai; Kong, Fantao; Beyly-Adriano, Audrey; Légeret, Bertrand; Billon, Emmanuelle; Cuiné, Stéphan; Beisson, Fred; Peltier, Gilles; Li-Beisson, Yonghua

    2016-01-01

    Microalgae have emerged as a promising source for biofuel production. Massive oil and starch accumulation in microalgae is possible, but occurs mostly when biomass growth is impaired. The molecular networks underlying the negative correlation between growth and reserve formation are not known. Thus isolation of strains capable of accumulating carbon reserves during optimal growth would be highly desirable. To this end, we screened an insertional mutant library of Chlamydomonas reinhardtii for alterations in oil content. A mutant accumulating five times more oil and twice more starch than wild-type during optimal growth was isolated and named constitutive oil accumulator 1 (coa1). Growth in photobioreactors under highly controlled conditions revealed that the increase in oil and starch content in coa1 was dependent on light intensity. Genetic analysis and DNA hybridization pointed to a single insertional event responsible for the phenotype. Whole genome re-sequencing identified in coa1 a >200 kb deletion on chromosome 14 containing 41 genes. This study demonstrates that, 1), the generation of algal strains accumulating higher reserve amount without compromising biomass accumulation is feasible; 2), light is an important parameter in phenotypic analysis; and 3), a chromosomal region (Quantitative Trait Locus) acts as suppressor of carbon reserve accumulation during optimal growth. PMID:27141848

  6. Identification and validation of quantitative trait loci (QTL for canine hip dysplasia (CHD in German Shepherd Dogs.

    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.

  7. Quantitative Trait Loci Associated with Pollen Fertility under High Temperature Stress at Flowering Stage in Rice (Oryza sativa)

    XIAO Ying-hui; PAN Yi; Luo Li-hua; DENG Hua-bing; ZHANG Gui-lian; TANG Wen-bang; CHEN Li-yun

    2011-01-01

    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-toleranca 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.

  8. Identification of Soat1 as a quantitative trait locus gene on mouse chromosome 1 contributing to hyperlipidemia.

    Lu, Zongji; Yuan, Zuobiao; Miyoshi, Toru; Wang, Qian; Su, Zhiguang; Chang, Catherine C; Shi, Weibin

    2011-01-01

    We previously identified two closely linked quantitative trait loci (QTL) on distal chromosome 1 contributing to major variations in plasma cholesterol and triglyceride levels in an intercross derived from C57BL/6 (B6) and C3H/HeJ (C3H) apolipoprotein E-deficient (apoE(-/-)) mice. Soat1, encoding sterol o-acyltransferase 1, is a functional candidate gene located underneath the proximal linkage peak. We sequenced the coding region of Soat1 and identified four single nucleotide polymorphisms (SNPs) between B6 and C3H mice. Two of the SNPs resulted in amino-acid substitutions (Ile147Val and His205Tyr). Functional assay revealed an increased enzyme activity of Soat1 in peritoneal macrophages of C3H mice relative to those of B6 mice despite comparable protein expression levels. Allelic variants of Soat1 were associated with variations in plasma cholesterol and triglyceride levels in an intercross between B6.apoE(-/-) and C3H.apoE(-/-) mice. Inheritance of the C3H allele resulted in significantly higher plasma lipid levels than inheritance of the B6 allele. Soat1 variants were also significantly linked to major variations in plasma esterified cholesterol levels but not with free cholesterol levels. Trangenic expression of C3H Soat1 in B6.apoE(-/-) mice resulted in elevations of plasma cholesterol and triglyceride levels. These results indicate that Soat1 is a QTL gene contributing to hyperlipidemia. PMID:22022387

  9. Identification of Quantitative Trait Loci Affecting Hemicellulose Characteristics Based on Cell Wall Composition in a Wild and Cultivated Rice Species

    Si-Ju Zhang; Xue-Qin Song; Bai-Sheng Yu; Bao-Cai Zhang; Chuan-Qing Sun; J. Paul Knox; Yi-Hua Zhou

    2012-01-01

    Cell wall hemicellulosic polysaccharides are structurally complex and diverse.Knowledge about the synthesisof cell wall hemicelluloses and their biological roles is limited.Quantitative trait loci (QTL) mapping is a helpful tool for the dissection of complex phenotypes for gene identification.In this study,we exploited the natural variation in cell wall monosaccharide levels between a common wild rice,Yuanj,and an elite indica cultivar,Teqing,and performed QTL mapping with their introgression lines (ILs).Chemical analyses conducted on the culms of Yuanj and Teqing showed that the major alterations are found in glucose and xylose levels,which are correlated with specific hemicellulosic polymers.Glycosidic linkage examination revealed that,in Yuanj,an increase in glucose content results from a higher level of mixed linkage β-glucan (MLG),whereas a reduction in xylose content reflects a low level of xylan backbone and a varied arabinoxylan (AX) structure.Seventeen QTLs for monosaccharides have been identified through composition analysis of the culm residues of 95 core ILs.Four major QTLs affecting xylose and glucose levels are responsible for 19 and 21% of the phenotypic variance,respectively.This study provides a unique resource for the genetic dissection of rice cell wall formation and remodeling in the vegetative organs.

  10. Quantitative trait Loci influencing abdominal fat deposition and functional variability of the HPA axis in the rat.

    Marissal-Arvy, N; Heliès, J-M; Tridon, C; Moisan, M-P; Mormède, P

    2014-08-01

    With the aim to reveal common genomic regions influencing phenotypes related to HPA axis function and metabolism, we did a quantitative trait loci (QTL) study in a F2 population obtained from the cross-breeding between 2 contrasted rat strains, LOU/C and Fischer 344. QTL determining phenotypes related first to corticotropic function were searched: plasma corticosterone (Cort) in control and stress conditions, after a dexamethasone suppression treatment (glucocorticoid receptor related-effect), and mineralocorticoid receptor-mediated urinary response to aldosterone. Then, phenotypes related to metabolism were studied on the same animals: body composition, basal and post-insulin plasma glucose, plasma free fatty acids, leptin, and insulin. Finally, we analyzed the overlapping regions between these QTL and looked for candidate genes within these regions. The gene NR3C1 encoding the glucocorticoid receptor was confirmed to be central in the link between hypothalamic-pituitary-adrenal (HPA) axis function and fat deposition, and its metabolic consequences. Among the other candidate genes detected, most contain a glucocorticoid responsive element, strengthening our hypothesis of common genetic determinism between HPA axis and metabolism. PMID:25003539

  11. Multilevel-analysis identify a cis-expression quantitative trait locus associated with risk of renal cell carcinoma.

    Shu, Xiang; Purdue, Mark P; Ye, Yuanqing; Wood, Christopher G; Chen, Meng; Wang, Zhaoming; Albanes, Demetrius; Pu, Xia; Huang, Maosheng; Stevens, Victoria L; Diver, W Ryan; Gapstur, Susan M; Virtamo, Jarmo; Chow, Wong-Ho; Tannir, Nizar M; Dinney, Colin P; Rothman, Nathaniel; Chanock, Stephen J; Wu, Xifeng

    2015-02-28

    We conducted multilevel analyses to identify potential susceptibility loci for renal cell carcinoma (RCC), which may be overlooked in traditional genome-wide association studies (GWAS). A gene set enrichment analysis was performed utilizing a GWAS dataset comprised of 894 RCC cases and 1,516 controls using GenGen, SNP ratio test, and ALIGATOR. The antigen processing and presentation pathway was consistently significant (P = 0.001, = 0.004, and < 0.001, respectively). Versatile gene-based association study approach was applied to the top-ranked pathway and identified the driven genes. By comparing the expression of the genes in RCC tumor and adjacent normal tissues, we observed significant overexpression of HLA genes in tumor tissues, which was also supported by public databases. We sought to validate genetic variants in antigen processing and presentation pathway in an independent GWAS dataset comprised of 1,311 RCC cases and 3,424 control subjects from the National Cancer Institute; one SNP, rs1063355, was significant in both populations (P(meta-analysis) = 9.15 × 10⁻⁴, P(heterogeneity) = 0.427). Strong correlation indicated that rs1063355 was a cis-expression quantitative trait loci which associated with HLA-DQB1 expression (Spearman's rank r = -0.59, p = 5.61 × 10⁻⁶). The correlation was further validated using a public dataset. Our results highlighted the role of immune-related pathway and genes in the etiology of RCC. PMID:25784652

  12. Identification of a major Quantitative Trait Locus determining resistance to the organophosphate temephos in the dengue vector mosquito Aedes aegypti.

    Paiva, Marcelo H S; Lovin, Diane D; Mori, Akio; Melo-Santos, Maria A V; Severson, David W; Ayres, Constância F J

    2016-01-01

    Organophosphate insecticides (OP) have extensively been used to control mosquitoes, such as the vector Aedes aegypti. Unfortunately, OP resistance has hampered control programs worldwide. We used Quantitative Trait Locus (QTL) mapping to evaluate temephos resistance in two F1 intercross populations derived from crosses between a resistant Ae. aegypti strain (RecR) and two susceptible strains (MoyoD and Red). A single major effect QTL was identified on chromosome 2 of both segregating populations, named rtt1 (resistance to temephos 1). Bioinformatics analyses identified a cluster of carboxylesterase genes (CCE) within the rtt1 interval. qRT-PCR demonstrated that different CCEs were up-regulated in F2 resistant individuals from both crosses. However, none exceeded the 2-fold expression. Primary mechanisms for temephos resistance may vary between Ae. aegypti populations, yet also appear to support previous findings suggesting that multiple linked esterase genes may contribute to temephos resistance in the RecR strain as well as other populations. PMID:26576515

  13. Gamma and X irradiation effects on variability and correlations between some quantitative traits of winter wheat in M2 generation

    The variability and correlations of 7 quantitative traits are analyzed using winter wheat species Kosutska (Triticum aestivum var. erythrospermum/koern./Mansf). The following single doses of gamma and X radiation were used in M0: D1 1.935 C.kg-1; D2 2.58 C.kg-1; D3 3.225 C.kg-1; D4 3.870 C.kg-1; D5 4.515 C.kg-1; D6 5.160 C.kg-1. The weight of grain and the length of ears showed the highest variability (D1 - gamma irradiation). The lowest variability of the tra+ts under study was found in D6 after the application of both types of irradiation. All correlation coefficients were significant in the controls. Lower correlations were found after lower doses of radiation while higher ones were observed after higher doses. After X rays a higher frequency of lower correlations was found. (author)

  14. Identification and validation of quantitative trait loci (QTL) for canine hip dysplasia (CHD) in German Shepherd Dogs.

    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. PMID:24802516

  15. Systems genetics of liver fibrosis: identification of fibrogenic and expression quantitative trait loci in the BXD murine reference population.

    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.

  16. Systems genetics of liver fibrosis: identification of fibrogenic and expression quantitative trait loci in the BXD murine reference population.

    Hall, Rabea A; Liebe, Roman; Hochrath, Katrin; Kazakov, Andrey; Alberts, Rudi; Laufs, Ulrich; Böhm, Michael; Fischer, Hans-Peter; Williams, Robert W; Schughart, Klaus; Weber, Susanne N; Lammert, Frank

    2014-01-01

    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. PMID:24586654

  17. Whole Genome Re-Sequencing Identifies a Quantitative Trait Locus Repressing Carbon Reserve Accumulation during Optimal Growth in Chlamydomonas reinhardtii

    Goold, Hugh Douglas; Nguyen, Hoa Mai; Kong, Fantao; Beyly-Adriano, Audrey; Légeret, Bertrand; Billon, Emmanuelle; Cuiné, Stéphan; Beisson, Fred; Peltier, Gilles; Li-Beisson, Yonghua

    2016-01-01

    Microalgae have emerged as a promising source for biofuel production. Massive oil and starch accumulation in microalgae is possible, but occurs mostly when biomass growth is impaired. The molecular networks underlying the negative correlation between growth and reserve formation are not known. Thus isolation of strains capable of accumulating carbon reserves during optimal growth would be highly desirable. To this end, we screened an insertional mutant library of Chlamydomonas reinhardtii for alterations in oil content. A mutant accumulating five times more oil and twice more starch than wild-type during optimal growth was isolated and named constitutive oil accumulator 1 (coa1). Growth in photobioreactors under highly controlled conditions revealed that the increase in oil and starch content in coa1 was dependent on light intensity. Genetic analysis and DNA hybridization pointed to a single insertional event responsible for the phenotype. Whole genome re-sequencing identified in coa1 a >200 kb deletion on chromosome 14 containing 41 genes. This study demonstrates that, 1), the generation of algal strains accumulating higher reserve amount without compromising biomass accumulation is feasible; 2), light is an important parameter in phenotypic analysis; and 3), a chromosomal region (Quantitative Trait Locus) acts as suppressor of carbon reserve accumulation during optimal growth. PMID:27141848

  18. Quantitative Trait Loci Mapping of Flag-leaf Ligule Length in Rice and Alignment with ZmLG1 Gene

    Dali Zeng; Jiang Hu; Guojun Dong; Jian Liu; Longjun Zeng; Guangheng Zhang; Longbiao Guo; Yihua Zhou; Qian Qian

    2009-01-01

    A doubled haploid (DH) population,which consists of 120 lines dedved from anther culture of a typical Indica and japonica hybrid 'CJ06'/'TN1',was used in this study.Ligule lengths of flag leaf were investigated for quantitative trait loci (QTL) mapping using the DH population.Five QTLs (qLL-2,qLL-4,qLL-6,qLL-10 and qLL-12) controlling the ligule length (LL) were detected on chromosomes 2,4,6,10 and 12,with the variances explained 11.4%,13.6%,27.8%,22.1% and 11.0%,respectively.Using four known genes of ZmGL1,ZmGL2,ZmGL3 and ZmGL4 in maize from the MaizeGDB,their homologs in rice were aligned and integrated into the existing simple sequence repeats linkage map by in silico mapping.A ZmLG1 homolog gene,OsLG1 encoding a squamosa promoter binding protein,was located between the markers RM255 and RM280,which is just identical to the interval of qLL-4 on the long arm of chromosome 4.The results are beneficial to dissection of the ligule molecular mechanism and the study of cereal evolution.

  19. Moo1 obesity quantitative trait locus in BTBR T+ Itpr3tf/J mice increases food intake.

    Karunakaran, Subashini; Manji, Akiff; Yan, Chenhua Serena; Wu, Zi-Jun John; Clee, Susanne M

    2013-03-01

    The rising prevalence of obesity is one of the greatest health challenges facing the world today. Discovery of genetic factors affecting obesity risk will provide important insight to its etiology that could suggest new therapeutic approaches. We have previously identified the Modifier of obese 1 (Moo1) quantitative trait locus (QTL) in a cross between leptin-deficient BTBR T(+) Itpr3(tf)/J (BTBR) and C57BL/6J (B6) mice. Understanding the mechanism by which this locus acts will aid in the identification of candidate genes. Here we refined the location of this QTL and sought to determine the mechanism by which Moo1 affects body weight. We found that the effects of Moo1 also alter high fat diet-induced obesity in mice having functional leptin. In detailed metabolic analyses we determined that this locus acts by increasing food intake in BTBR mice, without affecting energy expenditure. The expression levels of the main molecular mediators of food intake in the hypothalamus were not altered, suggesting this locus affects an independent pathway, consistent with its identification in mice lacking functional leptin. Finally, we show that the increased adiposity resulting from Moo1 is sufficient to affect glucose tolerance. These studies show that the Moo1 obesity QTL affects food intake, likely through a novel mechanism, and indicate that modulation of the underlying pathway may not only ameliorate obesity but also its clinical consequences. PMID:23341217

  20. Genetic mapping of quantitative trait loci associated with important agronomic traits in the spring wheat (Triticum aestivum L.) cross ‘Louise’ by ‘Penawawa’

    Understanding the genetic factors underlying agronomic traits in common wheat (Triticum aestivum L.) is essential to making gains from selection during the breeding process. A set of 188 recombinant inbred lines from a ‘Louise’ by ‘Penawawa’ mapping population was grown in two crop years at two loc...

  1. The genetic architecture of selection response. Inferences from fine-scale mapping of bristle number quantitative trait loci in Drosophila melanogaster.

    Nuzhdin, S V; Dilda, C L; Mackay, T F

    1999-01-01

    Quantitative trait loci (QTL) affecting responses and correlated responses to selection for abdominal and sternopleural bristle number have been mapped with high resolution to the X and third chromosomes. Advanced intercross recombinant isogenic chromosomes were constructed from high and low selection lines in an unselected inbred background, and QTL were detected using composite interval mapping and high density transposable element marker maps. We mapped a total of 26 bristle number QTL wit...

  2. Quantitative trait loci influencing cholesterol and phospholipid phenotypes map to chromosomes that contain genes regulating blood pressure in the spontaneously hypertensive rat.

    Bottger, A.; van Lith, H.A.; Kren, V.; Krenová, D; Bílá, V; Vorlícek, J; Zídek, V; Musilová, A; Zdobinská, M; J. M. Wang; van Zutphen, B F; Kurtz, T. W.; Pravenec, M.

    1996-01-01

    The frequent coincidence of hypertension and dyslipidemia suggests that related genetic factors might underlie these common risk factors for cardiovascular disease. To investigate whether quantitative trait loci (QTLs) regulating lipid levels map to chromosomes known to contain genes regulating blood pressure, we used a genome scanning approach to map QTLs influencing cholesterol and phospholipid phenotypes in a large set of recombinant inbred strains and in congenic strains derived from the ...

  3. Candidate gene selection and detailed morphological evaluations of fs8.1, a quantitative trait locus controlling tomato fruit shape

    Sun, Liang; Rodriguez, Gustavo R.; Clevenger, Josh P.; Illa-Berenguer, Eudald; Lin, Jinshan; Blakeslee, Joshua J.; Liu, Wenli; Fei, Zhangjun; Wijeratne, Asela; Meulia, Tea; van der Knaap, Esther

    2015-01-01

    fs8.1 is a major quantitative trait locus (QTL) that controls the elongated shape of tomato (Solanum lycopersicum) fruit. In this study, we fine-mapped the locus from a 47Mb to a 3.03Mb interval on the long arm of chromosome 8. Of the 122 annotated genes found in the fs8.1 region, 51 were expressed during floral development and six were differentially expressed in anthesis-stage ovaries in fs8.1 and wild-type (WT) lines. To identify possible nucleotide polymorphisms that may underlie the fruit shape phenotype, genome sequence analyses between tomato cultivars carrying the mutant and WT allele were conducted. This led to the identification of 158 single-nucleotide polymorphisms (SNPs) and five small indels in the fs8.1 interval, including 31 that could be associated with changes in gene expression or function. Morphological and histological analyses showed that the effects of fs8.1 were mainly on reproductive organ elongation by increasing cell number in the proximal–distal direction. Fruit weight was also increased in fs8.1 compared with WT, which was predominantly attributed to the increased fruit length. By combining the findings from the different analyses, we consider 12 likely candidate genes to underlie fs8.1, including Solyc08g062580 encoding a pentatricopeptide repeat protein, Solyc08g061560 encoding a putative orthologue of ERECTA, which is known to control fruit morphology and inflorescence architecture in Arabidopsis, Solyc08g061910 encoding a GTL2-like trihelix transcription factor, Solyc08g061930 encoding a protein that regulates cytokinin degradation, and two genes, Solyc08g062340 and Solyc08g062450, encoding 17.6kDa class II small heat-shock proteins. PMID:26175354

  4. Quantitative Trait Loci in Sweet Corn Associated with Partial Resistance to Stewart's Wilt, Northern Corn Leaf Blight, and Common Rust.

