Improving biological understanding and complex trait prediction by integrating prior information in genomic feature models

DEFF Research Database (Denmark)

Edwards, Stefan McKinnon

externally founded information, such as KEGG pathways, Gene Ontology gene sets, or genomic features, and estimate the joint contribution of the genetic variants within these sets to complex trait phenotypes. The analysis of complex trait phenotypes is hampered by the myriad of genes that control the trait...

Ubiquitous polygenicity of human complex traits: genome-wide analysis of 49 traits in Koreans.

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Jian Yang

Full Text Available Recent studies in population of European ancestry have shown that 30% ~ 50% of heritability for human complex traits such as height and body mass index, and common diseases such as schizophrenia and rheumatoid arthritis, can be captured by common SNPs and that genetic variation attributed to chromosomes are in proportion to their length. Using genome-wide estimation and partitioning approaches, we analysed 49 human quantitative traits, many of which are relevant to human diseases, in 7,170 unrelated Korean individuals genotyped on 326,262 SNPs. For 43 of the 49 traits, we estimated a nominally significant (P<0.05 proportion of variance explained by all SNPs on the Affymetrix 5.0 genotyping array ([Formula: see text]. On average across 47 of the 49 traits for which the estimate of h(G(2 is non-zero, common SNPs explain approximately one-third (range of 7.8% to 76.8% of narrow sense heritability. The estimate of h(G(2 is highly correlated with the proportion of SNPs with association P<0.031 (r(2 = 0.92. Longer genomic segments tend to explain more phenotypic variation, with a correlation of 0.78 between the estimate of variance explained by individual chromosomes and their physical length, and 1% of the genome explains approximately 1% of the genetic variance. Despite the fact that there are a few SNPs with large effects for some traits, these results suggest that polygenicity is ubiquitous for most human complex traits and that a substantial proportion of the "missing heritability" is captured by common SNPs.

GlobAl Distribution of GEnetic Traits (GADGET) web server: polygenic trait scores worldwide.

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Chande, Aroon T; Wang, Lu; Rishishwar, Lavanya; Conley, Andrew B; Norris, Emily T; Valderrama-Aguirre, Augusto; Jordan, I King

2018-05-18

Human populations from around the world show striking phenotypic variation across a wide variety of traits. Genome-wide association studies (GWAS) are used to uncover genetic variants that influence the expression of heritable human traits; accordingly, population-specific distributions of GWAS-implicated variants may shed light on the genetic basis of human phenotypic diversity. With this in mind, we developed the GlobAl Distribution of GEnetic Traits web server (GADGET http://gadget.biosci.gatech.edu). The GADGET web server provides users with a dynamic visual platform for exploring the relationship between worldwide genetic diversity and the genetic architecture underlying numerous human phenotypes. GADGET integrates trait-implicated single nucleotide polymorphisms (SNPs) from GWAS, with population genetic data from the 1000 Genomes Project, to calculate genome-wide polygenic trait scores (PTS) for 818 phenotypes in 2504 individual genomes. Population-specific distributions of PTS are shown for 26 human populations across 5 continental population groups, with traits ordered based on the extent of variation observed among populations. Users of GADGET can also upload custom trait SNP sets to visualize global PTS distributions for their own traits of interest.

Genetic Parameters of Reproductive and Meat Quality Traits in Korean Berkshire Pigs

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Joon-Ho Lee

2015-10-01

carcass traits, an appropriate breeding scheme is required that carefully considers the complexity of genetic parameters and applicability of data.

Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean.

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Fang, Chao; Ma, Yanming; Wu, Shiwen; Liu, Zhi; Wang, Zheng; Yang, Rui; Hu, Guanghui; Zhou, Zhengkui; Yu, Hong; Zhang, Min; Pan, Yi; Zhou, Guoan; Ren, Haixiang; Du, Weiguang; Yan, Hongrui; Wang, Yanping; Han, Dezhi; Shen, Yanting; Liu, Shulin; Liu, Tengfei; Zhang, Jixiang; Qin, Hao; Yuan, Jia; Yuan, Xiaohui; Kong, Fanjiang; Liu, Baohui; Li, Jiayang; Zhang, Zhiwu; Wang, Guodong; Zhu, Baoge; Tian, Zhixi

2017-08-24

Soybean (Glycine max [L.] Merr.) is one of the most important oil and protein crops. Ever-increasing soybean consumption necessitates the improvement of varieties for more efficient production. However, both correlations among different traits and genetic interactions among genes that affect a single trait pose a challenge to soybean breeding. To understand the genetic networks underlying phenotypic correlations, we collected 809 soybean accessions worldwide and phenotyped them for two years at three locations for 84 agronomic traits. Genome-wide association studies identified 245 significant genetic loci, among which 95 genetically interacted with other loci. We determined that 14 oil synthesis-related genes are responsible for fatty acid accumulation in soybean and function in line with an additive model. Network analyses demonstrated that 51 traits could be linked through the linkage disequilibrium of 115 associated loci and these links reflect phenotypic correlations. We revealed that 23 loci, including the known Dt1, E2, E1, Ln, Dt2, Fan, and Fap loci, as well as 16 undefined associated loci, have pleiotropic effects on different traits. This study provides insights into the genetic correlation among complex traits and will facilitate future soybean functional studies and breeding through molecular design.

Adapting APSIM to model the physiology and genetics of complex adaptive traits in field crops.

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Hammer, Graeme L; van Oosterom, Erik; McLean, Greg; Chapman, Scott C; Broad, Ian; Harland, Peter; Muchow, Russell C

2010-05-01

Progress in molecular plant breeding is limited by the ability to predict plant phenotype based on its genotype, especially for complex adaptive traits. Suitably constructed crop growth and development models have the potential to bridge this predictability gap. A generic cereal crop growth and development model is outlined here. It is designed to exhibit reliable predictive skill at the crop level while also introducing sufficient physiological rigour for complex phenotypic responses to become emergent properties of the model dynamics. The approach quantifies capture and use of radiation, water, and nitrogen within a framework that predicts the realized growth of major organs based on their potential and whether the supply of carbohydrate and nitrogen can satisfy that potential. The model builds on existing approaches within the APSIM software platform. Experiments on diverse genotypes of sorghum that underpin the development and testing of the adapted crop model are detailed. Genotypes differing in height were found to differ in biomass partitioning among organs and a tall hybrid had significantly increased radiation use efficiency: a novel finding in sorghum. Introducing these genetic effects associated with plant height into the model generated emergent simulated phenotypic differences in green leaf area retention during grain filling via effects associated with nitrogen dynamics. The relevance to plant breeding of this capability in complex trait dissection and simulation is discussed.

Behavioral trait genetics in mice; Opportunities for translational research of psychiatric endophenotypes

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Mooij-van Malsen, J.G. de

2009-01-01

Mood disorders have powerful effects on the lives of many people. Finding the mechanisms underlying these disorders is essential to develop selective treatment. In this thesis, interspecies trait genetics are used on behavioural domains to unravel the complex genetics of involved endophenotypes. We

Worms under stress: unravelling genetic complex traits through perturbation

NARCIS (Netherlands)

Rodriguez Sanchez, M.

2014-01-01

The genetic architecture of an organism could be considered ‘the most amazing piece of engineering’ existing in nature. Looking from a certain distance, the genetic complexity of an organism could be described as an immense jigsaw puzzle. As in a real jigsaw, the connection between two pieces

Heritability and demographic analyses in the large isolated population of Val Borbera suggest advantages in mapping complex traits genes.

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Michela Traglia

2009-10-01

Full Text Available Isolated populations are a useful resource for mapping complex traits due to shared stable environment, reduced genetic complexity and extended Linkage Disequilibrium (LD compared to the general population. Here we describe a large genetic isolate from the North West Apennines, the mountain range that runs through Italy from the North West Alps to the South.The study involved 1,803 people living in 7 villages of the upper Borbera Valley. For this large population cohort, data from genealogy reconstruction, medical questionnaires, blood, anthropometric and bone status QUS parameters were evaluated. Demographic and epidemiological analyses indicated a substantial genetic component contributing to each trait variation as well as overlapping genetic determinants and family clustering for some traits.The data provide evidence for significant heritability of medical relevant traits that will be important in mapping quantitative traits. We suggest that this population isolate is suitable to identify rare variants associated with complex phenotypes that may be difficult to study in larger but more heterogeneous populations.

Genetic Analysis of Kernel Traits in Maize-Teosinte Introgression Populations

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Zhengbin Liu

2016-08-01

Full Text Available Seed traits have been targeted by human selection during the domestication of crop species as a way to increase the caloric and nutritional content of food during the transition from hunter-gather to early farming societies. The primary seed trait under selection was likely seed size/weight as it is most directly related to overall grain yield. Additional seed traits involved in seed shape may have also contributed to larger grain. Maize (Zea mays ssp. mays kernel weight has increased more than 10-fold in the 9000 years since domestication from its wild ancestor, teosinte (Z. mays ssp. parviglumis. In order to study how size and shape affect kernel weight, we analyzed kernel morphometric traits in a set of 10 maize-teosinte introgression populations using digital imaging software. We identified quantitative trait loci (QTL for kernel area and length with moderate allelic effects that colocalize with kernel weight QTL. Several genomic regions with strong effects during maize domestication were detected, and a genetic framework for kernel traits was characterized by complex pleiotropic interactions. Our results both confirm prior reports of kernel domestication loci and identify previously uncharacterized QTL with a range of allelic effects, enabling future research into the genetic basis of these traits.

Quantitative genetics of disease traits.

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Wray, N R; Visscher, P M

2015-04-01

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

Genetic relationships between detailed reproductive traits and performance traits in Holstein-Friesian dairy cattle.

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Carthy, T R; Ryan, D P; Fitzgerald, A M; Evans, R D; Berry, D P

2016-02-01

The objective of the study was to estimate the genetic relationships between detailed reproductive traits derived from ultrasound examination of the reproductive tract and a range of performance traits in Holstein-Friesian dairy cows. The performance traits investigated included calving performance, milk production, somatic cell score (i.e., logarithm transformation of somatic cell count), carcass traits, and body-related linear type traits. Detailed reproductive traits included (1) resumed cyclicity at the time of examination, (2) multiple ovulations, (3) early ovulation, (4) heat detection, (5) ovarian cystic structures, (6) embryo loss, and (7) uterine score, measured on a 1 (little or no fluid with normal tone) to 4 (large quantity of fluid with a flaccid tone) scale, based on the tone of the uterine wall and the quantity of fluid present in the uterus. (Co)variance components were estimated using a repeatability animal linear mixed model. Genetic merit for greater milk, fat, and protein yield was associated with a reduced ability to resume cyclicity postpartum (genetic correlations ranged from -0.25 to -0.15). Higher genetic merit for milk yield was also associated with a greater genetic susceptibility to multiple ovulations. Genetic predisposition to elevated somatic cell score was associated with a decreased likelihood of cyclicity postpartum (genetic correlation of -0.32) and a greater risk of both multiple ovulations (genetic correlation of 0.25) and embryo loss (genetic correlation of 0.32). Greater body condition score was genetically associated with an increased likelihood of resumption of cyclicity postpartum (genetic correlation of 0.52). Genetically heavier, fatter carcasses with better conformation were also associated with an increased likelihood of resumed cyclicity by the time of examination (genetic correlations ranged from 0.24 to 0.41). Genetically heavier carcasses were associated with an inferior uterine score as well as a greater

Genetic correlations between wool traits and meat quality traits in Merino sheep.

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Mortimer, S I; Hatcher, S; Fogarty, N M; van der Werf, J H J; Brown, D J; Swan, A A; Jacob, R H; Geesink, G H; Hopkins, D L; Edwards, J E Hocking; Ponnampalam, E N; Warner, R D; Pearce, K L; Pethick, D W

2017-10-01

Genetic correlations between 29 wool production and quality traits and 25 meat quality and nutritional value traits were estimated for Merino sheep from an Information Nucleus (IN). Genetic correlations among the meat quality and nutritional value traits are also reported. The IN comprised 8 flocks linked genetically and managed across a range of sheep production environments in Australia. The wool traits included over 5,000 yearling and 3,700 adult records for fleece weight, fiber diameter, staple length, staple strength, fiber diameter variation, scoured wool color, and visual scores for breech and body wrinkle. The meat quality traits were measured on samples from the and included over 1,200 records from progeny of over 170 sires for intramuscular fat (IMF), shear force of meat aged for 5 d (SF5), 24 h postmortem pH (pHLL; also measured in the , pHST), fresh and retail meat color and meat nutritional value traits such as iron and zinc levels, and long-chain omega-3 and omega-6 polyunsaturated fatty acid levels. Estimated heritabilities for IMF, SF5, pHLL, pHST, retail meat color lightness (), myoglobin, iron, zinc and across the range of long-chain fatty acids were 0.58 ± 0.11, 0.10 ± 0.09, 0.15 ± 0.07, 0.20 ± 0.10, 0.59 ± 0.15, 0.31 ± 0.09, 0.20 ± 0.09, 0.11 ± 0.09, and range of 0.00 (eicosapentaenoic, docosapentaenoic, and arachidonic acids) to 0.14 ± 0.07 (linoleic acid), respectively. The genetic correlations between the wool production and meat quality traits were low to negligible and indicate that wool breeding programs will have little or no effect on meat quality. There were moderately favorable genetic correlations between important yearling wool production traits and the omega-3 fatty acids that were reduced for corresponding adult wool production traits, but these correlations are unlikely to be important in wool/meat breeding programs because they have high SE, and the omega-3 traits have little or no genetic variance. Significant genetic

Genetic correlations among and between wool, growth and reproduction traits in Merino sheep.

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Safari, E; Fogarty, N M; Gilmour, A R; Atkins, K D; Mortimer, S I; Swan, A A; Brien, F D; Greeff, J C; van der Werf, J H J

2007-04-01

Data from seven research resource flocks across Australia were combined to provide accurate estimates of genetic correlations among production traits in Merino sheep. The flocks represented contemporary Australian Merino fine, medium and broad wool strains over the past 30 years. Over 110,000 records were available for analysis for each of the major wool traits, and 50,000 records for reproduction and growth traits with over 2700 sires and 25,000 dams. Individual models developed from the single trait analyses were extended to the various combinations of two-trait models to obtain genetic correlations among six wool traits [clean fleece weight (CFW), greasy fleece weight, fibre diameter (FD), yield, coefficient of variation of fibre diameter and standard deviation of fibre diameter], four growth traits [birth weight, weaning weight, yearling weight (YWT), and hogget weight] and four reproduction traits [fertility, litter size, lambs born per ewe joined, lambs weaned per ewe joined (LW/EJ)]. This study has provided for the first time a comprehensive matrix of genetic correlations among these 14 wool, growth and reproduction traits. The large size of the data set has also provided estimates with very low standard errors. A moderate positive genetic correlation was observed between CFW and FD (0.29 +/- 0.02). YWT was positively correlated with CFW (0.23 +/- 0.04), FD (0.17 +/- 0.04) and LWEJ (0.58 +/- 0.06), while LW/EJ was negatively correlated with CFW (-0.26 +/- 0.05) and positively correlated with FD (0.06 +/- 0.04) and LS (0.68 +/- 0.04). These genetic correlations, together with the estimates of heritability and other parameters provide the basis for more accurate prediction of outcomes in complex sheep-breeding programmes designed to improve several traits.

Early warm-rewarding parenting moderates the genetic contributions to callous-unemotional traits in childhood.

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Henry, Jeffrey; Dionne, Ginette; Viding, Essi; Vitaro, Frank; Brendgen, Mara; Tremblay, Richard E; Boivin, Michel

2018-04-23

Previous gene-environment interaction studies of CU traits have relied on the candidate gene approach, which does not account for the entire genetic load of complex phenotypes. Moreover, these studies have not examined the role of positive environmental factors such as warm/rewarding parenting. The aim of the present study was to determine whether early warm/rewarding parenting moderates the genetic contributions (i.e., heritability) to callous-unemotional (CU) traits at school age. Data were collected in a population sample of 662 twin pairs (Quebec Newborn Twin Study - QNTS). Mothers reported on their warm/rewarding parenting. Teachers assessed children's CU traits. These reports were subjected to twin modeling. Callous-unemotional traits were highly heritable, with the remaining variance accounted for by nonshared environmental factors. Warm/rewarding parenting significantly moderated the role of genes in CU traits; heritability was lower when children received high warm/rewarding parenting than when they were exposed to low warm/rewarding parenting. High warm/rewarding parenting may partly impede the genetic expression of CU traits. Developmental models of CU traits need to account for such gene-environment processes. © 2018 Association for Child and Adolescent Mental Health.

Estimation of genetic parameters for reproductive traits in alpacas.

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Cruz, A; Cervantes, I; Burgos, A; Morante, R; Gutiérrez, J P

2015-12-01

One of the main deficiencies affecting animal breeding programs in Peruvian alpacas is the low reproductive performance leading to low number of animals available to select from, decreasing strongly the selection intensity. Some reproductive traits could be improved by artificial selection, but very few information about genetic parameters exists for these traits in this specie. The aim of this study was to estimate genetic parameters for six reproductive traits in alpacas both in Suri (SU) and Huacaya (HU) ecotypes, as well as their genetic relationship with fiber and morphological traits. Dataset belonging to Pacomarca experimental farm collected between 2000 and 2014 was used. Number of records for age at first service (AFS), age at first calving (AFC), copulation time (CT), pregnancy diagnosis (PD), gestation length (GL), and calving interval (CI) were, respectively, 1704, 854, 19,770, 5874, 4290 and 934. Pedigree consisted of 7742 animals. Regarding reproductive traits, model of analysis included additive and residual random effects for all traits, and also permanent environmental effect for CT, PD, GL and CI traits, with color and year of recording as fixed effects for all the reproductive traits and also age at mating and sex of calf for GL trait. Estimated heritabilities, respectively for HU and SU were 0.19 and 0.09 for AFS, 0.45 and 0.59 for AFC, 0.04 and 0.05 for CT, 0.07 and 0.05 for PD, 0.12 and 0.20 for GL, and 0.14 and 0.09 for CI. Genetic correlations between them ranged from -0.96 to 0.70. No important genetic correlations were found between reproductive traits and fiber or morphological traits in HU. However, some moderate favorable genetic correlations were found between reproductive and either fiber and morphological traits in SU. According to estimated genetic correlations, some reproductive traits might be included as additional selection criteria in HU. Copyright © 2015 Elsevier B.V. All rights reserved.

Natural Genetic Variation and Candidate Genes for Morphological Traits in Drosophila melanogaster

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Carreira, Valeria Paula; Mensch, Julián; Hasson, Esteban; Fanara, Juan José

2016-01-01

Body size is a complex character associated to several fitness related traits that vary within and between species as a consequence of environmental and genetic factors. Latitudinal and altitudinal clines for different morphological traits have been described in several species of Drosophila and previous work identified genomic regions associated with such variation in D. melanogaster. However, the genetic factors that orchestrate morphological variation have been barely studied. Here, our main objective was to investigate genetic variation for different morphological traits associated to the second chromosome in natural populations of D. melanogaster along latitudinal and altitudinal gradients in Argentina. Our results revealed weak clinal signals and a strong population effect on morphological variation. Moreover, most pairwise comparisons between populations were significant. Our study also showed important within-population genetic variation, which must be associated to the second chromosome, as the lines are otherwise genetically identical. Next, we examined the contribution of different candidate genes to natural variation for these traits. We performed quantitative complementation tests using a battery of lines bearing mutated alleles at candidate genes located in the second chromosome and six second chromosome substitution lines derived from natural populations which exhibited divergent phenotypes. Results of complementation tests revealed that natural variation at all candidate genes studied, invected, Fasciclin 3, toucan, Reticulon-like1, jing and CG14478, affects the studied characters, suggesting that they are Quantitative Trait Genes for morphological traits. Finally, the phenotypic patterns observed suggest that different alleles of each gene might contribute to natural variation for morphological traits. However, non-additive effects cannot be ruled out, as wild-derived strains differ at myriads of second chromosome loci that may interact

Simple, standardized incorporation of genetic risk into non-genetic risk prediction tools for complex traits: coronary heart disease as an example

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Benjamin A Goldstein

2014-08-01

Full Text Available Purpose: Genetic risk assessment is becoming an important component of clinical decision-making. Genetic Risk Scores (GRSs allow the composite assessment of genetic risk in complex traits. A technically and clinically pertinent question is how to most easily and effectively combine a GRS with an assessment of clinical risk derived from established non-genetic risk factors as well as to clearly present this information to patient and health care providers. Materials & Methods: We illustrate a means to combine a GRS with an independent assessment of clinical risk using a log-link function. We apply the method to the prediction of coronary heart disease (CHD in the Atherosclerosis Risk in Communities (ARIC cohort. We evaluate different constructions based on metrics of effect change, discrimination, and calibration.Results: The addition of a GRS to a clinical risk score (CRS improves both discrimination and calibration for CHD in ARIC. Results are similar regardless of whether external vs. internal coefficients are used for the CRS, risk factor SNPs are included in the GRS, or subjects with diabetes at baseline are excluded. We outline how to report the construction and the performance of a GRS using our method and illustrate a means to present genetic risk information to subjects and/or their health care provider. Conclusion: The proposed method facilitates the standardized incorporation of a GRS in risk assessment.

Multiple-trait estimates of genetic parameters for metabolic disease traits, fertility disorders, and their predictors in Canadian Holsteins.

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Jamrozik, J; Koeck, A; Kistemaker, G J; Miglior, F

2016-03-01

Producer-recorded health data for metabolic disease traits and fertility disorders on 35,575 Canadian Holstein cows were jointly analyzed with selected indicator traits. Metabolic diseases included clinical ketosis (KET) and displaced abomasum (DA); fertility disorders were metritis (MET) and retained placenta (RP); and disease indicators were fat-to-protein ratio, milk β-hydroxybutyrate, and body condition score (BCS) in the first lactation. Traits in first and later (up to fifth) lactations were treated as correlated in the multiple-trait (13 traits in total) animal linear model. Bayesian methods with Gibbs sampling were implemented for the analysis. Estimates of heritability for disease incidence were low, up to 0.06 for DA in first lactation. Among disease traits, the environmental herd-year variance constituted 4% of the total variance for KET and less for other traits. First- and later-lactation disease traits were genetically correlated (from 0.66 to 0.72) across all traits, indicating different genetic backgrounds for first and later lactations. Genetic correlations between KET and DA were relatively strong and positive (up to 0.79) in both first- and later-lactation cows. Genetic correlations between fertility disorders were slightly lower. Metritis was strongly genetically correlated with both metabolic disease traits in the first lactation only. All other genetic correlations between metabolic and fertility diseases were statistically nonsignificant. First-lactation KET and MET were strongly positively correlated with later-lactation performance for these traits due to the environmental herd-year effect. Indicator traits were moderately genetically correlated (from 0.30 to 0.63 in absolute values) with both metabolic disease traits in the first lactation. Smaller and mostly nonsignificant genetic correlations were among indicators and metabolic diseases in later lactations. The only significant genetic correlations between indicators and fertility

Genetic and phenotypic variation of some reproductive traits in ...

African Journals Online (AJOL)

Unknown

sasas.co.za/Sajas.html. 195. Genetic and phenotypic variation of some reproductive traits in Egyptian buffalo ..... Mourad, Kawthar A., Khattab, A.S. & Ibrahim, M.A.R., 1989. Effect of genetic and non-genetic factors on reproductive traits in Egyptian ...

Genetic Marker Discovery in Complex Traits: A Field Example on Fat Content and Composition in Pigs

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Ramona Natacha Pena

2016-12-01

Full Text Available Among the large number of attributes that define pork quality, fat content and composition have attracted the attention of breeders in the recent years due to their interaction with human health and technological and sensorial properties of meat. In livestock species, fat accumulates in different depots following a temporal pattern that is also recognized in humans. Intramuscular fat deposition rate and fatty acid composition change with life. Despite indication that it might be possible to select for intramuscular fat without affecting other fat depots, to date only one depot-specific genetic marker (PCK1 c.2456C>A has been reported. In contrast, identification of polymorphisms related to fat composition has been more successful. For instance, our group has described a variant in the stearoyl-coA desaturase (SCD gene that improves the desaturation index of fat without affecting overall fatness or growth. Identification of mutations in candidate genes can be a tedious and costly process. Genome-wide association studies can help in narrowing down the number of candidate genes by highlighting those which contribute most to the genetic variation of the trait. Results from our group and others indicate that fat content and composition are highly polygenic and that very few genes explain more than 5% of the variance of the trait. Moreover, as the complexity of the genome emerges, the role of non-coding genes and regulatory elements cannot be disregarded. Prediction of breeding values from genomic data is discussed in comparison with conventional best linear predictors of breeding values. An example based on real data is given, and the implications in phenotype prediction are discussed in detail. The benefits and limitations of using large SNP sets versus a few very informative markers as predictors of genetic merit of breeding candidates are evaluated using field data as an example.

Detection of expression quantitative trait Loci in complex mouse crosses: impact and alleviation of data quality and complex population substructure.

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Iancu, Ovidiu D; Darakjian, Priscila; Kawane, Sunita; Bottomly, Daniel; Hitzemann, Robert; McWeeney, Shannon

2012-01-01

Complex Mus musculus crosses, e.g., heterogeneous stock (HS), provide increased resolution for quantitative trait loci detection. However, increased genetic complexity challenges detection methods, with discordant results due to low data quality or complex genetic architecture. We quantified the impact of theses factors across three mouse crosses and two different detection methods, identifying procedures that greatly improve detection quality. Importantly, HS populations have complex genetic architectures not fully captured by the whole genome kinship matrix, calling for incorporating chromosome specific relatedness information. We analyze three increasingly complex crosses, using gene expression levels as quantitative traits. The three crosses were an F(2) intercross, a HS formed by crossing four inbred strains (HS4), and a HS (HS-CC) derived from the eight lines found in the collaborative cross. Brain (striatum) gene expression and genotype data were obtained using the Illumina platform. We found large disparities between methods, with concordance varying as genetic complexity increased; this problem was more acute for probes with distant regulatory elements (trans). A suite of data filtering steps resulted in substantial increases in reproducibility. Genetic relatedness between samples generated overabundance of detected eQTLs; an adjustment procedure that includes the kinship matrix attenuates this problem. However, we find that relatedness between individuals is not evenly distributed across the genome; information from distinct chromosomes results in relatedness structure different from the whole genome kinship matrix. Shared polymorphisms from distinct chromosomes collectively affect expression levels, confounding eQTL detection. We suggest that considering chromosome specific relatedness can result in improved eQTL detection.

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

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

2013-11-01

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

Association genetics of growth and adaptive traits in loblolly pine (Pinus taeda L.) using whole-exome-discovered polymorphisms

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Mengmeng Lu; Konstantin V. Krutovsky; C. Dana Nelson; Jason B. West; Nathalie A. Reilly; Carol A. Loopstra

2017-01-01

In the USA, forest genetics research began over 100 years ago and loblolly pine breeding programs were established in the 1950s. However, the genetics underlying complex traits of loblolly pine remains to be discovered. To address this, adaptive and growth traits were measured and analyzed in a clonally tested loblolly pine (Pinus taeda L.) population. Over 2.8 million...

Genetic diversity, population structure and marker trait associations ...

Indian Academy of Sciences (India)

Supplementary data: Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum). Ashok Badigannavar and Gerald O. Myers. J. Genet. 94, 87–94. Table 1. List of cotton germplasm lines used in this study. Germplasm no. Cultivar. Region. Germplasm no. Cultivar.

Genetic mapping of quantitative trait loci for aseasonal reproduction in sheep.

