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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. 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

  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. 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.

  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. 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

  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. 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

  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. 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

  12. 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

  13. 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)

  14. 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.

  15. 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.

  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. 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

  18. 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

  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. 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

  4. 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.

  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. 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

  11. 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.

  12. 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.

  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. 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 ...

  12. 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...

  13. 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...

  14. 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...

  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. 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.

  19. 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.

  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. 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

  5. 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).

  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. 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 ...

  11. 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...

  12. #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 ...

  13. 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…

  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. 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...

  16. 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...

  17. 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 ...

  18. 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...

  19. 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...

  20. 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...

  1. 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 ...

  2. 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...

  3. %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 ...

  4. 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 ...

  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. 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

  8. 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...

  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. 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.

  14. 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

  15. 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

  16. 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.

  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. 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

  8. 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

  9. 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.

  10. 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

  11. 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)

  12. 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.

  13. 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

  14. 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

  15. 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.

  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. 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

  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. 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...

  4. 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...

  5. 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…

  6. 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...

  7. 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

  8. 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.

  9. 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.

  10. 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.

  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. 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

  13. 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

  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. 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...

  17. 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...

  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. 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

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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...