    Brown, A F; Juvik, J A; Pataky, J K

    2001-03-01

    ABSTRACT Partial resistance to Stewart's wilt (Erwina stewartii, syn. Pantoea stewartii), northern corn leaf blight (NCLB) (Exserohilum turcicum), and common rust (Puccinia sorghi) was observed in an F(2:3) population developed from a cross between the inbred sweet corn lines IL731a and W6786. The objective of this study was to identify quantitative trait loci (QTL) associated with partial resistance using restriction fragment length polymorphic markers. Phenotypic data were collected for 2 years for Stewart's wilt, NCLB, and common rust but, due to significant family-environment interaction, analysis was conducted individually on data from each year. In 2 years of evaluation for the three diseases, a total of 33 regions in the maize genome were associated with partial resistance describing from 5.9 to 18% of the total phenotypic variability. Of six regions common in both years, three were associated with partial resistance to Stewart's wilt (chromosomes 4:07, 5:03, and 6:04), one was associated with NCLB (chromosome 9:05), and two were associated with common rust (chromosomes 2:04 and 3:04). The rust QTL on 3S mapped to within 20 cM of the rp3 locus and explained 17.7% of the phenotypic variability. Some of the QTL associated with partial resistance to the three diseases have been reported previously, and some are described here for the first time. Results suggest it may be possible to consolidate QTL from various elite backgrounds in a manner analogous to the pyramiding of major resistance genes. We also report here on two QTL associated with anthocyanin production on chromosomes 10:6 and 5:03 in the general location of the a2 gene. PMID:18943349

  5. Identification and mapping of leaf, stem and stripe rust resistance quantitative trait loci and their interactions in durum wheat.

    Singh, A; Pandey, M P; Singh, A K; Knox, R E; Ammar, K; Clarke, J M; Clarke, F R; Singh, R P; Pozniak, C J; Depauw, R M; McCallum, B D; Cuthbert, R D; Randhawa, H S; Fetch, T G

    2013-02-01

    Leaf rust (Puccinia triticina Eriks.), stripe rust (Puccinia striiformis f. tritici Eriks.) and stem rust (Puccinia graminis f. sp. tritici) cause major production losses in durum wheat (Triticum turgidum L. var. durum). The objective of this research was to identify and map leaf, stripe and stem rust resistance loci from the French cultivar Sachem and Canadian cultivar Strongfield. A doubled haploid population from Sachem/Strongfield and parents were phenotyped for seedling reaction to leaf rust races BBG/BN and BBG/BP and adult plant response was determined in three field rust nurseries near El Batan, Obregon and Toluca, Mexico. Stripe rust response was recorded in 2009 and 2011 nurseries near Toluca and near Njoro, Kenya in 2010. Response to stem rust was recorded in field nurseries near Njoro, Kenya, in 2010 and 2011. Sachem was resistant to leaf, stripe and stem rust. A major leaf rust quantitative trait locus (QTL) was identified on chromosome 7B at Xgwm146 in Sachem. In the same region on 7B, a stripe rust QTL was identified in Strongfield. Leaf and stripe rust QTL around DArT marker wPt3451 were identified on chromosome 1B. On chromosome 2B, a significant leaf rust QTL was detected conferred by Strongfield, and at the same QTL, a Yr gene derived from Sachem conferred resistance. Significant stem rust resistance QTL were detected on chromosome 4B. Consistent interactions among loci for resistance to each rust type across nurseries were detected, especially for leaf rust QTL on 7B. Sachem and Strongfield offer useful sources of rust resistance genes for durum rust breeding. PMID:23396999

  6. Genome-wide association analysis for quantitative trait loci influencing Warner–Bratzler shear force in five taurine cattle breeds

    McClure, M C; Ramey, H R; Rolf, M M; McKay, S D; Decker, J E; Chapple, R H; Kim, J W; Taxis, T M; Weaber, R L; Schnabel, R D; Taylor, J F

    2012-01-01

    Summary We performed a genome-wide association study for Warner–Bratzler shear force (WBSF), a measure of meat tenderness, by genotyping 3360 animals from five breeds with 54 790 BovineSNP50 and 96 putative single-nucleotide polymorphisms (SNPs) within μ-calpain [HUGO nomenclature calpain 1, (mu/I) large subunit; CAPN1] and calpastatin (CAST). Within- and across-breed analyses estimated SNP allele substitution effects (ASEs) by genomic best linear unbiased prediction (GBLUP) and variance components by restricted maximum likelihood under an animal model incorporating a genomic relationship matrix. GBLUP estimates of ASEs from the across-breed analysis were moderately correlated (0.31–0.66) with those from the individual within-breed analyses, indicating that prediction equations for molecular estimates of breeding value developed from across-breed analyses should be effective for genomic selection within breeds. We identified 79 genomic regions associated with WBSF in at least three breeds, but only eight were detected in all five breeds, suggesting that the within-breed analyses were underpowered, that different quantitative trait loci (QTL) underlie variation between breeds or that the BovineSNP50 SNP density is insufficient to detect common QTL among breeds. In the across-breed analysis, CAPN1 was followed by CAST as the most strongly associated WBSF QTL genome-wide, and associations with both were detected in all five breeds. We show that none of the four commercialized CAST and CAPN1SNP diagnostics are causal for associations with WBSF, and we putatively fine-map the CAPN1 causal mutation to a 4581-bp region. We estimate that variation in CAST and CAPN1 explains 1.02 and 1.85% of the phenotypic variation in WBSF respectively. PMID:22497286

  7. PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies

    Dai, Xinbin; Wang, Qishan; Xu, Shizhong; Zhao, Patrick X.

    2016-01-01

    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 the original prototype R code, but the computational time was reduced from more than one month to about five minutes. These advances will help overcome the bottleneck frequently encountered in genome wide epistatic genetic effect analysis and enable accommodation of the high computational demand. The PEPIS is publically available at http://bioinfo.noble.org/PolyGenic_QTL/. PMID:27224861

  8. QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

    Lei; Meng; Huihui; Li; Luyan; Zhang; Jiankang; Wang

    2015-01-01

    QTL Ici Mapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci(QTL) in biparental populations. Eight functionalities are integrated in this software package:(1) BIN: binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations;(3) CMP: consensus map construction from multiple linkage maps sharing common markers;(4) SDL: mapping of segregation distortion loci;(5) BIP: mapping of additive, dominant, and digenic epistasis genes;(6) MET: QTL-by-environment interaction analysis;(7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and(8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL,and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci,and to perform analysis of variance for multi-environmental trials.

  9. QTL IciMapping:Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

    Lei Meng; Huihui Li; Luyan Zhang; Jiankang Wang

    2015-01-01

    QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight func-tionalities are integrated in this software package: (1) BIN:binning of redundant markers;(2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci;(5) BIP:mapping of additive, dominant, and digenic epistasis genes;(6) MET:QTL-by-environment interaction analysis;(7) CSL:mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials.

  10. Quantitative Trait Loci (QTL) Mapping for Glycinin and β-Conglycinin Contents in Soybean (Glycine max L. Merr.).

    Ma, Yujie; Kan, Guizhen; Zhang, Xinnan; Wang, Yongli; Zhang, Wei; Du, Hongyang; Yu, Deyue

    2016-05-01

    Compared to β-conglycinin, glycinin contains 3-4 times the methionine and cysteine (sulfur-containing amino acids), accounting for approximately 40 and 30%, respectively, of the total storage protein in soybean. Increasing the soybean storage protein content while improving the ratio of glycinin to β-conglycinin is of great significance for soybean breeding and soy food products. The objective of this study is to analyze the genetic mechanism regulating the glycinin and β-conglycinin contents of soybean by using a recombinant inbred line (RIL) population derived from a cross between Kefeng No. 1 and Nannong 1138-2. Two hundred and twenty-one markers were used to map quantitative trait loci (QTLs) for glycinin (11S) and β-conglycinin (7S) contents, the ratio of glycinin to β-conglycinin (RGC), and the sum of glycinin and β-conglycinin (SGC). A total of 35 QTLs, 3 pairs of epistatic QTLs, and 5 major regions encompassing multiple QTLs were detected. Genes encoding the subunits of β-conglycinin were localized to marker intervals sat_418-satt650 and sat_196-sat_303, which are linked to RGC and SGC; marker sat_318, associated with 11S, 7S, and SGC, was located near Glyma10g04280 (Gy4), which encodes a subunit of glycinin. These results, which take epistatic interactions into account, will improve our understanding of the genetic basis of 11S and 7S contents and will lay a foundation for marker-assisted selection (MAS) breeding of soybean and improving the quality of soybean products. PMID:27070305

  11. A genome-wide search for quantitative trait loci affecting the cortical surface area and thickness of Heschl's gyrus.

    Cai, D-C; Fonteijn, H; Guadalupe, T; Zwiers, M; Wittfeld, K; Teumer, A; Hoogman, M; Arias-Vásquez, A; Yang, Y; Buitelaar, J; Fernández, G; Brunner, H G; van Bokhoven, H; Franke, B; Hegenscheid, K; Homuth, G; Fisher, S E; Grabe, H J; Francks, C; Hagoort, P

    2014-09-01

    Heschl's gyrus (HG) is a core region of the auditory cortex whose morphology is highly variable across individuals. This variability has been linked to sound perception ability in both speech and music domains. Previous studies show that variations in morphological features of HG, such as cortical surface area and thickness, are heritable. To identify genetic variants that affect HG morphology, we conducted a genome-wide association scan (GWAS) meta-analysis in 3054 healthy individuals using HG surface area and thickness as quantitative traits. None of the single nucleotide polymorphisms (SNPs) showed association P values that would survive correction for multiple testing over the genome. The most significant association was found between right HG area and SNP rs72932726 close to gene DCBLD2 (3q12.1; P=2.77 × 10(-7) ). This SNP was also associated with other regions involved in speech processing. The SNP rs333332 within gene KALRN (3q21.2; P=2.27 × 10(-6) ) and rs143000161 near gene COBLL1 (2q24.3; P=2.40 × 10(-6) ) were associated with the area and thickness of left HG, respectively. Both genes are involved in the development of the nervous system. The SNP rs7062395 close to the X-linked deafness gene POU3F4 was associated with right HG thickness (Xq21.1; P=2.38 × 10(-6) ). This is the first molecular genetic analysis of variability in HG morphology. PMID:25130324

  12. Identification of Quantitative Trait Loci and Water Environmental Interactions for Developmental Behaviors of Leaf Greenness in Wheat.

    Yang, Delong; Li, Mengfei; Liu, Yuan; Chang, Lei; Cheng, Hongbo; Chen, Jingjing; Chai, Shouxi

    2016-01-01

    The maintenance of leaf greenness in wheat, highly responsible for yield potential and resistance to drought stress, has been proved to be quantitatively inherited and susceptible to interact with environments by traditional genetic analysis. In order to further dissect the developmental genetic behaviors of flag leaf greenness under terminal drought, unconditional and conditional QTL mapping strategies were performed with a mixed linear model in 120 F8-derived recombinant inbred lines (RILs) from two Chinese common wheat cultivars (Longjian 19 × Q9086) in different water environments. A total of 65 additive QTLs (A-QTLs) and 42 pairs of epistatic QTLs (AA-QTLs) were identified as distribution on almost all 21 chromosomes except 5A, explaining from 0.24 to 3.29 % of the phenotypic variation. Of these, 22 A-QTLs and 25 pairs of AA-QTLs were common in two sets of mapping methods but the others differed. These putative QTLs were essentially characteristic of time- and environmentally-dependent expression patterns. Indeed some loci were expressed at two or more stages, while no single QTL was continually active through whole measuring duration. More loci were detected in early growth periods but most of QTL × water environment interactions (QEIs) happened in mid-anaphase, where drought stress was more conducted with negative regulation on QTL expressions. Compared to other genetic components, epistatic effects and additive QEIs effects could be predominant in regulating phenotypic variations during the ontogeny of leaf greenness. Several QTL cluster regions were suggestive of tight linkage or expression pleiotropy in the inheritance of these traits. Some reproducibly-expressed QTLs or common loci consistent with previously detected would be useful to the genetic improvement of staygreen types in wheat through MAS, especially in water-deficit environments. PMID:27014298

  13. Quantitative trait loci affecting response to crowding stress in an F2 generation of rainbow trout produced through phenotypic selection

    Selective breeding programs for salmonids typically aim to improve traits associated with growth and disease resistance. It has been established that stressors common to production environments can adversely affect these and other traits which are important to producers and consumers. Previously,...

  14. Quantitative Assessment of Autism Symptom-Related Traits in Probands and Parents: Broader Phenotype Autism Symptom Scale

    Dawson, Geraldine; Estes, Annette; Munson, Jeffrey; Schellenberg, Gerard; Bernier, Raphael; Abbott, Robert

    2007-01-01

    Autism susceptibility genes likely have effects on continuously distributed autism-related traits, yet few measures of such traits exist. The Broader Phenotype Autism Symptom Scale (BPASS), developed for use with affected children and family members, measures social motivation, social expressiveness, conversational skills, and flexibility. Based…

  15. Quantitative Trait Loci for Maysin Synthesis in Maize (Zea mays L.) Lines Selected for High Silk Maysin Content

    Recurrent selection has been utilized for over a century to increase desired traits in crop plants. One notable trait of interest to plant breeders is insect resistance. Maysin is a naturally occurring C-glycosyl flavone found in maize (Zea mays L.) silk tissue that confers resistance to corn earwor...

  16. Combining Quantitative Trait Loci Analysis and an Ecophysiological Model to Analyze the Genetic Variability of the Responses of Maize Leaf Growth to Temperature and Water Deficit1

    Reymond, Matthieu; Muller, Bertrand; Leonardi, Agnès; Charcosset, Alain; Tardieu, François

    2003-01-01

    Ecophysiological models predict quantitative traits of one genotype in any environment, whereas quantitative trait locus (QTL) models predict the contribution of alleles to quantitative traits under a limited number of environments. We have combined both approaches by dissecting into effects of QTLs the parameters of a model of maize (Zea mays) leaf elongation rate (LER; H. Ben Haj Salah, F. Tardieu [1997] Plant Physiol 114: 893–900). Response curves of LER to meristem temperature, water vapor pressure difference, and soil water status were established in 100 recombinant inbred lines (RILs) of maize in six experiments carried out in the field or in the greenhouse. All responses were linear and common to different experiments, consistent with the model. A QTL analysis was carried out on the slopes of these responses by composite interval mapping confirmed by bootstrap analysis. Most QTLs were specific of one response only. QTLs of abscisic acid concentration in the xylem sap colocalized with QTLs of response to soil water deficit and conferred a low response. Each parameter of the ecophysiological model was computed as the sum of QTL effects, allowing calculation of parameters for 11 new RILs and two parental lines. LERs were simulated and compared with measurements in a growth chamber experiment. The combined model accounted for 74% of the variability of LER, suggesting that it has a general value for any RIL under any environment. PMID:12586890

  17. Validation and dissection of quantitative trait loci for leaf traits in interval RM4923-RM402 on the short arm of rice chromosome 6

    Bo Shen; Wei-Dong Yu; Jing-Hong Du; Ye-Yang Fan; Ji-Rong Wu; Jie-Yun Zhuang

    2011-04-01

    Validation and dissection of a QTL region for leaf traits in rice which has been reported in a number of independent studies were conducted. Three sets of near isogenic lines (NILs) were originated from a residual heterozygous line derived the indica cross Zhenshan 97B/Milyang 46. They were overlapping and totally covered a 4.2-Mb heterogenous region extending from RM4923 to RM402 on the short arm of rice chromosome 6. Each NIL set consisted of 10 maternal lines and 10 paternal lines. They were measured for the length, width, perimeter and area of the top three leaves and the number of spikelets per panicle, number of grains per panicle and grain weight per panicle. In NIL sets 6-4 and 6-7, differing in intervals RM4923-RM225 and RM19410-RM6119, respectively, significant variations with the enhancing alleles from the female parent ZS97 were shown for the length, perimeter and area except for the area of the third leaf from top in 6-4, but the effects were lower in 6-4 than in 6-7. No significant effects were detected for the three traits in the remaining NIL set. It was shown that flag leaf length (FLL) is the primary target of the QTLs detected. Two QTLs for FLL linked in repulsion phase were resolved, of which qFLL6.2 located in the 1.19-Mb interval RM3414-RM6917 had a major effect with the enhancing allele from Zhenshan 97B, and qFLL6.1 located in the 946.8-kb interval RM19350-RM19410 had a smaller effect with the enhancing allele from Milyang 46. The two QTLs also exerted pleiotropic effects on the yield traits.

  18. Quantitative Trait Loci for Yield Traits Located Between Hd3a and Hd1 on Short Arm of Chromosome 6 in Rice

    FAN Ye-yang; CHEN Chen; Wu Ji-rong; CHENG Shi-hua; ZHUANG Jie-yun

    2011-01-01

    QTLs for heading date located in the regions of Hd3a and Hd1 were detected using an F2:3 population developed from a residual heterozygous line (RHL) identified from the recombinant inbred lines of the indica rice cross Zhenshan 97B /Milyang 46.Linkage in coupling phase between the QTLs for heading date and yield traits detected in a previous study was found.Four more F2:3 populations were each developed from an RHL that was homozygous at Hd3a and Hd1 but heterozygous in a portion of the intervals flanked by Hd3a and Hd1.QTLs for grain yield per plant,number of panicles per plant,number of grains per panicle and 1000-grain weight were detected in the heterozygous region.Five sets of near-isogenic lines (NILs) with overlapping heterogenous segments covering the interval RM6119-RM6779 were developed and used to validate and delimitate the QTLs.A QTL conferring a consistent effect for the number of grains per panicle was located within the interval RM19615-RM19652 that corresponded to a 514.4-kb region on chromosome 6.The same region might have pleiotropic effects on the other three yield-related traits analyzed,but the effects varied greatly among different populations and across different environments.This study suggests that it is possible to develop a population with little variation on heading date and to identify QTLs for yield traits that might not be associated with heading date by using the information of physical positions of DNA markers and cloned genes.

  19. Genetic Map Construction and Quantitative Trait Locus (QTL Detection of Six Economic Traits Using an F2 Population of the Hybrid from Saccharina longissima and Saccharina japonica.

    Jing Zhang

    Full Text Available Saccharina (Laminaria is one of the most important economic seaweeds. Previously, four genetic linkage maps of Saccharina have been constructed and five QTLs have been identified. However, they were not enough for its breeding. In this work, Saccharina longissima (♀ and Saccharina japonica (♂, which showed obvious differences in morphology and genetics, were applied in hybridization to yield the F2 mapping population with 102 individuals. Using these 102 F2 hybrids, the genetic linkage map of Saccharina was constructed by MapMaker software based on 37 amplified fragment length polymorphisms (AFLPs, 22 sequence-related amplified polymorphisms (SRAPs and 139 simple sequence repeats (SSRs markers. Meanwhile, QTL analysis was performed for six economic traits. The linkage map constructed in this research consisted of 422 marker loci (137 AFLPs, 57 SRAPs and 228 SSRs, which formed 45 linkage groups (LGs with an average marker space of 7.92 cM; they spanned a total length of 2233.1 cM, covering the whole estimated genome size. A total of 29 QTLs were identified for six economic traits, which explained 1.06 to 64.00% of phenotypic variation, including three QTLs for frond length (FL and raw weight (RW, five QTLs for frond width (FW, two QTLs for frond fascia width (FFW and frond thickness (FT, and fourteen QTLs for base shape (BS. The results of this research will improve the breeding efficiency and be beneficial for marker-assisted selection (MAS schemes in Saccharina breeding.

  20. Quantitative Trait Locus and Brain Expression of HLA-DPA1 Offers Evidence of Shared Immune Alterations in Psychiatric Disorders.