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Mateescu, R G; Thonney, M L

2010-10-01

The productivity and economic prosperity of sheep farming could benefit greatly from more effective methods of selection for year-round lambing. Identification of QTL for aseasonal reproduction in sheep could lead to more accurate selection and faster genetic improvement. One hundred and twenty microsatellite markers were genotyped on 159 backcross ewes from a Dorset × East Friesian crossbred pedigree. Interval mapping was undertaken to map the QTL underlying several traits describing aseasonal reproduction including the number of oestrous cycles, maximum level of progesterone prior to breeding, pregnancy status determined by progesterone level, pregnancy status determined by ultrasound, lambing status and number of lambs born. Seven chromosomes (1, 3, 12, 17, 19, 20 and 24) were identified to harbour putative QTL for one or more component traits used to describe aseasonal reproduction. Ovine chromosomes 12, 17, 19 and 24 harbour QTL significant at the 5% chromosome-wide level, chromosomes 3 and 20 harbour QTL that exceeded the threshold at the 1% chromosome-wide level, while the QTL identified on chromosome 1 exceeded the 1% experiment-wide significance level. These results are a first step towards understanding the genetic mechanism of this complex trait and show that variation in aseasonal reproduction is associated with multiple chromosomal regions. © 2010 The Authors, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.

An Efficient Stepwise Statistical Test to Identify Multiple Linked Human Genetic Variants Associated with Specific Phenotypic Traits.

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Iksoo Huh

Full Text Available Recent advances in genotyping methodologies have allowed genome-wide association studies (GWAS to accurately identify genetic variants that associate with common or pathological complex traits. Although most GWAS have focused on associations with single genetic variants, joint identification of multiple genetic variants, and how they interact, is essential for understanding the genetic architecture of complex phenotypic traits. Here, we propose an efficient stepwise method based on the Cochran-Mantel-Haenszel test (for stratified categorical data to identify causal joint multiple genetic variants in GWAS. This method combines the CMH statistic with a stepwise procedure to detect multiple genetic variants associated with specific categorical traits, using a series of associated I × J contingency tables and a null hypothesis of no phenotype association. Through a new stratification scheme based on the sum of minor allele count criteria, we make the method more feasible for GWAS data having sample sizes of several thousands. We also examine the properties of the proposed stepwise method via simulation studies, and show that the stepwise CMH test performs better than other existing methods (e.g., logistic regression and detection of associations by Markov blanket for identifying multiple genetic variants. Finally, we apply the proposed approach to two genomic sequencing datasets to detect linked genetic variants associated with bipolar disorder and obesity, respectively.

Estimates of genetic parameters and genetic gains for growth traits ...

African Journals Online (AJOL)

Estimates of genetic parameters and genetic gains for growth traits of two Eucalyptus ... In South Africa, Eucalyptus urophylla is an important species due to its ... as hybrid parents to cross with E. grandis was 59.8% over the population mean.

cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture

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Jennifer Yihong Tan

2017-02-01

Full Text Available Summary: Intergenic long noncoding RNAs (lincRNAs are the largest class of transcripts in the human genome. Although many have recently been linked to complex human traits, the underlying mechanisms for most of these transcripts remain undetermined. We investigated the regulatory roles of a high-confidence and reproducible set of 69 trait-relevant lincRNAs (TR-lincRNAs in human lymphoblastoid cells whose biological relevance is supported by their evolutionary conservation during recent human history and genetic interactions with other trait-associated loci. Their enrichment in enhancer-like chromatin signatures, interactions with nearby trait-relevant protein-coding loci, and preferential location at topologically associated domain (TAD boundaries provide evidence that TR-lincRNAs likely regulate proximal trait-relevant gene expression in cis by modulating local chromosomal architecture. This is consistent with the positive and significant correlation found between TR-lincRNA abundance and intra-TAD DNA-DNA contacts. Our results provide insights into the molecular mode of action by which TR-lincRNAs contribute to complex human traits. : Tan et al. identify and characterize 69 human complex trait/disease-associated lincRNAs in LCLs. They show that these loci are often associated with cis-regulation of gene expression and tend to be localized at TAD boundaries, suggesting that these lincRNAs may influence chromosomal architecture. Keywords: intergenic long noncoding RNA, lincRNA, GWAS, expression quantitative trait loci, eQTL, complex trait and disease, enhancer, cis-regulation, topologically associated domains, TAD

Plasticity first: molecular signatures of a complex morphological trait in filamentous cyanobacteria.

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Koch, Robin; Kupczok, Anne; Stucken, Karina; Ilhan, Judith; Hammerschmidt, Katrin; Dagan, Tal

2017-08-31

Filamentous cyanobacteria that differentiate multiple cell types are considered the peak of prokaryotic complexity and their evolution has been studied in the context of multicellularity origins. Species that form true-branching filaments exemplify the most complex cyanobacteria. However, the mechanisms underlying the true-branching morphology remain poorly understood despite of several investigations that focused on the identification of novel genes or pathways. An alternative route for the evolution of novel traits is based on existing phenotypic plasticity. According to that scenario - termed genetic assimilation - the fixation of a novel phenotype precedes the fixation of the genotype. Here we show that the evolution of transcriptional regulatory elements constitutes a major mechanism for the evolution of new traits. We found that supplementation with sucrose reconstitutes the ancestral branchless phenotype of two true-branching Fischerella species and compared the transcription start sites (TSSs) between the two phenotypic states. Our analysis uncovers several orthologous TSSs whose transcription level is correlated with the true-branching phenotype. These TSSs are found in genes that encode components of the septosome and elongasome (e.g., fraC and mreB). The concept of genetic assimilation supplies a tenable explanation for the evolution of novel traits but testing its feasibility is hindered by the inability to recreate and study the evolution of present-day traits. We present a novel approach to examine transcription data for the plasticity first route and provide evidence for its occurrence during the evolution of complex colony morphology in true-branching cyanobacteria. Our results reveal a route for evolution of the true-branching phenotype in cyanobacteria via modification of the transcription level of pre-existing genes. Our study supplies evidence for the 'plasticity-first' hypothesis and highlights the importance of transcriptional regulation in

Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs.

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Camarinha-Silva, Amelia; Maushammer, Maria; Wellmann, Robin; Vital, Marius; Preuss, Siegfried; Bennewitz, Jörn

2017-07-01

The aim of the present study was to analyze the interplay between gastrointestinal tract (GIT) microbiota, host genetics, and complex traits in pigs using extended quantitative-genetic methods. The study design consisted of 207 pigs that were housed and slaughtered under standardized conditions, and phenotyped for daily gain, feed intake, and feed conversion rate. The pigs were genotyped with a standard 60 K SNP chip. The GIT microbiota composition was analyzed by 16S rRNA gene amplicon sequencing technology. Eight from 49 investigated bacteria genera showed a significant narrow sense host heritability, ranging from 0.32 to 0.57. Microbial mixed linear models were applied to estimate the microbiota variance for each complex trait. The fraction of phenotypic variance explained by the microbial variance was 0.28, 0.21, and 0.16 for daily gain, feed conversion, and feed intake, respectively. The SNP data and the microbiota composition were used to predict the complex traits using genomic best linear unbiased prediction (G-BLUP) and microbial best linear unbiased prediction (M-BLUP) methods, respectively. The prediction accuracies of G-BLUP were 0.35, 0.23, and 0.20 for daily gain, feed conversion, and feed intake, respectively. The corresponding prediction accuracies of M-BLUP were 0.41, 0.33, and 0.33. Thus, in addition to SNP data, microbiota abundances are an informative source of complex trait predictions. Since the pig is a well-suited animal for modeling the human digestive tract, M-BLUP, in addition to G-BLUP, might be beneficial for predicting human predispositions to some diseases, and, consequently, for preventative and personalized medicine. Copyright © 2017 by the Genetics Society of America.

Genetic parameters and genetic and phenotypic trends of performance traits of equines from the Brazilian Army

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Mariana de Almeida Dornelles

2012-06-01

Full Text Available The objective of this research was to compare the magnitude of genetic parameters (coefficients of heritability and genetic correlation as estimated by the Restricted Maximum Likelihood (REML method and Bayesian Inference, and to estimate the genetic and phenotypic trends to the traits height at the withers (HW24 and weight at 24 months of age (W24. The average heritability estimated by Bayesian Inference to HW24 was 0.47, and it was lower than that obtained by REML bi-trait analysis (0.52; however, the value estimated to W24 (0.39 was higher than that obtained by REML bi-trait analysis (0.38. The genetic correlation estimate between W24 and HW24 traits obtained by the REML method (0.66 was lower than that obtained by the Bayesian Inference Method (0.72. From the regression of the average additive genetic merit in the year of birth of the animals, it was found that the averaged genetic values of the animals for HW24 showed a genetic trend near zero (-0.0008cm/year, and the averaged genetic values for W24 showed a negative trend of -0.38 kg/year. The values to the direct heritability estimated for HW24 and W24 suggest that the direct selection for these traits can provide genetic gain in this population. The genetic correlation between the traits, high and positive, suggests that the selection for HW24 should promote increase in W24 at this age. The genetic trends obtained for the traits studied, near zero, indicate that the selection performed produced a slight reduction of the weight of the animals at 24 months of age; however, it did not promote increase in height at the wither at this same age, in this population.

Use of genetic data to infer population-specific ecological and phenotypic traits from mixed aggregations.

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Paul Moran

Full Text Available Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions.

Use of genetic data to infer population-specific ecological and phenotypic traits from mixed aggregations

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Moran, Paul; Bromaghin, Jeffrey F.; Masuda, Michele

2014-01-01

Many applications in ecological genetics involve sampling individuals from a mixture of multiple biological populations and subsequently associating those individuals with the populations from which they arose. Analytical methods that assign individuals to their putative population of origin have utility in both basic and applied research, providing information about population-specific life history and habitat use, ecotoxins, pathogen and parasite loads, and many other non-genetic ecological, or phenotypic traits. Although the question is initially directed at the origin of individuals, in most cases the ultimate desire is to investigate the distribution of some trait among populations. Current practice is to assign individuals to a population of origin and study properties of the trait among individuals within population strata as if they constituted independent samples. It seemed that approach might bias population-specific trait inference. In this study we made trait inferences directly through modeling, bypassing individual assignment. We extended a Bayesian model for population mixture analysis to incorporate parameters for the phenotypic trait and compared its performance to that of individual assignment with a minimum probability threshold for assignment. The Bayesian mixture model outperformed individual assignment under some trait inference conditions. However, by discarding individuals whose origins are most uncertain, the individual assignment method provided a less complex analytical technique whose performance may be adequate for some common trait inference problems. Our results provide specific guidance for method selection under various genetic relationships among populations with different trait distributions.

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.

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Astle, William J; Elding, Heather; Jiang, Tao; Allen, Dave; Ruklisa, Dace; Mann, Alice L; Mead, Daniel; Bouman, Heleen; Riveros-Mckay, Fernando; Kostadima, Myrto A; Lambourne, John J; Sivapalaratnam, Suthesh; Downes, Kate; Kundu, Kousik; Bomba, Lorenzo; Berentsen, Kim; Bradley, John R; Daugherty, Louise C; Delaneau, Olivier; Freson, Kathleen; Garner, Stephen F; Grassi, Luigi; Guerrero, Jose; Haimel, Matthias; Janssen-Megens, Eva M; Kaan, Anita; Kamat, Mihir; Kim, Bowon; Mandoli, Amit; Marchini, Jonathan; Martens, Joost H A; Meacham, Stuart; Megy, Karyn; O'Connell, Jared; Petersen, Romina; Sharifi, Nilofar; Sheard, Simon M; Staley, James R; Tuna, Salih; van der Ent, Martijn; Walter, Klaudia; Wang, Shuang-Yin; Wheeler, Eleanor; Wilder, Steven P; Iotchkova, Valentina; Moore, Carmel; Sambrook, Jennifer; Stunnenberg, Hendrik G; Di Angelantonio, Emanuele; Kaptoge, Stephen; Kuijpers, Taco W; Carrillo-de-Santa-Pau, Enrique; Juan, David; Rico, Daniel; Valencia, Alfonso; Chen, Lu; Ge, Bing; Vasquez, Louella; Kwan, Tony; Garrido-Martín, Diego; Watt, Stephen; Yang, Ying; Guigo, Roderic; Beck, Stephan; Paul, Dirk S; Pastinen, Tomi; Bujold, David; Bourque, Guillaume; Frontini, Mattia; Danesh, John; Roberts, David J; Ouwehand, Willem H; Butterworth, Adam S; Soranzo, Nicole

2016-11-17

Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (<5%) and rare (<1%) variants with a strong impact on blood cell phenotypes. Our data highlight general properties of the allelic architecture of complex traits, including the proportion of the heritable component of each blood trait explained by the polygenic signal across different genome regulatory domains. Finally, through Mendelian randomization, we provide evidence of shared genetic pathways linking blood cell indices with complex pathologies, including autoimmune diseases, schizophrenia, and coronary heart disease and evidence suggesting previously reported population associations between blood cell indices and cardiovascular disease may be non-causal. Copyright © 2016 Elsevier Inc. All rights reserved.

Multiple-Trait Genomic Selection Methods Increase Genetic Value Prediction Accuracy

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Jia, Yi; Jannink, Jean-Luc

2012-01-01

Genetic correlations between quantitative traits measured in many breeding programs are pervasive. These correlations indicate that measurements of one trait carry information on other traits. Current single-trait (univariate) genomic selection does not take advantage of this information. Multivariate genomic selection on multiple traits could accomplish this but has been little explored and tested in practical breeding programs. In this study, three multivariate linear models (i.e., GBLUP, BayesA, and BayesCπ) were presented and compared to univariate models using simulated and real quantitative traits controlled by different genetic architectures. We also extended BayesA with fixed hyperparameters to a full hierarchical model that estimated hyperparameters and BayesCπ to impute missing phenotypes. We found that optimal marker-effect variance priors depended on the genetic architecture of the trait so that estimating them was beneficial. We showed that the prediction accuracy for a low-heritability trait could be significantly increased by multivariate genomic selection when a correlated high-heritability trait was available. Further, multiple-trait genomic selection had higher prediction accuracy than single-trait genomic selection when phenotypes are not available on all individuals and traits. Additional factors affecting the performance of multiple-trait genomic selection were explored. PMID:23086217

Genetic parameters of wool colour and skin traits in Corriedale sheep

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M.V. Benavides

2003-01-01

Full Text Available Clean wool colour (CWC is an important wool price determinant and has been related to suint characteristics, i.e. sudoriparous and sebaceous gland secretions, such as suint percentage and suint K content. In this work heritability, phenotypic and genetic correlations among wool colour and skin traits were examined. The genetic estimates were assessed by Restricted Maximum Likelihood (REML procedures using average information algorithm (AIREML in a Corriedale flock. The traits analysed were wool colour traits (CWC, yellow predictive colour (YPC, and Visual Score; suint traits such as suint percentage and potassium and sodium concentrations in suint, and physiological traits such as potassium and sodium concentrations in the skin, including plasma and red blood cells. The objectives of this study were to assess phenotypic and genetic correlations between wool colour and skin traits, and to find the suitability of these traits as indirect selection criteria for clean wool colour. Suint traits were highly genetically correlated to YPC. Suint K, but not suint percentage, was found to have a high genetic correlation with CWC. Skin K, Visual Score, YPC and suint K were amongst the best indirect selection criteria for clean wool colour. However, selection using these traits was expected to reduce CWC from 52% to 49% of that estimated under direct selection.

Missing heritability : Is the gap closing? An analysis of 32 complex traits in the Lifelines Cohort Study

NARCIS (Netherlands)

Nolte, Ilja M.; van der Most, Peter J.; Alizadeh, Behrooz Z.; de Bakker, Paul I. W.; Boezen, H. Marike; Bruinenberg, Marcel; Franke, Lude; van der Harst, Pim; Navis, Gerjan; Postma, Dirkje S.; Rots, Marianne G.; Stolk, Ronald P.; Swertz, Morris A.; Wolffenbuttel, Bruce H. R.; Wijmenga, Cisca; Snieder, Harold

Despite the recent explosive rise in number of genetic markers for complex disease traits identified in genome-wide association studies, there is still a large gap between the known heritability of these traits and the part explained by these markers. To gauge whether this 'heritability gap' is

High-precision genetic mapping of behavioral traits in the diversity outbred mouse population

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Logan, R W; Robledo, R F; Recla, J M; Philip, V M; Bubier, J A; Jay, J J; Harwood, C; Wilcox, T; Gatti, D M; Bult, C J; Churchill, G A; Chesler, E J

2013-01-01

Historically our ability to identify genetic variants underlying complex behavioral traits in mice has been limited by low mapping resolution of conventional mouse crosses. The newly developed Diversity Outbred (DO) population promises to deliver improved resolution that will circumvent costly fine-mapping studies. The DO is derived from the same founder strains as the Collaborative Cross (CC), including three wild-derived strains. Thus the DO provides more allelic diversity and greater potential for discovery compared to crosses involving standard mouse strains. We have characterized 283 male and female DO mice using open-field, light–dark box, tail-suspension and visual-cliff avoidance tests to generate 38 behavioral measures. We identified several quantitative trait loci (QTL) for these traits with support intervals ranging from 1 to 3 Mb in size. These intervals contain relatively few genes (ranging from 5 to 96). For a majority of QTL, using the founder allelic effects together with whole genome sequence data, we could further narrow the positional candidates. Several QTL replicate previously published loci. Novel loci were also identified for anxiety- and activity-related traits. Half of the QTLs are associated with wild-derived alleles, confirming the value to behavioral genetics of added genetic diversity in the DO. In the presence of wild-alleles we sometimes observe behaviors that are qualitatively different from the expected response. Our results demonstrate that high-precision mapping of behavioral traits can be achieved with moderate numbers of DO animals, representing a significant advance in our ability to leverage the mouse as a tool for behavioral genetics PMID:23433259

Genetic basis of a cognitive complexity metric.

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Narelle K Hansell

Full Text Available Relational complexity (RC is a metric reflecting capacity limitation in relational processing. It plays a crucial role in higher cognitive processes and is an endophenotype for several disorders. However, the genetic underpinnings of complex relational processing have not been investigated. Using the classical twin model, we estimated the heritability of RC and genetic overlap with intelligence (IQ, reasoning, and working memory in a twin and sibling sample aged 15-29 years (N = 787. Further, in an exploratory search for genetic loci contributing to RC, we examined associated genetic markers and genes in our Discovery sample and selected loci for replication in four independent samples (ALSPAC, LBC1936, NTR, NCNG, followed by meta-analysis (N>6500 at the single marker level. Twin modelling showed RC is highly heritable (67%, has considerable genetic overlap with IQ (59%, and is a major component of genetic covariation between reasoning and working memory (72%. At the molecular level, we found preliminary support for four single-marker loci (one in the gene DGKB, and at a gene-based level for the NPS gene, having influence on cognition. These results indicate that genetic sources influencing relational processing are a key component of the genetic architecture of broader cognitive abilities. Further, they suggest a genetic cascade, whereby genetic factors influencing capacity limitation in relational processing have a flow-on effect to more complex cognitive traits, including reasoning and working memory, and ultimately, IQ.

Genetic parameters of ovarian and uterine reproductive traits in dairy cows.

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Carthy, T R; Ryan, D P; Fitzgerald, A M; Evans, R D; Berry, D P

2015-06-01

The objective of the study was to estimate genetic parameters of detailed reproductive traits derived from ultrasound examination of the reproductive tract as well as their genetic correlations with traditional reproductive traits. A total of 226,141 calving and insemination records as well as 74,134 ultrasound records from Irish dairy cows were used. Traditional reproductive traits included postpartum interval to first service, conception, and next calving, as well as the interval from first to last service; number of inseminations, pregnancy rate to first service, pregnant within 42 d of the herd breeding season, and submission in the first 21 d of the herd breeding season were also available. Detailed reproductive traits included resumed cyclicity at the time of ultrasound examination, incidence of multiple ovulations, incidence of early postpartum ovulation, heat detection, ovarian cystic structures, embryo loss, and uterine score; the latter was a subjectively assessed on a scale of 1 (little fluid with normal uterine tone) to 4 (large quantity of fluid with a flaccid uterine tone). Variance (and covariance) components were estimated using repeatability animal linear mixed models. Heritability for all reproductive traits were generally low (0.001-0.05), with the exception of traits related to cyclicity postpartum, regardless if defined traditionally (0.07; calving to first service) or from ultrasound examination [resumed cyclicity at the time of examination (0.07) or early postpartum ovulation (0.10)]. The genetic correlations among the detailed reproductive traits were generally favorable. The exception was the genetic correlation (0.29) between resumed cyclicity and uterine score; superior genetic merit for cyclicity postpartum was associated with inferior uterine score. Superior genetic merit for most traditional reproductive traits was associated with superior genetic merit for resumed cyclicity (genetic correlations ranged from -0.59 to -0.36 and from 0

Genetic, Genomic, and Breeding Approaches to Further Explore Kernel Composition Traits and Grain Yield in Maize

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Da Silva, Helena Sofia Pereira

2009-01-01

Maize ("Zea mays L.") is a model species well suited for the dissection of complex traits which are often of commercial value. The purpose of this research was to gain a deeper understanding of the genetic control of maize kernel composition traits starch, protein, and oil concentration, and also kernel weight and grain yield. Germplasm with…

A population genetic interpretation of GWAS findings for human quantitative traits

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Bullaughey, Kevin; Hudson, Richard R.; Sella, Guy

2018-01-01

Human genome-wide association studies (GWASs) are revealing the genetic architecture of anthropomorphic and biomedical traits, i.e., the frequencies and effect sizes of variants that contribute to heritable variation in a trait. To interpret these findings, we need to understand how genetic architecture is shaped by basic population genetics processes—notably, by mutation, natural selection, and genetic drift. Because many quantitative traits are subject to stabilizing selection and because genetic variation that affects one trait often affects many others, we model the genetic architecture of a focal trait that arises under stabilizing selection in a multidimensional trait space. We solve the model for the phenotypic distribution and allelic dynamics at steady state and derive robust, closed-form solutions for summary statistics of the genetic architecture. Our results provide a simple interpretation for missing heritability and why it varies among traits. They predict that the distribution of variances contributed by loci identified in GWASs is well approximated by a simple functional form that depends on a single parameter: the expected contribution to genetic variance of a strongly selected site affecting the trait. We test this prediction against the results of GWASs for height and body mass index (BMI) and find that it fits the data well, allowing us to make inferences about the degree of pleiotropy and mutational target size for these traits. Our findings help to explain why the GWAS for height explains more of the heritable variance than the similarly sized GWAS for BMI and to predict the increase in explained heritability with study sample size. Considering the demographic history of European populations, in which these GWASs were performed, we further find that most of the associations they identified likely involve mutations that arose shortly before or during the Out-of-Africa bottleneck at sites with selection coefficients around s = 10−3. PMID

Genetic analyses for conformation traits in South African Jersey and ...

African Journals Online (AJOL)

JACO

Genetic trends for conformation traits of the South African Holstein show that ... conformation traits can be used to improve stayability, fertility and disease resistance (Rogers et al., 1999; .... Genetic correlations among protein yield, productive.

Dominance genetic variance for traits under directional selection in Drosophila serrata.

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Sztepanacz, Jacqueline L; Blows, Mark W

2015-05-01

In contrast to our growing understanding of patterns of additive genetic variance in single- and multi-trait combinations, the relative contribution of nonadditive genetic variance, particularly dominance variance, to multivariate phenotypes is largely unknown. While mechanisms for the evolution of dominance genetic variance have been, and to some degree remain, subject to debate, the pervasiveness of dominance is widely recognized and may play a key role in several evolutionary processes. Theoretical and empirical evidence suggests that the contribution of dominance variance to phenotypic variance may increase with the correlation between a trait and fitness; however, direct tests of this hypothesis are few. Using a multigenerational breeding design in an unmanipulated population of Drosophila serrata, we estimated additive and dominance genetic covariance matrices for multivariate wing-shape phenotypes, together with a comprehensive measure of fitness, to determine whether there is an association between directional selection and dominance variance. Fitness, a trait unequivocally under directional selection, had no detectable additive genetic variance, but significant dominance genetic variance contributing 32% of the phenotypic variance. For single and multivariate morphological traits, however, no relationship was observed between trait-fitness correlations and dominance variance. A similar proportion of additive and dominance variance was found to contribute to phenotypic variance for single traits, and double the amount of additive compared to dominance variance was found for the multivariate trait combination under directional selection. These data suggest that for many fitness components a positive association between directional selection and dominance genetic variance may not be expected. Copyright © 2015 by the Genetics Society of America.

Integrating modelling and phenotyping approaches to identify and screen complex traits - Illustration for transpiration efficiency in cereals.

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Chenu, K; van Oosterom, E J; McLean, G; Deifel, K S; Fletcher, A; Geetika, G; Tirfessa, A; Mace, E S; Jordan, D R; Sulman, R; Hammer, G L

2018-02-21

Following advances in genetics, genomics, and phenotyping, trait selection in breeding is limited by our ability to understand interactions within the plants and with their environments, and to target traits of most relevance for the target population of environments. We propose an integrated approach that combines insights from crop modelling, physiology, genetics, and breeding to identify traits valuable for yield gain in the target population of environments, develop relevant high-throughput phenotyping platforms, and identify genetic controls and their values in production environments. This paper uses transpiration efficiency (biomass produced per unit of water used) as an example of a complex trait of interest to illustrate how the approach can guide modelling, phenotyping, and selection in a breeding program. We believe that this approach, by integrating insights from diverse disciplines, can increase the resource use efficiency of breeding programs for improving yield gains in target populations of environments.

How powerful are summary-based methods for identifying expression-trait associations under different genetic architectures?

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Veturi, Yogasudha; Ritchie, Marylyn D

2018-01-01

Transcriptome-wide association studies (TWAS) have recently been employed as an approach that can draw upon the advantages of genome-wide association studies (GWAS) and gene expression studies to identify genes associated with complex traits. Unlike standard GWAS, summary level data suffices for TWAS and offers improved statistical power. Two popular TWAS methods include either (a) imputing the cis genetic component of gene expression from smaller sized studies (using multi-SNP prediction or MP) into much larger effective sample sizes afforded by GWAS - TWAS-MP or (b) using summary-based Mendelian randomization - TWAS-SMR. Although these methods have been effective at detecting functional variants, it remains unclear how extensive variability in the genetic architecture of complex traits and diseases impacts TWAS results. Our goal was to investigate the different scenarios under which these methods yielded enough power to detect significant expression-trait associations. In this study, we conducted extensive simulations based on 6000 randomly chosen, unrelated Caucasian males from Geisinger's MyCode population to compare the power to detect cis expression-trait associations (within 500 kb of a gene) using the above-described approaches. To test TWAS across varying genetic backgrounds we simulated gene expression and phenotype using different quantitative trait loci per gene and cis-expression /trait heritability under genetic models that differentiate the effect of causality from that of pleiotropy. For each gene, on a training set ranging from 100 to 1000 individuals, we either (a) estimated regression coefficients with gene expression as the response using five different methods: LASSO, elastic net, Bayesian LASSO, Bayesian spike-slab, and Bayesian ridge regression or (b) performed eQTL analysis. We then sampled with replacement 50,000, 150,000, and 300,000 individuals respectively from the testing set of the remaining 5000 individuals and conducted GWAS on each

Complex Genetics of Behavior: BXDs in the Automated Home-Cage.

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Loos, Maarten; Verhage, Matthijs; Spijker, Sabine; Smit, August B

2017-01-01

This chapter describes a use case for the genetic dissection and automated analysis of complex behavioral traits using the genetically diverse panel of BXD mouse recombinant inbred strains. Strains of the BXD resource differ widely in terms of gene and protein expression in the brain, as well as in their behavioral repertoire. A large mouse resource opens the possibility for gene finding studies underlying distinct behavioral phenotypes, however, such a resource poses a challenge in behavioral phenotyping. To address the specifics of large-scale screening we describe how to investigate: (1) how to assess mouse behavior systematically in addressing a large genetic cohort, (2) how to dissect automation-derived longitudinal mouse behavior into quantitative parameters, and (3) how to map these quantitative traits to the genome, deriving loci underlying aspects of behavior.

Efficient algorithms for multidimensional global optimization in genetic mapping of complex traits

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Kajsa Ljungberg

2010-10-01

Full Text Available Kajsa Ljungberg1, Kateryna Mishchenko2, Sverker Holmgren11Division of Scientific Computing, Department of Information Technology, Uppsala University, Uppsala, Sweden; 2Department of Mathematics and Physics, Mälardalen University College, Västerås, SwedenAbstract: We present a two-phase strategy for optimizing a multidimensional, nonconvex function arising during genetic mapping of quantitative traits. Such traits are believed to be affected by multiple so called QTL, and searching for d QTL results in a d-dimensional optimization problem with a large number of local optima. We combine the global algorithm DIRECT with a number of local optimization methods that accelerate the final convergence, and adapt the algorithms to problem-specific features. We also improve the evaluation of the QTL mapping objective function to enable exploitation of the smoothness properties of the optimization landscape. Our best two-phase method is demonstrated to be accurate in at least six dimensions and up to ten times faster than currently used QTL mapping algorithms.Keywords: global optimization, QTL mapping, DIRECT 

Directional selection can drive the evolution of modularity in complex traits.

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Melo, Diogo; Marroig, Gabriel

2015-01-13

Modularity is a central concept in modern biology, providing a powerful framework for the study of living organisms on many organizational levels. Two central and related questions can be posed in regard to modularity: How does modularity appear in the first place, and what forces are responsible for keeping and/or changing modular patterns? We approached these questions using a quantitative genetics simulation framework, building on previous results obtained with bivariate systems and extending them to multivariate systems. We developed an individual-based model capable of simulating many traits controlled by many loci with variable pleiotropic relations between them, expressed in populations subject to mutation, recombination, drift, and selection. We used this model to study the problem of the emergence of modularity, and hereby show that drift and stabilizing selection are inefficient at creating modular variational structures. We also demonstrate that directional selection can have marked effects on the modular structure between traits, actively promoting a restructuring of genetic variation in the selected population and potentially facilitating the response to selection. Furthermore, we give examples of complex covariation created by simple regimes of combined directional and stabilizing selection and show that stabilizing selection is important in the maintenance of established covariation patterns. Our results are in full agreement with previous results for two-trait systems and further extend them to include scenarios of greater complexity. Finally, we discuss the evolutionary consequences of modular patterns being molded by directional selection.

Quantitative genetic analysis of anxiety trait in bipolar disorder.

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Contreras, J; Hare, E; Chavarría, G; Raventós, H

2018-01-01

Bipolar disorder type I (BPI) affects approximately 1% of the world population. Although genetic influences on bipolar disorder are well established, identification of genes that predispose to the illness has been difficult. Most genetic studies are based on categorical diagnosis. One strategy to overcome this obstacle is the use of quantitative endophenotypes, as has been done for other medical disorders. We studied 619 individuals, 568 participants from 61 extended families and 51 unrelated healthy controls. The sample was 55% female and had a mean age of 43.25 (SD 13.90; range 18-78). Heritability and genetic correlation of the trait scale from the Anxiety State and Trait Inventory (STAI) was computed by using the general linear model (SOLAR package software). we observed that anxiety trait meets the following criteria for an endophenotype of bipolar disorder type I (BPI): 1) association with BPI (individuals with BPI showed the highest trait score (F = 15.20 [5,24], p = 0.009), 2) state-independence confirmed after conducting a test-retest in 321 subjects, 3) co-segregation within families 4) heritability of 0.70 (SE: 0.060), p = 2.33 × 10 -14 and 5) genetic correlation with BPI was 0.20, (SE = 0.17, p = 3.12 × 10 -5 ). Confounding factors such as comorbid disorders and pharmacological treatment could affect the clinical relationship between BPI and anxiety trait. Further research is needed to evaluate if anxiety traits are specially related to BPI in comparison with other traits such as anger, attention or response inhibition deficit, pathological impulsivity or low self-directedness. Anxiety trait is a heritable phenotype that follows a normal distribution when measured not only in subjects with BPI but also in unrelated healthy controls. It could be used as an endophenotype in BPI for the identification of genomic regions with susceptibility genes for this disorder. Published by Elsevier B.V.

A behavioral genetic analysis of callous-unemotional traits and Big Five personality in adolescence.

Science.gov (United States)

Mann, Frank D; Briley, Daniel A; Tucker-Drob, Elliot M; Harden, K Paige

2015-11-01

Callous-unemotional (CU) traits, such as lacking empathy and emotional insensitivity, predict the onset, severity, and persistence of antisocial behavior. CU traits are heritable, and genetic influences on CU traits contribute to antisocial behavior. This study examines genetic overlap between CU traits and general domains of personality. We measured CU traits using the Inventory of Callous-Unemotional Traits (ICU) and Big Five personality using the Big Five Inventory in a sample of adolescent twins from the Texas Twin Project. Genetic influences on the Big Five personality dimensions could account for the entirety of genetic influences on CU traits. Item Response Theory results indicate that the Inventory of Callous and Unemotional Traits is better at detecting clinically relevant personality variation at lower extremes of personality trait continua, particularly low agreeableness and low conscientiousness. The proximate biological mechanisms that mediate genetic liabilities for CU traits remain an open question. The results of the current study suggest that understanding the development of normal personality may inform understanding of the genetic underpinnings of callous and unemotional behavior. (c) 2015 APA, all rights reserved).

Trait variation and genetic diversity in a banana genomic selection training population

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Nyine, Moses; Uwimana, Brigitte; Swennen, Rony; Batte, Michael; Brown, Allan; Christelová, Pavla; Hřibová, Eva; Lorenzen, Jim

2017-01-01

Banana (Musa spp.) is an important crop in the African Great Lakes region in terms of income and food security, with the highest per capita consumption worldwide. Pests, diseases and climate change hamper sustainable production of bananas. New breeding tools with increased crossbreeding efficiency are being investigated to breed for resistant, high yielding hybrids of East African Highland banana (EAHB). These include genomic selection (GS), which will benefit breeding through increased genetic gain per unit time. Understanding trait variation and the correlation among economically important traits is an essential first step in the development and selection of suitable GS models for banana. In this study, we tested the hypothesis that trait variations in bananas are not affected by cross combination, cycle, field management and their interaction with genotype. A training population created using EAHB breeding material and its progeny was phenotyped in two contrasting conditions. A high level of correlation among vegetative and yield related traits was observed. Therefore, genomic selection models could be developed for traits that are easily measured. It is likely that the predictive ability of traits that are difficult to phenotype will be similar to less difficult traits they are highly correlated with. Genotype response to cycle and field management practices varied greatly with respect to traits. Yield related traits accounted for 31–35% of principal component variation under low and high input field management conditions. Resistance to Black Sigatoka was stable across cycles but varied under different field management depending on the genotype. The best cross combination was 1201K-1xSH3217 based on selection response (R) of hybrids. Genotyping using simple sequence repeat (SSR) markers revealed that the training population was genetically diverse, reflecting a complex pedigree background, which was mostly influenced by the male parents. PMID:28586365

Trait variation and genetic diversity in a banana genomic selection training population.

Directory of Open Access Journals (Sweden)

Moses Nyine

Full Text Available Banana (Musa spp. is an important crop in the African Great Lakes region in terms of income and food security, with the highest per capita consumption worldwide. Pests, diseases and climate change hamper sustainable production of bananas. New breeding tools with increased crossbreeding efficiency are being investigated to breed for resistant, high yielding hybrids of East African Highland banana (EAHB. These include genomic selection (GS, which will benefit breeding through increased genetic gain per unit time. Understanding trait variation and the correlation among economically important traits is an essential first step in the development and selection of suitable GS models for banana. In this study, we tested the hypothesis that trait variations in bananas are not affected by cross combination, cycle, field management and their interaction with genotype. A training population created using EAHB breeding material and its progeny was phenotyped in two contrasting conditions. A high level of correlation among vegetative and yield related traits was observed. Therefore, genomic selection models could be developed for traits that are easily measured. It is likely that the predictive ability of traits that are difficult to phenotype will be similar to less difficult traits they are highly correlated with. Genotype response to cycle and field management practices varied greatly with respect to traits. Yield related traits accounted for 31-35% of principal component variation under low and high input field management conditions. Resistance to Black Sigatoka was stable across cycles but varied under different field management depending on the genotype. The best cross combination was 1201K-1xSH3217 based on selection response (R of hybrids. Genotyping using simple sequence repeat (SSR markers revealed that the training population was genetically diverse, reflecting a complex pedigree background, which was mostly influenced by the male parents.

Trait variation and genetic diversity in a banana genomic selection training population.

Science.gov (United States)

Nyine, Moses; Uwimana, Brigitte; Swennen, Rony; Batte, Michael; Brown, Allan; Christelová, Pavla; Hřibová, Eva; Lorenzen, Jim; Doležel, Jaroslav

2017-01-01

Banana (Musa spp.) is an important crop in the African Great Lakes region in terms of income and food security, with the highest per capita consumption worldwide. Pests, diseases and climate change hamper sustainable production of bananas. New breeding tools with increased crossbreeding efficiency are being investigated to breed for resistant, high yielding hybrids of East African Highland banana (EAHB). These include genomic selection (GS), which will benefit breeding through increased genetic gain per unit time. Understanding trait variation and the correlation among economically important traits is an essential first step in the development and selection of suitable GS models for banana. In this study, we tested the hypothesis that trait variations in bananas are not affected by cross combination, cycle, field management and their interaction with genotype. A training population created using EAHB breeding material and its progeny was phenotyped in two contrasting conditions. A high level of correlation among vegetative and yield related traits was observed. Therefore, genomic selection models could be developed for traits that are easily measured. It is likely that the predictive ability of traits that are difficult to phenotype will be similar to less difficult traits they are highly correlated with. Genotype response to cycle and field management practices varied greatly with respect to traits. Yield related traits accounted for 31-35% of principal component variation under low and high input field management conditions. Resistance to Black Sigatoka was stable across cycles but varied under different field management depending on the genotype. The best cross combination was 1201K-1xSH3217 based on selection response (R) of hybrids. Genotyping using simple sequence repeat (SSR) markers revealed that the training population was genetically diverse, reflecting a complex pedigree background, which was mostly influenced by the male parents.

Kernel-based whole-genome prediction of complex traits: a review.

Science.gov (United States)

Morota, Gota; Gianola, Daniel

2014-01-01

Prediction of genetic values has been a focus of applied quantitative genetics since the beginning of the 20th century, with renewed interest following the advent of the era of whole genome-enabled prediction. Opportunities offered by the emergence of high-dimensional genomic data fueled by post-Sanger sequencing technologies, especially molecular markers, have driven researchers to extend Ronald Fisher and Sewall Wright's models to confront new challenges. In particular, kernel methods are gaining consideration as a regression method of choice for genome-enabled prediction. Complex traits are presumably influenced by many genomic regions working in concert with others (clearly so when considering pathways), thus generating interactions. Motivated by this view, a growing number of statistical approaches based on kernels attempt to capture non-additive effects, either parametrically or non-parametrically. This review centers on whole-genome regression using kernel methods applied to a wide range of quantitative traits of agricultural importance in animals and plants. We discuss various kernel-based approaches tailored to capturing total genetic variation, with the aim of arriving at an enhanced predictive performance in the light of available genome annotation information. Connections between prediction machines born in animal breeding, statistics, and machine learning are revisited, and their empirical prediction performance is discussed. Overall, while some encouraging results have been obtained with non-parametric kernels, recovering non-additive genetic variation in a validation dataset remains a challenge in quantitative genetics.

Kernel-based whole-genome prediction of complex traits: a review

Directory of Open Access Journals (Sweden)

Gota eMorota

2014-10-01

Full Text Available Prediction of genetic values has been a focus of applied quantitative genetics since the beginning of the 20th century, with renewed interest following the advent of the era of whole genome-enabled prediction. Opportunities offered by the emergence of high-dimensional genomic data fueled by post-Sanger sequencing technologies, especially molecular markers, have driven researchers to extend Ronald Fisher and Sewall Wright's models to confront new challenges. In particular, kernel methods are gaining consideration as a regression method of choice for genome-enabled prediction. Complex traits are presumably influenced by many genomic regions working in concert with others (clearly so when considering pathways, thus generating interactions. Motivated by this view, a growing number of statistical approaches based on kernels attempt to capture non-additive effects, either parametrically or non-parametrically. This review centers on whole-genome regression using kernel methods applied to a wide range of quantitative traits of agricultural importance in animals and plants. We discuss various kernel-based approaches tailored to capturing total genetic variation, with the aim of arriving at an enhanced predictive performance in the light of available genome annotation information. Connections between prediction machines born in animal breeding, statistics, and machine learning are revisited, and their empirical prediction performance is discussed. Overall, while some encouraging results have been obtained with non-parametric kernels, recovering non-additive genetic variation in a validation dataset remains a challenge in quantitative genetics.

Immunity traits in pigs: substantial genetic variation and limited covariation.

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Laurence Flori

Full Text Available BACKGROUND: Increasing robustness via improvement of resistance to pathogens is a major selection objective in livestock breeding. As resistance traits are difficult or impossible to measure directly, potential indirect criteria are measures of immune traits (ITs. Our underlying hypothesis is that levels of ITs with no focus on specific pathogens define an individual's immunocompetence and thus predict response to pathogens in general. Since variation in ITs depends on genetic, environmental and probably epigenetic factors, our aim was to estimate the relative importance of genetics. In this report, we present a large genetic survey of innate and adaptive ITs in pig families bred in the same environment. METHODOLOGY/PRINCIPAL FINDINGS: Fifty four ITs were studied on 443 Large White pigs vaccinated against Mycoplasma hyopneumoniae and analyzed by combining a principal component analysis (PCA and genetic parameter estimation. ITs include specific and non specific antibodies, seric inflammatory proteins, cell subsets by hemogram and flow cytometry, ex vivo production of cytokines (IFNα, TNFα, IL6, IL8, IL12, IFNγ, IL2, IL4, IL10, phagocytosis and lymphocyte proliferation. While six ITs had heritabilities that were weak or not significantly different from zero, 18 and 30 ITs had moderate (0.10.4 heritability values, respectively. Phenotypic and genetic correlations between ITs were weak except for a few traits that mostly include cell subsets. PCA revealed no cluster of innate or adaptive ITs. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that variation in many innate and adaptive ITs is genetically controlled in swine, as already reported for a smaller number of traits by other laboratories. A limited redundancy of the traits was also observed confirming the high degree of complementarity between innate and adaptive ITs. Our data provide a genetic framework for choosing ITs to be included as selection criteria in multitrait selection

Identification of genetic loci shared between schizophrenia and the Big Five personality traits.

Science.gov (United States)

Smeland, Olav B; Wang, Yunpeng; Lo, Min-Tzu; Li, Wen; Frei, Oleksandr; Witoelar, Aree; Tesli, Martin; Hinds, David A; Tung, Joyce Y; Djurovic, Srdjan; Chen, Chi-Hua; Dale, Anders M; Andreassen, Ole A

2017-05-22

Schizophrenia is associated with differences in personality traits, and recent studies suggest that personality traits and schizophrenia share a genetic basis. Here we aimed to identify specific genetic loci shared between schizophrenia and the Big Five personality traits using a Bayesian statistical framework. Using summary statistics from genome-wide association studies (GWAS) on personality traits in the 23andMe cohort (n = 59,225) and schizophrenia in the Psychiatric Genomics Consortium cohort (n = 82,315), we evaluated overlap in common genetic variants. The Big Five personality traits neuroticism, extraversion, openness, agreeableness and conscientiousness were measured using a web implementation of the Big Five Inventory. Applying the conditional false discovery rate approach, we increased discovery of genetic loci and identified two loci shared between neuroticism and schizophrenia and six loci shared between openness and schizophrenia. The study provides new insights into the relationship between personality traits and schizophrenia by highlighting genetic loci involved in their common genetic etiology.

Shared genetic influences between attention-deficit/hyperactivity disorder (ADHD) traits in children and clinical ADHD.

Science.gov (United States)

Stergiakouli, Evie; Martin, Joanna; Hamshere, Marian L; Langley, Kate; Evans, David M; St Pourcain, Beate; Timpson, Nicholas J; Owen, Michael J; O'Donovan, Michael; Thapar, Anita; Davey Smith, George

2015-04-01

Twin studies and genome-wide complex trait analysis (GCTA) are not in agreement regarding heritability estimates for behavioral traits in children from the general population. This has sparked a debate on the possible difference in genetic architecture between behavioral traits and psychiatric disorders. In this study, we test whether polygenic risk scores associated with variation in attention-deficit/hyperactivity disorder (ADHD) trait levels in children from the general population predict ADHD diagnostic status and severity in an independent clinical sample. Single nucleotide polymorphisms (SNPs) with p ADHD traits in 4,546 children (mean age, 7 years 7 months) from the Avon Longitudinal Study of Parents and Children (ALSPAC; general population sample) were selected to calculate polygenic risk scores in 508 children with an ADHD diagnosis (independent clinical sample) and 5,081 control participants. Polygenic scores were tested for association with case-control status and severity of disorder in the clinical sample. Increased polygenic score for ADHD traits predicted ADHD case-control status (odds ratio = 1.17 [95% CI = 1.08-1.28], p = .0003), higher ADHD symptom severity (β = 0.29 [95% CI = 0.04-0.54], p = 0.02), and symptom domain severity in the clinical sample. This study highlights the relevance of additive genetic variance in ADHD, and provides evidence that shared genetic factors contribute to both behavioral traits in the general population and psychiatric disorders at least in the case of ADHD. Copyright © 2015 American Academy of Child and Adolescent Psychiatry. Published by Elsevier Inc. All rights reserved.

Genetic Relationships of Carcass Traits with Retail Cut Productivity of Hanwoo Cattle

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Daeyoung Koh

2014-10-01

Full Text Available This study aimed to estimate genetic correlation between carcass grading and retail productivity traits and to estimate the correlated response on retail productivity traits through selection for carcass grading traits in order to assess the efficacy of indirect selection. Genetic parameters were estimated with the data from 4240 Hanwoo steers using mixed models, and phenotypes included carcass weight (CWT, back fat thickness (BFT, eye muscle area (EMA, marbling (MAR, and estimated lean yield percentage (ELP as the carcass grading traits, and weight and portion of retail cuts (RCW and RCP, trimmed fats (TFW and TFP and trimmed bones (TBW and TBP as the lean productivity traits. The CWT had positive genetic correlations with RCW (0.95 and TFW (0.73, but its genetic correlation with RCP was negligible (0.02. The BFT was negatively correlated with RCP (−0.63, but positively correlated with TFW and TFP (0.77 and 0.70. Genetic correlations of MAR with TFW and TFP were low. Among the carcass grading traits, only EMA was positively correlated with both RCW (0.60 and RCP (0.72. The EMA had a relatively strong negative genetic correlation with TFW (−0.64. The genetic correlation coefficients of ELP with RCP, TFW, and TFP were 0.76, −0.90, and −0.82, respectively. These correlation coefficients suggested that the ELP and EMA might be favorable traits in regulating lean productivity of carcass.

Genetic relationships between calving interval and linear type traits in

African Journals Online (AJOL)

Genetic correlations between first calving interval (CI) and linear type traits in South African Holstein and Jersey cattle were estimated to assess the possibility of using type information as selection criteria for CI. All linear type traits routinely evaluated under the National Genetic Evaluation Programme (18 for Jersey and 17 ...

Genetic parameters for fitness and neonatal behavior traits in sheep.

Science.gov (United States)

Matheson, S M; Bünger, L; Dwyer, C M

2012-11-01

Poor neonatal survival constrains productivity and good welfare. The heritability of survival in sheep is very low, suggesting that genetic progress will be slow. Previously we have shown that a difficult birth and low neonatal lamb vigor are important predictors of future survival. In this study we investigated the heritability of these traits, and their relationship to production traits, as an alternative indirect route to improve lamb survival. Neonatal lamb data from 11,092 animals were collected over 2 years from 290 commercial sheep flocks, using previously developed methods to rapidly assess three traits (birth assistance, lamb vigor, sucking ability) on farm. Heritabilities for neonatal traits were moderate: birth assistance (mean ± standard error; 0.26 ± 0.03), lamb vigor (0.40 ± 0.04) and sucking ability (0.32 ± 0.03). Genetic correlations between neonatal traits were moderate to high, and positive. Heritabilities for production traits were also moderate: 8-week weight (0.27 ± 0.06), 20-week weight (0.39 ± 0.07), ultrasound muscle depth (0.37 ± 0.06). Genetic and phenotypic correlations between the neonatal traits and production traits were not significantly different from zero. However, lambs that were scored as of poor vigor at birth were less likely to be recorded at 8 or 20 weeks, indicating that they may have died. The data demonstrate that the neonatal survival traits of birth assistance, lamb vigor and sucking assistance are moderately heritable when treated as a lamb trait, indicating that selection to target these lamb traits would successfully, and efficiently, improve survival without influencing productivity.

Appearance traits in fish farming: progress from classical genetics to genomics, providing insight into current and potential genetic improvement

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Nelson eColihueque

2014-08-01

Full Text Available Appearance traits in fish, those external body characteristics that influence consumer acceptance at point of sale, have come to the forefront of commercial fish farming, as culture profitability is closely linked to management of these traits. Appearance traits comprise mainly body shape and skin pigmentation. Analysis of the genetic basis of these traits in different fish reveals significant genetic variation within populations, indicating potential for their genetic improvement. Work into ascertaining the minor or major genes underlying appearance traits for commercial fish is emerging, with substantial progress in model fish in terms of identifying genes that control body shape and skin colors. In this review, we describe research progress to date, especially with regard to commercial fish, and discuss genomic findings in model fish in order to better address the genetic basis of the traits. Given that appearance traits are important in commercial fish, the genomic information related to this issue promises to accelerate the selection process in coming years.

Appearance traits in fish farming: progress from classical genetics to genomics, providing insight into current and potential genetic improvement

Science.gov (United States)

Colihueque, Nelson; Araneda, Cristian

2014-01-01

Appearance traits in fish, those external body characteristics that influence consumer acceptance at point of sale, have come to the forefront of commercial fish farming, as culture profitability is closely linked to management of these traits. Appearance traits comprise mainly body shape and skin pigmentation. Analysis of the genetic basis of these traits in different fish reveals significant genetic variation within populations, indicating potential for their genetic improvement. Work into ascertaining the minor or major genes underlying appearance traits for commercial fish is emerging, with substantial progress in model fish in terms of identifying genes that control body shape and skin colors. In this review, we describe research progress to date, especially with regard to commercial fish, and discuss genomic findings in model fish in order to better address the genetic basis of the traits. Given that appearance traits are important in commercial fish, the genomic information related to this issue promises to accelerate the selection process in coming years. PMID:25140172

Nutritional habits, lifestyle, and genetic predisposition in cardiovascular and metabolic traits in Turkish population.

Science.gov (United States)

Karaca, Sefayet; Erge, Sema; Cesuroglu, Tomris; Polimanti, Renato

2016-06-01

Cardiovascular and metabolic traits (CMT) are influenced by complex interactive processes including diet, lifestyle, and genetic predisposition. The present study investigated the interactions of these risk factors in relation to CMTs in the Turkish population. We applied bootstrap agglomerative hierarchical clustering and Bayesian network learning algorithms to identify the causative relationships among genes involved in different biological mechanisms (i.e., lipid metabolism, hormone metabolism, cellular detoxification, aging, and energy metabolism), lifestyle (i.e., physical activity, smoking behavior, and metropolitan residency), anthropometric traits (i.e., body mass index, body fat ratio, and waist-to-hip ratio), and dietary habits (i.e., daily intakes of macro- and micronutrients) in relation to CMTs (i.e., health conditions and blood parameters). We identified significant correlations between dietary habits (soybean and vitamin B12 intakes) and different cardiometabolic diseases that were confirmed by the Bayesian network-learning algorithm. Genetic factors contributed to these disease risks also through the pleiotropy of some genetic variants (i.e., F5 rs6025 and MTR rs180508). However, we also observed that certain genetic associations are indirect since they are due to the causative relationships among the CMTs (e.g., APOC3 rs5128 is associated with low-density lipoproteins cholesterol and, by extension, total cholesterol). Our study applied a novel approach to integrate various sources of information and dissect the complex interactive processes related to CMTs. Our data indicated that complex causative networks are present: causative relationships exist among CMTs and are affected by genetic factors (with pleiotropic and non-pleiotropic effects) and dietary habits. Copyright © 2016 Elsevier Inc. All rights reserved.

Comparison of whole-genome prediction models for traits with contrasting genetic architecture in a diversity panel of maize inbred lines

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Riedelsheimer Christian

2012-09-01

Full Text Available Abstract Background There is increasing empirical evidence that whole-genome prediction (WGP is a powerful tool for predicting line and hybrid performance in maize. However, there is a lack of knowledge about the sensitivity of WGP models towards the genetic architecture of the trait. Whereas previous studies exclusively focused on highly polygenic traits, important agronomic traits such as disease resistances, nutrifunctional or climate adaptational traits have a genetic architecture which is either much less complex or unknown. For such cases, information about model robustness and guidelines for model selection are lacking. Here, we compared five WGP models with different assumptions about the distribution of the underlying genetic effects. As contrasting model traits, we chose three highly polygenic agronomic traits and three metabolites each with a major QTL explaining 22 to 30% of the genetic variance in a panel of 289 diverse maize inbred lines genotyped with 56,110 SNPs. Results We found the five WGP models to be remarkable robust towards trait architecture with the largest differences in prediction accuracies ranging between 0.05 and 0.14 for the same trait, most likely as the result of the high level of linkage disequilibrium prevailing in elite maize germplasm. Whereas RR-BLUP performed best for the agronomic traits, it was inferior to LASSO or elastic net for the three metabolites. We found the approach of genome partitioning of genetic variance, first applied in human genetics, as useful in guiding the breeder which model to choose, if prior knowledge of the trait architecture is lacking. Conclusions Our results suggest that in diverse germplasm of elite maize inbred lines with a high level of LD, WGP models differ only slightly in their accuracies, irrespective of the number and effects of QTL found in previous linkage or association mapping studies. However, small gains in prediction accuracies can be achieved if the WGP model is

Intelligence : shared genetic basis between Mendelian disorders and a polygenic trait

NARCIS (Netherlands)

Franić, Sanja; Groen-Blokhuis, Maria M; Dolan, Conor V; Kattenberg, Mathijs V; Pool, René; Xiao, Xiangjun; Scheet, Paul A; Ehli, Erik A; Davies, Gareth E; van der Sluis, Sophie; Abdellaoui, Abdel; Hansell, Narelle K; Martin, Nicholas G; Hudziak, James J; van Beijsterveldt, Catherina E M; Swagerman, Suzanne C; Hulshoff Pol, Hilleke E; de Geus, Eco J C; Bartels, Meike; Ropers, H Hilger; Hottenga, Jouke-Jan; Boomsma, Dorret I

2015-01-01

Multiple inquiries into the genetic etiology of human traits indicated an overlap between genes underlying monogenic disorders (eg, skeletal growth defects) and those affecting continuous variability of related quantitative traits (eg, height). Extending the idea of a shared genetic basis between a

The genetic variance but not the genetic covariance of life-history traits changes towards the north in a time-constrained insect.