    Morgan, Ling Z; Rollins, Brandi; Sequeira, Adolfo; Byerley, William; DeLisi, Lynn E; Schatzberg, Alan F; Barchas, Jack D; Myers, Richard M; Watson, Stanley J; Akil, Huda; Bunney, William E; Vawter, Marquis P

    2016-01-01

    Genome-wide association studies of schizophrenia encompassing the major histocompatibility locus (MHC) were highly significant following genome-wide correction. This broad region implicates many genes including the MHC complex class II. Within this interval we examined the expression of two MHC II genes (HLA-DPA1 and HLA-DRB1) in brain from individual subjects with schizophrenia (SZ), bipolar disorder (BD), major depressive disorder (MDD), and controls by differential gene expression methods. A third MHC II mRNA, CD74, was studied outside of the MHC II locus, as it interacts within the same immune complex. Exon microarrays were performed in anterior cingulate cortex (ACC) in BD compared to controls, and both HLA-DPA1 and CD74 were decreased in expression in BD. The expression of HLA-DPA1 and CD74 were both reduced in hippocampus, amygdala, and dorsolateral prefrontal cortex regions in SZ and BD compared to controls by specific qPCR assay. We found several novel HLA-DPA1 mRNA variants spanning HLA-DPA1 exons 2-3-4 as suggested by exon microarrays. The intronic rs9277341 SNP was a significant cis expression quantitative trait locus (eQTL) that was associated with the total expression of HLA-DPA1 in five brain regions. A biomarker study of MHC II mRNAs was conducted in SZ, BD, MDD, and control lymphoblastic cell lines (LCL) by qPCR assay of 87 subjects. There was significantly decreased expression of HLA-DPA1 and CD74 in BD, and trends for reductions in SZ in LCLs. The discovery of multiple splicing variants in brain for HLA-DPA1 is important as the HLA-DPA1 gene is highly conserved, there are no reported splicing variants, and the functions in brain are unknown. Future work on the function and localization of MHC Class II proteins in brain will help to understand the role of alterations in neuropsychiatric disorders. The HLA-DPA1 eQTL is located within a large linkage disequilibrium block that has an irrefutable association with schizophrenia. Future tests in a

  1. The nucleoside diphosphate kinase gene Nme3 acts as quantitative trait locus promoting non-Mendelian inheritance.

    Hermann Bauer

    Full Text Available The t-haplotype, a variant form of the t-complex region on mouse chromosome 17, acts as selfish genetic element and is transmitted at high frequencies (> 95% from heterozygous (t/+ males to their offspring. This phenotype is termed transmission ratio distortion (TRD and is caused by the interaction of the t-complex responder (Tcr with several quantitative trait loci (QTL, the t-complex distorters (Tcd1 to Tcd4, all located within the t-haplotype region. Current data suggest that the distorters collectively impair motility of all sperm derived from t/+ males; t-sperm is rescued by the responder, whereas (+-sperm remains partially dysfunctional. Recently we have identified two distorters as regulators of RHO small G proteins. Here we show that the nucleoside diphosphate kinase gene Nme3 acts as a QTL on TRD. Reduction of the Nme3 dosage by gene targeting of the wild-type allele enhanced the transmission rate of the t-haplotype and phenocopied distorter function. Genetic and biochemical analysis showed that the t-allele of Nme3 harbors a mutation (P89S that compromises enzymatic activity of the protein and genetically acts as a hypomorph. Transgenic overexpression of the Nme3 t-allele reduced t-haplotype transmission, proving it to be a distorter. We propose that the NME3 protein interacts with RHO signaling cascades to impair sperm motility through hyperactivation of SMOK, the wild-type form of the responder. This deleterious effect of the distorters is counter-balanced by the responder, SMOK(Tcr, a dominant-negative protein kinase exclusively expressed in t-sperm, thus permitting selfish behaviour and preferential transmission of the t-haplotype. In addition, the previously reported association of NME family members with RHO signaling in somatic cell motility and metastasis, in conjunction with our data involving RHO signaling in sperm motility, suggests a functional conservation between mechanisms for motility control in somatic cells and

  2. Mapping of quantitative trait locus (QTLs) that contribute to germination and early seedling drought tolerance in the interspecific cross Setaria italica×Setaria viridis.

    Qie, Lufeng; Jia, Guanqing; Zhang, Wenying; Schnable, James; Shang, Zhonglin; Li, Wei; Liu, Binhui; Li, Mingzhe; Chai, Yang; Zhi, Hui; Diao, Xianmin

    2014-01-01

    Drought tolerance is an important breeding target for enhancing the yields of grain crop species in arid and semi-arid regions of the world. Two species of Setaria, domesticated foxtail millet (S. italica) and its wild ancestor green foxtail (S. viridis) are becoming widely adopted as models for functional genomics studies in the Panicoid grasses. In this study, the genomic regions controlling germination and early seedling drought tolerance in Setaria were identified using 190 F7 lines derived from a cross between Yugu1, a S. italica cultivar developed in China, and a wild S. viridis genotype collected from Uzbekistan. Quantitative trait loci were identified which contribute to a number of traits including promptness index, radical root length, coleoptile length and lateral root number at germinating stage and seedling survival rate was characterized by the ability of desiccated seedlings to revive after rehydration. A genetic map with 128 SSR markers which spans 1293.9 cM with an average of 14 markers per linkage group of the 9 linkage groups was constructed. A total of eighteen QTLs were detected which included nine that explained over 10% of the phenotypic variance for a given trait. Both the wild green foxtail genotype and the foxtail millet cultivar contributed the favorite alleles for traits detected in this trial, indicating that wild Setaria viridis populations may serve as a reservoir for novel stress tolerance alleles which could be employed in foxtail millet breeding. PMID:25033201

  3. Effects of chronic gamma irradiation and inbreeding on manifestations of some quantitative traits in G3I1 generation of winter rye

    The effects of 3 doses of radiation upon the manifestation and extension of phenotypic variability in some quantitative traits (4 experimental treatments A to D) were estimated in the G3I1 generation after chronic irradiation with 60Co and inbreeding in the G2 generation. Treatment A involved doses of 0.8927 to 0.6966 C.kg-1, treatment B 0.3354 to 0.3011 C.kg-1, treatment C 0.1014 to 0.0916 C.kg-1 and treatment D no irradiation (controls). The efficiency of the doses was evaluated according to the height of plants, the weight of 1000 grains, the number of grains per ear, and gross protein content in grains. An increase in the phenotypic variability was demonstrated in the major part of traits under study. Statistically significant differences between individual treatments were found. (author)

  4. Genetic Variation, Heritability, and Diversity Analysis of Upland Rice (Oryza sativa L.) Genotypes Based on Quantitative Traits.

    Tuhina-Khatun, Mst; Hanafi, Mohamed M; Rafii Yusop, Mohd; Wong, M Y; Salleh, Faezah M; Ferdous, Jannatul

    2015-01-01

    Upland rice is important for sustainable crop production to meet future food demands. The expansion in area of irrigated rice faces limitations due to water scarcity resulting from climate change. Therefore, this research aimed to identify potential genotypes and suitable traits of upland rice germplasm for breeding programmes. Forty-three genotypes were evaluated in a randomised complete block design with three replications. All genotypes exhibited a wide and significant variation for 22 traits. The highest phenotypic and genotypic coefficient of variation was recorded for the number of filled grains/panicle and yields/plant (g). The highest heritability was found for photosynthetic rate, transpiration rate, stomatal conductance, intercellular CO₂, and number of filled grains/panicle and yields/plant (g). Cluster analysis based on 22 traits grouped the 43 rice genotypes into five clusters. Cluster II was the largest and consisted of 20 genotypes mostly originating from the Philippines. The first four principle components of 22 traits accounted for about 72% of the total variation and indicated a wide variation among the genotypes. The selected best trait of the number of filled grains/panicle and yields/plant (g), which showed high heritability and high genetic advance, could be used as a selection criterion for hybridisation programmes in the future. PMID:26258135

  5. Genetic Variation, Heritability, and Diversity Analysis of Upland Rice (Oryza sativa L. Genotypes Based on Quantitative Traits

    Mst. Tuhina-Khatun

    2015-01-01

    Full Text Available Upland rice is important for sustainable crop production to meet future food demands. The expansion in area of irrigated rice faces limitations due to water scarcity resulting from climate change. Therefore, this research aimed to identify potential genotypes and suitable traits of upland rice germplasm for breeding programmes. Forty-three genotypes were evaluated in a randomised complete block design with three replications. All genotypes exhibited a wide and significant variation for 22 traits. The highest phenotypic and genotypic coefficient of variation was recorded for the number of filled grains/panicle and yields/plant (g. The highest heritability was found for photosynthetic rate, transpiration rate, stomatal conductance, intercellular CO2, and number of filled grains/panicle and yields/plant (g. Cluster analysis based on 22 traits grouped the 43 rice genotypes into five clusters. Cluster II was the largest and consisted of 20 genotypes mostly originating from the Philippines. The first four principle components of 22 traits accounted for about 72% of the total variation and indicated a wide variation among the genotypes. The selected best trait of the number of filled grains/panicle and yields/plant (g, which showed high heritability and high genetic advance, could be used as a selection criterion for hybridisation programmes in the future.

  6. Quantitative variation in obesity-related traits and insulin precursors linked to the OB gene region on human chromosome 7

    Duggirala, R.; Stern, M.P.; Reinhart, L.J. [Univ. of Texas Health Science Center, San Antonio, TX (United States)] [and others

    1996-09-01

    Despite the evidence that human obesity has strong genetic determinants, efforts at identifying specific genes that influence human obesity have largely been unsuccessful. Using the sibship data obtained from 32 low-income Mexican American pedigrees ascertained on a type II diabetic proband and a multipoint variance-components method, we tested for linkage between various obesity-related traits plus associated metabolic traits and 15 markers on human chromosome 7. We found evidence for linkage between markers in the OB gene region and various traits, as follows: D7S514 and extremity skinfolds (LOD = 3.1), human carboxypeptidase A1 (HCPA1) and 32,33-split proinsulin level (LOD = 4.2), and HCPA1 and proinsulin level (LOD = 3.2). A putative susceptibility locus linked to the marker D7S514 explained 56% of the total phenotypic variation in extremity skinfolds. Variation at the HCPA1 locus explained 64% of phenotypic variation in proinsulin level and {approximately}73% of phenotypic variation in split proinsulin concentration, respectively. Weaker evidence for linkage to several other obesity-related traits (e.g., waist circumference, body-mass index, fat mass by bioimpedance, etc.) was observed for a genetic location, which is {approximately}15 cM telomeric to OB. In conclusion, our study reveals that the OB region plays a significant role in determining the phenotypic variation of both insulin precursors and obesity-related traits, at least in Mexican Americans. 66 refs., 3 figs., 4 tabs.

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

    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 illustratin...

  8. Identification and mapping of quantitative trait loci controlling cold-tolerance of Chinese common wild rice (O. rufipogon Griff.) at booting to flowering stages

    LIU Fengxia; SUN Chuanqing; TAN Lubin; FU Yongcai; LI Dejun; WANG Xiangkun

    2003-01-01

    An advanced backcross population of rice was used to identify the quantitative trait locus (QTL) controlling the cold-tolerance at booting to flowering stages. The recipient, Guichao 2 (GC2), was a commercial Indica rice; the donor Dongxiang common wild rice, was an accession of common wild rice (DXCWR, Oryza rufipogon Griff.). Three QTLs for cold-tolerance were detected on chromosomes 1, 6and 11. Two of them coming from DXCWR could enhance the cold-tolerance of the backcross progenies. Moreover, one sterility QTL that could reduce the seed set rate of the backcross progenies by 78% was mapped on chromosome 5.

  9. Exercise Capacity and Response to Training Quantitative Trait Loci in a NZW X 129S1 Intercross and Combined Cross Analysis of Inbred Mouse Strains

    Michael P. Massett; Avila, Joshua J; Seung Kyum Kim

    2015-01-01

    Genetic factors determining exercise capacity and the magnitude of the response to exercise training are poorly understood. The aim of this study was to identify quantitative trait loci (QTL) associated with exercise training in mice. Based on marked differences in training responses in inbred NZW (-0.65 ± 1.73 min) and 129S1 (6.18 ± 3.81 min) mice, a reciprocal intercross breeding scheme was used to generate 285 F2 mice. All F2 mice completed an exercise performance test before and after a 4...

  10. Studies of association of the CASQ1 rs2275703 polymorphism in relation to type 2 diabetes and related quantitative metabolic traits among 7,088 Danish whites

    Sparsø, Thomas; Hussain, Meena Shaheen; Borch-Johnsen, Knut; Jørgensen, Torben; Madsbad, Sten; Hansen, Torben; Pedersen, Oluf; Andersen, Gitte

    2007-01-01

    Calsequestrin 1 (CASQ1) is a calcium storage protein of fast-twitch skeletal muscle cells. In previous human association studies the results have been contradictory regarding the association between a CASQ1 rs2275703 polymorphism and type 2 diabetes. In the present study of the CASQ1 rs2275703 po...... polymorphism in 7,088 Danish whites the allele frequency and genotype distribution did not differ between type 2 diabetic patients and glucose-tolerant control subjects, neither was found any association with diabetes-related quantitative traits....

  11. Mapping of quantitative trait loci for phytic acid and phosphorus contents in seed and seedling of mungbean (Vigna radiata (L.) Wilczek)

    Sompong, Utumporn; Somta, Prakit; Raboy, Victor; Srinives, Peerasak

    2012-01-01

    Phytic acid (PA) is the storage form of phosphorus (P) in seeds and plays an important role in the nutritional quality of food crops. There is little information on the genetics of seed and seedling PA in mungbean [Vigna radiata (L.) Wilczek]. Quantitative trait loci (QTL) were identified for phytic acid P (PAP), total P (TP), and inorganic P (IP) in mungbean seeds and seedlings, and for flowering, maturity and seed weight, in an F2 population developed from a cross between low PAP cultivated...

  12. Validation of a brief quantitative measure of autistic traits: comparison of the social responsiveness scale with the autism diagnostic interview-revised.

    Constantino, John N; Davis, Sandra A; Todd, Richard D; Schindler, Matthew K; Gross, Maggie M; Brophy, Susan L; Metzger, Lisa M; Shoushtari, Christiana S; Splinter, Reagan; Reich, Wendy

    2003-08-01

    Studies of the broader autism phenotype, and of subtle changes in autism symptoms over time, have been compromised by a lack of established quantitative assessment tools. The Social Responsiveness Scale (SRS-formerly known as the Social Reciprocity Scale) is a new instrument that can be completed by parents and/or teachers in 15-20 minutes. We compared the SRS with the Autism Diagnostic Interview-Revised (ADI-R) in 61 child psychiatric patients. Correlations between SRS scores and ADI-R algorithm scores for DSM-IV criterion sets were on the order of 0.7. SRS scores were unrelated to I.Q. and exhibited inter-rater reliability on the order of 0.8. The SRS is a valid quantitative measure of autistic traits, feasible for use in clinical settings and for large-scale research studies of autism spectrum conditions. PMID:12959421

  13. Simulating the yield impacts of organ-level quantitative trait loci associated with drought response in maize: a "gene-to-phenotype" modeling approach.

    Chenu, Karine; Chapman, Scott C; Tardieu, François; McLean, Greg; Welcker, Claude; Hammer, Graeme L

    2009-12-01

    Under drought, substantial genotype-environment (G x E) interactions impede breeding progress for yield. Identifying genetic controls associated with yield response is confounded by poor genetic correlations across testing environments. Part of this problem is related to our inability to account for the interplay of genetic controls, physiological traits, and environmental conditions throughout the crop cycle. We propose a modeling approach to bridge this "gene-to-phenotype" gap. For maize under drought, we simulated the impact of quantitative trait loci (QTL) controlling two key processes (leaf and silk elongation) that influence crop growth, water use, and grain yield. Substantial G x E interaction for yield was simulated for hypothetical recombinant inbred lines (RILs) across different seasonal patterns of drought. QTL that accelerated leaf elongation caused an increase in crop leaf area and yield in well-watered or preflowering water deficit conditions, but a reduction in yield under terminal stresses (as such "leafy" genotypes prematurely exhausted the water supply). The QTL impact on yield was substantially enhanced by including pleiotropic effects of these QTL on silk elongation and on consequent grain set. The simulations obtained illustrated the difficulty of interpreting the genetic control of yield for genotypes influenced only by the additive effects of QTL associated with leaf and silk growth. The results highlight the potential of integrative simulation modeling for gene-to-phenotype prediction and for exploiting G x E interactions for complex traits such as drought tolerance. PMID:19786622

  14. Transcriptomics-assisted quantitative trait locus fine mapping for the rapid identification of a nodulin 26-like intrinsic protein gene regulating boron efficiency in allotetraploid rapeseed.

    Hua, Yingpeng; Zhang, Didi; Zhou, Ting; He, Mingliang; Ding, Guangda; Shi, Lei; Xu, Fangsen

    2016-07-01

    Allotetraploid rapeseed (Brassica napus L., An An Cn Cn , 2n = 4x = 38) is extraordinarily susceptible to boron (B) deficiency, a ubiquitous problem causing severe losses in seed yield. The breeding of B-efficient rapeseed germ plasm is a cost-effective and environmentally friendly strategy for the agricultural industry; however, genes regulating B efficiency in allotetraploid rapeseed have not yet been isolated. In this research, quantitative trait locus (QTL) fine mapping and digital gene expression (DGE) profiling were combined to identify the candidate genes underlying the major-effect QTL qBEC-A3a, which regulates B efficiency. Comparative phenotype analyses of the near-isogenic lines (NILs) indicated that qBEC-A3a plays a significant role in improving B efficiency under B deficiency. Exploiting QTL fine mapping and DGE analyses revealed a nodulin 26-like intrinsic protein (NIP) gene, which encodes a likely boric acid channel. The gene co-expression network for putative B transporters also highlighted its central role in the efficiency of B uptake. An integration of whole-genome re-sequencing (WGS) with bulked segregant analysis (BSA) authenticated the emerging availability of QTL-seq for the QTL analyses in allotetraploid rapeseed. Transcriptomics-assisted QTL mapping and comparative genomics provided novel insights into the rapid identification of quantitative trait genes (QTGs) in plant species with complex genomes. PMID:26934080

  15. A Quantitative Genomic Approach for Analysis of Fitness and Stress Related Traits in a Drosophila melanogaster Model Population

    Duun Rohde, Palle; Krag, Kristian; Loeschcke, Volker; Overgaard, Johannes; Sørensen, Peter; Nygaard Kristensen, Torsten

    2016-01-01

    The ability of natural populations to withstand environmental stresses relies partly on their adaptive ability. In this study, we used a subset of the Drosophila Genetic Reference Panel, a population of inbred, genome-sequenced lines derived from a natural population of Drosophila melanogaster, to investigate whether this population harbors genetic variation for a set of stress resistance and life history traits. Using a genomic approach, we found substantial genetic variation for metabolic rate, heat stress resistance, expression of a major heat shock protein, and egg-to-adult viability investigated at a benign and a higher stressful temperature. This suggests that these traits will be able to evolve. In addition, we outline an approach to conduct pathway associations based on genomic linear models, which has potential to identify adaptive genes and pathways, and therefore can be a valuable tool in conservation genomics.

  16. Genetic Variation, Heritability, and Diversity Analysis of Upland Rice (Oryza sativa L.) Genotypes Based on Quantitative Traits

    Mst. Tuhina-Khatun; Hanafi, Mohamed M.; Mohd Rafii Yusop; Wong, M. Y.; Salleh, Faezah M.; Jannatul Ferdous

    2015-01-01

    Upland rice is important for sustainable crop production to meet future food demands. The expansion in area of irrigated rice faces limitations due to water scarcity resulting from climate change. Therefore, this research aimed to identify potential genotypes and suitable traits of upland rice germplasm for breeding programmes. Forty-three genotypes were evaluated in a randomised complete block design with three replications. All genotypes exhibited a wide and significant variation for 22 tra...

  17. A general statistical framework for mapping quantitative trait loci in nonmodel systems: issue for characterizing linkage phases.

    Lin, Min; Lou, Xiang-Yang; Chang, Myron; Wu, Rongling

    2003-01-01

    Because of uncertainty about linkage phases of founders, linkage mapping in nonmodel, outcrossing systems using molecular markers presents one of the major statistical challenges in genetic research. In this article, we devise a statistical method for mapping QTL affecting a complex trait by incorporating all possible QTL-marker linkage phases within a mapping framework. The advantage of this model is the simultaneous estimation of linkage phases and QTL location and effect parameters. These ...

  18. Multiple regression approach to mapping of quantitative trait loci (QTL) based on sib-pair data: a theoretical analysis

    Xiong, Momiao; Guo, Sunwei

    2000-01-01

    The interval mapping method has been shown to be a powerful tool for mapping QTL. However, it is still a challenge to perform a simultaneous analysis of several linked QTLs, and to isolate multiple linked QTLs. To circumvent these problems, multiple regression analysis has been suggested for experimental species. In this paper, the multiple regression approach is extended to human sib-pair data through multiple regression of the squared difference in trait values between two...

  19. Mapping quantitative trait loci associated with yield and yield components under reproductive stage salinity stress in rice (Oryza sativa L.)