Science.gov (United States)

Sniegula, Szymon; Golab, Maria J; Drobniak, Szymon M; Johansson, Frank

2018-03-22

Seasonal time constraints are usually stronger at higher than lower latitudes and can exert strong selection on life-history traits and the correlations among these traits. To predict the response of life-history traits to environmental change along a latitudinal gradient, information must be obtained about genetic variance in traits and also genetic correlation between traits, that is the genetic variance-covariance matrix, G. Here, we estimated G for key life-history traits in an obligate univoltine damselfly that faces seasonal time constraints. We exposed populations to simulated native temperatures and photoperiods and common garden environmental conditions in a laboratory set-up. Despite differences in genetic variance in these traits between populations (lower variance at northern latitudes), there was no evidence for latitude-specific covariance of the life-history traits. At simulated native conditions, all populations showed strong genetic and phenotypic correlations between traits that shaped growth and development. The variance-covariance matrix changed considerably when populations were exposed to common garden conditions compared with the simulated natural conditions, showing the importance of environmentally induced changes in multivariate genetic structure. Our results highlight the importance of estimating variance-covariance matrixes in environments that mimic selection pressures and not only trait variances or mean trait values in common garden conditions for understanding the trait evolution across populations and environments. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Genetic variation of inbreeding depression among floral and fitness traits in Silene nutans

DEFF Research Database (Denmark)

Thiele, Jan; Hansen, Thomas Møller; Siegismund, Hans Redlef

2010-01-01

The magnitude and variation of inbreeding depression (ID) within populations is important for the evolution and maintenance of mixed mating systems. We studied ID and its genetic variation in a range of floral and fitness traits in a small and large population of the perennial herb Silene nutans......, using controlled pollinations in a fully factorial North Carolina II design. Floral traits and early fitness traits, that is seed mass and germination rate, were not much affected by inbreeding (delta0.4). Lack of genetic correlations indicated that ID in floral, early and late traits is genetically...... was statistically significant in most floral and all seed traits, but not in late fitness traits. However, some paternal families had delta...

Genetic divergence in sesame based on morphological and agronomic traits

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Nair Helena Castro Arriel

2007-01-01

Full Text Available The evaluation of diversity in germplasm collections is important for both plant breeders and germplasmcurators to optimize the use of the variability available. Diversity can be estimated by different genetic markers. The purposeof this study was to estimate the genetic divergence of 30 morphological and agronomic traits in 108 sesame genotypes bymultivariate analysis. The Cole-Rodgers index was used to establish the dissimilarity matrices. The principal componentanalysis identified the traits that contributed most to the divergence and the genotypes were clustered by Tocher’s optimization.Despite the narrow genetic basis, the markers were efficient to characterize the genotypes and identify the most similar groupsor duplicate and divergent genotypes. Greatest variation was found for the traits number of capsules per plant and grain yield.

Using genetic markers to orient the edges in quantitative trait networks: the NEO software.

Science.gov (United States)

Aten, Jason E; Fuller, Tova F; Lusis, Aldons J; Horvath, Steve

2008-04-15

Systems genetic studies have been used to identify genetic loci that affect transcript abundances and clinical traits such as body weight. The pairwise correlations between gene expression traits and/or clinical traits can be used to define undirected trait networks. Several authors have argued that genetic markers (e.g expression quantitative trait loci, eQTLs) can serve as causal anchors for orienting the edges of a trait network. The availability of hundreds of thousands of genetic markers poses new challenges: how to relate (anchor) traits to multiple genetic markers, how to score the genetic evidence in favor of an edge orientation, and how to weigh the information from multiple markers. We develop and implement Network Edge Orienting (NEO) methods and software that address the challenges of inferring unconfounded and directed gene networks from microarray-derived gene expression data by integrating mRNA levels with genetic marker data and Structural Equation Model (SEM) comparisons. The NEO software implements several manual and automatic methods for incorporating genetic information to anchor traits. The networks are oriented by considering each edge separately, thus reducing error propagation. To summarize the genetic evidence in favor of a given edge orientation, we propose Local SEM-based Edge Orienting (LEO) scores that compare the fit of several competing causal graphs. SEM fitting indices allow the user to assess local and overall model fit. The NEO software allows the user to carry out a robustness analysis with regard to genetic marker selection. We demonstrate the utility of NEO by recovering known causal relationships in the sterol homeostasis pathway using liver gene expression data from an F2 mouse cross. Further, we use NEO to study the relationship between a disease gene and a biologically important gene co-expression module in liver tissue. The NEO software can be used to orient the edges of gene co-expression networks or quantitative trait

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

Science.gov (United States)

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

2018-06-01

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

Genetic parameters for reproductive traits in a beef cattle herd ...

African Journals Online (AJOL)

Unknown

Keywords: beef cattle, breeding, genetics, heritability, reproduction .... nature of the female reproductive traits or to the large influence of unidentified environmental effects on ..... Factors affecting some performance traits in Friesian cattle.

The genetic basis of traits regulating sperm competition and polyandry: can selection favour the evolution of good- and sexy-sperm?

Science.gov (United States)

Evans, Jonathan P; Simmons, Leigh W

2008-09-01

The good-sperm and sexy-sperm (GS-SS) hypotheses predict that female multiple mating (polyandry) can fuel sexual selection for heritable male traits that promote success in sperm competition. A major prediction generated by these models, therefore, is that polyandry will benefit females indirectly via their sons' enhanced fertilization success. Furthermore, like classic 'good genes' and 'sexy son' models for the evolution of female preferences, GS-SS processes predict a genetic correlation between genes for female mating frequency (analogous to the female preference) and those for traits influencing fertilization success (the sexually selected traits). We examine the premise for these predictions by exploring the genetic basis of traits thought to influence fertilization success and female mating frequency. We also highlight recent debates that stress the possible genetic constraints to evolution of traits influencing fertilization success via GS-SS processes, including sex-linked inheritance, nonadditive effects, interacting parental genotypes, and trade-offs between integrated ejaculate components. Despite these possible constraints, the available data suggest that male traits involved in sperm competition typically exhibit substantial additive genetic variance and rapid evolutionary responses to selection. Nevertheless, the limited data on the genetic variation in female mating frequency implicate strong genetic maternal effects, including X-linkage, which is inconsistent with GS-SS processes. Although the relative paucity of studies on the genetic basis of polyandry does not allow us to draw firm conclusions about the evolutionary origins of this trait, the emerging pattern of sex linkage in genes for polyandry is more consistent with an evolutionary history of antagonistic selection over mating frequency. We advocate further development of GS-SS theory to take account of the complex evolutionary dynamics imposed by sexual conflict over mating frequency.

Genetic analysis of relative traits for a drought-sensitive mutant

International Nuclear Information System (INIS)

Gao Kangning; Wang Huaqi

2009-01-01

A drought-sensitive mutant (M616), selected from Handao 616 (HD616) by 60 Co γ-irradiation at 200Gy, was used. Some morphological and yield related traits of M166 and HD616 related to drought resistance were investigated. We further developed F 1 and F 2 reciprocal hybrid combinations derived from the crosses between M616 and HD616, between M616 and IRAT109, respectively, and genetic analysis of 3 traits including plant height, culm width of main stem and seed setting rate on main panicle were camed out. The results showed that M616 showed obviously sensitive to drought stress. Analysis of variance for three traits in upland and paddy between F 1 reciprocal hybrid combinations showed that each trait had no significant difference, and indicated that there were no differences of cytoplasmic hereditary effect. In addition, 3 traits of F 2 populations, were found that the frequency distributions of culm width showed normal distribution, indicating that culm width was polygenic trait, and the frequency distribution of plant height and seed setting rate did not show normal distribution, indicating that the two traits were qualitative-quantitative traits. Genetic analysis of relative traits for a drought-sensitive mutant of upland rice was a basic work for the gene location and cloning. (authors)

The genetic architecture of growth and fillet traits in farmed Atlantic salmon (Salmo salar).

Science.gov (United States)

Tsai, Hsin Yuan; Hamilton, Alastair; Guy, Derrick R; Tinch, Alan E; Bishop, Stephen C; Houston, Ross D

2015-05-19

Performance and quality traits such as harvest weight, fillet weight and flesh color are of economic importance to the Atlantic salmon aquaculture industry. The genetic factors underlying these traits are of scientific and commercial interest. However, such traits are typically polygenic in nature, with the number and size of QTL likely to vary between studies and populations. The aim of this study was to investigate the genetic basis of several growth and fillet traits measured at harvest in a large farmed salmon population by using SNP markers. Due to the marked heterochiasmy in salmonids, an efficient two-stage mapping approach was applied whereby QTL were detected using a sire-based linkage analysis, a sparse SNP marker map and exploiting low rates of recombination, while a subsequent dam-based analysis focused on the significant chromosomes with a denser map to confirm QTL and estimate their position. The harvest traits all showed significant heritability, ranging from 0.05 for fillet yield up to 0.53 for the weight traits. In the sire-based analysis, 1695 offspring with trait records and their 20 sires were successfully genotyped for the SNPs on the sparse map. Chromosomes 13, 18, 19 and 20 were shown to harbor genome-wide significant QTL affecting several growth-related traits. The QTL on chr. 13, 18 and 20 were detected in the dam-based analysis using 512 offspring from 10 dams and explained approximately 6-7 % of the within-family variation in these traits. We have detected several QTL affecting economically important complex traits in a commercial salmon population. Overall, the results suggest that the traits are relatively polygenic and that QTL tend to be pleiotropic (affecting the weight of several components of the harvested fish). Comparison of QTL regions across studies suggests that harvest trait QTL tend to be relatively population-specific. Therefore, the application of marker or genomic selection for improvement in these traits is likely to be

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

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Huang Yung-Fen

2012-02-01

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

Innate and adaptive immune traits are differentially affected by genetic and environmental factors

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Mangino, Massimo; Roederer, Mario; Beddall, Margaret H.; Nestle, Frank O.; Spector, Tim D.

2017-01-01

The diversity and activity of leukocytes is controlled by genetic and environmental influences to maintain balanced immune responses. However, the relative contribution of environmental compared with genetic factors that affect variations in immune traits is unknown. Here we analyse 23,394 immune phenotypes in 497 adult female twins. 76% of these traits show a predominantly heritable influence, whereas 24% are mostly influenced by environment. These data highlight the importance of shared childhood environmental influences such as diet, infections or microbes in shaping immune homeostasis for monocytes, B1 cells, γδ T cells and NKT cells, whereas dendritic cells, B2 cells, CD4+ T and CD8+ T cells are more influenced by genetics. Although leukocyte subsets are influenced by genetics and environment, adaptive immune traits are more affected by genetics, whereas innate immune traits are more affected by environment. PMID:28054551

Genetic diversity and population structure of Pisum sativum accessions for marker-trait association of lipid content

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Sajjad Ahmad

2015-06-01

Full Text Available Field pea (Pisum sativum L. is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germplasm is important and a prerequisite for genetic dissection of complex characteristics and marker-trait associations. Fifty polymorphic microsatellite markers detecting a total of 207 alleles were used to obtain information on genetic diversity, population structure and marker-trait associations. Cluster analysis was performed using UPGMA to construct a dendrogram from a pairwise similarity matrix. Pea genotypes were divided into five major clusters. A model-based population structure analysis divided the pea accessions into four groups. Percentage lipid content in 35 diverse pea accessions was used to find potential associations with the SSR markers. Markers AD73, D21, and AA5 were significantly associated with lipid content using a mixed linear model (MLM taking population structure (Q and relative kinship (K into account. The results of this preliminary study suggested that the population could be used for marker-trait association mapping studies.

Genetic parameters and genetic and phenotypic trends of performance traits of equines from the Brazilian Army

OpenAIRE

Dornelles, Mariana de Almeida; Araújo, Ronyere Olegário de; Everling, Dionéia Magda; Weber, Tomás; Lopes, Jader Silva; Pacheco, Paulo Santana; Breda, Fernanda Cristina; Rorato, Paulo Roberto Nogara

2012-01-01

The objective of this research was to compare the magnitude of genetic parameters (coefficients of heritability and genetic correlation) as estimated by the Restricted Maximum Likelihood (REML) method and Bayesian Inference, and to estimate the genetic and phenotypic trends to the traits height at the withers (HW24) and weight at 24 months of age (W24). The average heritability estimated by Bayesian Inference to HW24 was 0.47, and it was lower than that obtained by REML bi-trait analysis (0.5...

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

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Jaeyong Yee

2015-01-01

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

Genetic divergence among interspecific Paspalum hybrids based on seed production traits

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Rodrigo Ramos Lopes

Full Text Available ABSTRACT The use of genetic divergence as a basis for identifying superior individuals, with greater heterozygosity, is important in view of the difficulty when selecting of dissimilar genotypes exhibiting high average for interest traits. The aim of this study was to evaluate the genetic divergence and the expression of seed production traits in seventeen apomictic Paspalum plicatulum × Paspalum guenoarum hybrids and two male parents (P. guenoarum. A randomized block design was used, with genotypes individually arranged into ten blocks. The following traits were assessed: total number of tillers/plant (TT, reproductive tiller/plant (RT, number of racemes per inflorescence (NRI, reproductive tiller height (RTH, inflorescence rachis length (IRL, number of seeds/inflorescence (NSI, weight of a thousand seeds (WTS and seed production (SP. Genetic divergence among the genotypes was estimated using the Tocher method and UPGMA clustering, based on the generalized Mahalanobis distance (D2 ii’. The Tocher and UPGMA optimization methods showed high concordance. The traits that most contributed to genetic divergence were RTH (23.59%, IRL (21.63%, WTS (16.67% and SP (14.23%. The presence of genetic diversity made it possible to identify divergent genotypes and those with high means for the traits studied, allowing the selection of genotypes with significant breeding potential. Repeated cross-breeding of female superior plants with the genotypes Azulão and H20 can result in a high heterosis effect on seed production characteristics.

Genetic parameters for lactose and its correlation with other milk production traits and fitness traits in pasture-based production systems.

Science.gov (United States)

Haile-Mariam, M; Pryce, J E

2017-05-01

Lactose is a major component of milk (typically around 5% of composition) that is not usually directly considered in national genetic improvement programs of dairy cattle. Daily test-day lactose yields and percentage data from pasture-based seasonal calving herds in Australia were analyzed to assess if lactose content can be used for predicting fitness traits and if an additional benefit is achieved by including lactose yield in selecting for milk yield traits. Data on lactose percentage collected from 2007 to 2014, from about 600 herds, were used to estimated genetic parameters for lactose percentage and lactose yield and correlations with other milk yield traits, somatic cell count (SCC), calving interval (CIV), and survival. Daily test-day data were analyzed using bivariate random regression models. In addition, multi-trait models were also performed mainly to assess the value of lactose to predict fitness traits. The heritability of lactose percentage (0.25 to 0.37) was higher than lactose yield (0.11 to 0.20) in the first parity. Genetically, the correlation of lactose percentage with protein percentage varied from 0.3 at the beginning of lactation to -0.24 at the end of the lactation in the first parity. Similar patterns in genetic correlations were also observed in the second and third parity. At all levels (i.e., genetic, permanent environmental, and residual), the correlation between milk yield and lactose yield was close to 1. The genetic and permanent environmental correlations between lactose percentage and SCC were stronger in the second and third parity and toward the end of the lactation (-0.35 to -0.50) when SCC levels are at their maximum. The genetic correlation between lactose percentage in the first 120 d and CIV (-0.23) was similar to correlation of CIV with protein percentage (-0.28), another component trait with the potential to predict fertility. Furthermore, the correlations of estimated breeding values of lactose percentage and estimated

Resolving the Complex Genetic Basis of Phenotypic Variation and Variability of Cellular Growth.

Science.gov (United States)

Ziv, Naomi; Shuster, Bentley M; Siegal, Mark L; Gresham, David

2017-07-01

In all organisms, the majority of traits vary continuously between individuals. Explaining the genetic basis of quantitative trait variation requires comprehensively accounting for genetic and nongenetic factors as well as their interactions. The growth of microbial cells can be characterized by a lag duration, an exponential growth phase, and a stationary phase. Parameters that characterize these growth phases can vary among genotypes (phenotypic variation), environmental conditions (phenotypic plasticity), and among isogenic cells in a given environment (phenotypic variability). We used a high-throughput microscopy assay to map genetic loci determining variation in lag duration and exponential growth rate in growth rate-limiting and nonlimiting glucose concentrations, using segregants from a cross of two natural isolates of the budding yeast, Saccharomyces cerevisiae We find that some quantitative trait loci (QTL) are common between traits and environments whereas some are unique, exhibiting gene-by-environment interactions. Furthermore, whereas variation in the central tendency of growth rate or lag duration is explained by many additive loci, differences in phenotypic variability are primarily the result of genetic interactions. We used bulk segregant mapping to increase QTL resolution by performing whole-genome sequencing of complex mixtures of an advanced intercross mapping population grown in selective conditions using glucose-limited chemostats. We find that sequence variation in the high-affinity glucose transporter HXT7 contributes to variation in growth rate and lag duration. Allele replacements of the entire locus, as well as of a single polymorphic amino acid, reveal that the effect of variation in HXT7 depends on genetic, and allelic, background. Amplifications of HXT7 are frequently selected in experimental evolution in glucose-limited environments, but we find that HXT7 amplifications result in antagonistic pleiotropy that is absent in naturally

Dominance genetic and maternal effects for genetic evaluation of egg production traits in dual-purpose chickens.

Science.gov (United States)

Jasouri, M; Zamani, P; Alijani, S

2017-10-01

1. A study was conducted to study direct dominance genetic and maternal effects on genetic evaluation of production traits in dual-purpose chickens. The data set consisted of records of body weight and egg production of 49 749 Mazandaran fowls from 19 consecutive generations. Based on combinations of different random effects, including direct additive and dominance genetic and maternal additive genetic and environmental effects, 8 different models were compared. 2. Inclusion of a maternal genetic effect in the models noticeably improved goodness of fit for all traits. Direct dominance genetic effect did not have noticeable effects on goodness of fit but simultaneous inclusion of both direct dominance and maternal additive genetic effects improved fitting criteria and accuracies of genetic parameter estimates for hatching body weight and egg production traits. 3. Estimates of heritability (h 2 ) for body weights at hatch, 8 weeks and 12 weeks of age (BW0, BW8 and BW12, respectively), age at sexual maturity (ASM), average egg weights at 28-32 weeks of laying period (AEW), egg number (EN) and egg production intensity (EI) were 0.08, 0.21, 0.22, 0.22, 0.21, 0.09 and 0.10, respectively. For BW0, BW8, BW12, ASM, AEW, EN and EI, proportion of dominance genetic to total phenotypic variance (d 2 ) were 0.06, 0.08, 0.01, 0.06, 0.06, 0.08 and 0.07 and maternal heritability estimates (m 2 ) were 0.05, 0.04, 0.03, 0.13, 0.21, 0.07 and 0.03, respectively. Negligible coefficients of maternal environmental effect (c 2 ) from 0.01 to 0.08 were estimated for all traits, other than BW0, which had an estimate of 0.30. 4. Breeding values (BVs) estimated for body weights at early ages (BW0 and BW8) were considerably affected by components of the models, but almost similar BVs were estimated by different models for higher age body weight (BW12) and egg production traits (ASM, AEW, EN and EI). Generally, it could be concluded that inclusion of maternal effects (both genetic and

Genetic basis of haloperidol resistance in Saccharomyces cerevisiae is complex and dose dependent.

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Xin Wang

2014-12-01

Full Text Available The genetic basis of most heritable traits is complex. Inhibitory compounds and their effects in model organisms have been used in many studies to gain insights into the genetic architecture underlying quantitative traits. However, the differential effect of compound concentration has not been studied in detail. In this study, we used a large segregant panel from a cross between two genetically divergent yeast strains, BY4724 (a laboratory strain and RM11_1a (a vineyard strain, to study the genetic basis of variation in response to different doses of a drug. Linkage analysis revealed that the genetic architecture of resistance to the small-molecule therapeutic drug haloperidol is highly dose-dependent. Some of the loci identified had effects only at low doses of haloperidol, while other loci had effects primarily at higher concentrations of the drug. We show that a major QTL affecting resistance across all concentrations of haloperidol is caused by polymorphisms in SWH1, a homologue of human oxysterol binding protein. We identify a complex set of interactions among the alleles of the genes SWH1, MKT1, and IRA2 that are most pronounced at a haloperidol dose of 200 µM and are only observed when the remainder of the genome is of the RM background. Our results provide further insight into the genetic basis of drug resistance.

Genetic Basis of Haloperidol Resistance in Saccharomyces cerevisiae Is Complex and Dose Dependent

Science.gov (United States)

Wang, Xin; Kruglyak, Leonid

2014-01-01

The genetic basis of most heritable traits is complex. Inhibitory compounds and their effects in model organisms have been used in many studies to gain insights into the genetic architecture underlying quantitative traits. However, the differential effect of compound concentration has not been studied in detail. In this study, we used a large segregant panel from a cross between two genetically divergent yeast strains, BY4724 (a laboratory strain) and RM11_1a (a vineyard strain), to study the genetic basis of variation in response to different doses of a drug. Linkage analysis revealed that the genetic architecture of resistance to the small-molecule therapeutic drug haloperidol is highly dose-dependent. Some of the loci identified had effects only at low doses of haloperidol, while other loci had effects primarily at higher concentrations of the drug. We show that a major QTL affecting resistance across all concentrations of haloperidol is caused by polymorphisms in SWH1, a homologue of human oxysterol binding protein. We identify a complex set of interactions among the alleles of the genes SWH1, MKT1, and IRA2 that are most pronounced at a haloperidol dose of 200 µM and are only observed when the remainder of the genome is of the RM background. Our results provide further insight into the genetic basis of drug resistance. PMID:25521586

Genetic Factors Affecting Performance Traits of Sahiwal Cattle in Pakistan

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Z. Rehman*§ and M. S. Khan1

2012-06-01

Full Text Available Data on 23925 lactations of 5897 Sahiwal cows in five Government herds of Punjab province were collected to estimate the genetic control and genetic correlations among performance traits. A repeatability animal model having herd-year-season and parity was used for this purpose. The repeatability estimates for 305-d milk yield, total milk yield, lactation length, dry period, calving interval and service period were 0.40±0.015, 0.40±0.016, 0.33±0.013, 0.14±0.005, 0.15±0.004, and 0.14±0.005 respectively. The heritability estimates for these traits were 0.10±0.016, 0.09±0.016, 0.06±0.013, 0.14±0.009, 0.15±0.010, and 0.14±0.010, respectively. The phenotypic, genetic and environmental correlation of 305-d milk yield with lactation length was 0.71, 0.48 and 0.70, respectively, with dry period was -0.31, -0.43 and -0.22, respectively while with calving interval and service period exhibited similar pattern (0.08, 0.25 and 0.08, respectively. The estimated breeding values ranged from -447 to 1254 kg, -442 to 1265 kg, -24 to 38, -78 to 116, -84 to 107 and -81 to 91, days for 305-day milk yield, total milk yield, lactation length, dry period, calving interval and service period, respectively. No specific genetic trend was observed for performance traits during the period under study. Cows have not improved in their ability to perform in various economic traits. Accurate recording of pedigree and performance is necessary for improving the performance traits of Sahiwal. Due to high repeatability estimates of yield traits selection or culling may be practised from first few records.

Genetic analysis for grain quality traits in pakistani wheat varieties

International Nuclear Information System (INIS)

Minhas, N.M.; Ajmal, S.U.; Iqbal, Z.; Munir, M.

2014-01-01

A set of eight parental diallel involving seven commercial wheat cultivars and one breeding line was made to investigate the nature of gene action determining inheritance pattern of grain quality characters. Highly significant differences were observed among the genotypes for 1000 grain weight, protein content, wet gluten and lysine content. Adequacy tests were employed to estimate the fitness of data sets to additive dominance model. Both the tests i.e. analysis of uniformity of Wr, Vr and joint regression analysis validated the data of these traits for genetic analysis. Gene actions for grain quality traits were ascertained following Hayman's analysis of variance. Results of the genetic analysis revealed that both additive and dominance genetic components were involved in the manifestation of characters under study. However, additive gene effects were more pronounced in the genetic control of these traits. Non significance of b1, b2 and b3 values revealed the absence of directional dominance, symmetrical distribution of genes among the parental lines and absence of specific genes action respectively in all the traits. Maternal effects were also noted in 1000 grain weight, protein content and wet gluten percentage. It is concluded that additive effects are crucial in the expression of grain quality characters of wheat in germplasm under study and single plant selection may be recommended in segregating generations for effective improvement in these characters. (author)

Phenotypic and genetic associations between the big five and trait emotional intelligence.

Science.gov (United States)

Vernon, Philip A; Villani, Vanessa C; Schermer, Julie Aitken; Petrides, K V

2008-10-01

This study reports the first behavioral genetic investigation of the extent to which genetic and/or environmental factors contribute to the relationship between the Big Five personality factors and trait emotional intelligence. 213 pairs of adult monozygotic twins and 103 pairs of same-sex dizygotic twins completed the NEO-PI-R and the Trait Emotional Intelligence Questionnaire (TEIQue). Replicating previous non-twin studies, many significant phenotypic correlations were found between the Big Five factors - especially Neuroticism, Extraversion, and Conscientiousness - and the facets, factors, and global scores derived from the TEIQue. Bivariate behavioral genetic model-fitting analyses revealed that these phenotypic correlations were primarily attributable to correlated genetic factors and secondarily to correlated non-shared environmental factors. The results support the feasibility of incorporating EI as a trait within existing personality taxonomies.

Alternative Somatic Cell Count Traits as Mastitis Indicators for Genetic Selection

NARCIS (Netherlands)

Haas, de Y.; Ouweltjes, W.; Napel, ten J.; Windig, J.J.; Jong, de G.

2008-01-01

The aim of this study was to define alternative traits of somatic cell count (SCC) that can be used to decrease genetic susceptibility to clinical and subclinical mastitis (CM and SCM, respectively). Three kinds of SCC traits were evaluated: 1) lactation-averages of SCC, 2) traits derived from the

Personality disorder traits, family environment, and alcohol misuse: a multivariate behavioural genetic analysis.

Science.gov (United States)

Jang, K L; Vernon, P A; Livesley, W J

2000-06-01

This study seeks to estimate the extent to which a common genetic and environmental basis is shared between (i) traits delineating specific aspects of antisocial personality and alcohol misuse, and (ii) childhood family environments, traits delineating broad domains of personality pathology and alcohol misuse. Postal survey data were collected from monozygotic and dizygotic twin pairs. Twin pairs were recruited from Vancouver, British Columbia and London, Ontario, Canada using newspaper advertisements, media stories and twin clubs. Data obtained from 324 monozygotic and 335 dizygotic twin pairs were used to estimate the extent to which traits delineating specific antisocial personality traits and alcohol misuse shared a common genetic and environmental aetiology. Data from 81 monozygotic and 74 dizygotic twin pairs were used to estimate the degree to which traits delineating personality pathology, childhood family environment and alcohol misuse shared a common aetiology. Current alcohol misuse and personality pathology were measured using scales contained in the self-report Dimensional Assessment of Personality Pathology. Perceptions of childhood family environment were measured using the self-report Family Environment Scale. Multivariate genetic analyses showed that a subset of traits delineating components of antisocial personality (i.e. grandiosity, attention-seeking, failure to adopt social norms, interpersonal violence and juvenile antisocial behaviours) are influenced by genetic factors in common to alcohol misuse. Genetically based perceptions of childhood family environment had little relationship with alcohol misuse. Heritable personality factors that influence the perception of childhood family environment play only a small role in the liability to alcohol misuse. Instead, liability to alcohol misuse is related to genetic factors common a specific subset of antisocial personality traits describing conduct problems, narcissistic and stimulus

Simultaneous discovery, estimation and prediction analysis of complex traits using a bayesian mixture model.