    Reza Mohammadi; Merlyn S. Mendioro; Genaleen Q. Diaz; Glenn B. Gregorio; Rakesh K. Singh

    2013-12-01

    Salinity tolerance in rice is critical at reproductive stage because it ultimately determines grain yield. An F2 mapping population derived from a Sadri/FL478 cross was exposed to saline field conditions (6–8 dS m-1) after the active tillering stage to 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 be significant based on permutation test. Three major QTL clusters were found on chromosomes 2 (RM423–RM174), 4 (RM551–RM518) and 6 (RM20224–RM528) for multiple traits under salinity stress. Both parental lines contributed additively for QTLs identified for the yield components. A majority of the QTLs detected in our study are reported for the first time for reproductive stage salinity stress. Fine-mapping of selected putative QTLs will be the next step to facilitate marker-assisted backcrossing and to detect useful genes for salinity tolerance at the reproductive stage in rice.

  20. Correlation studies of some qualitative and quantitative traits with grain yield in spring wheat across two environments

    A 8x8 complete diallel population was studied to estimate correlation coefficients of seven quality and morphological traits in wheat. Sowing was done on 15 November and 15 December 2007-08. The differences among all the traits were statistically significant. Grain yield per plant under normal planting was significantly and positively correlated with plant height, peduncle length and 1000-grain weight. It was also positively correlated with spike length and gluten at genotypic level at P=0.01. Only grain yield per plant was negatively and significantly correlated with protein under both planting dates at genotypic level. Genotypic correlation of grain yield per plant in case of late planting was positive and non-significant with plant height, peduncle length and spike length, while it was negatively correlated with gluten. Phenotypic correlation of grain yield per plant with plant height, peduncle length, spike length, 1000-grain weight and gluten was positive and significant under both plantings while grain yield per plant was negatively and significantly associated with protein. It is therefore suggested that 1000-grain weight, peduncle length and gluten should be given more emphasis to improve yield and quality in wheat. (author)

  1. Correlation studies of some qualitative and quantitative traits with grain yield in spring wheat across two environments

    A 8 X 8 complete diallel population was studied to estimate correlation coefficients of seven quality and morphological traits in wheat. Sowing was done on 15 November and 15 December 2007-08. The differences among all the traits were statistically significant. Grain yield per plant under normal planting was significantly and positively correlated with plant height, peduncle length and 1000-grain weight. It was also positively correlated with spike length and gluten at genotypic level at P.0.01. Only grain yield per plant was negatively and significantly correlated with protein under both planting dates at genotypic level. Genotypic correlation of grain yield per plant in case of late planting was positive and non-significant with plant height, peduncle length and spike length, while it was negatively correlated with gluten. Phenotypic correlation of grain yield per plant with plant height, peduncle length, spike length, 1000-grain weight and gluten was positive and significant under both plantings while grain yield per plant was negatively and significantly associated with protein. It is therefore suggested that 1000-grain weight, peduncle length and gluten should be given more emphasis to improve yield and quality in wheat. (author)

  2. Evidence of 13C non-covalent isotope effects obtained by quantitative 13C nuclear magnetic resonance spectroscopy at natural abundance during normal phase liquid chromatography.

    Botosoa, Eliot P; Silvestre, Virginie; Robins, Richard J; Rojas, Jose Manuel Moreno; Guillou, Claude; Remaud, Gérald S

    2009-10-16

    Quantitative isotopic (13)C NMR at natural abundance has been used to determine the site-by-site (13)C/(12)C ratios in vanillin and a number of related compounds eluted from silica gel chromatography columns under similar conditions. Head-to-tail isotope fractionation is observed in all compounds at the majority of carbon positions. Furthermore, the site-specific isotope deviations show signatures characteristic of the position and functionality of the substituents present. The observed effects are more complex than would be obtained by simply summing the individual effects. Such detail is hidden when only the global (13)C content is measured by mass spectrometry. In particular, carbon positions within the aromatic ring are found to show site-specific isotope fractionation between the solute and the stationary phase. These interactions, defined as non-covalent isotope effects, can be normal or inverse and vary with the substitution pattern present. PMID:19748628

  3. Mapping quantitative trait loci (QTL in sheep. I. A new male framework linkage map and QTL for growth rate and body weight

    Attard Gina

    2009-04-01

    Full Text Available Abstract A male sheep linkage map comprising 191 microsatellites was generated from a single family of 510 Awassi-Merino backcross progeny. Except for ovine chromosomes 1, 2, 10 and 17, all other chromosomes yielded a LOD score difference greater than 3.0 between the best and second-best map order. The map is on average 11% longer than the Sheep Linkage Map v4.7 male-specific map. This map was employed in quantitative trait loci (QTL analyses on body-weight and growth-rate traits between birth and 98 weeks of age. A custom maximum likelihood program was developed to map QTL in half-sib families for non-inbred strains (QTL-MLE and is freely available on request. The new analysis package offers the advantage of enabling QTL × fixed effect interactions to be included in the model. Fifty-four putative QTL were identified on nine chromosomes. Significant QTL with sex-specific effects (i.e. QTL × sex interaction in the range of 0.4 to 0.7 SD were found on ovine chromosomes 1, 3, 6, 11, 21, 23, 24 and 26.

  4. Mapping quantitative trait loci affecting fatness and breast muscle weight in meat-type chicken lines divergently selected on abdominal fatness

    Neau André

    2006-01-01

    Full Text Available Abstract Quantitative trait loci (QTL for abdominal fatness and breast muscle weight were investigated in a three-generation design performed by inter-crossing two experimental meat-type chicken lines that were divergently selected on abdominal fatness. A total of 585 F2 male offspring from 5 F1 sires and 38 F1 dams were recorded at 8 weeks of age for live body, abdominal fat and breast muscle weights. One hundred-twenty nine microsatellite markers, evenly located throughout the genome and heterozygous for most of the F1 sires, were used for genotyping the F2 birds. In each sire family, those offspring exhibiting the most extreme values for each trait were genotyped. Multipoint QTL analyses using maximum likelihood methods were performed for abdominal fat and breast muscle weights, which were corrected for the effects of 8-week body weight, dam and hatching group. Isolated markers were assessed by analyses of variance. Two significant QTL were identified on chromosomes 1 and 5 with effects of about one within-family residual standard deviation. One breast muscle QTL was identified on GGA1 with an effect of 2.0 within-family residual standard deviation.

  5. A genome-wide association study reveals a quantitative trait locus for days open on chromosome 2 in Japanese Black cattle.

    Sasaki, Shinji; Ibi, Takayuki; Kojima, Takatoshi; Sugimoto, Yoshikazu

    2016-02-01

    Days open (DO), which is the interval from calving to conception, is an important trait related to reproductive performance in cattle. To identify quantitative trait loci for DO in Japanese Black cattle, we conducted a genome-wide association study with 33,303 single nucleotide polymorphisms (SNPs) using 459 animals with extreme DO values selected from a larger group of 15,488 animals. We identified a SNP on bovine chromosome 2 (BTA2) that was associated with DO. After imputation using phased haplotype data inferred from 586 812 SNPs of 1041 Japanese Black cattle, six SNPs associated with DO were located in an 8.5-kb region of high linkage disequilibrium on BTA2. These SNPs were located on the telomeric side at a distance of 177 kb from the parathyroid hormone 2 receptor (PTH2R) gene. The association was replicated in a sample of 1778 animals. In the replicated population, the frequency of the reduced-DO allele (Q) was 0.63, and it accounted for 1.72% of the total genetic variance. The effect of a Q-to-q allele substitution on DO was a decrease of 3.74 days. The results suggest that the Q allele could serve as a marker in Japanese Black cattle to select animals with superior DO performance. PMID:26374166

  6. Studies of CTNNBL1 and FDFT1 variants and measures of obesity: analyses of quantitative traits and case-control studies in 18,014 Danes

    Andreasen, Camilla Helene; Mogensen, Mette Sloth; Borch-Johnsen, Knut; Sandbaek, Annelli; Lauritzen, Torsten; Almind, Katrine; Hansen, Lars; Jørgensen, Torben; Pedersen, Oluf; Hansen, Torben

    2009-01-01

    obesity-related quantitative traits, and case-control studies in large study samples of Danes. METHODS: The FDFT1 rs7001819, CTNNBL1 rs6013029 and rs6020846 were genotyped, using TaqMan allelic discrimination, in a combined study sample comprising 18,014 participants ascertained from; the population...... most significantly associating variants within CTNNBL1 including rs6013029 and rs6020846 were additionally confirmed to associate with morbid obesity in a French Caucasian case-control sample. The aim of this study was to investigate the impact of these three variants on obesity, through analyses of......-based Inter99 cohort (n = 6,514), the ADDITION Denmark screening study cohort (n = 8,662), and a population-based sample (n = 680) and a type 2 diabetic patients group (n = 2,158) from Steno Diabetes Center. RESULTS: Both CTNNBL1 variants associated with body weight and height with per allele effect sizes of...

  7. High-resolution mapping of a fruit firmness-related quantitative trait locus in tomato reveals epistatic interactions associated with a complex combinatorial locus.

    Chapman, Natalie H; Bonnet, Julien; Grivet, Laurent; Lynn, James; Graham, Neil; Smith, Rebecca; Sun, Guiping; Walley, Peter G; Poole, Mervin; Causse, Mathilde; King, Graham J; Baxter, Charles; Seymour, Graham B

    2012-08-01

    Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir(s.p.)QTL2.1 to Fir(s.p.)QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir(s.p.)QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir(s.p.)QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus. PMID:22685170

  8. Effects of spermidine and calcium sulfate on quantitative and qualitative traits and vase life of rose (Rosa hybrida cv. Dolcvita grown in hydroponic system

    M. Hosseini Farahi

    2013-07-01

    Full Text Available In order to improve quantitative and qualitative properties and vase life of rose cv. Dolcvita, an experiment was conducted in a randomized complete blocks design with ten treatments and three replications in a hydroponic greenhouse adjacent to Yasouj city, Iran. Treatments included control, spermidine (0.5, 1 and 1.5 mM, calcium sulfate (2.5 and 5 mM, spermidine 0.5 mM+ calcium sulfate 2.5 mM, spermidine 0.5 mM + calcium sulfate 5 mM, spermidine 1 mM + calcium sulfate 2.5 mM and spermidine 1 mM + calcium sulfate 5 mM. Traits such as length of flower stalk, stem diameter, flower bud diameter, fresh weight of stem, chlorophyll content and vase life were measured. Results showed that effect of spermidine and calcium sulfate on all traits, except chlorophyll content, was significant (P<0.05. The highest and lowest length of flower stalk, stem diameter and fresh weight of stem was obtained in the 1.5 mM spermidine and control treatments, respectively. The highest diameter of flower bud was observed in the 0.5 mM spermidine and 2.5 mM calcium sulfate treatments. Flower vase life in the 0.5 mM spermidine + 5 mM calcium sulfate treatment was higher than that in the other treatments. Therefore, application of 1.5 mM spermidine is recommended for improving quantitative properties and combination of 0.5 mM spermidine with 5 mM calcium sulfate for increasing vase life of rose, cultivar Dolcvita, in hydroponic system.

  9. Mapping genomic features to functional traits through microbial whole genome sequences.

    Zhang, Wei; Zeng, Erliang; Liu, Dan; Jones, Stuart E; Emrich, Scott

    2014-01-01

    Recently, the utility of trait-based approaches for microbial communities has been identified. Increasing availability of whole genome sequences provide the opportunity to explore the genetic foundations of a variety of functional traits. We proposed a machine learning framework to quantitatively link the genomic features with functional traits. Genes from bacteria genomes belonging to different functional traits were grouped to Cluster of Orthologs (COGs), and were used as features. Then, TF-IDF technique from the text mining domain was applied to transform the data to accommodate the abundance and importance of each COG. After TF-IDF processing, COGs were ranked using feature selection methods to identify their relevance to the functional trait of interest. Extensive experimental results demonstrated that functional trait related genes can be detected using our method. Further, the method has the potential to provide novel biological insights. PMID:24989863

  10. Quantitative trait loci involved in sex determination and body growth in the gilthead sea bream (Sparus aurata L. through targeted genome scan.

    Dimitrios Loukovitis

    Full Text Available Among vertebrates, teleost fish exhibit a considerably wide range of sex determination patterns that may be influenced by extrinsic parameters. However even for model fish species like the zebrafish Danio rerio the precise mechanisms involved in primary sex determination have not been studied extensively. The zebrafish, a gonochoristic species, is lacking discernible sex chromosomes and the sex of juvenile fish is difficult to determine. Sequential protandrous hermaphrodite species provide distinct determination of the gender and allow studying the sex determination process by looking at the mechanism of sex reversal. This is the first attempt to understand the genetic basis of phenotypic variation for sex determination and body weight in a sequential protandrous hermaphrodite species, the gilthead sea bream (Sparus aurata. This work demonstrates a fast and efficient strategy for Quantitative Trait Loci (QTL detection in the gilthead sea bream, a non-model but target hermaphrodite fish species. Therefore a comparative mapping approach was performed to query syntenies against two other Perciformes, the European sea bass (Dicentrarchus labrax, a gonochoristic species and the Asian sea bass (Lates calcarifer a protandrous hermaphrodite. In this manner two significant QTLs, one QTL affecting both body weight and sex and one QTL affecting sex, were detected on the same linkage group. The co-segregation of the two QTLs provides a genomic base to the observed genetic correlation between these two traits in sea bream as well as in other teleosts. The identification of QTLs linked to sex reversal and growth, will contribute significantly to a better understanding of the complex nature of sex determination in S. aurata where most individuals reverse to the female sex at the age of two years through development and maturation of the ovarian portion of the gonad and regression of the testicular area. [Genomic sequences reported in this manuscript have been

  11. Short communication: Effects of Bos taurus autosome 9-located quantitative trait loci haplotypes on enzymatic mastitis indicators of milk from dairy cows experimentally inoculated with Escherichia coli.

    Sørensen, L P; Engberg, R M; Løvendahl, P; Larsen, T

    2015-08-01

    The aim of this study was to investigate the effect of a quantitative trait locus associated with mastitis caused by Escherichia coli, with one haplotype being more susceptible (HH) and another being more resistant (HL) to E. coli mastitis, on the activity of 4 inflammatory related milk enzymes. In particular, we investigated the suitability of β-glucuronidase (GLU) as an early indicator of E. coli mastitis. Besides GLU, the enzymes l-lactate dehydrogenase (LDH), N-acetyl-β-d-glucosaminidase (NAGase), and alkaline phosphatase were included. The study was conducted in an experimental setup with 31 Holstein cows divided into 4 groups representing repeated experiments and, within group, divided according to quantitative trait locus haplotype. All cows were inoculated with viable E. coli, and milk samples were collected 27 times from -6 to 396 h post-E. coli inoculation (PI). Activity of the 4 enzymes in milk, somatic cell count (SCC), daily milk yield, viable E. coli counts, and results of a semiquantitative polymerase chain reaction for pathogen detection, were all analyzed with a repeatability model. The response variables all expressed a strong reaction to the E. coli infection. Daily milk yield decreased significantly at 12 h PI and bacteria counts increased 100-fold and peaked at 18 h PI, which was validated by PCR. Also, SCC started to increase at 12 h PI and increased on average 70 times; however, no significant differences in SCC level were detected between HH and HL cows at any sampling point. The enzymes LDH, NAGase, and alkaline phosphatase showed similar responses, with a significantly increased activity and higher peak values for the HH than the HL cows. Significant differences between HH and HL cows were detected at different time points for these 3 enzymes, but not after adjusting P-values for multiple testing. A different pattern was also observed for GLU, where HL cows expressed the highest peak activity. Indication of differences in GLU activity

  12. The natural abundance of 15N in litter and soil profiles under six temperate tree species: N cycling depends on tree species traits and site fertility

    Callesen, Ingeborg; Nilsson, Lars Ola; Schmidt, Inger Kappel;

    2013-01-01

    We investigated the influence of tree species on the natural 15N abundance in forest stands under elevated ambient N deposition.We analysed δ15N in litter, the forest floor and three mineral soil horizons along with ecosystem N status variables at six sites planted three decades ago with five...... European broadleaved tree species and Norway spruce.Litter δ15N and 15N enrichment factor (δ15Nlitter–δ15Nsoil) were positively correlated with N status based on soil and litter N pools, nitrification, subsoil nitrate concentration and forest growth. Tree species differences were also significant...... for these N variables and for the litter δ15N and enrichment factor. Litter from ash and sycamore maple with high N status and low fungal mycelia activity was enriched in 15N (+0.9 delta units) relative to other tree species (European beech, pedunculate oak, lime and Norway spruce) even though the latter...

  13. Refined positioning of a quantitative trait locus affecting somatic cell score on chromosome 18 in the German Holstein using linkage disequilibrium.

    Baes, C; Brand, B; Mayer, M; Kühn, C; Liu, Z; Reinhardt, F; Reinsch, N

    2009-08-01

    Combined linkage and linkage disequilibrium analysis (LALD) was conducted to more accurately map a previously reported quantitative trait locus (QTL) affecting somatic cell score on bovine chromosome 18. A grand-daughter design consisting of 6 German Holstein grandsire families with 1,054 progeny-tested genotyped sons was used in this study. Twenty microsatellite markers, 5 single nucleotide polymorphisms, and an erythrocyte antigen marker with an average marker spacing of 1.95 cM were analyzed along a chromosomal segment of 50.80 cM. Variance components were estimated and restricted maximum likelihood test statistics were calculated at the midpoint of each marker interval. The test statistics calculated in single-QTL linkage analysis exceeded the genome-wide significance threshold at several putative QTL positions. Using LALD, we were successful in assigning a genome-wide significant QTL to a confidence interval of 10.8 cM between the markers ILSTS002 and BMS833. The QTL in this marker interval was estimated to be responsible for between 5.89 and 13.86% of the genetic variation in somatic cell score. In contrast to the single-QTL linkage analysis model, LALD analyses with a 2-QTL model confirmed the position of one QTL, but gave no conclusive evidence for the existence or position of a second QTL. Ultimately, the QTL position was narrowed down considerably compared with previous results with a refined confidence interval of less than 11 cM. PMID:19620688

  14. An interaction quantitative trait loci tool implicates epistatic functional variants in an apoptosis pathway in smallpox vaccine eQTL data.

    Lareau, C A; White, B C; Oberg, A L; Kennedy, R B; Poland, G A; McKinney, B A

    2016-06-01

    Expression quantitative trait loci (eQTL) studies have functionalized nucleic acid variants through the regulation of gene expression. Although most eQTL studies only examine the effects of single variants on transcription, a more complex process of variant-variant interaction (epistasis) may regulate transcription. Herein, we describe a tool called interaction QTL (iQTL) designed to efficiently detect epistatic interactions that regulate gene expression. To maximize biological relevance and minimize the computational and hypothesis testing burden, iQTL restricts interactions such that one variant is within a user-defined proximity of the transcript (cis-regulatory). We apply iQTL to a data set of 183 smallpox vaccine study participants with genome-wide association study and gene expression data from unstimulated samples and samples stimulated by inactivated vaccinia virus. While computing only 0.15% of possible interactions, we identify 11 probe sets whose expression is regulated through a variant-variant interaction. We highlight the functional epistatic interactions among apoptosis-related genes, DIABLO, TRAPPC4 and FADD, in the context of smallpox vaccination. We also use an integrative network approach to characterize these iQTL interactions in a posterior network of known prior functional interactions. iQTL is an efficient, open-source tool to analyze variant interactions in eQTL studies, providing better understanding of the function of epistasis in immune response and other complex phenotypes. PMID:27052692

  15. Quantitative trait locus mapping of genes that regulate HDL cholesterol in SM/J and NZB/B1NJ inbred mice.

    Pitman, Wendy A; Korstanje, Ron; Churchill, Gary A; Nicodeme, Edwige; Albers, John J; Cheung, Marian C; Staton, Megan A; Sampson, Stephen S; Harris, Stephen; Paigen, Beverly

    2002-01-01

    To investigate the quantitative trait loci (QTL) regulating plasma cholesterol, the female progeny of an (SMxNZB/ B1NJ)xNZB/B1NJ backcross were fed an atherogenic diet. After 18 wk, plasma total cholesterol and high-density lipoprotein cholesterol (HDL-C) was measured. HDL-C concentrations were greater in NZB than in SM mice. For standard chow-fed mice, QTL were found near D5Mit370 and D18Mit34. For mice fed an atherogenic diet, a QTL was found near D5Mit239. The QTL for chow-fed and atherogenic-fed mice on chromosome 5 seem to be two different loci. We used a multitrait analysis to rule out pleiotropy in favor of a two-QTL hypothesis. Furthermore, the HDL-C in these strains was induced by the high-fat diet. For inducible HDL-C, one significant locus was found near D15Mit39. The gene for an HDL receptor, Srb1, maps close to the HDL-C QTL at D5Mit370, but the concentrations of Srb1 mRNA and SR-B1 protein and the gene sequence of NZB/B1NJ and SM/J did not support Srb1 as a candidate gene. With these QTL, we have identified chromosomal regions that affect lipoprotein profiles in these strains. PMID:12006675

  16. Characterization of variation and quantitative trait loci related to terpenoid indole alkaloid yield in a recombinant inbred line mapping population of Catharanthus roseus

    Vishakha Sharma; Swati Chaudhary; Suchi Srivastava; Richa Pandey; Sushil Kumar

    2011-04-01

    Improved Catharanthus roseus cultivars are required for high yields of vinblastine, vindoline and catharanthine and/or serpentine and ajmalicine, the pharmaceutical terpenoid indole alkaloids. An approach to derive them is to map QTL for terpenoid indole alkaloids yields, identify DNA markers tightly linked to the QTL and apply marker assisted selection. Towards the end, 197 recombinant inbred lines from a cross were grown over two seasons to characterize variability for seven biomass and 23 terpenoid indole alkaloids content-traits and yield-traits. The recombinant inbred lines were genotyped for 178 DNA markers which formed a framework genetic map of eight linkage groups (LG), spanning 1786.5 cM, with 10.0 cM average intermarker distance. Estimates of correlations between traits allowed selection of seven relatively more important traits for terpenoid indole alkaloids yields. QTL analysis was performed on them using single marker (regression) analysis, simple interval mapping and composite interval mapping procedures. A total of 20 QTL were detected on five of eight LG, 10 for five traits on LG1, five for four traits on LG2, three for one trait on LG3 and one each for different traits on LG three and four. QTL for the same or different traits were found clustered on three LG. Co-location of two QTL for biomass traits was in accord of correlation between them. The QTL were validated for use in marker assisted selection by the recombinant inbred line which transgressively expressed 16 traits contributory to the yield vinblastine, vindoline and catharanthine from leaves and roots that possessed favourable alleles of 13 relevant QTL.

  17. Studies of a genetic variant in HK1 in relation to quantitative metabolic traits and to the prevalence of type 2 diabetes

    Bonnefond Amélie

    2011-07-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs within the gene encoding Hexokinase 1 (HK1 are associated with changes in glycated haemoglobin (HbA1c levels. Our aim was to investigate the effect of HK1 rs7072268 on measures of glucose- and lipid-metabolism in a Danish non-diabetic population and combine the outcome of these analyses in a meta-analysis with previously published results. Furthermore, our aim was to perform a type 2 diabetes case-control analysis and meta-analysis with two previous case-control studies. Methods SNP rs7072268 was genotyped in 9,724 Danes. The quantitative trait study included 5,604 non-diabetic individuals from the Inter99 cohort. The case-control study included 4,449 glucose tolerant individuals and 3,398 patients with type 2 diabetes. Meta-analyses on quantitative traits included 24,560 Caucasian individuals and 30,802 individuals were included in the combined analysis of present and previous type 2 diabetes case-control studies. Results Using an additive model, we confirmed that the T-allele of rs7072268 associates with increased HbA1c of 0.6% (CI: 0.4 - 0.9, p = 3*10-7 per allele. The same allele associated with an increased area under the curve (AUC for glucose of 5.0 mmol/l*min (0.1 - 10.0, p = 0.045 following an oral glucose tolerance test (OGTT and increased fasting levels of cholesterol of 0.06 mmol/l (0.03 - 1.0, p = 0.001 and triglycerides of 2.0% (0.2 - 3.8, p = 0.03 per allele in the same study sample of non-diabetic individuals from the Inter99 cohort. However, the T-allele did not show any association with estimates of insulin release or insulin sensitivity neither in Inter99 nor in combined analyses. The prevalence of type 2 diabetes was increased among carriers of the rs7072268 T-allele both in the Danish study-population with an OR of 1.11 (1.02-1.21 and in a meta-analysis including the two additional sample sets with an OR of 1.06 (1.02-1.11. However, after Bonferroni correction the T

  18. Quantitative trait loci (QTLs) analysis of palm oil fatty acid composition in an interspecific pseudo-backcross from Elaeis oleifera (HBK) Cortés and oil palm (Elaeis guineensis Jacq.)

    Montoya, Carmenza; Lopes, Ricardo; Flori, Albert; Cros, David; Cuellar, Teresa; Summo, Maryline; Espeout, Sandra; Rivallan, Ronan; Risterucci, Ange-Marie; Bittencourt, Daniela; Zambrano, Jorge R.; Alarcon G, Wilmar H.; Villeneuve, Pierre; Pina, Michel; Nouy, Bruno

    2013-01-01

    We chose an Elaeis interspecific pseudo-backcross of first generation (E. oleifera x E. guineensis) x E. guineensis to identify quantitative trait loci (QTLs) for fatty acid composition of palm oil. A dense microsatellite linkage map of 362 loci spanned 1.485 cM, representing the 16 pairs of homologous chromosomes in the Elaeis genus from which we traced segregating alleles from both E. oleifera and E. guineensis grandparents. The relative linear orders of mapped loci suggested the probable a...

  19. Identification of quantitative trait loci affecting resistance to gastrointestinal parasites in a double backcross population of Red Maasai and Dorper sheep

    Full text: A genome-wide scan for quantitative trait loci (QTL) affecting gastrointestinal nematode resistance in sheep was completed using a double backcross population derived from Red Maasai and Dorper ewes bred to F1 rams. This design provided an opportunity to map potentially unique genetic variation associated with a parasite-tolerant breed like Red Maasai, a breed developed to survive East African grazing conditions. Parasite indicator phenotypes (blood packed cell volume - PCV and faecal egg count - FEC) were collected on a weekly basis from 1064 lambs during a single 3-month post-weaning grazing challenge on infected pastures. The averages of last measurements for FEC (AVFEC) and PCV (AV-PCV), along with decline in PCV from challenge start to end (PCVD), were used to select lambs (N = 371) for genotyping that represented the tails (10% threshold) of the phenotypic distributions. Marker genotypes for 172 microsatellite loci covering 25 of 26 autosomes (1560.7 cM) were scored and corrected by GENOPROB prior to QXPAK analysis that included Box-Cox transformed AVFEC and arcsine transformed PCV statistics. Significant QTL for AVFEC and AVPCV were detected on four chromosomes, and this included a novel AVFEC QTL on chromosome 6 that would have remained undetected without Box-Cox transformation methods. The most significant P-values for AVFEC, AVPCV and PCVD overlapped the same marker interval on chromosome 22, suggesting the potential for a single causative mutation, which remains unknown. In all cases, the favourable QTL allele was always contributed from Red Maasai, providing support for the idea that future marker-assisted selection for genetic improvement of production in East Africa will rely on markers in linkage disequilibrium with these QTL. (author)

  20. Identification of distinct quantitative trait loci associated with defence against the closely related aphids Acyrthosiphon pisum and A. kondoi in Medicago truncatula

    Guo, Su-Min

    2012-03-21

    Aphids are a major family of plant insect pests. Medicago truncatula and Acyrthosiphon pisum (pea aphid, PA) are model species with a suite of resources available to help dissect the mechanism underlying plant-aphid interactions. A previous study focused on monogenic and relatively strong resistance in M. truncatula to PA and other aphid species. In this study a moderate resistance to PA was characterized in detail in the M. truncatula line A17 and compared with the highly susceptible line A20 and the more resistant line Jester. The results show that PA resistance in A17 involves both antibiosis and tolerance, and that resistance is phloem based. Quantitative trait locus (QTL) analysis using a recombinant inbred line (RIL) population (n=114) from a cross between A17 and A20 revealed that one locus, which co-segregated with AIN (Acyrthosiphon-induced necrosis) on chromosome 3, is responsible for the reduction of aphid biomass (indicator of antibiosis) for both PA and bluegreen aphid (BGA, A. kondoi), albeit to a lesser degree for PA than BGA. Interestingly, two independent loci on chromosomes 5 and 3 were identified for the plant biomass reduction (indicator of plant tolerance) by PA and BGA, respectively, demonstrating that the plant\\'s tolerance response to these two closely related aphid species is distinct. Together with previously identified major resistant (R) genes, the QTLs identified in this study are powerful tools to understand fully the spectrum of plant defence against sap-sucking insects and provide opportunities for breeders to generate effective and sustainable strategies for aphid control. 2012 The Author.

  1. High-resolution genetic linkage mapping, high-temperature tolerance and growth-related quantitative trait locus (QTL) identification in Marsupenaeus japonicus.

    Lu, Xia; Luan, Sheng; Hu, Long Yang; Mao, Yong; Tao, Ye; Zhong, Sheng Ping; Kong, Jie

    2016-06-01

    The Kuruma prawn, Marsupenaeus japonicus, is one of the most promising marine invertebrates in the industry in Asia, Europe and Australia. However, the increasing global temperatures result in considerable economic losses in M. japonicus farming. In the present study, to select genetically improved animals for the sustainable development of the Kuruma prawn industry, a high-resolution genetic linkage map and quantitative trait locus (QTL) identification were performed using the RAD technology. The maternal map contained 5849 SNP markers and spanned 3127.23 cM, with an average marker interval of 0.535 cM. Instead, the paternal map contained 3927 SNP markers and spanned 3326.19 cM, with an average marker interval of 0.847 cM. The consensus map contained 9289 SNP markers and spanned 3610.90 cM, with an average marker interval of 0.388 cM and coverage of 99.06 % of the genome. The markers were grouped into 41 linkage groups in the maps. Significantly, negative correlation was detected between high-temperature tolerance (UTT) and body weight (BW). The QTL mapping revealed 129 significant QTL loci for UTT and four significant QTL loci for BW at the genome-wide significance threshold. Among these QTLs, 129 overlapped with linked SNPs, and the remaining four were located in regions between contiguous SNPs. They explained the total phenotypic variance ranging from 8.9 to 12.4 %. Because of a significantly negative correlation between growth and high-temperature tolerance, we demonstrate that this high-resolution linkage map and QTLs would be useful for further marker-assisted selection in the genetic improvement of M. japonicus. PMID:26965508

  2. Identification of aortic arch-specific quantitative trait loci for atherosclerosis by an intercross of DBA/2J and 129S6 apolipoprotein E-deficient mice.

    Yukako Kayashima

    Full Text Available The genetic background of apolipoprotein E (apoE deficient mice influences atherosclerotic plaque development. We previously reported three quantitative trait loci (QTL, Aath1-Aath3, that affect aortic arch atherosclerosis independently of those in the aortic root in a cross between C57BL6 apoEKO mice (B6-apoE and 129S6 apoEKO mice (129-apoE. To gain further insight into genetic factors that influence atherosclerosis at different vascular locations, we analyzed 335 F2 mice from an intercross between 129-apoE and apoEKO mice on a DBA/2J genetic background (DBA-apoE. The extent of atherosclerosis in the aortic arch was very similar in the two parental strains. Nevertheless, a genome-wide scan identified two significant QTL for plaque size in the aortic arch: Aath4 on Chromosome (Chr 2 at 137 Mb and Aath5 on Chr 10 at 51 Mb. The DBA alleles of Aath4 and Aath5 respectively confer susceptibility and resistance to aortic arch atherosclerosis over 129 alleles. Both QTL are also independent of those affecting plaque size at the aortic root. Genome analysis suggests that athero-susceptibility of Aath4 in DBA may be contributed by multiple genes, including Mertk and Cd93, that play roles in phagocytosis of apoptotic cells and modulate inflammation. A candidate gene for Aath5 is Stab2, the DBA allele of which is associated with 10 times higher plasma hyaluronan than the 129 allele. Overall, our identification of two new QTL that affect atherosclerosis in an aortic arch-specific manner further supports the involvement of distinct pathological processes at different vascular locations.

  3. Identification of quantitative trait loci affecting resistance to gastrointestinal parasites in a double backcross population of Red Maasai and Dorper sheep.

    Silva, M V B; Sonstegard, T S; Hanotte, O; Mugambi, J M; Garcia, J F; Nagda, S; Gibson, J P; Iraqi, F A; McClintock, A E; Kemp, S J; Boettcher, P J; Malek, M; Van Tassell, C P; Baker, R L

    2012-02-01

    A genome-wide scan for quantitative trait loci (QTL) affecting gastrointestinal nematode resistance in sheep was completed using a double backcross population derived from Red Maasai and Dorper ewes bred to F(1) rams. This design provided an opportunity to map potentially unique genetic variation associated with a parasite-tolerant breed like Red Maasai, a breed developed to survive East African grazing conditions. Parasite indicator phenotypes (blood packed cell volume - PCV and faecal egg count - FEC) were collected on a weekly basis from 1064 lambs during a single 3-month post-weaning grazing challenge on infected pastures. The averages of last measurements for FEC (AVFEC) and PCV (AVPCV), along with decline in PCV from challenge start to end (PCVD), were used to select lambs (N = 371) for genotyping that represented the tails (10% threshold) of the phenotypic distributions. Marker genotypes for 172 microsatellite loci covering 25 of 26 autosomes (1560.7 cm) were scored and corrected by Genoprob prior to qxpak analysis that included Box-Cox transformed AVFEC and arcsine transformed PCV statistics. Significant QTL for AVFEC and AVPCV were detected on four chromosomes, and this included a novel AVFEC QTL on chromosome 6 that would have remained undetected without Box-Cox transformation methods. The most significant P-values for AVFEC, AVPCV and PCVD overlapped the same marker interval on chromosome 22, suggesting the potential for a single causative mutation, which remains unknown. In all cases, the favourable QTL allele was always contributed from Red Maasai, providing support for the idea that future marker-assisted selection for genetic improvement of production in East Africa will rely on markers in linkage disequilibrium with these QTL. PMID:22221026

  4. Quantitative trait loci for non-race-specific, high-temperature adult-plant resistance to stripe rust in wheat cultivar Express.

    Lin, F; Chen, X M

    2009-02-01

    Wheat cultivar Express has durable, high-temperature adult-plant (HTAP) resistance to stripe rust (Puccinia striiformis f. sp. tritici). To elucidate the genetic basis of the resistance, Express was crossed with 'Avocet Susceptible' (AVS). A mapping population of 146 F(5) recombinant inbred lines (RILs) was developed using single-seed descent. The RILs were evaluated at two sites near Pullman in eastern Washington and one site near Mount Vernon in western Washington in 2005, and were evaluated near Pullman in 2006 under natural stripe rust infection of predominant races virulent on seedlings of Express. Infection type (IT) and disease severity (DS) were recorded three times for each line during each growing season. The DS data were used to calculate relative area under the disease progress curve (rAUDPC) values. Both IT and rAUDPC data showed continuous distributions, indicating that the Express HTAP resistance was controlled by quantitative trait loci (QTL). Resistance gene analog polymorphism (RGAP) and simple sequence repeat (SSR) techniques were used to map the HTAP resistance QTL. Three QTL were detected with significant additive effects, explaining 49.5-69.6% of the phenotypic variation for rAUDPC. Two of the QTL explained 30.8-42.7% of the phenotypic variation for IT. The three QTL were mapped to wheat chromosomes 6AS, 3BL and 1BL, and were designated as QYrex.wgp-6AS, QYrex.wgp-3BL and QYrex.wgp-1BL, respectively. QYrex.wgp-6AS and QYrex.wgp-3BL, which had higher effects than QYrex.wgp-1BL, were different from previously reported QTL/genes for adult-plant resistance. Markers Xgwm334-Xwgp56 and Xgwm299-Xwgp66 flanking the two major QTL were highly polymorphic in various wheat genotypes, suggesting that these markers are useful in marker-assisted selection. PMID:18815766

  5. Targeted mapping of quantitative trait locus regions for rhizomatousness in chromosome SBI-01 and analysis of overwintering in a Sorghum bicolor × S. propinquum population

    Washburn, Jacob D.; Murray, Seth C.; Burson, Byron L.; Klein, Robert R.; Jessup, Russell W.

    2012-01-01

    While rhizome formation is intimately associated with perennialism and the derived benefit of sustainability, the introduction of this trait into temperate-zone adapted Sorghum cultivars requires precise knowledge of the genetics conditioning this trait in order to minimize the risk of weediness (e.g., Johnsongrass, S. halepense) while maximizing the productivity of perennial sorghum. As an incremental step towards dissecting the genetics of perennialism, a segregating F4 heterogeneous inbred...

  6. Quantitative Trait Loci for Salinity Tolerance Identified under Drained and Waterlogged Conditions and Their Association with Flowering Time in Barley (Hordeum vulgare. L.

    Yanling Ma

    Full Text Available Salinity is one of the major abiotic stresses affecting crop production via adverse effects of osmotic stress, specific ion toxicity, and stress-related nutritional disorders. Detrimental effects of salinity are also often exacerbated by low oxygen availability when plants are grown under waterlogged conditions. Developing salinity-tolerant varieties is critical to overcome these problems, and molecular marker assisted selection can make breeding programs more effective.In this study, a double haploid (DH population consisting of 175 lines, derived from a cross between a Chinese barley variety Yangsimai 1 (YSM1 and an Australian malting barley variety Gairdner, was used to construct a high density molecular map which contained more than 8,000 Diversity Arrays Technology (DArT markers and single nucleotide polymorphism (SNP markers. Salinity tolerance of parental and DH lines was evaluated under drained (SalinityD and waterlogged (SalinityW conditions at two different sowing times.Three quantitative trait loci (QTL located on chromosome 1H, single QTL located on chromosomes 1H, 2H, 4H, 5H and 7H, were identified to be responsible for salinity tolerance under different environments. Waterlogging stress, daylight length and temperature showed significant effects on barley salinity tolerance. The QTL for salinity tolerance mapped on chromosomes 4H and 7H, QSlwd.YG.4H, QSlwd.YG.7H and QSlww.YG.7H were only identified in winter trials, while the QTL on chromosome 2H QSlsd.YG.2H and QSlsw.YG.2H were only detected in summer trials. Genes associated with flowering time were found to pose significant effects on the salinity QTL mapped on chromosomes 2H and 5H in summer trials. Given the fact that the QTL for salinity tolerance QSlsd.YG.1H and QSlww.YG.1H-1 reported here have never been considered in the literature, this warrants further investigation and evaluation for suitability to be used in breeding programs.

  7. Exercise Capacity and Response to Training Quantitative Trait Loci in a NZW X 129S1 Intercross and Combined Cross Analysis of Inbred Mouse Strains.

    Michael P Massett

    Full Text Available Genetic factors determining exercise capacity and the magnitude of the response to exercise training are poorly understood. The aim of this study was to identify quantitative trait loci (QTL associated with exercise training in mice. Based on marked differences in training responses in inbred NZW (-0.65 ± 1.73 min and 129S1 (6.18 ± 3.81 min mice, a reciprocal intercross breeding scheme was used to generate 285 F2 mice. All F2 mice completed an exercise performance test before and after a 4-week treadmill running program, resulting in an increase in exercise capacity of 1.54 ± 3.69 min (range = -10 to +12 min. Genome-wide linkage scans were performed for pre-training, post-training, and change in run time. For pre-training exercise time, suggestive QTL were identified on Chromosomes 5 (57.4 cM, 2.5 LOD and 6 (47.8 cM, 2.9 LOD. A significant QTL for post-training exercise capacity was identified on Chromosome 5 (43.4 cM, 4.1 LOD and a suggestive QTL on Chromosomes 1 (55.7 cM, 2.3 LOD and 8 (66.1 cM, 2.2 LOD. A suggestive QTL for the change in run time was identified on Chromosome 6 (37.8 cM, 2.7 LOD. To identify shared QTL, this data set was combined with data from a previous F2 cross between B6 and FVB strains. In the combined cross analysis, significant novel QTL for pre-training exercise time and change in exercise time were identified on Chromosome 12 (54.0 cM, 3.6 LOD and Chromosome 6 (28.0 cM, 3.7 LOD, respectively. Collectively, these data suggest that combined cross analysis can be used to identify novel QTL and narrow the confidence interval of QTL for exercise capacity and responses to training. Furthermore, these data support the use of larger and more diverse mapping populations to identify the genetic basis for exercise capacity and responses to training.