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Gerhard Moser

2015-04-01

Full Text Available Gene discovery, estimation of heritability captured by SNP arrays, inference on genetic architecture and prediction analyses of complex traits are usually performed using different statistical models and methods, leading to inefficiency and loss of power. Here we use a Bayesian mixture model that simultaneously allows variant discovery, estimation of genetic variance explained by all variants and prediction of unobserved phenotypes in new samples. We apply the method to simulated data of quantitative traits and Welcome Trust Case Control Consortium (WTCCC data on disease and show that it provides accurate estimates of SNP-based heritability, produces unbiased estimators of risk in new samples, and that it can estimate genetic architecture by partitioning variation across hundreds to thousands of SNPs. We estimated that, depending on the trait, 2,633 to 9,411 SNPs explain all of the SNP-based heritability in the WTCCC diseases. The majority of those SNPs (>96% had small effects, confirming a substantial polygenic component to common diseases. The proportion of the SNP-based variance explained by large effects (each SNP explaining 1% of the variance varied markedly between diseases, ranging from almost zero for bipolar disorder to 72% for type 1 diabetes. Prediction analyses demonstrate that for diseases with major loci, such as type 1 diabetes and rheumatoid arthritis, Bayesian methods outperform profile scoring or mixed model approaches.

Genetic parameters and trends of morphometric traits of GIFT tilapia under selection for weight gain

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Rafael Vilhena Reis Neto

2014-08-01

Full Text Available The main factor considered in breeding programs for fish is growth, which can be assessed in terms of a gain in either weight or body measurements. This study was undertaken to evaluate the morphometric traits of GIFT strain tilapia (Oreochromis sp. selected for weight gain. The data set used contained information on 6,650 animals. The genetic values of 8,590 animals in a relationship matrix of five generations were predicted. The following morphometric measurements were evaluated: standard length; body depth and body width. Body area and volume were also calculated. Bi-character analyses involving morphometric traits were used to estimate (covariance components. Heritability, larval and fingerling common environmental effects were estimated for each trait, together with the genetic and phenotypic correlations between traits. Bayesian procedures were utilised by Gibbs chains, and the convergence of the chains was tested using the Heidelberger and Welch method. Genetic trends were estimated by segmented regression of the fish breeding values of the generations considered in this study. Estimates of heritability (0.28 a 0.31 had moderate to high magnitudes for all traits. Genetic correlations between traits were all above 0.8, and the genetic gains were satisfactory from the third generation onwards. From the estimates of the genetic parameters and genetic gain the morphometric traits evaluated have good potential for selection.

Do gender and personality traits (BFI-10) influence attitude towards genetic research?

DEFF Research Database (Denmark)

Sudzina, Frantisek

2016-01-01

There is a continuing trend of making genetic research commercially available. It is not only 23andme that offers various types of genetic tests anymore. People do not need to rely on doctor's opinion, they can purchase genetic testing kits and test themselves. Unfortunately, not all available te...... tests are reliable; as the case of Theranos showed recently. The paper aims to investigate if there is any impact of gender and of personality traits on attitude towards genetic research. Big Five Inventory is used to measure personality traits....

Genetic diversity of Iranian rice germplasm based on morphological traits

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nade ali bagheri

2009-06-01

Full Text Available Study of genetic diversity of rice is very important for rice breeders. In this study 64 genotypes for 14 agronomic traits were evaluated. Phenotypic variation coefficients of some of traits were high which showed essential variation in this traits. Principal component analysis detected 6 components which explained 74.66 percent of the total variations. The first component was related to generative traits such as number of spiklet per panicle, number of full grain per panicle, date of 50% flowering and length of panicle. In the third component, the date of complete maturity with -0.730 has negative effects on yield. Correlation analysis of morphological traits indicated a negative and significant relationship between early maturity and plant height, which showed early maturity cultivars had higher plant type. Results of stepwise regression analysis for early maturity, indicated that three traits such as date of 50% flowering, number of full grain per panicle and plant height showed higher variation and explained 54.3 percent of total early maturity variations. All traits were classified into 2 groups, by cluster analysis and traits belonged to early maturity classified as a sub-group. Genotypes were classified into 4 groups by using method of Ward,s minimum variance and squared Euclidean distance. Native cultivars from the view point of early maturity and yield components had useful information for rice breeding. Key words: Genetic diversity, rice, morphological traits.

Assessing the evidence for shared genetic risks across psychiatric disorders and traits.

Science.gov (United States)

Martin, Joanna; Taylor, Mark J; Lichtenstein, Paul

2017-12-04

Genetic influences play a significant role in risk for psychiatric disorders, prompting numerous endeavors to further understand their underlying genetic architecture. In this paper, we summarize and review evidence from traditional twin studies and more recent genome-wide molecular genetic analyses regarding two important issues that have proven particularly informative for psychiatric genetic research. First, emerging results are beginning to suggest that genetic risk factors for some (but not all) clinically diagnosed psychiatric disorders or extreme manifestations of psychiatric traits in the population share genetic risks with quantitative variation in milder traits of the same disorder throughout the general population. Second, there is now evidence for substantial sharing of genetic risks across different psychiatric disorders. This extends to the level of characteristic traits throughout the population, with which some clinical disorders also share genetic risks. In this review, we summarize and evaluate the evidence for these two issues, for a range of psychiatric disorders. We then critically appraise putative interpretations regarding the potential meaning of genetic correlation across psychiatric phenotypes. We highlight several new methods and studies which are already using these insights into the genetic architecture of psychiatric disorders to gain additional understanding regarding the underlying biology of these disorders. We conclude by outlining opportunities for future research in this area.

The causes of variation in the presence of genetic covariance between sexual traits and preferences.

Science.gov (United States)

Fowler-Finn, Kasey D; Rodríguez, Rafael L

2016-05-01

Mating traits and mate preferences often show patterns of tight correspondence across populations and species. These patterns of apparent coevolution may result from a genetic association between traits and preferences (i.e. trait-preference genetic covariance). We review the literature on trait-preference covariance to determine its prevalence and potential biological relevance. Of the 43 studies we identified, a surprising 63% detected covariance. We test multiple hypotheses for factors that may influence the likelihood of detecting this covariance. The main predictor was the presence of genetic variation in mate preferences, which is one of the three main conditions required for the establishment of covariance. In fact, 89% of the nine studies where heritability of preference was high detected covariance. Variables pertaining to the experimental methods and type of traits involved in different studies did not greatly influence the detection of trait-preference covariance. Trait-preference genetic covariance appears to be widespread and therefore represents an important and currently underappreciated factor in the coevolution of traits and preferences. © 2015 Cambridge Philosophical Society.

A Genome-Wide mQTL Analysis in Human Adipose Tissue Identifies Genetic Variants Associated with DNA Methylation, Gene Expression and Metabolic Traits

DEFF Research Database (Denmark)

Volkov, Petr; Olsson, Anders H; Gillberg, Linn

2016-01-01

Little is known about the extent to which interactions between genetics and epigenetics may affect the risk of complex metabolic diseases and/or their intermediary phenotypes. We performed a genome-wide DNA methylation quantitative trait locus (mQTL) analysis in human adipose tissue of 119 men, w...... and epigenetic variation in both cis and trans positions influencing gene expression in adipose tissue and in vivo (dys)metabolic traits associated with the development of obesity and diabetes.......Little is known about the extent to which interactions between genetics and epigenetics may affect the risk of complex metabolic diseases and/or their intermediary phenotypes. We performed a genome-wide DNA methylation quantitative trait locus (mQTL) analysis in human adipose tissue of 119 men......, where 592,794 single nucleotide polymorphisms (SNPs) were related to DNA methylation of 477,891 CpG sites, covering 99% of RefSeq genes. SNPs in significant mQTLs were further related to gene expression in adipose tissue and obesity related traits. We found 101,911 SNP-CpG pairs (mQTLs) in cis and 5...

Genetic variability and heritability studies of some reproductive traits ...

African Journals Online (AJOL)

GRACE

2006-07-03

Jul 3, 2006 ... The success of most crop improvement programs largely depends upon the genetic variability and the heritability of desirable traits. The magnitude and type of genetic variability help the breeder to determine the selection criteria and breeding schemes to be used for improvement purposes. A screen.

Genomic prediction of complex human traits: relatedness, trait architecture and predictive meta-models

Science.gov (United States)

Spiliopoulou, Athina; Nagy, Reka; Bermingham, Mairead L.; Huffman, Jennifer E.; Hayward, Caroline; Vitart, Veronique; Rudan, Igor; Campbell, Harry; Wright, Alan F.; Wilson, James F.; Pong-Wong, Ricardo; Agakov, Felix; Navarro, Pau; Haley, Chris S.

2015-01-01

We explore the prediction of individuals' phenotypes for complex traits using genomic data. We compare several widely used prediction models, including Ridge Regression, LASSO and Elastic Nets estimated from cohort data, and polygenic risk scores constructed using published summary statistics from genome-wide association meta-analyses (GWAMA). We evaluate the interplay between relatedness, trait architecture and optimal marker density, by predicting height, body mass index (BMI) and high-density lipoprotein level (HDL) in two data cohorts, originating from Croatia and Scotland. We empirically demonstrate that dense models are better when all genetic effects are small (height and BMI) and target individuals are related to the training samples, while sparse models predict better in unrelated individuals and when some effects have moderate size (HDL). For HDL sparse models achieved good across-cohort prediction, performing similarly to the GWAMA risk score and to models trained within the same cohort, which indicates that, for predicting traits with moderately sized effects, large sample sizes and familial structure become less important, though still potentially useful. Finally, we propose a novel ensemble of whole-genome predictors with GWAMA risk scores and demonstrate that the resulting meta-model achieves higher prediction accuracy than either model on its own. We conclude that although current genomic predictors are not accurate enough for diagnostic purposes, performance can be improved without requiring access to large-scale individual-level data. Our methodologically simple meta-model is a means of performing predictive meta-analysis for optimizing genomic predictions and can be easily extended to incorporate multiple population-level summary statistics or other domain knowledge. PMID:25918167

Genetic analysis of growth traits in Iranian Makuie sheep breed

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Mohammad Farhadian

2012-01-01

Full Text Available The Makuie sheep is a fat-tailed sheep breed which can be found in the Azerbaijan province of Iran. In 1986, a Makuie sheep breeding station was established in the city of Maku in order to breed, protect and purify this breed. The genetic parameters for birth weight, weaning weight (3 months, 6-month, 9-month and yearling weight, and average daily gain from birth to weaning traits were estimated based on 25 years of data using DFREML software. Six different models were applied and a likelihood ratio test (LRT was used to select the appropriate model. Bivariate analysis was used to define the genetic correlation between studied traits. Based on the LRT, model II was selected as an appropriate model for all studied traits. Direct heritability estimates of birth, weaning, 6-month, 9-month and yearling weights and average daily gain from birth to weaning were 0.36, 0.41, 0.48, 0.42, 0.36 and 0.37, respectively. Estimates of direct genetic correlation between birth and weaning weights, birth and 6-month weights, birth and 9-month weights, as well as between birth and yearling weights were 0.57, 0.49, 0.46 and 0.32, respectively. The results suggest there is a substantial additive genetic variability for studied traits in the Makuie sheep breed population, and the direct additive effect and maternal permanent environment variance are the main source of phenotypic variance.

Genetic parameters and environmental effects on temperament score and reproductive traits of Nellore cattle.

Science.gov (United States)

Barrozo, D; Buzanskas, M E; Oliveira, J A; Munari, D P; Neves, H H R; Queiroz, S A

2012-01-01

Animal temperament is a trait of economic relevance and its use as a selection criterion requires the identification of environmental factors that influence this trait, as well as the estimation of its genetic variability and interrelationship with other traits. The objectives of this study were to evaluate the effect of the covariates dam age at calving (ADC), long yearling age (YA) and long yearling weight (YW) on temperament score (T) and to estimate genetic parameters for T, scrotal circumference (SC) at long YA and age at first calving (AFC) in Nellore cattle participating in a selection program. The traits were analyzed by the restricted maximum likelihood method under a multiple-trait animal model. For all traits, contemporary group was included as a fixed effect and additive genetic and residual as random effects. In addition to these effects, YA, YW and ADC were considered for analyzing T. In the case of SC and AFC, the effect of long YW was included as a covariate. Genetic parameters were estimated for and between traits. The three covariates significantly influenced T. The heritability estimates for T, SC and AFC were 0.18 ± 0.02, 0.53 ± 0.04 and 0.23 ± 0.08, respectively. The genetic correlations between T and SC, and T and AFC were -0.07 ± 0.17 and -0.06 ± 0.19, respectively. The genetic correlation estimated between SC and AFC was -0.57 ± 0.16. In conclusion, a response to selection for T, SC and AFC is expected and selection for T does not imply correlated responses with the other traits.

Accounting for genetic architecture improves sequence based genomic prediction for a Drosophila fitness trait.

Science.gov (United States)

Ober, Ulrike; Huang, Wen; Magwire, Michael; Schlather, Martin; Simianer, Henner; Mackay, Trudy F C

2015-01-01

The ability to predict quantitative trait phenotypes from molecular polymorphism data will revolutionize evolutionary biology, medicine and human biology, and animal and plant breeding. Efforts to map quantitative trait loci have yielded novel insights into the biology of quantitative traits, but the combination of individually significant quantitative trait loci typically has low predictive ability. Utilizing all segregating variants can give good predictive ability in plant and animal breeding populations, but gives little insight into trait biology. Here, we used the Drosophila Genetic Reference Panel to perform both a genome wide association analysis and genomic prediction for the fitness-related trait chill coma recovery time. We found substantial total genetic variation for chill coma recovery time, with a genetic architecture that differs between males and females, a small number of molecular variants with large main effects, and evidence for epistasis. Although the top additive variants explained 36% (17%) of the genetic variance among lines in females (males), the predictive ability using genomic best linear unbiased prediction and a relationship matrix using all common segregating variants was very low for females and zero for males. We hypothesized that the low predictive ability was due to the mismatch between the infinitesimal genetic architecture assumed by the genomic best linear unbiased prediction model and the true genetic architecture of chill coma recovery time. Indeed, we found that the predictive ability of the genomic best linear unbiased prediction model is markedly improved when we combine quantitative trait locus mapping with genomic prediction by only including the top variants associated with main and epistatic effects in the relationship matrix. This trait-associated prediction approach has the advantage that it yields biologically interpretable prediction models.

Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize.

Science.gov (United States)

Riedelsheimer, Christian; Lisec, Jan; Czedik-Eysenberg, Angelika; Sulpice, Ronan; Flis, Anna; Grieder, Christoph; Altmann, Thomas; Stitt, Mark; Willmitzer, Lothar; Melchinger, Albrecht E

2012-06-05

The diversity of metabolites found in plants is by far greater than in most other organisms. Metabolic profiling techniques, which measure many of these compounds simultaneously, enabled investigating the regulation of metabolic networks and proved to be useful for predicting important agronomic traits. However, little is known about the genetic basis of metabolites in crops such as maize. Here, a set of 289 diverse maize inbred lines was genotyped with 56,110 SNPs and assayed for 118 biochemical compounds in the leaves of young plants, as well as for agronomic traits of mature plants in field trials. Metabolite concentrations had on average a repeatability of 0.73 and showed a correlation pattern that largely reflected their functional grouping. Genome-wide association mapping with correction for population structure and cryptic relatedness identified for 26 distinct metabolites strong associations with SNPs, explaining up to 32.0% of the observed genetic variance. On nine chromosomes, we detected 15 distinct SNP-metabolite associations, each of which explained more then 15% of the genetic variance. For lignin precursors, including p-coumaric acid and caffeic acid, we found strong associations (P values to ) with a region on chromosome 9 harboring cinnamoyl-CoA reductase, a key enzyme in monolignol synthesis and a target for improving the quality of lignocellulosic biomass by genetic engineering approaches. Moreover, lignin precursors correlated significantly with lignin content, plant height, and dry matter yield, suggesting that metabolites represent promising connecting links for narrowing the genotype-phenotype gap of complex agronomic traits.

Genetic and environmental trends of early growth traits in the ...

African Journals Online (AJOL)

Data from the Elsenburg Dormer sheep stud were used to estimate genetic and environmental change in early growth traits from 1943 to 1990. .... The Elsenburg stud is not only the foundation Dormer stud, ... derivative-free algorithm. Genet.

Assessment of Genetic Parameters of Agronomic Traits in Bread Wheat using Generation Means Analysis under water-limited Conditions

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M Dorrani-Nejad

2017-10-01

Full Text Available Introduction Wheat is the oldest and most important cultivated crop in the world and has fundamental role in human food security. Drought is one of the most common environmental stresses that affect growth and development of plants. Most parts of Iran’s cultivation land are located in arid and semiarid regions and because of water deficiency, plant stress appear and wheat performance reduces severely in these regions. In such circumstances, the production of drought tolerant varieties has special importance. Understand the genetic basis of yield and yield related traits is necessary in breeding programs. One of the best approaches to determine genetic parameters is generation means analysis method, due to it allows breeders to predict epistasis. In order to estimate genetic parameters and evaluation of gene action controlling agronomic traits in bread wheat under moisture stress, F4 families derived from cross between Roushan and Kavir along with F2, F3 and parents, were evaluated under moisture stress. Materials and Methods Field experiment was carried out in research field of Shahid Bahonar University of Kerman, during growing season of year 2013-2014 using Augmented design with 5 known check cultivars (Roushan, Falat, Mahdavi, Karchia and Shahpasand. Stress treatment was cut off irrigation at heading stage. Grain yield and some agronomic traits were measured. Generation means analysis method was used to determine genetic parameters including additive effect (d, dominance effect (h, additive × additive [i], and dominance × dominance effect [l] were evaluated for different traits. Generation means analysis was carried out using equation 1. Y= m+α[d]+β[h]+α2[i]+2αβ[j]+β2[l] (1 Broad and narrow sense heritability of evaluated traits were estimated according to equation 2 and 3. Results and Discussion The study revealed a complex genetic control for studied traits. Genetic variation in F2, F3 and F4 was more than parents. Five

Estimation of Genetic Parameters of Kleiber Ratio and Growth Traits in Kurdish Sheep

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Davoud Ali Saghi

2016-11-01

Full Text Available Introduction Kurdish sheep breed is one of the most important native breeds of Iran. They are fat-tailed, large-sized, well adapted to the mountainous regions in northern Khorasan province and mainly raising for meat production under pastoral production system (28. Feed efficiency is a major component in the profitability of the small ruminant enterprise, because quality of range and pasture is low in poor environmental conditions in Iran. Growth rate and feed efficiency are two traits of great economic importance in sheep production and also Kleiber ratio has been suggested to be a useful indicator for these traits (2. There was no information regarding genetic parameters for growth traits in Kurdish sheep. Thus, the main objective of the present research was to estimate (covariance components and genetic parameters for pre- and post-weaning growth traits and Kleiber ratio in Kurdish sheep. Material and Methods In this study, the records of growth traits from 5144 lambs (from 161 rams and 1982 ewes were used. The data were collected during a 17-year period (1996–2013 in Kurdish sheep Breeding Station located in Shirvan city of northern Khorasan province. Traits investigated were average daily gain from birth to weaning (ADG0-3, average daily gain from weaning to six months of age (ADG3-6, average daily gain from six to nine months of age (ADG6-9, average daily gain from nine to twelve months of age (ADG9-12 and Kleiber ratios (KR defined as: KR1=ADG0-3/(BW30.75 KR2=ADG3-6/(BW60.75 KR3=ADG6-9/(BW90.75 KR4=ADG9-12/(BW120.75 Test of significance for the fixed effects to be included in the final functional model for each trait and calculation of least squares means was accomplished using GLM procedure of SAS software (24. The considered fixed effects were year of lambing (1996-2013, sex of lamb (male and female, type of birth (single and twin and age of ewe (1–7 years old. (Co variance components and genetic parameters were estimated applying

Genetic parameters for uniformity of harvest weight and body size traits in the GIFT strain of Nile tilapia.

Science.gov (United States)

Marjanovic, Jovana; Mulder, Han A; Khaw, Hooi L; Bijma, Piter

2016-06-10

Animal breeding programs have been very successful in improving the mean levels of traits through selection. However, in recent decades, reducing the variability of trait levels between individuals has become a highly desirable objective. Reaching this objective through genetic selection requires that there is genetic variation in the variability of trait levels, a phenomenon known as genetic heterogeneity of environmental (residual) variance. The aim of our study was to investigate the potential for genetic improvement of uniformity of harvest weight and body size traits (length, depth, and width) in the genetically improved farmed tilapia (GIFT) strain. In order to quantify the genetic variation in uniformity of traits and estimate the genetic correlations between level and variance of the traits, double hierarchical generalized linear models were applied to individual trait values. Our results showed substantial genetic variation in uniformity of all analyzed traits, with genetic coefficients of variation for residual variance ranging from 39 to 58 %. Genetic correlation between trait level and variance was strongly positive for harvest weight (0.60 ± 0.09), moderate and positive for body depth (0.37 ± 0.13), but not significantly different from 0 for body length and width. Our results on the genetic variation in uniformity of harvest weight and body size traits show good prospects for the genetic improvement of uniformity in the GIFT strain. A high and positive genetic correlation was estimated between level and variance of harvest weight, which suggests that selection for heavier fish will also result in more variation in harvest weight. Simultaneous improvement of harvest weight and its uniformity will thus require index selection.

Genetic parameters of growth, body, and egg traits in Japanese quails

African Journals Online (AJOL)

SARAH

2014-07-31

Jul 31, 2014 ... egg traits as well as genetic and phenotypic relationships between these traits in Japanese quails reared in the ... Japanese quail is the smallest avian species farmed .... 2 = cross classified “family” variance component.

Genetic parameters of growth, body, and egg traits in Japanese ...

African Journals Online (AJOL)

Objective: This study on Japanese quails was undertaken to estimate heritability values for growth, body and egg traits as well as genetic and phenotypic relationships between these traits in Japanese quails reared in the Southern Guinea Savannah Zone of Nigeria. Methodology and Results: One hundred and sixty nine ...

Dissecting Genetic Network of Fruit Branch Traits in Upland Cotton by Association Mapping Using SSR Markers.

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Yongjun Mei

Full Text Available Genetic architecture of branch traits has large influences on the morphological structure, photosynthetic capacity, planting density, and yield of Upland cotton (Gossypium hirsutum L.. This research aims to reveal the genetic effects of six branch traits, including bottom fruit branch node number (BFBNN, bottom fruit branch length (BFBL, middle fruit branch node number (MFBNN, middle fruit branch length (MFBL, upper fruit branch node number (UFBNN, and upper fruit branch length (UFBL. Association mapping was conducted for these traits of 39 lines and their 178 F1 hybrids in three environments. There were 20 highly significant Quantitative Trait SSRs (QTSs detected by mixed linear model approach analyzing a full genetic model with genetic effects of additive, dominance, epistasis and their environment interaction. The phenotypic variation explained by genetic effects ranged from 32.64 ~ 91.61%, suggesting these branch traits largely influenced by genetic factors.

The Hidden Complexity of Mendelian Traits across Natural Yeast Populations

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Jing Hou

2016-07-01

Full Text Available Mendelian traits are considered to be at the lower end of the complexity spectrum of heritable phenotypes. However, more than a century after the rediscovery of Mendel’s law, the global landscape of monogenic variants, as well as their effects and inheritance patterns within natural populations, is still not well understood. Using the yeast Saccharomyces cerevisiae, we performed a species-wide survey of Mendelian traits across a large population of isolates. We generated offspring from 41 unique parental pairs and analyzed 1,105 cross/trait combinations. We found that 8.9% of the cases were Mendelian. Further tracing of causal variants revealed background-specific expressivity and modified inheritances, gradually transitioning from Mendelian to complex traits in 30% of the cases. In fact, when taking into account the natural population diversity, the hidden complexity of traits could be substantial, confounding phenotypic predictability even for simple Mendelian traits.

Ecosensitivity and genetic polymorphism of somatic traits in the perinatal development of twins.

Science.gov (United States)

Waszak, Małgorzata; Cieślik, Krystyna; Skrzypczak-Zielińska, Marzena; Szalata, Marlena; Wielgus, Karolina; Kempiak, Joanna; Bręborowicz, Grzegorz; Słomski, Ryszard

2016-04-01

In view of criticism regarding the usefulness of heritability coefficients, the aim of this study was to analyze separately the information on genetic and environmental variability. Such an approach, based on the normalization of trait's variability for its value, is determined by the coefficients of genetic polymorphism (Pg) and ecosensitivity (De). The studied material included 1263 twin pairs of both sexes (among them 424 pairs of monozygotic twins and 839 pairs of dizygotic twins) born between the 22nd and 41st week of gestation. Variability of six somatic traits was analyzed. The zygosity of same-sex twins was determined based on the polymorphism of DNA from lymphocytes of the umbilical cord blood, obtained at birth. The coefficients of genetic polymorphism and ecosensitivity for analyzed traits of male and female twins born at various months of gestation were calculated. Our study revealed that a contribution of the genetic component predominated over that of the environmental component in determining the phenotypic variability of somatic traits of newborns from twin pregnancies. The genetically determined phenotypic variability in male twins was greater than in the females. The genetic polymorphism and ecosensitivity of somatic traits were relatively stable during the period of fetal ontogeny analyzed in this study. Only in the case of body weight, a slight increase in the genetic contribution of polygenes to the phenotypic variance could be observed with gestational age, along with a slight decrease in the influence of environmental factors. Copyright © 2015 Elsevier GmbH. All rights reserved.

The genetic basis of natural variation in oenological traits in Saccharomyces cerevisiae.

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Francisco Salinas

Full Text Available Saccharomyces cerevisiae is the main microorganism responsible for wine alcoholic fermentation. The oenological phenotypes resulting from fermentation, such as the production of acetic acid, glycerol, and residual sugar concentration are regulated by multiple genes and vary quantitatively between different strain backgrounds. With the aim of identifying the quantitative trait loci (QTLs that regulate oenological phenotypes, we performed linkage analysis using three crosses between highly diverged S. cerevisiae strains. Segregants from each cross were used as starter cultures for 20-day fermentations, in synthetic wine must, to simulate actual winemaking conditions. Linkage analysis on phenotypes of primary industrial importance resulted in the mapping of 18 QTLs. We tested 18 candidate genes, by reciprocal hemizygosity, for their contribution to the observed phenotypic variation, and validated five genes and the chromosome II right subtelomeric region. We observed that genes involved in mitochondrial metabolism, sugar transport, nitrogen metabolism, and the uncharacterized ORF YJR030W explained most of the phenotypic variation in oenological traits. Furthermore, we experimentally validated an exceptionally strong epistatic interaction resulting in high level of succinic acid between the Sake FLX1 allele and the Wine/European MDH2 allele. Overall, our work demonstrates the complex genetic basis underlying wine traits, including natural allelic variation, antagonistic linked QTLs and complex epistatic interactions between alleles from strains with different evolutionary histories.

Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

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Daniel Garrido-Sanz

Full Text Available The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as

Accounting for genetic architecture improves sequence based genomic prediction for a Drosophila fitness trait.