  8. Multiple quantitative trait loci for cortical and trabecular bone regulation map to mid-distal mouse chromosome 4 that shares linkage homology to human chromosome 1p36.

    Beamer, Wesley G; Shultz, Kathryn L; Coombs, Harold F; Horton, Lindsay G; Donahue, Leah Rae; Rosen, Clifford J

    2012-01-01

    The mid-distal region of mouse chromosome 4 (Chr 4) is homologous with human Chr 1p36. Previously, we reported that mouse Chr 4 carries a quantitative trait locus (QTL) with strong regulatory effect on volumetric bone mineral density (vBMD). The intent of this study is to utilize nested congenic strains to decompose the genetic complexity of this gene-rich region. Adult females and males from 18 nested congenic strains carrying discrete C3H sequences were phenotyped for femoral mineral and volume by pQCT and for trabecular bone volume (BV), tissue volume (TV), trabecular number (Trab.no), and trabecular thickness (Trab.thk) by MicroCT 40. Our data show that the mouse Chr 4 region consists of at least 10 regulatory QTL regions that affected either or both pQCT and MicroCT 40 phenotypes. The pQCT phenotypes were typically similar between sexes, whereas the MicroCT 40 phenotypes were divergent. Individual congenic strains contained one to seven QTL regions. These regions conferred large positive or negative effects in some congenic strains, depending on the particular bone phenotype. The QTL regions II to X are syntenic with human 1p36, containing from 1 to 102 known genes. We identified 13 candidate genes that can be linked to bone within these regions. Six of these genes were linked to osteoblasts, three linked to osteoclasts, and two linked to skeletal development. Three of these genes have been identified in Genome Wide Association Studies (GWAS) linked to 1p36. In region III, there is only one gene, Lck, which conferred negative pQCT and MicroCT 40 phenotypes in both sexes. This gene is important to development and functioning of T cells, has been associated with osteoclast activity, and represents a novel bone regulatory gene that merits further experimental evaluation. In summary, congenic strains are powerful tools for identifying regulatory regions that influence bone biology and offer models for testing hypotheses about gene-gene and gene

  9. The effects of different levels of nitrogen and molybdenum in nutrient solution on quantitative and qualitative traits and nitrate concentration of cucumber in hydroponic culture

    S. Beigi

    2011-07-01

    Full Text Available Abstract In order to study the effects of different levels of nitrogen (N and molybdenum (Mo in nutrient solution on quantitative and qualitative traits and nitrate concentration of cucumber (Sultan cv., a factorial hydroponic-experiment with completely randomized design and three replications was conducted in the greenhouse of Soil Science Department, Zanjan University, in 2009. The concentrations of N in nutrient solution were 238 and 310 mg/L, and Mo was used at the rates of 0.01, 0.1 and 1 mg/L. The results showed that the effects of N and Mo levels were significant (P≤0.01 on plant yield and growth indices such as average weight, length and diameter of fruit and chlorophyll content of leaf. The chlorophyll content of leaf increased but fruit yield and average weight, length and diameter of fruits decreased as the N concentration of the nutrient solution increased. Increasing the Mo level in the nutrient solution decreased the growth indices and yield of cucumber. The highest fruit yield was obtained when the concentration of Mo in the nutrient solution was 0.01 mg/L. But it didn’t have significant difference with 0.1 mg/L treatment. However, the yield decreased significantly as the Mo concentration increased to 1 mg/L. The effects of N and Mo levels of nutrient solution were significant (P ≤ 0.01 on nitrate concentration of the fruits. As the N level of nutrient solution increased, the nitrate concentration of cucumber fruit increased from 1356 to 2122 mg/kg (on dry weight basis, and exceeded the toxicity limit of 1500 mg/L. Increasing the concentration of Mo of the nutrient solution from 0.01 to 0.1 mg/L decreased nitrate concentration of fruits from 1961 to 1703 mg/kg, without decreasing the fruit yield. With an increase in N concentration of the nutrient solution, the fruit concentrations of N, potassium and calcium increased, but those of phosphorus, magnesium and Mo decreased significantly. Also, as the concentration of Mo in the

  10. Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus ‘Robusta 5’ accessions

    Gardiner Susan E

    2012-04-01

    Full Text Available Abstract Background Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL for fire blight resistance has been reported on linkage group 3 of Malus ‘Robusta 5’. In this study we identified markers derived from putative fire blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. Results When several defined E.amylovora strains were used to inoculate three progenies from international breeding programs, all with ‘Robusta 5’ as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand ‘Malling 9’ X ‘Robusta 5’ population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein ( MxdRLP1 and a closely linked class 3 peroxidase gene. While the QTL detected in the German ‘Idared’ X ‘Robusta 5’ population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6 cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene ( HSP90. In the US ‘Otawa3’ X ‘Robusta5’ population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in fire blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY

  11. Label-free Quantitative Proteomics for the Extremely Thermophilic Bacterium Caldicellulosiruptor obsidiansis Reveal Distinct Abundance Patterns upon Growth on Cellobiose, Crystalline Cellulose, and Switchgrass

    Giannone, Richard J [ORNL; Lochner, Adriane [ORNL; Keller, Martin [ORNL; Antranikian, Garabed [Technische Universitat Hamburg-Harburg (Hamburg University of Technology); Graham, David E [ORNL; Hettich, Robert {Bob} L [ORNL

    2011-01-01

    Mass spectrometric analysis of Caldicellulosiruptor obsidiansis cultures grown on four different carbon sources identified 65% of the cells predicted proteins in cell lysates and supernatants. Biological and technical replication together with sophisticated statistical analysis were used to reliably quantify protein abundances and their changes as a function of carbon source. Extracellular, multifunctional glycosidases were significantly more abundant on cellobiose than on the crystalline cellulose substrates Avicel and filter paper, indicating either disaccharide induction or constitutive protein expression. Highly abundant flagellar, chemotaxis, and pilus proteins were detected during growth on insoluble substrates, suggesting motility or specific substrate attachment. The highly abundant extracellular binding protein COB47-0549 together with the COB47-1616 ATPase might comprise the primary ABC-transport system for cellooligosaccharides, while COB47-0096 and COB47-0097 could facilitate monosaccharide uptake. Oligosaccharide degradation can occur either via extracellular hydrolysis by a GH1 {beta}-glycosidase or by intracellular phosphorolysis using two GH94 enzymes. When C. obsidiansis was grown on switchgrass, the abundance of hemicellulases (including GH3, GH5, GH51, and GH67 enzymes) and certain sugar transporters increased significantly. Cultivation on biomass also caused a concerted increase in cytosolic enzymes for xylose and arabinose fermentation.

  12. Changes in protein abundance between tender and tough meat from bovine Longissimus thoracis muscle assessed by isobaric Tag for Relative and Absolute Quantitation (iTRAQ) and 2-dimensional gel electrophoresis analysis

    Bjarnadóttir, S G; Hollung, K; Høy, M; Bendixen, Emøke; Codrea, Marius Cosmin; Veiseth-Kent, E

    2012-01-01

    The aim of this study was to find potential biomarkers for meat tenderness in bovine Longissimus thoracis muscle and to compare results from isobaric Tag for Relative and Absolute Quantitation (iTRAQ) and 2-dimensional gel electrophoresis (2-DE) analysis. The experiment included 4 tender and 4...... tough samples, based on shear force measurements at 7 d postmortem, from young Norwegian red (NRF) bulls, taken at 1 h postmortem. A number of the proteins which have previously been related to tenderness were found to change in abundance between tender and tough samples, both in iTRAQ (P < 0.1) and 2......-DE analysis (P < 0.05). Furthermore, 3 proteins that have not previously been related to tenderness were found to change significantly in abundance between tender and tough meat samples in the present study. These include proteins related to control of flux through the tricarboxylate cycle [2...

  13. Detection and quantitation of twenty-seven cytokines, chemokines and growth factors pre- and post-high abundance protein depletion in human plasma

    Seong-Beom Ahn

    2014-06-01

    Full Text Available Cytokines, chemokines and growth factors (CCGFs in human plasma are analyzed for identification of biomarkers. However concentrations of CCGFs are very low; it is difficult to identify and quantify low abundance proteins in the presence of the high abundance proteins (HAPs unless HAPs are removed prior to analysis. However, there is a concern that the low abundance proteins such as CCGFs may also be removed during the HAP depletion process. In this study, we have examined whether or not depletion of the HAPs enhances detection of the CCGFs by immuno-assays. Top 14 HAPs were depleted from 10 healthy volunteers’ plasma using MARS-14 immuno-depletion column and a total of 27 CCGFs were analyzed by bead-based multiplexed immuno-assay. All 27 CCGFs were detected in neat plasma (NP, 25 were detected in flow through fraction (FT and 21 were detected in bound protein (BP fraction. Concentrations of 22 CCGFs were significantly higher in NP compared to FT and BP. Only one CCGF had higher concentration in FT compared to NP. The remaining 2 CCGFs were not different between NP and FT. It was counter-productive for the detection of 24 CCGFs after HAP removal, primarily due to post-depletion protein precipitation and/or re-suspension of pellets.

  14. Comparison of multipoint linkage analyses for quantitative traits in the CEPH data: parametric LOD scores, variance components LOD scores, and Bayes factors

    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...

  15. Simulating the Yield Impacts of Organ-Level Quantitative Trait Loci Associated With Drought Response in Maize: A “Gene-to-Phenotype” Modeling Approach

    Chenu, Karine; Chapman, Scott C.; Tardieu, François; McLean, Greg; Welcker, Claude; Hammer, Graeme L.

    2009-01-01

    Under drought, substantial genotype–environment (G × E) interactions impede breeding progress for yield. Identifying genetic controls associated with yield response is confounded by poor genetic correlations across testing environments. Part of this problem is related to our inability to account for the interplay of genetic controls, physiological traits, and environmental conditions throughout the crop cycle. We propose a modeling approach to bridge this “gene-to-phenotype” gap. For maize un...

  16. Linkage scan for quantitative traits identifies new regions of interest for substance dependence in the Collaborative Study on the Genetics of Alcoholism (COGA) Sample

    Agrawal, Arpana; Hinrichs, Anthony L.; Dunn, Gerald; Bertelsen, Sarah; Dick, Danielle M; Saccone, Scott F; Saccone, Nancy L.; Grucza, Richard A.; Wang, Jen C.; Robert Cloninger, C.; Edenberg, Howard J.; Foroud, Tatiana; Hesselbrock, Victor; Kramer, John; Bucholz, Kathleen K.

    2007-01-01

    Dependence on alcohol and illicit drugs frequently co-occur. Results from a number of twin studies suggest that heritable influences on alcohol dependence and drug dependence may substantially overlap. Using large, genetically informative pedigrees from the Collaborative Study on the Genetics of Alcoholism (COGA), we performed quantitative linkage analyses using a panel of 1717 SNPs. Genome-wide linkage analyses were conducted for quantitative measures of DSM-IV alcohol dependence criteria, c...

  17. Genetic alterations as determined by quantitative morphological, viability and social behavioral traits in postirradiation generations of an inbred strain of the platyfish, Xiphophorus maculatus (Guenther)(Pisces: Poecliidae), induced by 1000 R of X-rays to spermatogonia and oogonia

    Spermatogonia and oogonia were X-irradiated with 258 mC/kg in neonatal platyfish. This procedure corresponds to an exposure of immature spermatogonia and oogonia. The postirradiation (PI) F2 generation was compared with controls of the same origin regarding viability characters (brood size, postnatal mortality, and sex ratio), quantitative morphological (number of vertebrae, body proportions) and social behavioral traits (cohesiveness of both sexes, male sexual and agonistic behavior patterns). Each of 5 pairs of F2 fish were used as the founders for a one-year lasting population experiment in which the fish had been subjected to either mutation pressure through derivation from irradiated spermatogonia and oogonia as mentioned above or to selection pressure through predation by the convict cichlid, Cichlasoma nigrofasciatum, or to a combination of both in order to compare the outcome of this experiment with that of a control population. The PI F2 exhibited a higher mortality rate than the controls. A unidirectional shift of the mean values of the quantitative morphological characters towards a more compact fish was observed in the postirradiation generations. The social cohesiveness of PI F2 was higher than that of the controls. Male sexual activity was enhanced in PI F2, and there was a similar trend to higher intraspecific aggressiveness among PI F2 males. The single effects of mutation and selection pressures were beneficial in so far as the number of individuals and the biomass were enhanced, while a combination of both was deleterious endangering the population to extinction. Contrary to expectation, the coefficient of variation for the quantitative morphological traits was higher in the controls than in the Pi F2. (author)

  18. Genomic scan for quantitative trait loci of chemical and physical body composition and deposition on pig chromosome X including the pseudoautosomal region of males

    Kalm Ernst; Doeschl-Wilson Andrea; Pérez-Enciso Miguel; Simm Geoff; Duthie Carol-Anne; Knap Pieter W; Roehe Rainer

    2009-01-01

    Abstract A QTL analysis of pig chromosome X (SSCX) was carried out using an approach that accurately takes into account the specific features of sex chromosomes i.e. their heterogeneity, the presence of a pseudoautosomal region and the dosage compensation phenomenon. A three-generation full-sib population of 386 animals was created by crossing Pietrain sires with a crossbred dam line. Phenotypic data on 72 traits were recorded for at least 292 and up to 315 F2 animals including chemical body ...

  19. Structural and temporal variation in the genetic diversity of a European collection of spring two-row barley cultivars and utility for association mapping of quantitative traits

    Tondelli, Alessandro; Xu, Xin; Moragues, Marc;

    2013-01-01

    barley, namely, i) directional selection for approximately 14% of total genetic variation of the population in the last approximately 50 yr and ii) highly uneven genomic distribution of genetic diversity. Association analysis of the phenotypic and genotypic data identified multiple loci affecting the...... traits investigated, some of which co-map with selected regions. Collectively, these data show that the genetic makeup of European two-row spring barley is evolving under breeder selection, with signs of extinction of diversity in some genomic regions, suggesting that “breeding the best with the best” is...

  20. Clonal growth and plant species abundance

    Herben, Tomáš; Nováková, Zuzana; Klimešová, Jitka

    2014-01-01

    Background and Aims Both regional and local plant abundances are driven by species' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf–height–seed) traits and by actual performance in the botanical garden. Methods Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area – height – seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates. Key Results After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level. Conclusions Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially

  1. A genome scan for quantitative trait loci affecting grain yield and its components of maize both in single-and two-locus levels

    YAN Jianbing; TANG Hua; HUANG Yiqin; ZHENG Yonglian; SUBHASH Chander; LI Jiansheng

    2006-01-01

    By adding thirty-one markers in the previous linkage map, a new genetic linkage map containing 205 markers was constructed, spanning a total of 2305.4 cM with an average interval of 11.2 cM. The genotypic errors in the whole genome were detected by the statistical method and removed manually. The precision of the linkage map was improved significantly. Main and epistatic QTL were detected by R/qtl, and main QTL were confirmed and refined by multiple interval mapping (MIM). Finally, MIM detected seven QTL for rows number, and five QTL for each grain yield, kernels per row and 100-kernel weight. The contribution to genetic variations of QTL varied from 35.3% for grain yield to 61.5% for rows number. Only kernels per row exhibited significant epistatic interactions between QTL. Twenty-four epistatic QTL were detected which distributed on almost all the ten chromosomes. About two-third epistatic QTL were observed between main QTL and another locus, which had no significant effects. These results indicate rather clearly that there are a number of QTL affecting trait expressions, not directly but indirectly through interactions with other loci. Thus, epistatic QTL effects may play a crucial role, if not more important than main QTL effects, in the genetic variation for the measured traits in present study.

  2. Structured exploratory data analysis (SEDA) for determining mode of inheritance of quantitative traits. I. Simulation studies on the effect of background distributions.

    Karlin, S; Williams, P T; Carmelli, D

    1981-03-01

    We examine through simulations the effectiveness of a new methodology to help distinguish among monogenic, multifactorial, and sporadic trait transmission from parents to offspring in nuclear family data sets. The major gene index (MGI), which compares the deviation of the offspring from the midparental value with a function of the individual deviations between parents and offspring, aids in the discrimination of multifactorial from sporadic and monogenic models. In contrast with other methodologies, the ability of the MGI to separate multifactorial, monogenic, and sporadic models improves with increased skewness in the trait distribution. The midparental correlation coefficient serves as a further guide for indicating mode of inheritance. A new class of techniques, the offspring between parents function (OBP), is introduced that provides a more sensitive tool to help in assessing mode of transmission through the analysis of the level, shape, and undulation characteristics of the curves. Four data examples are used to illustrate the methodology: erythrocyte catechol-O-methyltransferase (COMT) activity, height, weight, and triglyceride measurements. Height appears largely multifactorial, and weight appears to be mostly sporadic, while COMT and triglyceride measurements suggest the presence of some major gene influences. PMID:7211841

  3. Quantitative Genomics of Male Reproduction

    The objective of the review was to establish the current status of quantitative genomics for male reproduction. Genetic variation exists for male reproduction traits. These traits are expensive and time consuming traits to evaluate through conventional breeding schemes. Genomics is an alternative to...

  4. Quantitative genomics of female reproduction

    Numerous quantitative trait loci (QTL) for reproductive traits in domestic livestock have been described in the literature. In this chapter, the components needed for detection of reproductive trait QTL are described, including collection of phenotypes, genotypes, and the appropriate statistical ana...

  5. Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways.

    Kapil Dev Singh

    Full Text Available Complex traits, including common disease-related traits, are affected by many different genes that function in multiple pathways and networks. The apoptosis, MAPK, Notch, and Wnt signalling pathways play important roles in development and disease progression. At the moment we have a poor understanding of how allelic variation affects gene expression in these pathways at the level of translation. Here we report the effect of natural genetic variation on transcript and protein abundance involved in developmental signalling pathways in Caenorhabditis elegans. We used selected reaction monitoring to analyse proteins from the abovementioned four pathways in a set of recombinant inbred lines (RILs generated from the wild-type strains N2 (Bristol and CB4856 (Hawaii to enable quantitative trait locus (QTL mapping. About half of the cases from the 44 genes tested showed a statistically significant change in protein abundance between various strains, most of these were however very weak (below 1.3-fold change. We detected a distant QTL on the left arm of chromosome II that affected protein abundance of the phosphatidylserine receptor protein PSR-1, and two separate QTLs that influenced embryonic and ionizing radiation-induced apoptosis on chromosome IV. Our results demonstrate that natural variation in C. elegans is sufficient to cause significant changes in signalling pathways both at the gene expression (transcript and protein abundance and phenotypic levels.

  6. Taking species abundance distributions beyond individuals

    Morlon, Helene; White, Ethan P.; Etienne, Rampal S.; Green, Jessica L.; Ostling, Annette; Alonso, David; Enquist, Brian J.; He, Fangliang; Hurlbert, Allen; Magurran, Anne E.; Maurer, Brian A.; McGill, Brian J.; Olff, Han; Storch, David; Zillio, Tommaso; Chave, Jérôme

    2009-01-01

    The species abundance distribution (SAD) is one of the few universal patterns in ecology. Research on this fundamental distribution has primarily focused on the study of numerical counts, irrespective of the traits of individuals. Here we show that considering a set of Generalized Species Abundance

  7. A functional trait perspective on plant invasion

    Global environmental change affects exotic plant invasions, which profoundly impact native plant populations, communities and ecosystems. In this context, we review plant functional traits, including those that drive invader abundance (invasiveness), and impacts, as well as the integration of these...