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Ulrike Ober

Full Text Available The ability to predict quantitative trait phenotypes from molecular polymorphism data will revolutionize evolutionary biology, medicine and human biology, and animal and plant breeding. Efforts to map quantitative trait loci have yielded novel insights into the biology of quantitative traits, but the combination of individually significant quantitative trait loci typically has low predictive ability. Utilizing all segregating variants can give good predictive ability in plant and animal breeding populations, but gives little insight into trait biology. Here, we used the Drosophila Genetic Reference Panel to perform both a genome wide association analysis and genomic prediction for the fitness-related trait chill coma recovery time. We found substantial total genetic variation for chill coma recovery time, with a genetic architecture that differs between males and females, a small number of molecular variants with large main effects, and evidence for epistasis. Although the top additive variants explained 36% (17% of the genetic variance among lines in females (males, the predictive ability using genomic best linear unbiased prediction and a relationship matrix using all common segregating variants was very low for females and zero for males. We hypothesized that the low predictive ability was due to the mismatch between the infinitesimal genetic architecture assumed by the genomic best linear unbiased prediction model and the true genetic architecture of chill coma recovery time. Indeed, we found that the predictive ability of the genomic best linear unbiased prediction model is markedly improved when we combine quantitative trait locus mapping with genomic prediction by only including the top variants associated with main and epistatic effects in the relationship matrix. This trait-associated prediction approach has the advantage that it yields biologically interpretable prediction models.

Analysis of genetic effects of nuclear-cytoplasmic interaction on quantitative traits: genetic model for diploid plants.

Science.gov (United States)

Han, Lide; Yang, Jian; Zhu, Jun

2007-06-01

A genetic model was proposed for simultaneously analyzing genetic effects of nuclear, cytoplasm, and nuclear-cytoplasmic interaction (NCI) as well as their genotype by environment (GE) interaction for quantitative traits of diploid plants. In the model, the NCI effects were further partitioned into additive and dominance nuclear-cytoplasmic interaction components. Mixed linear model approaches were used for statistical analysis. On the basis of diallel cross designs, Monte Carlo simulations showed that the genetic model was robust for estimating variance components under several situations without specific effects. Random genetic effects were predicted by an adjusted unbiased prediction (AUP) method. Data on four quantitative traits (boll number, lint percentage, fiber length, and micronaire) in Upland cotton (Gossypium hirsutum L.) were analyzed as a worked example to show the effectiveness of the model.

Pollution breaks down the genetic architecture of life history traits in Caenorhabditis elegans.

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Morgan Dutilleul

Full Text Available When pollution occurs in an environment, populations present suffer numerous negative and immediate effects on their life history traits. Their evolutionary potential to live in a highly stressful environment will depend on the selection pressure strengths and on the genetic structure, the trait heritability, and the genetic correlations between them. If expression of this structure changes in a stressful environment, it becomes necessary to quantify these changes to estimate the evolutionary potential of the population in this new environment. We studied the genetic structure for survival, fecundity, and early and late growth in isogenic lines of a Caenorhabditis elegans population subject to three different environments: a control environment, an environment polluted with uranium, and a high salt concentration environment. We found a heritability decrease in the polluted environments for fecundity and early growth, two traits that were the most heritable in the control environment. The genetic structure of the traits was particularly affected in the uranium polluted environment, probably due to generally low heritability in this environment. This could prevent selection from acting on traits despite the strong selection pressures exerted on them. Moreover, phenotypic traits were more strongly affected in the salt than in the uranium environment and the heritabilities were also lower in the latter environment. Consequently the decrease in heritability was not proportional to the population fitness reduction in the polluted environments. Our results suggest that pollution can alter the genetic structure of a C. elegans population, and thus modify its evolutionary potential.

Genetic correlations between ewe reproduction and carcass and meat quality traits in Merino sheep.

Science.gov (United States)

Safari, E; Fogarty, N M; Hopkins, D L; Greeff, J C; Brien, F D; Atkins, K D; Mortimer, S I; Taylor, P J; van der Werf, J H J

2008-12-01

Genetic correlations between reproduction traits in ewes and carcass and meat quality traits in Merino rams were obtained using restricted maximum likelihood procedures. The carcass data were from 5870 Merino rams slaughtered at approximately 18 months of age that were the progeny of 543 sires from three research resource flocks over 7 years. The carcass traits included ultrasound scan fat and eye muscle depth (EMDUS) measured on live animals, dressing percentage and carcass tissue depth (at the GR site FATGR and C site FATC), eye muscle depth, width and area and the meat quality indicator traits of muscle final pH and colour (L*, a*, b*). The reproduction data consisted of 13 464 ewe joining records for number of lambs born and weaned and 9015 records for LS. The genetic correlations between reproduction and fat measurements were negative (range -0.06 +/- 0.12 to -0.37 +/- 0.12), with smaller correlations for live measurement than carcass traits. There were small favourable genetic correlations between reproduction traits and muscle depth in live rams (EMDUS, 0.10 +/- 0.12 to 0.20 +/- 0.12), although those with carcass muscle traits were close to zero. The reproduction traits were independent of meat colour L* (relative brightness), but tended to be favourably correlated with meat colour a* (relative redness, 0.12 +/- 0.17 to 0.19 +/- 0.16). There was a tendency for meat final pH to have small negative favourable genetic correlations with reproduction traits (0.05 +/- 0.11 to -0.17 +/- 0.12). This study indicates that there is no antagonism between reproduction traits and carcass and meat quality indicator traits, with scope for joint improvement of reproduction, carcass and meat quality traits in Merino sheep.

Genetic parameters for ostrich incubation traits in South Africa ...

African Journals Online (AJOL)

Genetic parameters for ostrich incubation traits in South Africa. Z Brand, S Cloete, I Malecki, C Brown. Abstract. Data obtained from a pair-mated ostrich flock located at Oudtshoorn, South Africa, were used to estimate genetic parameters for egg weight (EWT), weight of day-old chicks (CWT), water loss to 21 (WL21) and 35 ...

Regression-based approach for testing the association between multi-region haplotype configuration and complex trait

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Zhao Hongbo

2009-09-01

Full Text Available Abstract Background It is quite common that the genetic architecture of complex traits involves many genes and their interactions. Therefore, dealing with multiple unlinked genomic regions simultaneously is desirable. Results In this paper we develop a regression-based approach to assess the interactions of haplotypes that belong to different unlinked regions, and we use score statistics to test the null hypothesis of non-genetic association. Additionally, multiple marker combinations at each unlinked region are considered. The multiple tests are settled via the minP approach. The P value of the "best" multi-region multi-marker configuration is corrected via Monte-Carlo simulations. Through simulation studies, we assess the performance of the proposed approach and demonstrate its validity and power in testing for haplotype interaction association. Conclusion Our simulations showed that, for binary trait without covariates, our proposed methods prove to be equal and even more powerful than htr and hapcc which are part of the FAMHAP program. Additionally, our model can be applied to a wider variety of traits and allow adjustment for other covariates. To test the validity, our methods are applied to analyze the association between four unlinked candidate genes and pig meat quality.

Efficient multiple-trait association and estimation of genetic correlation using the matrix-variate linear mixed model.

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Furlotte, Nicholas A; Eskin, Eleazar

2015-05-01

Multiple-trait association mapping, in which multiple traits are used simultaneously in the identification of genetic variants affecting those traits, has recently attracted interest. One class of approaches for this problem builds on classical variance component methodology, utilizing a multitrait version of a linear mixed model. These approaches both increase power and provide insights into the genetic architecture of multiple traits. In particular, it is possible to estimate the genetic correlation, which is a measure of the portion of the total correlation between traits that is due to additive genetic effects. Unfortunately, the practical utility of these methods is limited since they are computationally intractable for large sample sizes. In this article, we introduce a reformulation of the multiple-trait association mapping approach by defining the matrix-variate linear mixed model. Our approach reduces the computational time necessary to perform maximum-likelihood inference in a multiple-trait model by utilizing a data transformation. By utilizing a well-studied human cohort, we show that our approach provides more than a 10-fold speedup, making multiple-trait association feasible in a large population cohort on the genome-wide scale. We take advantage of the efficiency of our approach to analyze gene expression data. By decomposing gene coexpression into a genetic and environmental component, we show that our method provides fundamental insights into the nature of coexpressed genes. An implementation of this method is available at http://genetics.cs.ucla.edu/mvLMM. Copyright © 2015 by the Genetics Society of America.

Genetic covariance components within and among linear type traits differ among contrasting beef cattle breeds.

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Doyle, Jennifer L; Berry, Donagh P; Walsh, Siobhan W; Veerkamp, Roel F; Evans, Ross D; Carthy, Tara R

2018-05-04

Linear type traits describing the skeletal, muscular, and functional characteristics of an animal are routinely scored on live animals in both the dairy and beef cattle industries. Previous studies have demonstrated that genetic parameters for certain performance traits may differ between breeds; no study, however, has attempted to determine if differences exist in genetic parameters of linear type traits among breeds or sexes. Therefore, the objective of the present study was to determine if genetic covariance components for linear type traits differed among five contrasting cattle breeds, and to also investigate if these components differed by sex. A total of 18 linear type traits scored on 3,356 Angus (AA), 31,049 Charolais (CH), 3,004 Hereford (HE), 35,159 Limousin (LM), and 8,632 Simmental (SI) were used in the analysis. Data were analyzed using animal linear mixed models which included the fixed effects of sex of the animal (except in the investigation into the presence of sexual dimorphism), age at scoring, parity of the dam, and contemporary group of herd-date of scoring. Differences (P covariance parameters estimated from the CH breed with a linear function of breeding values computed conditional on covariance parameters estimated from the other breeds was estimated. Replacing the genetic covariance components estimated in the CH breed with those of the LM had least effect but the impact was considerable when the genetic covariance components of the AA were used. Genetic correlations between the same linear type traits in the two sexes were all close to unity (≥0.90) suggesting little advantage in considering these as separate traits for males and females. Results for the present study indicate the potential increase in accuracy of estimated breeding value prediction from considering, at least, the British breed traits separate to continental breed traits.

A high-density genetic map and QTL analysis of agronomic traits in foxtail millet [Setaria italica (L.) P. Beauv.] using RAD-seq.

Science.gov (United States)

Wang, Jun; Wang, Zhilan; Du, Xiaofen; Yang, Huiqing; Han, Fang; Han, Yuanhuai; Yuan, Feng; Zhang, Linyi; Peng, Shuzhong; Guo, Erhu

2017-01-01

Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits. In this study, a high-throughput and cost-effective RAD-seq approach was employed to generate a high-density genetic map for foxtail millet. A total of 2,668,587 SNP loci were detected according to the reference genome sequence; meanwhile, 9,968 SNP markers were used to genotype 124 F2 progenies derived from the cross between Hongmiaozhangu and Changnong35; a high-density genetic map spanning 1648.8 cM, with an average distance of 0.17 cM between adjacent markers was constructed; 11 major QTLs for eight agronomic traits were identified; five co-dominant DNA markers were developed. These findings will be of value for the identification of candidate genes and marker-assisted selection in foxtail millet.

The IgA nephropathy Biobank. An important starting point for the genetic dissection of a complex trait

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Alexopoulos Efstathios

2005-12-01

from the study of Mendelian diseases has shown that the genetic dissection of a complex trait is more powerful when combined linkage-based, association-based, and sequence-based approaches are performed. This Biobank continuously expanded contains a sample size of adequately matched IgAN patients and healthy subjects, extended multiplex pedigrees, parent-child trios, thus permitting the combined genetic approaches with collaborative studies.

Genetic and environmental influences on Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition (DSM-5) maladaptive personality traits and their connections with normative personality traits.

Science.gov (United States)

Wright, Zara E; Pahlen, Shandell; Krueger, Robert F

2017-05-01

The Diagnostic and Statistical Manual for Mental Disorders-Fifth Edition (DSM-5) proposes an alternative model for personality disorders, which includes maladaptive-level personality traits. These traits can be operationalized by the Personality Inventory for the DSM-5 (PID-5). Although there has been extensive research on genetic and environmental influences on normative level personality, the heritability of the DSM-5 traits remains understudied. The present study addresses this gap in the literature by assessing traits indexed by the PID-5 and the International Personality Item Pool NEO (IPIP-NEO) in adult twins (N = 1,812 individuals). Research aims include (a) replicating past findings of the heritability of normative level personality as measured by the IPIP-NEO as a benchmark for studying maladaptive level traits, (b) ascertaining univariate heritability estimates of maladaptive level traits as measured by the PID-5, (c) establishing how much variation in personality pathology can be attributed to the same genetic components affecting variation in normative level personality, and (d) determining residual variance in personality pathology domains after variance attributable to genetic and environmental components of general personality has been removed. Results revealed that PID-5 traits reflect similar levels of heritability to that of IPIP-NEO traits. Further, maladaptive and normative level traits that correlate at the phenotypic level also correlate at the genotypic level, indicating overlapping genetic components contribute to variance in both. Nevertheless, we also found evidence for genetic and environmental components unique to maladaptive level personality traits, not shared with normative level traits. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Genetic variation and trait correlations in a birdresistant pearl millet ...

African Journals Online (AJOL)

selection indices for effective improvement. There was significant genetic variation for grain yield and most yield component traits, indicating that selection within the population would be feasible. Genetic variation was, however not significant for the percent incidence of downy mildew, implying that selection for improving ...

Genetic parameters and correlations among linear type traits in the ...

African Journals Online (AJOL)

The main objective of this study was to estimate the genetic parameters and relationships of 10 linear type traits in the first lactation of Holstein dairy cows. 3274 records for type traits was used (Ag, angularity; Sta, stature; Bdp, body depth; Rw, rump width; Rs, rear leg side view; Fa, foot angle; Fu, fore udder attachment; Ruh, ...

Relationships between structural complexity, coral traits, and reef fish assemblages

Science.gov (United States)

Darling, Emily S.; Graham, Nicholas A. J.; Januchowski-Hartley, Fraser A.; Nash, Kirsty L.; Pratchett, Morgan S.; Wilson, Shaun K.

2017-06-01

With the ongoing loss of coral cover and the associated flattening of reef architecture, understanding the links between coral habitat and reef fishes is of critical importance. Here, we investigate whether considering coral traits and functional diversity provides new insights into the relationship between structural complexity and reef fish communities, and whether coral traits and community composition can predict structural complexity. Across 157 sites in Seychelles, Maldives, the Chagos Archipelago, and Australia's Great Barrier Reef, we find that structural complexity and reef zone are the strongest and most consistent predictors of reef fish abundance, biomass, species richness, and trophic structure. However, coral traits, diversity, and life histories provided additional predictive power for models of reef fish assemblages, and were key drivers of structural complexity. Our findings highlight that reef complexity relies on living corals—with different traits and life histories—continuing to build carbonate skeletons, and that these nuanced relationships between coral assemblages and habitat complexity can affect the structure of reef fish assemblages. Seascape-level estimates of structural complexity are rapid and cost effective with important implications for the structure and function of fish assemblages, and should be incorporated into monitoring programs.

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

Science.gov (United States)

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

2018-03-01

The establishment of inflorescence architecture is critical for the reproduction of flowering plant species. The maize plant generates two types of inflorescences, the tassel and the ear, and their architectures have a large effect on grain yield and yield-related traits that are genetically controlled by quantitative trait loci (QTLs). Since ear and tassel architecture are deeply affected by the activity of inflorescence meristems, key QTLs and genes regulating meristematic activity have important impacts on inflorescence development and show great potential for optimizing grain yield. Isolation of yield trait-related QTLs is challenging, but these QTLs have direct application in maize breeding. Additionally, characterization and functional dissection of QTLs can provide genetic and molecular knowledge of quantitative variation in inflorescence architecture. In this review, we summarize currently identified QTLs responsible for the establishment of ear and tassel architecture and discuss the potential genetic control of four ear-related and four tassel-related traits. In recent years, several inflorescence architecture-related QTLs have been characterized at the gene level. We review the mechanisms of these characterized QTLs.

On the Origin of Complex Adaptive Traits: Progress Since the Darwin Versus Mivart Debate.

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Suzuki, Takao K

2017-06-01

The evolutionary origin of complex adaptive traits has been a controversial topic in the history of evolutionary biology. Although Darwin argued for the gradual origins of complex adaptive traits within the theory of natural selection, Mivart insisted that natural selection could not account for the incipient stages of complex traits. The debate starting from Darwin and Mivart eventually engendered two opposite views: gradualism and saltationism. Although this has been a long-standing debate, the issue remains unresolved. However, recent studies have interrogated classic examples of complex traits, such as the asymmetrical eyes of flatfishes and leaf mimicry of butterfly wings, whose origins were debated by Darwin and Mivart. Here, I review recent findings as a starting point to provide a modern picture of the evolution of complex adaptive traits. First, I summarize the empirical evidence that unveils the evolutionary steps toward complex traits. I then argue that the evolution of complex traits could be understood within the concept of "reducible complexity." Through these discussions, I propose a conceptual framework for the formation of complex traits, named as reducible-composable multicomponent systems, that satisfy two major characteristics: reducibility into a sum of subcomponents and composability to construct traits from various additional and combinatorial arrangements of the subcomponents. This conceptual framework provides an analytical foundation for exploring evolutionary pathways to build up complex traits. This review provides certain essential avenues for deciphering the origin of complex adaptive traits. © 2017 Wiley Periodicals, Inc.

Genetic parameters of reproductive traits in pigs: a contribution

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G. Pagnacco

2011-03-01

Full Text Available Generally pig breeding efficiency is defined as the number of piglets weaned per sow per year, so in every pig breeding programmes, great emphasis is placed on improving reproductive traits in sow lines and generally, the evaluation of litter size is carried out in most selection planes. Usually, the reproduction breeding goal is to increase the number of piglets born, but this trait, as reported by Hanenberg et al. (2001 gives an undesirable correlation with the number of stillborn piglets. Litter size is the result of a large number of traits as number of total piglets born, number of born alive, stillbirth, weaned survival; as reported by Tummaruk et al. (2000 the variation in these parameters is influenced by genetic value of the sow and by environmental factors, such as management and season. Regarding the genetic influence on the litter size, we know that the breed can influence the number of born, but its interaction with stillbirth is not significant, although Leenhouwers et al. (1999 found an higher stillbirth incidence in purebred than in crossbred litters........

A Genetically Informed Cross-lagged Analysis of Autistic-Like Traits and Affective Problems in Early Childhood

Science.gov (United States)

Micalizzi, Lauren; Ronald, Angelica; Saudino, Kimberly J.

2015-01-01

A genetically informed cross-lagged model was applied to twin data to explore etiological links between autistic-like traits and affective problems in early childhood. The sample comprised 310 same-sex twin pairs (143 monozygotic and 167 dizygotic; 53% male). Autistic-like traits and affective problems were assessed at ages 2 and 3 using parent ratings. Both constructs were related within and across age (r = .30−.53) and showed moderate stability (r = .45−.54). Autistic-like traits and affective problems showed genetic and environmental influences at both ages. Whereas at age 2, the covariance between autistic-like traits and affective problems was entirely due to environmental influences (shared and nonshared), at age 3, genetic factors also contributed to the covariance between constructs. The stability paths, but not the cross-lagged paths, were significant, indicating that there is stability in both autistic-like traits and affective problems but they do not mutually influence each other across age. Stability effects were due to genetic, shared, and nonshared environmental influences. Substantial novel genetic and nonshared environmental influences emerge at age 3 and suggest change in the etiology of these constructs over time. During early childhood, autistic-like traits tend to occur alongside affective problems and partly overlapping genetic and environmental influences explain this association. PMID:26456961

Phenotypic and genetic relations between the HEXACO dimensions and trait emotional intelligence.

Science.gov (United States)

Veselka, Livia; Petrides, K V; Schermer, Julie Aitken; Cherkas, Lynn F; Spector, Tim D; Vernon, Philip A

2010-02-01

The present study investigated the location of trait emotional intelligence (trait EI or trait emotional self-efficacy) within the context of the HEXACO model - a more comprehensive personality framework than the conventional Big Five structure. A total of 666 MZ and 526 DZ adult twin pairs from the United Kingdom completed the short form of the Trait Emotional Intelligence Questionnaire (TEIQue-SF) and the short form of the HEXACO Personality Inventory (HEXACO-60). Many significant phenotypic correlations between the TEIQue-SF and the HEXACO-60 were obtained, which were strongest for HEXACO Extraversion, and weakest for HEXACO Honesty-Humility. As was expected, Emotionality was the only HEXACO dimension to correlate negatively with TEIQue-SF scores. Bivariate behavioral genetic analyses revealed that all phenotypic correlations were attributable to common genetic and common nonshared environmental factors. The study confirms the validity of trait EI as a constellation of emotional self-perceptions located at the lower levels of personality.

Genetic analysis of some agronomic traits in groundnut (Arachis hypogaea L.

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M.K. Alam

2013-12-01

Full Text Available A 10×10 half diallel experiment was conducted on groundnut (Arachis hypogaea L. to ascertain the gene action and genetic parameters of ten traits including 50% flowering, no. of pods per plant, plant height, harvest index, pod index, 100 pod weight, 100 kernel weight, pod size, diseases infection and yield per plot. The experiments were carried out in the Department of Genetics and Plant Breeding, Bangladesh Agricultural University (BAU, Mymensingh during the cropping season of 2010-2011. The estimates of gene effects indicated that significance of both additive and non-additive variance for pod size, 100 pod weight and diseases infection among the traits and presence of over dominance satisfying assumptions of diallel except dormancy. However, both the additive and non-additive gene affects together importance to control of most quantitative traits in the groundnut. The average degree of dominance (H1/D 1/2 (H1 = dominance variance, D = additive variance was higher than one, indicating over dominance for all the traits. The narrow-sense heritability was high for 50% flowering (38%, harvest index (35%, pod size (52%, 100 pod weight (35% and yield per plot (41% indicating that great genetic gain could be achieved for them.

Evidence for genetic variation in human mate preferences for sexually dimorphic physical traits.

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Karin J H Verweij

Full Text Available Intersexual selection has been proposed as an important force in shaping a number of morphological traits that differ between human populations and/or between the sexes. Important to these accounts is the source of mate preferences for such traits, but this has not been investigated. In a large sample of twins, we assess forced-choice, dichotomous mate preferences for height, skin colour, hair colour and length, chest hair, facial hair, and breast size. Across the traits, identical twins reported more similar preferences than nonidentical twins, suggesting genetic effects. However, the relative magnitude of estimated genetic and environmental effects differed greatly and significantly between different trait preferences, with heritability estimates ranging from zero to 57%.

Complex Genotype by Environment interactions and changing genetic architectures across thermal environments in the Australian field cricket, Teleogryllus oceanicus

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Dowling Damian K

2011-07-01

Full Text Available Abstract Background Biologists studying adaptation under sexual selection have spent considerable effort assessing the relative importance of two groups of models, which hinge on the idea that females gain indirect benefits via mate discrimination. These are the good genes and genetic compatibility models. Quantitative genetic studies have advanced our understanding of these models by enabling assessment of whether the genetic architectures underlying focal phenotypes are congruent with either model. In this context, good genes models require underlying additive genetic variance, while compatibility models require non-additive variance. Currently, we know very little about how the expression of genotypes comprised of distinct parental haplotypes, or how levels and types of genetic variance underlying key phenotypes, change across environments. Such knowledge is important, however, because genotype-environment interactions can have major implications on the potential for evolutionary responses to selection. Results We used a full diallel breeding design to screen for complex genotype-environment interactions, and genetic architectures underlying key morphological traits, across two thermal environments (the lab standard 27°C, and the cooler 23°C in the Australian field cricket, Teleogryllus oceanicus. In males, complex three-way interactions between sire and dam parental haplotypes and the rearing environment accounted for up to 23 per cent of the scaled phenotypic variance in the traits we measured (body mass, pronotum width and testes mass, and each trait harboured significant additive genetic variance in the standard temperature (27°C only. In females, these three-way interactions were less important, with interactions between the paternal haplotype and rearing environment accounting for about ten per cent of the phenotypic variance (in body mass, pronotum width and ovary mass. Of the female traits measured, only ovary mass for crickets

The Genetic and Environmental Sources of Resemblance Between Normative Personality and Personality Disorder Traits.

Science.gov (United States)

Kendler, K S; Aggen, S H; Gillespie, Nathan; Neale, M C; Knudsen, G P; Krueger, R F; Czajkowski, Nikolai; Ystrom, Eivind; Reichborn-Kjennerud, T

2017-04-01

Recent work has suggested a high level of congruence between normative personality, most typically represented by the "big five" factors, and abnormal personality traits. In 2,293 Norwegian adult twins ascertained from a population-based registry, the authors evaluated the degree of sharing of genetic and environmental influences on normative personality, assessed by the Big Five Inventory (BFI), and personality disorder traits (PDTs), assessed by the Personality Inventory for DSM-5-Norwegian Brief Form (PID-5-NBF). For four of the five BFI dimensions, the strongest genetic correlation was observed with the expected PID-5-NBF dimension (e.g., neuroticism with negative affectivity [+], conscientiousness with disinhibition [-]). However, neuroticism, conscientiousness, and agreeableness had substantial genetic correlations with other PID-5-NBF dimensions (e.g., neuroticism with compulsivity [+], agreeableness with detachment [-]). Openness had no substantial genetic correlations with any PID-5-NBF dimension. The proportion of genetic risk factors shared in aggregate between the BFI traits and the PID-5-NBF dimensions was quite high for conscientiousness and neuroticism, relatively robust for extraversion and agreeableness, but quite low for openness. Of the six PID-5-NBF dimensions, three (negative affectivity, detachment, and disinhibition) shared, in aggregate, most of their genetic risk factors with normative personality traits. Genetic factors underlying psychoticism, antagonism, and compulsivity were shared to a lesser extent, suggesting that they are influenced by etiological factors not well indexed by the BFI.

Genetics of residual feed intake in growing pigs: Relationships with production traits, and nitrogen and phosphorus excretion traits.

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Saintilan, R; Mérour, I; Brossard, L; Tribout, T; Dourmad, J Y; Sellier, P; Bidanel, J; van Milgen, J; Gilbert, H

2013-06-01

Residual feed intake (RFI) is defined as the difference between the observed ADFI and the ADFI predicted from production and maintenance requirements. The objectives of this study were to evaluate RFI as a selection criterion to improve feed efficiency and its potential to reduce N and P excretion in 4 pig breeds. Data were collected between 2000 and 2009 in French central test stations for 2 dam breeds [French Landrace (LR) and Large White (LWD)], and 2 sire breeds [Large White (LWS) and Piétrain (PP)]. Numbers of recorded pigs were 6407, 10,694, 2342, and 2448 for the LR, LWD, LWS, and PP breeds, respectively. All PP animals were genotyped for the halothane mutation. This data set was used to calculate RFI equations for each of the 4 breeds, and to estimate genetic parameters for RFI together with growth, carcass, and meat quality traits, and N and P excretion during the test period (35 to 110 kg BW). The RFI explained 20.1% in PP, 26.5% in LWS, 27.6% in LWD, and 29.5% in LR of the phenotypic variability of ADFI. The PP breed differed from the others in this respect, probably due to a lower impact of the variation of body composition on ADFI. Heritability estimates of RFI ranged from 0.21 ± 0.03 (LWD) to 0.33 ± 0.06 (PP) depending on the breed. Heritabilities of N and P excretion traits ranged from 0.29 ± 0.06 to 0.40 ± 0.06. The RFI showed positive genetic correlations with feed conversion ratio (FCR) and excretion traits, these correlations being greater in the sire breeds (from 0.57 to 0.86) than in the dam breeds (from 0.38 to 0.53). Compared with FCR, RFI had weaker genetic correlations with carcass composition, growth rate, and excretion traits. Estimates of genetic correlations between FCR and excretion traits were very close to 1 for all breeds. Finally, excretion traits were, at the genetic level, correlated positively with ADFI, negatively with growth rate and carcass leanness, whereas the halothane n mutation in PP was shown to reduce N and P

Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops

Science.gov (United States)

Ru, Sushan; Hardner, Craig; Carter, Patrick A; Evans, Kate; Main, Dorrie; Peace, Cameron

2016-01-01

Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest. Traditionally, genetic potential is determined by phenotypic evaluation. With the availability of DNA tests for some agronomically important traits, breeders have the opportunity to include DNA information in their seedling selection operations—known as marker-assisted seedling selection. A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies. Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops, as clonal propagation captures all genetic effects, not just additive. This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation, based on a generalized seedling selection scheme of clonally propagated crops. Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns. Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability. Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available. PMID:27148453

Improvement in genetic evaluation of female fertility in dairy cattle using multiple-trait models including milk production traits

DEFF Research Database (Denmark)

Sun, C; Madsen, P; Lund, M S

2010-01-01

This study investigated the improvement in genetic evaluation of fertility traits by using production traits as secondary traits (MILK = 305-d milk yield, FAT = 305-d fat yield, and PROT = 305-d protein yield). Data including 471,742 records from first lactations of Denmark Holstein cows, covering...... the years of inseminations during first lactations from 1995 to 2004, were analyzed. Six fertility traits (i.e., interval in days from calving to first insemination, calving interval, days open, interval in days from first to last insemination, numbers of inseminations per conception, and nonreturn rate...... stability and predictive ability than single-trait models for all the fertility traits, except for nonreturn rate within 56 d after first service. The stability and predictive ability for the model including MILK or PROT were similar to the model including all 3 milk production traits and better than...

Host traits explain the genetic structure of parasites: a meta-analysis

Czech Academy of Sciences Publication Activity Database

Blasco-Costa, Maria Isabel; Poulin, R.

2013-01-01

Roč. 140, č. 10 (2013), s. 1316-1322 ISSN 0031-1820 EU Projects: European Commission(XE) 252124 - PARAPOPGENE Institutional support: RVO:60077344 Keywords : meta-analysis * host traits * parasite traits * F-statistics * population genetic structure * dispersal * autogenic life cycle * allogenic life cycle Subject RIV: EH - Ecology, Behaviour Impact factor: 2.350, year: 2013

Genetics of Obesity Traits: A Bivariate Genome-Wide Association Analysis

DEFF Research Database (Denmark)

Wu, Yili; Duan, Haiping; Tian, Xiaocao

2018-01-01

Previous genome-wide association studies on anthropometric measurements have identified more than 100 related loci, but only a small portion of heritability in obesity was explained. Here we present a bivariate twin study to look for the genetic variants associated with body mass index and waist......-hip ratio, and to explore the obesity-related pathways in Northern Han Chinese. Cholesky decompositionmodel for 242monozygotic and 140 dizygotic twin pairs indicated a moderate genetic correlation (r = 0.53, 95%CI: 0.42–0.64) between body mass index and waist-hip ratio. Bivariate genome-wide association.......05. Expression quantitative trait loci analysis identified rs2242044 as a significant cis-eQTL in both the normal adipose-subcutaneous (P = 1.7 × 10−9) and adipose-visceral (P = 4.4 × 10−15) tissue. These findings may provide an important entry point to unravel genetic pleiotropy in obesity traits....

Genetic and environmental effects on performance traits of ...

African Journals Online (AJOL)

Genetic and environmental effects on performance traits of Simmentaler cattle on the Transvaal Highveld. Tina Rust, J van der Westhuizen. Abstract. No Abstract. Full Text: EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT · AJOL African Journals Online. HOW TO USE ...

GENETIC STUDIES ON REPRODUCTION TRAITS IN CROSSBRED JERSEY CATTLE IN WESTERN ODISHA

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S.K.Dhal

2016-06-01

Full Text Available The present study was conducted on 412 crossbred (Jersey X Deshi cows sired by 24 bulls, maintained over the period from 2005 to 2014. The economic traits studied were age at first calving (AFC; months, calving interval (CI; days, dry period (DP; days and service period (SP; days. The averages for AFC, CI, DP and SP were 34.46±0.22 months, 505.95±3.24, 224.20±3.31 and 228.26±3.21 days, respectively. Effect of management system was significant for all the economic traits (AFC, CI and DP except SP. It may be inferred that rearing crossbred Jersey cows under intensive system of management may be advocated to utilize the maximum genetic potential of crossbred cattle for all the traits. Semi-intensive system may help moderate exploration of the traits. But exclusively pasture dependent management should be avoided for rearing crossbred Jersey cows. Heritability estimates for AFC, CI and DP were found to be 0.462 ±0.179; 0.062 ±0.088; 0.270 ±0.138, respectively. Genetic correlations of AFC with CI and SP were high and positive. For maximum genetic improvement and their correlated response, it is necessary to include all the economic traits with differential weightage for achieving accuracy in selection programs.

Genetic evaluation of claw health traits accounting for potential preselection of cows to be trimmed.

Science.gov (United States)

Croué, Iola; Fikse, Freddy; Johansson, Kjell; Carlén, Emma; Thomas, Gilles; Leclerc, Hélène; Ducrocq, Vincent

2017-10-01

Claw lesions are one of the most important health issues in dairy cattle. Although the frequency of claw lesions depends greatly on herd management, the frequency can be lowered through genetic selection. A genetic evaluation could be developed based on trimming records collected by claw trimmers; however, not all cows present in a herd are usually selected by the breeder to be trimmed. The objectives of this study were to investigate the importance of the preselection of cows for trimming, to account for this preselection, and to estimate genetic parameters of claw health traits. The final data set contained 25,511 trimming records of French Holstein cows. Analyzed claw lesion traits were digital dermatitis, heel horn erosion, interdigital hyperplasia, sole hemorrhage circumscribed, sole hemorrhage diffused, sole ulcer, and white line fissure. All traits were analyzed as binary traits in a multitrait linear animal model. Three scenarios were considered: including only trimmed cows in a 7-trait model (scenario 1); or trimmed cows and contemporary cows not trimmed but present at the time of a visit (considering that nontrimmed cows were healthy) in a 7-trait model (scenario 2); or trimmed cows and contemporary cows not trimmed but present at the time of a visit (considering lesion records for trimmed cows only), in an 8-trait model, including a 0/1 trimming status trait (scenario 3). For scenario 3, heritability estimates ranged from 0.02 to 0.09 on the observed scale. Genetic correlations clearly revealed 2 groups of traits (digital dermatitis, heel horn erosion, and interdigital hyperplasia on the one hand, and sole hemorrhage circumscribed, sole hemorrhage diffused, sole ulcer, and white line fissure on the other hand). Heritabilities on the underlying scale did not vary much depending on the scenario: the effect of the preselection of cows for trimming on the estimation of heritabilities appeared to be negligible. However, including untrimmed cows as healthy

Genetic architecture of clinical mastitis traits in dairy cattle

DEFF Research Database (Denmark)

Sahana, Goutam; Guldbrandtsen, Bernt; Lund, Mogens Sandø

2012-01-01

investigate the genetic architecture of clinical mastitis and somatic cell score traits in dairy cattle using a high density (HD) SNP panel. Mastitis, an inflammation of the mammary gland most commonly caused by bacterial infection, is a frequent disease in dairy cattle. Clinical mastitis and somatic cell...... score from first three lactations were studied for association with SNP markers in 4,200 progeny-tested Nordic Holstein bulls. Single trait breeding values were used as phenotypes. All the individuals were genotyped with BovineSNP50 Beadchip. Part of this population was also genotyped with the Bovine...... mixed model analysis. After Bonferroni correction 12, 372 SNP exhibited genome-wide significant associations with mastitis related traits. A total 61 QTL regions on 22 chromosomes associated with mastitis related traits were identified. The SNP with highest effect explained 5.6% of the variance...

Genetic Diversity of Upland Rice Germplasm in Malaysia Based on Quantitative Traits

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M. Sohrabi

2012-01-01

Full Text Available Genetic diversity is prerequisite for any crop improvement program as it helps in the development of superior recombinants. Fifty Malaysian upland rice accessions were evaluated for 12 growth traits, yield and yield components. All of the traits were significant and highly significant among the accessions. The higher magnitudes of genotypic and phenotypic coefficients of variation were recorded for flag leaf length-to-width ratio, spikelet fertility, and days to flowering. High heritability along with high genetic advance was registered for yield of plant, days to flowering, and flag leaf length-to-width ratio suggesting preponderance of additive gene action in the gene expression of these characters. Plant height showed highly significant positive correlation with most of the traits. According to UPGMA cluster analysis all accessions were clustered into six groups. Twelve morphological traits provided around 77% of total variation among the accessions.

Genetic and environmental effects on performance traits of ...

African Journals Online (AJOL)

Genetic and environmental effects on performance traits of Simmentaler cattle on the Transvaal Highveld. Tina Rust*. Highveld Region Agricultural Development Institute, .... ef'fect of the mtt' management system (m = 1,2,3,4),. bW = linear regression of the appropriate deviation from the mean of individual age at weaning (in ...

Genetic Diversity, Population Structure, and Heritability of Fruit Traits in Capsicum annuum

Science.gov (United States)

Naegele, Rachel P.; Mitchell, Jenna; Hausbeck, Mary K.

2016-01-01

Cultivated pepper (Capsicum annuum) is a phenotypically diverse species grown throughout the world. Wild and landrace peppers are typically small-fruited and pungent, but contain many important traits such as insect and disease resistance. Cultivated peppers vary dramatically in size, shape, pungency, and color, and often lack resistance traits. Fruit characteristics (e.g. shape and pericarp thickness) are major determinants for cultivar selection, and their association with disease susceptibility can reduce breeding efficacy. This study evaluated a diverse collection of peppers for mature fruit phenotypic traits, correlation among fruit traits and Phytophthora fruit rot resistance, genetic diversity, population structure, and trait broad sense heritability. Significant differences within all fruit phenotype categories were detected among pepper lines. Fruit from Europe had the thickest pericarp, and fruit from Ecuador had the thinnest. For fruit shape index, fruit from Africa had the highest index, while fruit from Europe had the lowest. Five genetic clusters were detected in the pepper population and were significantly associated with fruit thickness, end shape, and fruit shape index. The genetic differentiation between clusters ranged from little to very great differentiation when grouped by the predefined categories. Broad sense heritability for fruit traits ranged from 0.56 (shoulder height) to 0.98 (pericarp thickness). When correlations among fruit phenotypes and fruit disease were evaluated, fruit shape index was negatively correlated with pericarp thickness, and positively correlated with fruit perimeter. Pepper fruit pericarp, perimeter, and width had a slight positive correlation with Phytophthora fruit rot, whereas fruit shape index had a slight negative correlation. PMID:27415818

Genetics of Lipid and Lipoprotein Disorders and Traits.

Science.gov (United States)

Dron, Jacqueline S; Hegele, Robert A

2016-01-01

Plasma lipids, namely cholesterol and triglyceride, and lipoproteins, such as low-density lipoprotein (LDL) and high-density lipoprotein, serve numerous physiological roles. Perturbed levels of these traits underlie monogenic dyslipidemias, a diverse group of multisystem disorders. We are on the verge of having a relatively complete picture of the human dyslipidemias and their components. Recent advances in genetics of plasma lipids and lipoproteins include the following: (1) expanding the range of genes causing monogenic dyslipidemias, particularly elevated LDL cholesterol; (2) appreciating the role of polygenic effects in such traits as familial hypercholesterolemia and combined hyperlipidemia; (3) accumulating a list of common variants that determine plasma lipids and lipoproteins; (4) applying exome sequencing to identify collections of rare variants determining plasma lipids and lipoproteins that via Mendelian randomization have also implicated gene products such as NPC1L1 , APOC3 , LDLR , APOA5 , and ANGPTL4 as causal for atherosclerotic cardiovascular disease; and (5) using naturally occurring genetic variation to identify new drug targets, including inhibitors of apolipoprotein (apo) C-III, apo(a), ANGPTL3, and ANGPTL4. Here, we compile this disparate range of data linking human genetic variation to plasma lipids and lipoproteins, providing a "one stop shop" for the interested reader.

Heritability estimates of the Big Five personality traits based on common genetic variants.

Science.gov (United States)

Power, R A; Pluess, M

2015-07-14

According to twin studies, the Big Five personality traits have substantial heritable components explaining 40-60% of the variance, but identification of associated genetic variants has remained elusive. Consequently, knowledge regarding the molecular genetic architecture of personality and to what extent it is shared across the different personality traits is limited. Using genomic-relatedness-matrix residual maximum likelihood analysis (GREML), we here estimated the heritability of the Big Five personality factors (extraversion, agreeableness, conscientiousness, neuroticism and openness for experience) in a sample of 5011 European adults from 527,469 single-nucleotide polymorphisms across the genome. We tested for the heritability of each personality trait, as well as for the genetic overlap between the personality factors. We found significant and substantial heritability estimates for neuroticism (15%, s.e. = 0.08, P = 0.04) and openness (21%, s.e. = 0.08, P Big Five personality traits using the GREML approach. Findings should be considered exploratory and suggest that detectable heritability estimates based on common variants is shared between neuroticism and openness to experiences.

Genetic parameters for female fertility, locomotion, body condition score, and linear type traits in Czech Holstein cattle.

Science.gov (United States)

Zink, V; Štípková, M; Lassen, J

2011-10-01

The aim of this study was to estimate genetic parameters for fertility traits and linear type traits in the Czech Holstein dairy cattle population. Phenotypic data regarding 12 linear type traits, measured in first lactation, and 3 fertility traits, measured in each of first and second lactation, were collected from 2005 to 2009 in the progeny testing program of the Czech-Moravian Breeders Corporation. The number of animals for each linear type trait was 59,467, except for locomotion, where 53,436 animals were recorded. The 3-generation pedigree file included 164,125 animals. (Co)variance components were estimated using AI-REML in a series of bivariate analyses, which were implemented via the DMU package. Fertility traits included days from calving to first service (CF1), days open (DO1), and days from first to last service (FL1) in first lactation, and days from calving to first service (CF2), days open (DO2), and days from first to last service (FL2) in second lactation. The number of animals with fertility data varied between traits and ranged from 18,915 to 58,686. All heritability estimates for reproduction traits were low, ranging from 0.02 to 0.04. Heritability estimates for linear type traits ranged from 0.03 for locomotion to 0.39 for stature. Estimated genetic correlations between fertility traits and linear type traits were generally neutral or positive, whereas genetic correlations between body condition score and CF1, DO1, FL1, CF2 and DO2 were mostly negative, with the greatest correlation between BCS and CF2 (-0.51). Genetic correlations with locomotion were greatest for CF1 and CF2 (-0.34 for both). Results of this study show that cows that are genetically extreme for angularity, stature, and body depth tend to perform poorly for fertility traits. At the same time, cows that are genetically predisposed for low body condition score or high locomotion score are generally inferior in fertility. Copyright © 2011 American Dairy Science Association

Bayesian dissection for genetic architecture of traits associated with ...

African Journals Online (AJOL)

PRECIOUS

2009-12-15

Dec 15, 2009 ... model selection technique was used to dissect genetic architecture for traits of interest. A total of 28 main-effect ... nutrition elements for rice growth in natural ecosystems. In general ... All materials were sown on 28. April and ...

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

NARCIS (Netherlands)

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

2015-01-01

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

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

NARCIS (Netherlands)

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

2015-01-01

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

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

Directory of Open Access Journals (Sweden)

Brandon Jeffrey

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

Genetic Parameters for Reproduction Traits of Prolificacy and Conventional Purebred Sows

Directory of Open Access Journals (Sweden)

Vitomir Vidović

2012-05-01

Full Text Available Research was performed on four farms were included in 1567 a highly fertile females Landrace and Yorkshire, and 24 boars of Danish origin, or 5294 consecutive parities, and in period 2009 - 2011 year. Studies of evaluations genetic parameters conventional breeds Landrace and Yorkshire were included in 2987 female mating with 46 male or 11 674 litters in the same period. Evaluated genetic parameters for litter size traits show the same tendency as the legality of the pure breed sows that produce 11-14 piglets weaned less per sow per year. Environmental factors, HYS, food technology and management showed no significant effect on the traits. Heritability and repeatability of live and still born piglets, litter size and the fifth days after birth and the number of piglets weaned in category of low hereditary traits whose values vary within the limits of 0.08 to 0.11 for the heritability and from 0.14 to 0.18 for the repeatability. There was tendency to lower values of genetic parameters in the conventional compared to highly fertile cows, which is considered the effect of selection on gene frequency for the observed properties.

Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding.

Science.gov (United States)

Bhat, Javaid A; Ali, Sajad; Salgotra, Romesh K; Mir, Zahoor A; Dutta, Sutapa; Jadon, Vasudha; Tyagi, Anshika; Mushtaq, Muntazir; Jain, Neelu; Singh, Pradeep K; Singh, Gyanendra P; Prabhu, K V

2016-01-01

Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding, it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost-effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to earlier marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing. These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS-based genotyping have increased genomic-estimated breeding value prediction accuracies over other established marker platform in cereals and other crop species, and made the dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.

A methodology framework for weighting genetic traits that impact greenhouse gas emission intensities in selection indexes.

Science.gov (United States)

Amer, P R; Hely, F S; Quinton, C D; Cromie, A R

2018-01-01

A methodological framework was presented for deriving weightings to be applied in selection indexes to account for the impact genetic change in traits will have on greenhouse gas emissions intensities (EIs). Although the emission component of the breeding goal was defined as the ratio of total emissions relative to a weighted combination of farm outputs, the resulting trait-weighting factors can be applied as linear weightings in a way that augments any existing breeding objective before consideration of EI. Calculus was used to define the parameters and assumptions required to link each trait change to the expected changes in EI for an animal production system. Four key components were identified. The potential impact of the trait on relative numbers of emitting animals per breeding female first has a direct effect on emission output but, second, also has a dilution effect from the extra output associated with the extra animals. Third, each genetic trait can potentially change the amount of emissions generated per animal and, finally, the potential impact of the trait on product output is accounted for. Emission intensity weightings derived from this equation require further modifications to integrate them into an existing breeding objective. These include accounting for different timing and frequency of trait expressions as well as a weighting factor to determine the degree of selection emphasis that is diverted away from improving farm profitability in order to achieve gains in EI. The methodology was demonstrated using a simple application to dairy cattle breeding in Ireland to quantify gains in EI reduction from existing genetic trends in milk production as well as in fertility and survival traits. Most gains were identified as coming through the dilution effect of genetic increases in milk protein per cow, although gains from genetic improvements in survival by reducing emissions from herd replacements were also significant. Emission intensities in the Irish

Genetic line comparisons and genetic parameters for endoparasite infections and test-day milk production traits.

Science.gov (United States)

May, Katharina; Brügemann, Kerstin; Yin, Tong; Scheper, Carsten; Strube, Christina; König, Sven

2017-09-01

Keeping dairy cows in grassland systems relies on detailed analyses of genetic resistance against endoparasite infections, including between- and within-breed genetic evaluations. The objectives of this study were (1) to compare different Black and White dairy cattle selection lines for endoparasite infections and (2) the estimation of genetic (co)variance components for endoparasite and test-day milk production traits within the Black and White cattle population. A total of 2,006 fecal samples were taken during 2 farm visits in summer and autumn 2015 from 1,166 cows kept in 17 small- and medium-scale organic and conventional German grassland farms. Fecal egg counts were determined for gastrointestinal nematodes (FEC-GIN) and flukes (FEC-FLU), and fecal larvae counts for the bovine lungworm Dictyocaulus viviparus (FLC-DV). The lowest values for gastrointestinal nematode infections were identified for genetic lines adopted to pasture-based production systems, especially selection lines from New Zealand. Heritabilities were low for FEC-GIN (0.05-0.06 ± 0.04) and FLC-DV (0.05 ± 0.04), but moderate for FEC-FLU (0.33 ± 0.06). Almost identical heritabilities were estimated for different endoparasite trait transformations (log-transformation, square root). The genetic correlation between FEC-GIN and FLC-DV was 1.00 ± 0.60, slightly negative between FEC-GIN and FEC-FLU (-0.10 ± 0.27), and close to zero between FLC-DV and FEC-FLU (0.03 ± 0.30). Random regression test-day models on a continuous time scale [days in milk (DIM)] were applied to estimate genetic relationships between endoparasite and longitudinal test-day production traits. Genetic correlations were negative between FEC-GIN and milk yield (MY) until DIM 85, and between FEC-FLU and MY until DIM 215. Genetic correlations between FLC-DV and MY were negative throughout lactation, indicating improved disease resistance for high-productivity cows. Genetic relationships between FEC-GIN and FEC-FLU with milk

The genetic links between the big five personality traits and general interest domains.

Science.gov (United States)

Kandler, Christian; Bleidorn, Wiebke; Riemann, Rainer; Angleitner, Alois; Spinath, Frank M

2011-12-01

This is the first genetically informative study in which multiple informants were used to quantify the genetic and environmental sources of individual differences in general interests as well as the phenotypic and genetic links between general interests and Big Five personality traits. Self-reports and two peer ratings from 844 individuals, including 225 monozygotic and 113 dizygotic complete twin pairs, were collected. Multiple-rater scores (composites) revealed that the averaged levels of genetic and environmental effects on seven broad interest domains were similar to those on personality traits. Multivariate analyses showed that about 35% of the genetic and 9% of the environmental variance in interests were explained by personality domains, in particular by Openness. The findings suggest that interests cannot easily be considered as a byproduct of the interactions between personality genotypes and the environmental influences but rather as an internal regulation of behavior with an own genetic basis.

A Powerful Approach to Estimating Annotation-Stratified Genetic Covariance via GWAS Summary Statistics.

Science.gov (United States)

Lu, Qiongshi; Li, Boyang; Ou, Derek; Erlendsdottir, Margret; Powles, Ryan L; Jiang, Tony; Hu, Yiming; Chang, David; Jin, Chentian; Dai, Wei; He, Qidu; Liu, Zefeng; Mukherjee, Shubhabrata; Crane, Paul K; Zhao, Hongyu

2017-12-07

Despite the success of large-scale genome-wide association studies (GWASs) on complex traits, our understanding of their genetic architecture is far from complete. Jointly modeling multiple traits' genetic profiles has provided insights into the shared genetic basis of many complex traits. However, large-scale inference sets a high bar for both statistical power and biological interpretability. Here we introduce a principled framework to estimate annotation-stratified genetic covariance between traits using GWAS summary statistics. Through theoretical and numerical analyses, we demonstrate that our method provides accurate covariance estimates, thereby enabling researchers to dissect both the shared and distinct genetic architecture across traits to better understand their etiologies. Among 50 complex traits with publicly accessible GWAS summary statistics (N total ≈ 4.5 million), we identified more than 170 pairs with statistically significant genetic covariance. In particular, we found strong genetic covariance between late-onset Alzheimer disease (LOAD) and amyotrophic lateral sclerosis (ALS), two major neurodegenerative diseases, in single-nucleotide polymorphisms (SNPs) with high minor allele frequencies and in SNPs located in the predicted functional genome. Joint analysis of LOAD, ALS, and other traits highlights LOAD's correlation with cognitive traits and hints at an autoimmune component for ALS. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits.

Directory of Open Access Journals (Sweden)

Benjamin F Voight

Full Text Available Genome-wide association studies have identified hundreds of loci for type 2 diabetes, coronary artery disease and myocardial infarction, as well as for related traits such as body mass index, glucose and insulin levels, lipid levels, and blood pressure. These studies also have pointed to thousands of loci with promising but not yet compelling association evidence. To establish association at additional loci and to characterize the genome-wide significant loci by fine-mapping, we designed the "Metabochip," a custom genotyping array that assays nearly 200,000 SNP markers. Here, we describe the Metabochip and its component SNP sets, evaluate its performance in capturing variation across the allele-frequency spectrum, describe solutions to methodological challenges commonly encountered in its analysis, and evaluate its performance as a platform for genotype imputation. The metabochip achieves dramatic cost efficiencies compared to designing single-trait follow-up reagents, and provides the opportunity to compare results across a range of related traits. The metabochip and similar custom genotyping arrays offer a powerful and cost-effective approach to follow-up large-scale genotyping and sequencing studies and advance our understanding of the genetic basis of complex human diseases and traits.

An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus)

Science.gov (United States)

2014-01-01

Background Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Results Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. Conclusions The integrated map described herein enhances the utility of genomic tools over

An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon (Citrullus lanatus).

Science.gov (United States)

Ren, Yi; McGregor, Cecilia; Zhang, Yan; Gong, Guoyi; Zhang, Haiying; Guo, Shaogui; Sun, Honghe; Cai, Wantao; Zhang, Jie; Xu, Yong

2014-01-20

Modern watermelon (Citrullus lanatus L.) cultivars share a narrow genetic base due to many years of selection for desirable horticultural qualities. Wild subspecies within C. lanatus are important potential sources of novel alleles for watermelon breeding, but successful trait introgression into elite cultivars has had limited success. The application of marker assisted selection (MAS) in watermelon is yet to be realized, mainly due to the past lack of high quality genetic maps. Recently, a number of useful maps have become available, however these maps have few common markers, and were constructed using different marker sets, thus, making integration and comparative analysis among maps difficult. The objective of this research was to use single-nucleotide polymorphism (SNP) anchor markers to construct an integrated genetic map for C. lanatus. Under the framework of the high density genetic map, an integrated genetic map was constructed by merging data from four independent mapping experiments using a genetically diverse array of parental lines, which included three subspecies of watermelon. The 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel), 36 structure variation (SV) and 386 SNP markers from the four maps were used to construct an integrated map. This integrated map contained 1339 markers, spanning 798 cM with an average marker interval of 0.6 cM. Fifty-eight previously reported quantitative trait loci (QTL) for 12 traits in these populations were also integrated into the map. In addition, new QTL identified for brix, fructose, glucose and sucrose were added. Some QTL associated with economically important traits detected in different genetic backgrounds mapped to similar genomic regions of the integrated map, suggesting that such QTL are responsible for the phenotypic variability observed in a broad array of watermelon germplasm. The integrated map described herein enhances the utility of genomic tools over previous watermelon genetic maps. A

Makeup of the genetic correlation between milk production traits using genome-wide single nucleotide polymorphism information

NARCIS (Netherlands)

Binsbergen, van R.; Veerkamp, R.F.; Calus, M.P.L.

2012-01-01

The correlated responses between traits may differ depending on the makeup of genetic covariances, and may differ from the predictions of polygenic covariances Therefore, the objective of the present study was to investigate the makeup of the genetic covariances between the well-studied traits: milk

Genetic associations between reproductive and linear-type traits of Holstein cows in Brazil

OpenAIRE

Almeida, Tatiana Prestes; Kern, Elisandra Lurdes; Daltro, Darlene dos Santos; Braccini Neto, José; McManus, Concepta; Thaler Neto, André; Cobuci, Jaime Araujo

2017-01-01

ABSTRACT This study aimed to estimate heritability, genetic, and residual correlations between reproductive traits such as age at first calving, calving interval, dry period, and first service period and linear type traits measured in Holstein cows born between the years 1990 and 2008 in Brazil. The (co)variance components were estimated by restricted maximum likelihood, using the MTDFREML software. The heritability for reproductive traits and linear-type traits ranged from 0.02 to 0.03 and f...

Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study.

Science.gov (United States)

Bauchet, Guillaume; Grenier, Stéphane; Samson, Nicolas; Bonnet, Julien; Grivet, Laurent; Causse, Mathilde

2017-05-01

A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato. Until now GWAS in tomato has been performed on panels of heirloom and wild accessions. Using modern breeding materials would be of direct interest for breeding purpose. To implement GWAS on a large panel of 300 tomato accessions including 168 breeding lines, this study assessed the genetic diversity and linkage disequilibrium decay and revealed the population structure and performed GWA experiment. Genetic diversity and population structure analyses were based on molecular markers (>11,000 SNP) covering the whole genome. Six genetic subgroups were revealed and associated to traits of agronomical interest, such as fruit weight and disease resistance. Estimates of linkage disequilibrium highlighted the heterogeneity of its decay among genetic subgroups. Haplotype definition allowed a fine characterization of the groups and their recombination landscape revealing the patterns of admixture along the genome. Selection footprints showed results in congruence with introgressions. Taken together, all these elements refined our knowledge of the genetic material included in this panel and allowed the identification of several associations for fruit weight, plant growth and earliness, deciphering the genetic architecture of these complex traits and identifying several new loci useful for tomato breeding.