  8. Características quantitativas em matrizes de codorna de corte através de análises multicaracterística Quantitative traits in meat-type quail through two-trait analysis

    Bruno Bastos Teixeira

    2012-12-01

    most important variables. Then, two-trait analysis to estimate covariances and genetic correlations of traits. The characteristics of the analysis were: weight of the bird (P0, P7, P14, P21, P28, P35, P42, P77, P112 and P147, average egg weight (POM1, POM2, and POM3 POM4, average weight of the shell ( PCM1, pcm2, and PCM3 PCM4, average weight of yolk (PGM1, PGM2, and PGM3 PGM4, weight of albumen (PAM1, PAM2, and PAM3 PAM4, average egg specific gravity (DM1, DM2, DM3 and DM4 , average width of the egg (LOM1, LOM2, and LOM3 LOM4, average length of egg (COM1, COM2, COM3 and COM4, eggs (N1, N2, N3 and N4, total egg production (TXT and age at first egg (IDPO. For the group of genetic UFV1, an increase in weight of birds may result in an early and that IDPO to select for increased body weight of birds does not result in significant losses in egg quality. As for UFV2, a selection made at 35 days can identify the most weight matrices throughout the production cycle, and do not generate large losses in total egg production.

  9. Primary genome scan to identify putative quantitative trait loci for feedlot growth rate, feed intake, and feed efficiency of beef cattle.

    Nkrumah, J D; Sherman, E L; Li, C; Marques, E; Crews, D H; Bartusiak, R; Murdoch, B; Wang, Z; Basarab, J A; Moore, S S

    2007-12-01

    Feed intake and feed efficiency of beef cattle are economically relevant traits. The study was conducted to identify QTL for feed intake and feed efficiency of beef cattle by using genotype information from 100 microsatellite markers and 355 SNP genotyped across 400 progeny of 20 Angus, Charolais, or Alberta Hybrid bulls. Traits analyzed include feedlot ADG, daily DMI, feed-to-gain ratio [F:G, which is the reciprocal of the efficiency of gain (G:F)], and residual feed intake (RFI). A mixed model with sire as random and QTL effects as fixed was used to generate an F-statistic profile across and within families for each trait along each chromosome, followed by empirical permutation tests to determine significance thresholds for QTL detection. Putative QTL for ADG (chromosome-wise P detected across families on chromosomes 5 (130 cM), 6 (42 cM), 7 (84 cM), 11 (20 cM), 14 (74 cM), 16 (22 cM), 17 (9 cM), 18 (46 cM), 19 (53 cM), and 28 (23 cM). For DMI, putative QTL that exceeded the chromosome-wise P detected on chromosomes 1 (93 cM), 3 (123 cM), 15 (31 cM), 17 (81 cM), 18 (49 cM), 20 (56 cM), and 26 (69 cM) in the across-family analyses. Putative across-family QTL influencing F:G that exceeded the chromosome-wise P detected on chromosomes 3 (62 cM), 5 (129 cM), 7 (27 cM), 11 (16 cM), 16 (30 cM), 17 (81 cM), 22 (72 cM), 24 (55 cM), and 28 (24 cM). Putative QTL influencing RFI that exceeded the chromosome-wise P detected on chromosomes 1 (90 cM), 5 (129 cM), 7 (22 cM), 8 (80 cM), 12 (89 cM), 16 (41 cM), 17 (19 cM), and 26 (48 cM) in the across-family analyses. In addition, a total of 4, 6, 1, and 8 chromosomes showed suggestive evidence (chromosome-wise, P RFI QTL, respectively. Most of the QTL detected across families were also detected within families, although the locations across families were not necessarily the locations within families, which is likely because of differences among families in marker informativeness for the different linkage groups. The locations

  10. Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster

    Jordan Katherine W

    2010-05-01

    Full Text Available Abstract Background Obesity and phenotypic traits associated with this condition exhibit significant heritability in natural populations of most organisms. While a number of genes and genetic pathways have been implicated to play a role in obesity associated traits, the genetic architecture that underlies the natural variation in these traits is largely unknown. Here, we used 40 wild-derived inbred lines of Drosophila melanogaster to quantify genetic variation in body weight, the content of three major metabolites (glycogen, triacylglycerol, and glycerol associated with obesity, and metabolic rate in young flies. We chose these lines because they were previously screened for variation in whole-genome transcript abundance and in several adult life-history traits, including longevity, resistance to starvation stress, chill-coma recovery, mating behavior, and competitive fitness. This enabled us not only to identify candidate genes and transcriptional networks that might explain variation for energy metabolism traits, but also to investigate the genetic interrelationships among energy metabolism, behavioral, and life-history traits that have evolved in natural populations. Results We found significant genetically based variation in all traits. Using a genome-wide association screen for single feature polymorphisms and quantitative trait transcripts, we identified 337, 211, 237, 553, and 152 novel candidate genes associated with body weight, glycogen content, triacylglycerol storage, glycerol levels, and metabolic rate, respectively. Weighted gene co-expression analyses grouped transcripts associated with each trait in significant modules of co-expressed genes and we interpreted these modules in terms of their gene enrichment based on Gene Ontology analysis. Comparison of gene co-expression modules for traits in this study with previously determined modules for life-history traits identified significant modular pleiotropy between glycogen content

  11. Genomic scan for quantitative trait loci of chemical and physical body composition and deposition on pig chromosome X including the pseudoautosomal region of males

    Kalm Ernst

    2009-03-01

    Full Text Available Abstract A QTL analysis of pig chromosome X (SSCX was carried out using an approach that accurately takes into account the specific features of sex chromosomes i.e. their heterogeneity, the presence of a pseudoautosomal region and the dosage compensation phenomenon. A three-generation full-sib population of 386 animals was created by crossing Pietrain sires with a crossbred dam line. Phenotypic data on 72 traits were recorded for at least 292 and up to 315 F2 animals including chemical body composition measured on live animals at five target weights ranging from 30 to 140 kg, daily gain and feed intake measured throughout growth, and carcass characteristics obtained at slaughter weight (140 kg. Several significant and suggestive QTL were detected on pig chromosome X: (1 in the pseudoautosomal region of SSCX, a QTL for entire loin weight, which showed paternal imprinting, (2 closely linked to marker SW2456, a suggestive QTL for feed intake at which Pietrain alleles were found to be associated with higher feed intake, which is unexpected for a breed known for its low feed intake capacity, (3 at the telomeric end of the q arm of SSCX, QTL for jowl weight and lipid accretion and (4 suggestive QTL for chemical body composition at 30 kg. These results indicate that SSCX is important for physical and chemical body composition and accretion as well as feed intake regulation.

  12. Ecologically relevant stress resistance: from microarrays and quantitative trait loci to candidate genes – A research plan and preliminary results using Drosophila as a model organism and climatic and genetic stress as model stresses

    Volker Loeschcke; Jesper G Sørensen; Torsten N Kristensen

    2004-12-01

    We aim at studying adaptation to genetic and environmental stress and its evolutionary implications at different levels of biological organization. Stress influences cellular processes, individual physiology, genetic variation at the population level, and the process of natural selection. To investigate these highly connected levels of stress effects, it is advisable – if not critical – to integrate approaches from ecology, evolution, physiology, molecular biology and genetics. To investigate the mechanisms of stress resistance, how resistance evolves, and what factors contribute to and constrain its evolution, we use the well-defined model systems of Drosophila species, representing both cosmopolitan species such as D. melanogaster with a known genome map, and more specialized and ecologically well described species such as the cactophilic D. buzzatii. Various climate-related stresses are used as model stresses including desiccation, starvation, cold and heat. Genetic stress or genetic load is modelled by studying the consequences of inbreeding, the accumulation of (slightly) deleterious mutations, hybridization or the loss of genetic variability. We present here a research plan and preliminary results combining various approaches: molecular techniques such as microarrays, quantitative trait loci (QTL) analyses, quantitative PCR, ELISA or Western blotting are combined with population studies of resistance to climatic and genetic stress in natural populations collected across climatic gradients as well as in selection lines maintained in the laboratory.

  13. Long-range regulatory polymorphisms affecting a GABA receptor constitute a quantitative trait locus (QTL for social behavior in Caenorhabditis elegans.

    Andres Bendesky

    Full Text Available Aggregation is a social behavior that varies between and within species, providing a model to study the genetic basis of behavioral diversity. In the nematode Caenorhabditis elegans, aggregation is regulated by environmental context and by two neuromodulatory pathways, one dependent on the neuropeptide receptor NPR-1 and one dependent on the TGF-β family protein DAF-7. To gain further insight into the genetic regulation of aggregation, we characterize natural variation underlying behavioral differences between two wild-type C. elegans strains, N2 and CB4856. Using quantitative genetic techniques, including a survey of chromosome substitution strains and QTL analysis of recombinant inbred lines, we identify three new QTLs affecting aggregation in addition to the two known N2 mutations in npr-1 and glb-5. Fine-mapping with near-isogenic lines localized one QTL, accounting for 5%-8% of the behavioral variance between N2 and CB4856, 3' to the transcript of the GABA neurotransmitter receptor gene exp-1. Quantitative complementation tests demonstrated that this QTL affects exp-1, identifying exp-1 and GABA signaling as new regulators of aggregation. exp-1 interacts genetically with the daf-7 TGF-β pathway, which integrates food availability and population density, and exp-1 mutations affect the level of daf-7 expression. Our results add to growing evidence that genetic variation affecting neurotransmitter receptor genes is a source of natural behavioral variation.

  14. Quantitative trait loci with sex-specific effects for internal organs weights and hematocrit value in a broiler-layer cross.

    Moura, A S A M T; Ledur, M C; Boschiero, C; Nones, K; Pinto, L F B; Jaenisch, F R F; Burt, D W; Coutinho, L L

    2016-05-01

    Rapid growth in broilers is associated with susceptibility to metabolic disorders such as pulmonary hypertension syndrome (ascites) and sudden death. This study describes a genome search for QTL associated with relative weight of cardio respiratory and metabolically important organs (heart, lungs, liver and gizzard), and hematocrit value in a Brazilian broiler-layer cross. QTL with similar or different effects across sexes were investigated. At 42 days of age after fasted for 6 h, the F2 chickens were weighed and slaughtered. Weights and percentages of the weight relative to BW42 of gizzard, heart, lungs, liver and hematocrit were used in the QTL search. Parental, F1 and F2 individuals were genotyped with 128 genetic markers (127 microsatellites and 1 SNP) covering 22 linkage groups. QTL mapping analyses were carried out using mixed models. A total of 11 genome-wide significant QTL and five suggestive linkages were mapped. Thus, genome-wide significant QTL with similar effects across sexes were mapped to GGA2, 4 and 14 for heart weight, and to GGA2, 8 and 12 for gizzard %. Additionally, five genome-wide significant QTL with different effects across sexes were mapped to GGA 8, 19 and 26 for heart weight; GGA26 for heart % and GGA3 for hematocrit value. Five QTL were detected in chromosomal regions where QTL for similar traits were previously mapped in other F2 chicken populations. Seven novel genome-wide significant QTL are reported here, and 21 positional candidate genes in QTL regions were identified. PMID:26496990

  15. Traits-based approaches in bioassessment and ecological risk assessment: strengths, weaknesses, opportunities and threats.

    Van den Brink, Paul J; Alexander, Alexa C; Desrosiers, Mélanie; Goedkoop, Willem; Goethals, Peter L M; Liess, Matthias; Dyer, Scott D

    2011-04-01

    We discuss the application of traits-based bioassessment approaches in retrospective bioassessment as well as in prospective ecological risk assessments in regulatory frameworks. Both approaches address the interaction between species and stressors and their consequences at different levels of biological organization, but the fact that a specific species may be less abundant in a potentially impacted site compared with a reference site is, regrettably, insufficient to provide diagnostic information. Species traits may, however, overcome the problems associated with taxonomy-based bioassessment. Trait-based approaches could provide signals regarding what environmental factors may be responsible for the impairment and, thereby, provide causal insight into the interaction between species and stressors. For development of traits-based (TBA), traits should correspond to specific types of stressors or suites of stressors. In this paper, a strengths, weaknesses, opportunities, and threats (SWOT) analysis of TBA in both applications was used to identify challenges and potentials. This paper is part of a series describing the output of the TERA (Traits-based ecological risk assessment: Realising the potential of ecoinformatics approaches in ecotoxicology) Workshop held between 7 and 11 September, 2009, in Burlington, Ontario, Canada. The recognized strengths were that traits are transferrable across geographies, add mechanistic and diagnostic knowledge, require no new sampling methodology, have an old tradition, and can supplement taxonomic analysis. Weaknesses include autocorrelation, redundancy, and inability to protect biodiversity directly. Automated image analysis, combined with genetic and biotechnology tools and improved data analysis to solve autocorrelation problems were identified as opportunities, whereas low availability of trait data, their transferability, their quantitative interpretation, the risk of developing nonrelevant traits, low quality of historic

  16. Clonal traits

    Klimeš, Leoš; Klimešová, Jitka

    Groningen : LEDA Traitbase project, University of Groningen, Community and Conservation Ecology group, 2005 - (Knevel, I.C., Bekker, R.M., Kunzmann, D., Stadler, M., Thompson, K.), s. 66-88 Institutional research plan: CEZ:AV0Z6005908 Keywords : plant functional traits * clonality * vegetative regeneration Subject RIV: EF - Botanics

  17. Validation and Characterization of Ghd7.1, a Major Quantitative Trait Locus with Pleiotropic Effects on Spikelets per Panicle, Plant Height, and Heading Date in Rice (Oryza sativa L.)

    Touming Liu; Haiyang Liu; Huang Zhan; Yongzhong Xing

    2013-01-01

    A quantitative trait locus (QTL) that affects heading date (HD) and the number of spikelets per panicle (SPP) was previously identified in a small region on chromosome 7 in rice (Oryza sativa L.). In order to further characterize the QTL region, near isogenic lines (NILs) were quickly obtained by self-crossing recombinant inbred line 189, which is heterozygous in the vicinity of the target region. The pleiotropic effects of QTL Ghd7.1 on plant height (PH), SPP, and HD, were validated using an NIL-F2 population. Ghd7.1 explained 50.2%, 45.3%, and 76.9%of phenotypic variation in PH, SPP, and HD, respectively. Ghd7.1 was precisely mapped to a 357-kb region on the basis of analysis of the progeny of the NIL-F2 population. Day-length treatment confirmed that Ghd7.1 is sensitive to photoperiod, with long days delaying heading up to 12.5 d. Identification of panicle initiation and development for the pair of NILs showed that Ghd7.1 elongated the photoperiod-sensitive phase more than 10 d, but did not change the basic vegetative phase and the reproductive growth phase. These findings indicated that Ghd7.1 regulates SPP by controlling the rate of panicle differentiation rather than the duration of panicle development.

  18. Grey Correlation Analysis of Main Quantitative Traits and lint Yield of Cotton Variety%棉花品种主要数量性状与皮棉产量的灰色关联分析

    权月伟; 米换房; 翟雷霞; 李继军; 李文蕾; 唐光雷

    2013-01-01

      通过运用灰色关联分析方法对国家棉花品种区域试验中的参试品种(系)邯郸点试验数据进行了主要数量性状与皮棉产量分析。结果表明:对棉花品种皮棉产量影响较大的因素是单株结铃数和衣分,各个因素对皮棉产量的影响程度依次为:单株结铃数>衣分>霜前花率>始果枝节位>单铃重>果枝数>株高>籽指。%Main quantitative traits and lint yield were analyzed by grey correlation analysis in new cotton variety . The re-sults showed that :the numbers of bolls per plant and ginning outturn were the bigger influence factors to lint yield . The influ-ence degree to lint yields of every factor was as follows :the number of bolls per plant > ginning outturn > pre - frost yield > the first node of fruit branch > single boll weight > fruit branch number > stem height > seed index.

  19. Quantitative trait loci analysis of swine meat quality traits

    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...

  20. Genome-wide linkage analysis for ocular and nasal anthropometric traits in a Mongolian population

    Im, Sun-Wha; Kim, Hyun-Jin; Lee, Mi Kyeong; Yi, Jae-Hyuk; Jargal, Ganchimeg; Sung, Joohon; Cho, Sung-il; Kim, Jong-Il

    2010-01-01

    Anthropometric traits for eyes and nose are complex quantitative traits influenced by genetic and environmental factors. To date, there have been few reports on the contribution of genetic influence to these traits in Asian populations. The aim of this study was to determine the genetic effect and quantitative trait locus (QTL) of seven traits eyes- and nose-related anthropometric measurements in an isolated Mongolian population. Frontal and lateral photographs were obtained from 1,014 indivi...

  1. Bacteriocin Production: a Probiotic Trait?

    Dobson, Alleson; Cotter, Paul D.; Ross, R. Paul; Hill, Colin

    2012-01-01

    Bacteriocins are an abundant and diverse group of ribosomally synthesized antimicrobial peptides produced by bacteria and archaea. Traditionally, bacteriocin production has been considered an important trait in the selection of probiotic strains, but until recently, few studies have definitively demonstrated the impact of bacteriocin production on the ability of a strain to compete within complex microbial communities and/or positively influence the health of the host. Although research in th...

  2. Características quantitativas da carcaça de cordeiros de diferentes genótipos submetidos a duas dietas Quantitative traits of carcass from lambs of different genotypes submitted to two diets

    Felipe Queiroga Cartaxo

    2011-10-01

    Full Text Available Objetivou-se avaliar as características quantitativas de carcaça de cordeiros de diferentes genótipos recebendo diversos níveis de energia na dieta. Foram utilizados 54 cordeiros não-castrados, sendo 18 Santa Inês (SI, 18 F1Dorper × Santa Inês (Dp × SI e 18 F1 Santa Inês × Sem Raça Definida (SI × SRD, com idade média de 150 dias e peso médio de 22,60 kg no início do experimento. As dietas continham 17% de proteína bruta e 2,40 Mcal/kg MS ou 2,90 Mcal/kg MS. Os cordeiros alimentados com a dieta contendo 2,90 Mcal/kg MS apresentaram maior peso corporal e de carcaça, área de olho-de-lombo, percentual de gordura interna, índice de musculosidade, índice de compacidade da carcaça, percentual de gordura e menor relação músculo:gordura. As carcaças desses cordeiros obtiveram também menores perdas por resfriamento e maior peso e percentual de paleta e perna. As carcaças dos cordeiros Dorper × Santa Inês foram superiores em espessura de gordura subcutânea, medida GR (gordura sobre a 12ª costela a 11 cm de distância da linha média lombo, percentual de gordura, relação músculo:osso, índice de musculosidade, peso e percentual de lombo. Os cordeiros Santa Inês apresentaram maior relação músculo:gordura. A dieta e o genótipo influenciam as características quantitativas de carcaça de cordeiros.The objective of this study was to evaluate the quantitative carcass traits of lambs from different genotypes receiving different levels of energy in the diet. Fifty-four non-castrated lambs - 18 Santa Inês (SI, 18 F1Dorper × Santa Inês (Dp × SI and 18 F1Santa Inês × No defined breed (SI × NDB - of average 150 days old and 22.6-kg BW were used in the beginning of the experiment. Diets contained 17% crude protein and 2.40 Mcal/kg DM or 2.90 Mcal/kg DM. Lambs fed the diet containing 2.90 Mcal/kg DM showed higher final live and carcass weight, loin eye area, percentage of internal fat, muscularity index, compactness of the

  3. Identification of quantitative trait loci affecting ectomycorrhizal symbiosis in an interspecific F1 poplar cross and differential expression of genes in ectomycorrhizas of the two parents: Populus deltoides and Populus trichocarpa

    Labbe, Jessy L [ORNL; Jorge, Veronique [INRA, Nancy, France; Vion, Patrice [INRA, Nancy, France; Marcais, Benoit [INRA, Nancy, France; Bastien, Catherine [INRA, Orleans, France; Tuskan, Gerald A [ORNL; Martin, Francis [INRA, Nancy, France; Le Tacon, F [UMR, France

    2011-01-01

    A Populus deltoides Populus trichocarpa F1 pedigree was analyzed for quantitative trait loci (QTLs) affecting ectomycorrhizal development and for microarray characterization of gene networks involved in this symbiosis. A 300 genotype progeny set was evaluated for its ability to form ectomycorrhiza with the basidiomycete Laccaria bicolor. The percentage of mycorrhizal root tips was determined on the root systems of all 300 progeny and their two parents. QTL analysis identified four significant QTLs, one on the P. deltoides and three on the P. trichocarpa genetic maps. These QTLs were aligned to the P. trichocarpa genome and each contained several megabases and encompass numerous genes. NimbleGen whole-genome microarray, using cDNA from RNA extracts of ectomycorrhizal root tips from the parental genotypes P. trichocarpa and P. deltoides, was used to narrow the candidate gene list. Among the 1,543 differentially expressed genes (p value 0.05; 5.0-fold change in transcript level) having different transcript levels in mycorrhiza of the two parents, 41 transcripts were located in the QTL intervals: 20 in Myc_d1, 14 in Myc_t1, and seven in Myc_t2, while no significant differences among transcripts were found in Myc_t3. Among these 41 transcripts, 25 were overrepresented in P. deltoides relative to P. trichocarpa; 16 were overrepresented in P. trichocarpa. The transcript showing the highest overrepresentation in P. trichocarpa mycorrhiza libraries compared to P. deltoides mycorrhiza codes for an ethylene-sensitive EREBP-4 protein which may repress defense mechanisms in P. trichocarpa while the highest overrepresented transcripts in P. deltoides code for proteins/genes typically associated with pathogen resistance.

  4. Genetic dissection of functional traits in dairy cattle

    Holmberg, Mia

    2007-01-01

    The aims of this thesis were to improve the knowledge about the genetic background of health and reproduction traits in dairy cattle. This was accomplished by performing gene mapping studies of quantitative trait loci (QTL) affecting these traits and also by exploring the genetic variability for pathogen-specific mastitis. Ten sire families were used in a granddaughter design to map QTL. Several QTL were detected for most of the traits studied. Inclusion of cofactors in the analyses to adjust...

  5. Quantitative Trait Evolution and Environmental Change

    Björklund, Mats; Ranta, Esa; Kaitala, Veijo; Bach, Lars A.; Lundberg, Per; Stenseth, Nils Chr.

    2009-01-01

    Background Given the recent changes in climate, there is an urgent need to understand the evolutionary ability of populations to respond to these changes. Methodology/Principal Findings We performed individual-based simulations with different shapes of the fitness curve, different heritabilities, different levels of density compensation, and different autocorrelation of environmental noise imposed on an environmental trend to study the ability of a population to adapt to changing conditions. ...

  6. Sickle Cell Trait

    ... About Us Information For... Media Policy Makers Sickle Cell Trait Language: English Español (Spanish) Recommend on Facebook ... the trait on to their children. How Sickle Cell Trait is Inherited If both parents have SCT, ...

  7. Mapping of quantitative trait loci for thermosensitive genic male sterility in indica rice Mapeamento de controladores de caracteres quantitativos de macho-esterilidade gênica termossensível em arroz indica

    Antonio Alberto Neves de Alcochete

    2005-12-01

    Full Text Available The objective of this work was to select and use microsatellite markers, to map genomic regions associated with the genetic control of thermosensitive genic male sterility (TGMS in rice. An F2 population, derived from the cross between fertile and TGMS indica lines, was used to construct a microsatellite-based genetic map of rice. The TGMS phenotype showed a continuous variation in the segregant population. A low level of segregation distortion was detected in the F2 (14.65%, whose cause was found to be zygotic selection. There was no evidence suggesting a cause-effect relationship between zygotic selection and the control of TGMS in this cross. A linkage map comprising 1,213.3 cM was constructed based on the segregation data of the F2 population. Ninety-five out of 116 microsatellite polymorphic markers were assembled into 11 linkage groups, with an average of 12.77 cM between two adjacent marker loci. The phenotypic and genotypic data allowed for the identification of three new quantitative trait loci (QTL for thermosensitive genic male sterility in indica rice. Two of the QTL were mapped on chromosomes that, so far, have not been associated with the genetic control of the TGMS trait (chromosomes 1 and 12. The third QTL was mapped on chromosome 7, where a TGMS locus (tms2 has recently been mapped. Allelic tests will have to be developed, in order to clarify if the two regions are the same or not.O objetivo deste estudo foi selecionar e utilizar marcadores microssatélites, para mapear as regi��es genômicas associadas ao controle genético de macho-esterilidade termossensível (TGMS em arroz. Uma popu- lação F2, derivada do cruzamento entre linhagens indica fértil e TGMS, foi usada para construir um mapa genético de arroz, baseado em marcadores microssatélites. O fenótipo TGMS analisado apresentou uma variação contínua na população segregante. Um baixo nível de distorção da segregação foi detectado na população segregante

  8. 盐胁迫下小麦幼苗相关性状QTL加性及其上位性效应分析%Analysis on Quantitative Trait Loci Additive and Epistatic Effects of Wheat Seedling Under Salt Stress

    吴儒刚; 陈广凤; 李冬梅; 田纪春

    2015-01-01

    Seedling height and dry seedling weight are important indexes to evaluate salt tolerance of wheat seedlings. To detect quantitative trait loci (QTL) associated with seedling height and dry seedling weight at seedling stage in wheat, a set of 168 doubled haploid (DH) lines derived from the cross between Huapei 3 and Yumai 57 was treated with distilled water (CK), 50 and 100 mmol/L of NaCl. Based on inclusive composite interval mapping (ICIM) method, we identified 16 additive QTLs and 17 pairs of epistatic QTLs for seedling height and dry seedling weight under CK and salt stress. A total of eight QTLs for seedling height were detected distributed on chromosomes 2A, 2D, 3B, 4D, 6B and 7B, and explained phenotypic variation ranging from 3.38%to 22.96%. A total of eight QTLs for dry seedling weight were detected distributed on chromosomes 1A, 1B, 2B, 2D, 4D and 5B, which accounted for 4.53-9.10%of the phenotypic variation .The QDSW1A for dry seedling weight expressed both in CK and salt stress, which could be used in marker-assisted selection in wheat breeding programs. The results indicate that both additive effects and epistatic effects are important genetic bases for wheat seedling traits.%由小麦品种花培3号和豫麦57杂交获得了168个株系的DH群体为材料,分别用蒸馏水(对照)以及50、100 mmol/L NaCl溶液处理,对小麦幼苗的苗高、苗干重进行了QTL定位及效应分析。利用完备区间作图法,共检测到16个加性QTL和17对上位性互作QTL。其中,检测到8个控制苗高的QTL,分布在小麦2A、2D、3B、4D、6B和7B染色体上,单个QTL可解释3.38%~22.96%的遗传变异,位于4D和7B染色体上控制苗高的QSH4D和QSH7B两个QTL位点在两个环境中均被检测到,QSH4D在两个环境里的遗传贡献率分别为17.9%和22.96%,为一主效QTL位点;检测到8个控制苗干重的QTL,分布在小麦1A、1B、2B、2D、4D和5B染色体上,单个QTL可解释4.53%~9.10%

  9. Detecção de locos de características quantitativas nos cromossomos 9, 10 e 11 de suínos Detection of quantitative trait loci on chromosomes 9, 10 and 11 of swines

    Ana Paula Gomes Pinto

    2010-10-01

    Full Text Available Objetivou-se com este estudo mapear locos de características quantitativas (QTL nos cromossomos 9, 10 e 11 de suínos (Sus scrofa e associar seus efeitos em características de carcaça, cortes de carcaça, órgãos e vísceras, desempenho e qualidade de carne. Utilizaram-se amostras de DNA de animais pertencentes a uma população F2, oriunda do cruzamento entre machos da raça Piau e fêmeas Landrace õ Large White õ Pietrain. Um total de 13 locos microssatélites foi utilizado na construção dos mapas de ligação da população atual. As análises de associação foram feitas utilizando-se mapeamento de intervalo por regressão para detecção de QTL. Identificaram-se associações significativas, em nível cromossômico, entre regiões do cromossomo 9 e as características peso total do carré e peso do lombo. No cromossomo 10, foram detectados três QTL significativos para espessura de toucinho na linha dorso-lombar entre a última e a penúltima vértebra lombar, peso de pulmão e índice de vermelho e um QTL significativo, no nível genômico, para peso de fígado. No cromossomo 11, foi detectada apenas uma associação significativa, em nível cromossômico, relacionada à espessura de toucinho imediatamente após a última costela, a 6,5 cm da linha dorso-lombar. As informações dos QTL significativos encontrados são importantes para estudos futuros, como o mapeamento fino e a identificação de genes, que ajudem no melhor entendimento da fisiologia e das características de produção de suínos.The objective of this study was to map quantitative trait loci (QTL in chromosomes 9, 10 and 11 of swines (Sus scrofa and to associate their effects on traits of carcass, carcass cuts, organs and guts, performance and meat quality. Samples of DNA of animals from a F2 population originated from crosses between Piau breed males and Landrace õ Large White õ Pietrain females were used. A total of 13 microsatellite loci were used to build

  10. Mapping complex traits as a dynamic system

    Sun, Lidan; Wu, Rongling

    2015-06-01

    Despite increasing emphasis on the genetic study of quantitative traits, we are still far from being able to chart a clear picture of their genetic architecture, given an inherent complexity involved in trait formation. A competing theory for studying such complex traits has emerged by viewing their phenotypic formation as a "system" in which a high-dimensional group of interconnected components act and interact across different levels of biological organization from molecules through cells to whole organisms. This system is initiated by a machinery of DNA sequences that regulate a cascade of biochemical pathways to synthesize endophenotypes and further assemble these endophenotypes toward the end-point phenotype in virtue of various developmental changes. This review focuses on a conceptual framework for genetic mapping of complex traits by which to delineate the underlying components, interactions and mechanisms that govern the system according to biological principles and understand how these components function synergistically under the control of quantitative trait loci (QTLs) to comprise a unified whole. This framework is built by a system of differential equations that quantifies how alterations of different components lead to the global change of trait development and function, and provides a quantitative and testable platform for assessing the multiscale interplay between QTLs and development. The method will enable geneticists to shed light on the genetic complexity of any biological system and predict, alter or engineer its physiological and pathological states.

  11. Traits in Java

    2007-01-01

    A trait is a programming language feature which contains a collection of methods that can be reused across class hierarchies. Traits is a relatively new language feature that is beginning to be a part of some of the newest object-oriented programming languages. Traits have been implemented in some languages but it has not become a part of the Java language yet. In this thesis we apply traits to the Java 5 language by designing and implementing a traits aware preprocessor....

  12. Novel applications of multitask learning and multiple output regression to multiple genetic trait prediction

    He, Dan; Kuhn, David; Parida, Laxmi

    2016-01-01

    Given a set of biallelic molecular markers, such as SNPs, with genotype values encoded numerically on a collection of plant, animal or human samples, the goal of genetic trait prediction is to predict the quantitative trait values by simultaneously modeling all marker effects. Genetic trait prediction is usually represented as linear regression models. In many cases, for the same set of samples and markers, multiple traits are observed. Some of these traits might be correlated with each other...

  13. Genetic mapping of complex traits by minimizing integrated square errors

    Wu Song; Fu Guifang; Chen Yunmei; Wang Zhong; Wu Rongling

    2012-01-01

    Abstract Background Genetic mapping has been used as a tool to study the genetic architecture of complex traits by localizing their underlying quantitative trait loci (QTLs). Statistical methods for genetic mapping rely on a key assumption, that is, traits obey a parametric distribution. However, in practice real data may not perfectly follow the specified distribution. Results Here, we derive a robust statistical approach for QTL mapping that accommodates a certain degree of misspecification...

  14. Genetic Architecture of Leaf Ecophysiological Traits in Helianthus

    Brouillette, Larry C.; Rosenthal, David M.; Rieseberg, Loren H.; Lexer, Christian; Malmberg, Russell L; Donovan, Lisa A.

    2007-01-01

    We investigated quantitative trait loci (QTLs) for several leaf chemistry traits in early-generation hybrids between Helianthus annuus and Helianthus petiolaris, the parental species of the ancient diploid hybrid sunflower species Helianthus anomalus, Helianthus deserticola, and Helianthus paradoxus. We grew individuals of a second-generation backcross (BC2) toward H. petiolaris under optimum conditions in a glasshouse experiment. Trait values were measured once for each individual. In additi...

  15. The MRC-5 human embryonal lung fibroblast two-dimensional gel cellular protein database: quantitative identification of polypeptides whose relative abundance differs between quiescent, proliferating and SV40 transformed cells

    Celis, J E; Dejgaard, K; Madsen, Peder;

    1990-01-01

    proteins quantitated so far, the levels of 138 were up- or down-regulated (51 and 87, respectively) by two times or more in the transformed cells as compared to their normal proliferating counterparts, while only 14 behaved similarly in quiescent cells. Seven MRC-5 SV40 proteins, including plastin and two...

  16. Modelos alternativos para detecção de locos de características quantitativas (QTL de carcaça e crescimento nos cromossomos 4, 5 e 7 de suínos Alternative models for detection of quantitative trait loci (QTL for growth and carcass traits in pigs chromosomes 4, 5 and 7

    Tarcísio de Moraes Gonçalves

    2005-10-01

    Full Text Available O conhecimento do genoma pode auxiliar na identificação de regiões cromossômicas e, eventualmente, de genes que controlam características quantitativas (QTLs de importância econômica. Em um experimento com 1.129 suínos resultantes do cruzamento entre machos da raça Meishan e fêmeas Large White e Landrace, foram analisadas as características gordura intramuscular (GIM, em %, e ganho dos 25 aos 90 kg de peso vivo (GP, em g/dia, em 298 animais F1 e 831 F2, e espessura de toucinho (ET, em mm, em 324 F1 e 805 F2. Os animais das gerações F1 e F2 foram tipificados com 29 marcadores microsatélites. Estudou-se a ligação entre os cromossomos 4, 6 e 7 com GIM, ET e GP. Análises de QTL utilizando-se metodologia Bayesiana foram aplicadas mediante três modelos genéticos: modelo poligênico infinitesimal (MPI; modelo poligênico finito (MPF, considerando-se três locos; e MPF combinado com MPI. O número de QTLs, suas respectivas posições nos três cromossomos e o efeito fenotípico foram estimados simultaneamente. Os sumários dos parâmetros estimados foram baseados nas distribuições marginais a posteriori, obtidas por meio do uso da Cadeia de Markov, algoritmos de Monte Carlo (MCMC. Foi possível evidenciar dois QTLs relacionados a GIM nos cromossomos 4 e 6 e dois a ET nos cromossomos 4 e 7. Somente quando se ajustou o MPI, foram observados QTLs no cromossomo 4 para ET e GIM. Não foi possível detectar QTLs para a característica GP com a aplicação dessa metodologia, o que pode ter resultado do uso de marcadores não informativos ou da ausência de QTLs segregando nos cromossomos 4, 6 e 7 desta população. Foi evidenciada a vantagem de se analisar dados experimentais ajustando diferentes modelos genéticos; essas análises ilustram a utilidade e ampla aplicabilidade do método Bayesiano.Genome scans can be used to identify chromosomal regions and eventually genes that control quantitative traits (QTL of economic importance. In an

  17. Detecção de locos de características quantitativas (QTL afetando o crescimento e a carcaça de suínos: um enfoque Bayesiano com o uso de diferentes prioris Detection of quantitative trait loci (QTL affecting growth and carcass traits in swine: a Bayesian approach using differents priors

    Tarcisio de Moraes Gonçalves

    2008-02-01

    Full Text Available Foram utilizados 1.129 animais, 298 F1 e 831 F2 para gordura intramuscular (GIM, % e ganho de peso (GP, g/dia e 324 F1 e 805 F2 para espessura de toucinho (ET, mm, obtidos por meio do cruzamento de suínos machos da raça Meishan e fêmeas Large White e Landrace. Os animais foram genotipados para marcadores moleculares cobrindo todo o genoma. Foram estudados os cromossomos 1, 2, 4, 5, 6, 7, 13, 14 e19 para ET e GIM e os cromossomos 1, 2, 4, 6, 7, 8, 13, 17 e19 para GP entre 25 e 90 kg de peso vivo (PV. Análises de QTL usando metodologia Bayesiana foram aplicadas mediante o modelo genético estatístico combinando os efeitos Poligênico Infinito (MPI, Poligênico Finito (MPF e de QTL. Os sumários dos parâmetros estimados foram baseados nas distribuições marginais a posteriori obtidas por Cadeia de Markov, algoritmo de Monte Carlo (MCMC. De modo geral, por meio dos resultados, foi possível evidenciar um QTL para ET, independentemente da priori estudada. Não foi possível detectar QTL para as características GIM e GP com a aplicação desta metodologia, o que pode estar relacionado aos marcadores não-informativos ou à ausência de QTL segregando nos cromossomos estudados. Há vantagens em analisar dados experimentais ajustando modelos genéticos combinados e não considerando unicamente o modelo poligênico ou o oligogênico. As análises ilustraram a utilidade e aplicabilidade do método Bayesiano no qual foram utilizados modelos finitos.Genome scan was used to identify chromosomal regions and genes that control quantitative trait loci (QTL of economic importance using 1129 animals from F1 and F2 populations obtained from crosses between Meishan and commercial Dutch breeds (Large White and Landrace. Animals were genotyped for molecular markers covering the entire genome. The chromosomes 1, 2, 4, 5, 6, 7, 13, 14 and 19 were studied for intramuscular fat (IMF, % and backfat thickness (BT, mm and the chromosomes 1, 2, 4, 6, 7, 8, 13, 17 and

  18. Do community-weighted mean functional traits reflect optimal strategies?

    Muscarella, Robert; Uriarte, María

    2016-03-30

    The notion that relationships between community-weighted mean (CWM) traits (i.e. plot-level trait values weighted by species abundances) and environmental conditions reflect selection towards locally optimal phenotypes is challenged by the large amount of interspecific trait variation typically found within ecological communities. Reconciling these contrasting patterns is a key to advancing predictive theories of functional community ecology. We combined data on geographical distributions and three traits (wood density, leaf mass per area and maximum height) of 173 tree species in Puerto Rico. We tested the hypothesis that species are more likely to occur where their trait values are more similar to the local CWM trait values (the'CWM-optimality' hypothesis) by comparing species occurrence patterns (as a proxy for fitness) with the functional composition of forest plots across a precipitation gradient. While 70% of the species supported CWM-optimality for at least one trait, nearly 25% significantly opposed it for at least one trait, thereby contributing to local functional diversity. The majority (85%) of species that opposed CWM-optimality did so only for one trait and few species opposed CWM-optimality in multivariate trait space. Our study suggests that constraints to local functional variation act more strongly on multivariate phenotypes than on univariate traits. PMID:27030412

  19. Untangling the relationships among regional occupancy, species traits, and niche characteristics in stream invertebrates

    Heino, Jani; Grönroos, Mira

    2014-01-01

    The regional occupancy and local abundance of species are affected by various species traits, but their relative effects are poorly understood. We studied the relationships between species traits and occupancy (i.e., proportion of sites occupied) or abundance (i.e., mean local abundance at occupied sites) of stream invertebrates using small-grained data (i.e., local stream sites) across a large spatial extent (i.e., three drainage basins). We found a significant, yet rather weak, linear relat...

  20. Aspectos genético-quantitativos de características de desempenho, carcaça e composição corporal em frangos Genetic-quantitative aspects of performance, carcass and body composition traits in broilers

    Leila de Genova Gaya

    2006-04-01

    Full Text Available Os parâmetros genéticos são ferramentas importantes para se conhecer melhor as características utilizadas nos programas de melhoramento genético e para a avaliação do plano de seleção empregado, permitindo o direcionamento das estratégias a serem aplicadas. As características de desempenho e de carcaça vêm sendo utilizadas como critério durante a seleção genética dos frangos, a exemplo do peso vivo, do peso de peito e da conversão alimentar. Entretanto, algumas características de composição corporal vêm trazendo entraves para a produção e a indústria avícolas, especialmente o peso da gordura e o peso do coração. Assim, nesta revisão, são abordados os principais aspectos relacionados aos parâmetros genéticos das características de desempenho, de carcaça e de composição corporal em frangos com o objetivo de proporcionar um melhor entendimento das conseqüências trazidas pelos esquemas de seleção empregados e suas implicações na cadeia produtiva destes animais.Genetic parameters are important tools to know better the traits used in animal breeding programs and for assessment of the employed selection plan. Then, these parameters allow the establishment of strategies to be used in these programs. The performance and carcass traits are being used as criteria during broiler genetic selection, as body weight, breast weight and feeding conversion ratio. However, some of the body composition traits represent obstacles for avian production and processing, especially fat content and heart weight. Thus, in this review, the main aspects related to genetic parameters of these traits in broiler are addressed to provide a better understanding of the consequences brought from selection schemes employed and its involvement on the avian production.