Genetic and environmental contributions to the inverse association between specific autistic traits and experience seeking in adults.

Science.gov (United States)

Romero-Martínez, Ángel; Moya-Albiol, Luís; Vinkhuyzen, Anna A E; Polderman, Tinca J C

2016-12-01

Autistic traits are characterized by social and communication problems, restricted, repetitive and stereotyped patterns of behavior, interests and activities. The relation between autistic traits and personality characteristics is largely unknown. This study focused on the relation between five specific autistic traits measured with the abridged version of the Autism Spectrum Quotient ("social problems," "preference for routine," "attentional switching difficulties," "imagination impairments," "fascination for numbers and patterns") and Experience Seeking (ES) in a general population sample of adults, and subsequently investigated the genetic and environmental etiology between these traits. Self-reported data on autistic traits and ES were collected in a population sample (n = 559) of unrelated individuals, and in a population based family sample of twins and siblings (n = 560). Phenotypic, genetic and environmental associations between traits were examined in a bivariate model, accounting for sex and age differences. Phenotypically, ES correlated significantly with "preference for routine" and "imagination impairments" in both samples but was unrelated to the other autistic traits. Genetic analyses in the family sample revealed that the association between ES and "preference for routine" and "imagination impairments" could largely be explained by a shared genetic factor (89% and 70%, respectively). Our analyses demonstrated at a phenotypic and genetic level an inverse relationship between ES and specific autistic traits in adults. ES is associated with risk taking behavior such as substance abuse, antisocial behavior and financial problems. Future research could investigate whether autistic traits, in particular strong routine preference and impaired imagination skills, serve as protective factors for such risky behaviors. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Sex-stratified Genome-wide Association Studies Including 270,000 Individuals Show Sexual Dimorphism in Genetic Loci for Anthropometric Traits

Science.gov (United States)

Jackson, Anne U.; Monda, Keri L.; Kilpeläinen, Tuomas O.; Esko, Tõnu; Mägi, Reedik; Li, Shengxu; Workalemahu, Tsegaselassie; Feitosa, Mary F.; Croteau-Chonka, Damien C.; Day, Felix R.; Fall, Tove; Ferreira, Teresa; Gustafsson, Stefan; Locke, Adam E.; Mathieson, Iain; Scherag, Andre; Vedantam, Sailaja; Wood, Andrew R.; Liang, Liming; Steinthorsdottir, Valgerdur; Thorleifsson, Gudmar; Dermitzakis, Emmanouil T.; Dimas, Antigone S.; Karpe, Fredrik; Min, Josine L.; Nicholson, George; Clegg, Deborah J.; Person, Thomas; Krohn, Jon P.; Bauer, Sabrina; Buechler, Christa; Eisinger, Kristina; Bonnefond, Amélie; Froguel, Philippe; Hottenga, Jouke-Jan; Prokopenko, Inga; Waite, Lindsay L.; Harris, Tamara B.; Smith, Albert Vernon; Shuldiner, Alan R.; McArdle, Wendy L.; Caulfield, Mark J.; Munroe, Patricia B.; Grönberg, Henrik; Chen, Yii-Der Ida; Li, Guo; Beckmann, Jacques S.; Johnson, Toby; Thorsteinsdottir, Unnur; Teder-Laving, Maris; Khaw, Kay-Tee; Wareham, Nicholas J.; Zhao, Jing Hua; Amin, Najaf; Oostra, Ben A.; Kraja, Aldi T.; Province, Michael A.; Cupples, L. Adrienne; Heard-Costa, Nancy L.; Kaprio, Jaakko; Ripatti, Samuli; Surakka, Ida; Collins, Francis S.; Saramies, Jouko; Tuomilehto, Jaakko; Jula, Antti; Salomaa, Veikko; Erdmann, Jeanette; Hengstenberg, Christian; Loley, Christina; Schunkert, Heribert; Lamina, Claudia; Wichmann, H. Erich; Albrecht, Eva; Gieger, Christian; Hicks, Andrew A.; Johansson, Åsa; Pramstaller, Peter P.; Kathiresan, Sekar; Speliotes, Elizabeth K.; Penninx, Brenda; Hartikainen, Anna-Liisa; Jarvelin, Marjo-Riitta; Gyllensten, Ulf; Boomsma, Dorret I.; Campbell, Harry; Wilson, James F.; Chanock, Stephen J.; Farrall, Martin; Goel, Anuj; Medina-Gomez, Carolina; Rivadeneira, Fernando; Estrada, Karol; Uitterlinden, André G.; Hofman, Albert; Zillikens, M. Carola; den Heijer, Martin; Kiemeney, Lambertus A.; Maschio, Andrea; Hall, Per; Tyrer, Jonathan; Teumer, Alexander; Völzke, Henry; Kovacs, Peter; Tönjes, Anke; Mangino, Massimo; Spector, Tim D.; Hayward, Caroline; Rudan, Igor; Hall, Alistair S.; Samani, Nilesh J.; Attwood, Antony Paul; Sambrook, Jennifer G.; Hung, Joseph; Palmer, Lyle J.; Lokki, Marja-Liisa; Sinisalo, Juha; Boucher, Gabrielle; Huikuri, Heikki; Lorentzon, Mattias; Ohlsson, Claes; Eklund, Niina; Eriksson, Johan G.; Barlassina, Cristina; Rivolta, Carlo; Nolte, Ilja M.; Snieder, Harold; Van der Klauw, Melanie M.; Van Vliet-Ostaptchouk, Jana V.; Gejman, Pablo V.; Shi, Jianxin; Jacobs, Kevin B.; Wang, Zhaoming; Bakker, Stephan J. L.; Mateo Leach, Irene; Navis, Gerjan; van der Harst, Pim; Martin, Nicholas G.; Medland, Sarah E.; Montgomery, Grant W.; Yang, Jian; Chasman, Daniel I.; Ridker, Paul M.; Rose, Lynda M.; Lehtimäki, Terho; Raitakari, Olli; Absher, Devin; Iribarren, Carlos; Basart, Hanneke; Hovingh, Kees G.; Hyppönen, Elina; Power, Chris; Anderson, Denise; Beilby, John P.; Hui, Jennie; Jolley, Jennifer; Sager, Hendrik; Bornstein, Stefan R.; Schwarz, Peter E. H.; Kristiansson, Kati; Perola, Markus; Lindström, Jaana; Swift, Amy J.; Uusitupa, Matti; Atalay, Mustafa; Lakka, Timo A.; Rauramaa, Rainer; Bolton, Jennifer L.; Fowkes, Gerry; Fraser, Ross M.; Price, Jackie F.; Fischer, Krista; KrjutÅ¡kov, Kaarel; Metspalu, Andres; Mihailov, Evelin; Langenberg, Claudia; Luan, Jian'an; Ong, Ken K.; Chines, Peter S.; Keinanen-Kiukaanniemi, Sirkka M.; Saaristo, Timo E.; Edkins, Sarah; Franks, Paul W.; Hallmans, Göran; Shungin, Dmitry; Morris, Andrew David; Palmer, Colin N. A.; Erbel, Raimund; Moebus, Susanne; Nöthen, Markus M.; Pechlivanis, Sonali; Hveem, Kristian; Narisu, Narisu; Hamsten, Anders; Humphries, Steve E.; Strawbridge, Rona J.; Tremoli, Elena; Grallert, Harald; Thorand, Barbara; Illig, Thomas; Koenig, Wolfgang; Müller-Nurasyid, Martina; Peters, Annette; Boehm, Bernhard O.; Kleber, Marcus E.; März, Winfried; Winkelmann, Bernhard R.; Kuusisto, Johanna; Laakso, Markku; Arveiler, Dominique; Cesana, Giancarlo; Kuulasmaa, Kari; Virtamo, Jarmo; Yarnell, John W. G.; Kuh, Diana; Wong, Andrew; Lind, Lars; de Faire, Ulf; Gigante, Bruna; Magnusson, Patrik K. E.; Pedersen, Nancy L.; Dedoussis, George; Dimitriou, Maria; Kolovou, Genovefa; Kanoni, Stavroula; Stirrups, Kathleen; Bonnycastle, Lori L.; Njølstad, Inger; Wilsgaard, Tom; Ganna, Andrea; Rehnberg, Emil; Hingorani, Aroon; Kivimaki, Mika; Kumari, Meena; Assimes, Themistocles L.; Barroso, Inês; Boehnke, Michael; Borecki, Ingrid B.; Deloukas, Panos; Fox, Caroline S.; Frayling, Timothy; Groop, Leif C.; Haritunians, Talin; Hunter, David; Ingelsson, Erik; Kaplan, Robert; Mohlke, Karen L.; O'Connell, Jeffrey R.; Schlessinger, David; Strachan, David P.; Stefansson, Kari; van Duijn, Cornelia M.; Abecasis, Gonçalo R.; McCarthy, Mark I.; Hirschhorn, Joel N.; Qi, Lu; Loos, Ruth J. F.; Lindgren, Cecilia M.; North, Kari E.; Heid, Iris M.

2013-01-01

Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723 individuals) and took forward 348 SNPs into follow-up (additional 137,052 individuals) in a total of 94 studies. Seven loci displayed significant sex-difference (FDR<5%), including four previously established (near GRB14/COBLL1, LYPLAL1/SLC30A10, VEGFA, ADAMTS9) and three novel anthropometric trait loci (near MAP3K1, HSD17B4, PPARG), all of which were genome-wide significant in women (P<5×10−8), but not in men. Sex-differences were apparent only for waist phenotypes, not for height, weight, BMI, or hip circumference. Moreover, we found no evidence for genetic effects with opposite directions in men versus women. The PPARG locus is of specific interest due to its role in diabetes genetics and therapy. Our results demonstrate the value of sex-specific GWAS to unravel the sexually dimorphic genetic underpinning of complex traits. PMID:23754948

Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits.

Directory of Open Access Journals (Sweden)

Joshua C Randall

2013-06-01

Full Text Available Given the anthropometric differences between men and women and previous evidence of sex-difference in genetic effects, we conducted a genome-wide search for sexually dimorphic associations with height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip-ratio (133,723 individuals and took forward 348 SNPs into follow-up (additional 137,052 individuals in a total of 94 studies. Seven loci displayed significant sex-difference (FDR<5%, including four previously established (near GRB14/COBLL1, LYPLAL1/SLC30A10, VEGFA, ADAMTS9 and three novel anthropometric trait loci (near MAP3K1, HSD17B4, PPARG, all of which were genome-wide significant in women (P<5×10(-8, but not in men. Sex-differences were apparent only for waist phenotypes, not for height, weight, BMI, or hip circumference. Moreover, we found no evidence for genetic effects with opposite directions in men versus women. The PPARG locus is of specific interest due to its role in diabetes genetics and therapy. Our results demonstrate the value of sex-specific GWAS to unravel the sexually dimorphic genetic underpinning of complex traits.

Genetic and environmental influences underlying the relationship between autistic traits and temperament and character dimensions in adulthood.

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Picardi, Angelo; Fagnani, Corrado; Medda, Emanuela; Toccaceli, Virgilia; Brambilla, Paolo; Stazi, Maria Antonietta

2015-04-01

In recent years, several twin studies adopted a dimensional approach to Autism Spectrum Disorders (ASD) and estimated the contribution of genetic and environmental influences to variation in autistic traits. However, no study was performed on adults over 18 years of age and all but two studies were based on parent or teacher ratings. Also, the genetic and environmental contributions to the interplay between autistic traits and adult personality dimensions have not been investigated. A sample of 266 complete twin pairs (30% males, mean age 40 ± 12 years) drawn from the population-based Italian Twin Register was administered the Autism-Spectrum Quotient, Temperament and Character Inventory (TCI-125), and General Health Questionnaire (GHQ-12). Genetic structural equation modelling was performed with the Mx program. Estimates were adjusted for gender, age, and GHQ-12 score. Genetic factors accounted for 44% and 20%-49% of individual differences in autistic traits and TCI dimensions, respectively. Unshared environmental factors explained the remaining proportion of variance. Consistently with the notion of a personality profile in ASD characterised by obsessive temperament, autistic traits showed significant phenotypic correlations with several TCI dimensions (positive: HA; negative: NS, RD, SD, C). Genetic and unshared environmental correlations between AQ and these TCI dimensions were significant. The degree of genetic overlap was generally greater than the degree of environmental overlap. Despite some limitations, this study suggests that genetic factors contribute substantially to individual differences in autistic traits in adults, with unshared environmental influences also playing an important role. It also suggests that autistic traits and the majority of temperament and character dimensions share common genetic and environmental aetiological factors. Copyright © 2014 Elsevier Inc. All rights reserved.

Evaluation of the Genetic Variation of Cowpea Landraces (Vigna unguiculata from Western Cameroon Using Qualitative Traits

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Toscani NGOMPE-DEFFO

2017-12-01

Full Text Available Characterization of the genetic diversity and analysis of the genetic relationship between accessions of a crop species is a key step in breeding superior cultivars. The main objective of the hereby study was to determine the genetic variation between 30 cowpea accessions collected throughout the eight divisions of the Western Region of Cameroon using qualitative traits. Phenotypic variation of these accessions was evaluated using diversity indices and cluster analyses. A total of twenty qualitative traits were used for the study. Fifteen of them (75% were polymorphic, displaying each at least two phenotypic classes. The monomorphic characters were growth pattern, leaf color, leaf hairiness, plant hairiness and pod hairiness, each with only one phenotypic class. Results showed a relatively significant level of genetic diversity among the studied cowpea accessions. Overall, the average of the observed and effective number of phenotypic classes per qualitative trait were Na = 2.350 and Ne = 1.828 respectively. The Nei’s genetic diversity and the Shannon weaver diversity index were He = 0.369, ranging from zero (monomorphic trait to 0.655 (growth habit and H’ = 0.609, ranging from zero (monomorphic trait to 0.996 (seed crowding, respectively. The dendrogram constructed from the twenty qualitative traits revealed 05 accessions clusters with the number of accessions in each cluster varying from one to eleven. Information obtained from this study is likely be useful for future cowpea breeding program.

Models for genetic evaluations of claw health traits in Spanish dairy cattle.

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Pérez-Cabal, M A; Charfeddine, N

2015-11-01

Genetic parameters of 7 claw health traits from Spanish dairy cattle were estimated and the predictive ability of linear and ordinal threshold models were compared and assessed. This study included data on interdigital and digital dermatitis (DE), sole ulcer (SU), white line disease (WL), interdigital hyperplasia (IH), interdigital phlegmon (IP), and chronic laminitis (CL) collected between July 2012 and June 2013 from 834 dairy herds visited by 21 trained trimmers. An overall claw disorder (OCD) was also considered an indicator the absence or the presence of at least 1 of the 6 disorders. Claw health traits were scored as categorical traits with 3 degrees of severity (nonaffected, mild, and severe disorder). Genetic parameters were estimated by fitting both a standard linear model and an ordinal threshold animal model. Around 21% of cows had at least 1 claw disorder, and the most frequent disorders were SU, DE, WL, and CL. Heritabilities of claw disorders estimated with a linear model ranged from 0.01 (IP) to 0.05 (OCD), whereas estimates from the ordinal threshold models ranged from 0.06 to 0.39 (for IP and IH, respectively). Repeatabilities of claw health estimated with the linear model varied from 0.03 to 0.18 and estimates with the ordinal threshold model ranged from 0.33 to 0.69. The global trait OCD was correlated with all disorders, except for IH and IP when the linear model was fitted. Two different genetic backgrounds of claw disorders were found. Digital dermatitis showed positive correlations with IH and IP, whereas SU was positively correlated with WL and CL. The predictive ability of the models was assessed using mean squared error and Pearson correlation between the real observation and the corresponding prediction using cross-validation. Regardless of the claw health status, the linear model led to smaller mean squared error. However, differences in predictive ability were found when predicting nonaffected and affected animals. For most traits

Genome-wide prediction of traits with different genetic architecture through efficient variable selection.

Science.gov (United States)

Wimmer, Valentin; Lehermeier, Christina; Albrecht, Theresa; Auinger, Hans-Jürgen; Wang, Yu; Schön, Chris-Carolin

2013-10-01

In genome-based prediction there is considerable uncertainty about the statistical model and method required to maximize prediction accuracy. For traits influenced by a small number of quantitative trait loci (QTL), predictions are expected to benefit from methods performing variable selection [e.g., BayesB or the least absolute shrinkage and selection operator (LASSO)] compared to methods distributing effects across the genome [ridge regression best linear unbiased prediction (RR-BLUP)]. We investigate the assumptions underlying successful variable selection by combining computer simulations with large-scale experimental data sets from rice (Oryza sativa L.), wheat (Triticum aestivum L.), and Arabidopsis thaliana (L.). We demonstrate that variable selection can be successful when the number of phenotyped individuals is much larger than the number of causal mutations contributing to the trait. We show that the sample size required for efficient variable selection increases dramatically with decreasing trait heritabilities and increasing extent of linkage disequilibrium (LD). We contrast and discuss contradictory results from simulation and experimental studies with respect to superiority of variable selection methods over RR-BLUP. Our results demonstrate that due to long-range LD, medium heritabilities, and small sample sizes, superiority of variable selection methods cannot be expected in plant breeding populations even for traits like FRIGIDA gene expression in Arabidopsis and flowering time in rice, assumed to be influenced by a few major QTL. We extend our conclusions to the analysis of whole-genome sequence data and infer upper bounds for the number of causal mutations which can be identified by LASSO. Our results have major impact on the choice of statistical method needed to make credible inferences about genetic architecture and prediction accuracy of complex traits.

Genetic parameters for reproductive traits in female Nile tilapia (Oreochromis niloticus): II. Fecundity and fertility

NARCIS (Netherlands)

Trong, T.Q.; Arendonk, van J.A.M.; Komen, J.

2013-01-01

Harvest weight is the main trait in Nile tilapia (Oreochromis niloticus) breeding programmes. The effects of selection for harvest weight on female reproductive traits are unknown. In this paper we estimate genetic parameters for reproductive traits and their correlation with harvest weight using

Genetic risk for attention-deficit/hyperactivity disorder contributes to neurodevelopmental traits in the general population.

Science.gov (United States)

Martin, Joanna; Hamshere, Marian L; Stergiakouli, Evangelia; O'Donovan, Michael C; Thapar, Anita

2014-10-15

Attention-deficit/hyperactivity disorder (ADHD) can be viewed as the extreme end of traits in the general population. Epidemiological and twin studies suggest that ADHD frequently co-occurs with and shares genetic susceptibility with autism spectrum disorder (ASD) and ASD-related traits. The aims of this study were to determine whether a composite of common molecular genetic variants, previously found to be associated with clinically diagnosed ADHD, predicts ADHD and ASD-related traits in the general population. Polygenic risk scores were calculated in the Avon Longitudinal Study of Parents and Children (ALSPAC) population sample (N = 8229) based on a discovery case-control genome-wide association study of childhood ADHD. Regression analyses were used to assess whether polygenic scores predicted ADHD traits and ASD-related measures (pragmatic language abilities and social cognition) in the ALSPAC sample. Polygenic scores were also compared in boys and girls endorsing any (rating ≥ 1) ADHD item (n = 3623). Polygenic risk for ADHD showed a positive association with ADHD traits (hyperactive-impulsive, p = .0039; inattentive, p = .037). Polygenic risk for ADHD was also negatively associated with pragmatic language abilities (p = .037) but not with social cognition (p = .43). In children with a rating ≥ 1 for ADHD traits, girls had a higher polygenic score than boys (p = .003). These findings provide molecular genetic evidence that risk alleles for the categorical disorder of ADHD influence hyperactive-impulsive and attentional traits in the general population. The results further suggest that common genetic variation that contributes to ADHD diagnosis may also influence ASD-related traits, which at their extreme are a characteristic feature of ASD. Copyright © 2014 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Genome-Wide Association Uncovers Shared Genetic Effects Among Personality Traits and Mood States

NARCIS (Netherlands)

Luciano, Michelle; Huffman, Jennifer E.; Arias-Vásquez, Alejandro; Vinkhuyzen, Anna A. E.; Middeldorp, Christel M.; Giegling, Ina; Payton, Antony; Davies, Gail; Zgaga, Lina; Janzing, Joost; Ke, Xiayi; Galesloot, Tessel; Hartmann, Annette M.; Ollier, William; Tenesa, Albert; Hayward, Caroline; Verhagen, Maaike; Montgomery, Grant W.; Hottenga, Jouke-Jan; Konte, Bettina; Starr, John M.; Vitart, Veronique; Vos, Pieter E.; Madden, Pamela A. F.; Willemsen, Gonneke; Konnerth, Heike; Horan, Michael A.; Porteous, David J.; Campbell, Harry; Vermeulen, Sita H.; Heath, Andrew C.; Wright, Alan; Polasek, Ozren; Kovacevic, Sanja B.; Hastie, Nicholas D.; Franke, Barbara; Boomsma, Dorret I.; Martin, Nicholas G.; Rujescu, Dan; Wilson, James F.; Buitelaar, Jan; Pendleton, Neil; Rudan, Igor; Deary, Ian J.

2012-01-01

Measures of personality and psychological distress are correlated and exhibit genetic covariance. We conducted univariate genome-wide SNP (similar to 2.5 million) and gene-based association analyses of these traits and examined the overlap in results across traits, including a prediction analysis of

Cryptic Genetic Variation in Evolutionary Developmental Genetics

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Annalise B. Paaby

2016-06-01

Full Text Available Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits.

Random regression analysis for body weights and main morphological traits in genetically improved farmed tilapia (Oreochromis niloticus).

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He, Jie; Zhao, Yunfeng; Zhao, Jingli; Gao, Jin; Xu, Pao; Yang, Runqing

2018-02-01

To genetically analyse growth traits in genetically improved farmed tilapia (GIFT), the body weight (BWE) and main morphological traits, including body length (BL), body depth (BD), body width (BWI), head length (HL) and length of the caudal peduncle (CPL), were measured six times in growth duration on 1451 fish from 45 mixed families of full and half sibs. A random regression model (RRM) was used to model genetic changes of the growth traits with days of age and estimate the heritability for any growth point and genetic correlations between pairwise growth points. Using the covariance function based on optimal RRMs, the heritabilities were estimated to be from 0.102 to 0.662 for BWE, 0.157 to 0.591 for BL, 0.047 to 0.621 for BD, 0.018 to 0.577 for BWI, 0.075 to 0.597 for HL and 0.032 to 0.610 for CPL between 60 and 140 days of age. All genetic correlations exceeded 0.5 between pairwise growth points. Moreover, the traits at initial days of age showed less correlation with those at later days of age. With phenotypes observed repeatedly, the model choice showed that the optimal RRMs could more precisely predict breeding values at a specific growth time than repeatability models or multiple trait animal models, which enhanced the efficiency of selection for the BWE and main morphological traits.

Estimation of genetic parameters for growth traits in a breeding program for rainbow trout (Oncorhynchus mykiss) in China.

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Hu, G; Gu, W; Bai, Q L; Wang, B Q

2013-04-26

Genetic parameters and breeding values for growth traits were estimated in the first and, currently, the only family selective breeding program for rainbow trout (Oncorhynchus mykiss) in China. Genetic and phenotypic data were collected for growth traits from 75 full-sibling families with a 2-generation pedigree. Genetic parameters and breeding values for growth traits of rainbow trout were estimated using the derivative-free restricted maximum likelihood method. The goodness-of-fit of the models was tested using Akaike and Bayesian information criteria. Genetic parameters and breeding values were estimated using the best-fit model for each trait. The values for heritability estimating body weight and length ranged from 0.20 to 0.45 and from 0.27 to 0.60, respectively, and the heritability of condition factor was 0.34. Our results showed a moderate degree of heritability for growth traits in this breeding program and suggested that the genetic and phenotypic tendency of body length, body weight, and condition factor were similar. Therefore, the selection of phenotypic values based on pedigree information was also suitable in this research population.

A Chromosome Segment Substitution Library of Weedy Rice for Genetic Dissection of Complex Agronomic and Domestication Traits.

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Prasanta K Subudhi

Full Text Available Chromosome segment substitution lines (CSSLs are a powerful alternative for locating quantitative trait loci (QTL, analyzing gene interactions, and providing starting materials for map-based cloning projects. We report the development and characterization of a CSSL library of a U.S. weedy rice accession 'PSRR-1' with genome-wide coverage in an adapted rice cultivar 'Bengal' background. The majority of the CSSLs carried a single defined weedy rice segment with an average introgression segment of 2.8 % of the donor genome. QTL mapping results for several agronomic and domestication traits from the CSSL population were compared with those obtained from two recombinant inbred line (RIL populations involving the same weedy rice accession. There was congruence of major effect QTLs between both types of populations, but new and additional QTLs were detected in the CSSL population. Although, three major effect QTLs for plant height were detected on chromosomes 1, 4, and 8 in the CSSL population, the latter two escaped detection in both RIL populations. Since this was observed for many traits, epistasis may play a major role for the phenotypic variation observed in weedy rice. High levels of shattering and seed dormancy in weedy rice might result from an accumulation of many small effect QTLs. Several CSSLs with desirable agronomic traits (e.g. longer panicles, longer grains, and higher seed weight identified in this study could be useful for rice breeding. Since weedy rice is a reservoir of genes for many weedy and agronomic attributes, the CSSL library will serve as a valuable resource to discover latent genetic diversity for improving crop productivity and understanding the plant domestication process through cloning and characterization of the underlying genes.

Genetic analyses of agronomic and seed quality traits of synthetic ...

Indian Academy of Sciences (India)

As for protein content, similar results were found in the F2 plants and their maternal parents. ... doubled haploid; genetic analysis; gene interaction; agronomic traits; seed ..... Han J. Q. and Liu H. L. 1993 Principal component analysis for main.

When three traits make a line: evolution of phenotypic plasticity and genetic assimilation through linear reaction norms in stochastic environments.

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Ergon, T; Ergon, R

2017-03-01

Genetic assimilation emerges from selection on phenotypic plasticity. Yet, commonly used quantitative genetics models of linear reaction norms considering intercept and slope as traits do not mimic the full process of genetic assimilation. We argue that intercept-slope reaction norm models are insufficient representations of genetic effects on linear reaction norms and that considering reaction norm intercept as a trait is unfortunate because the definition of this trait relates to a specific environmental value (zero) and confounds genetic effects on reaction norm elevation with genetic effects on environmental perception. Instead, we suggest a model with three traits representing genetic effects that, respectively, (i) are independent of the environment, (ii) alter the sensitivity of the phenotype to the environment and (iii) determine how the organism perceives the environment. The model predicts that, given sufficient additive genetic variation in environmental perception, the environmental value at which reaction norms tend to cross will respond rapidly to selection after an abrupt environmental change, and eventually becomes equal to the new mean environment. This readjustment of the zone of canalization becomes completed without changes in genetic correlations, genetic drift or imposing any fitness costs of maintaining plasticity. The asymptotic evolutionary outcome of this three-trait linear reaction norm generally entails a lower degree of phenotypic plasticity than the two-trait model, and maximum expected fitness does not occur at the mean trait values in the population. © 2016 The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.

Estimating non-genetic and genetic parameters of pre-weaning growth traits in Raini Cashmere goat.

Science.gov (United States)

Barazandeh, Arsalan; Moghbeli, Sadrollah Molaei; Vatankhah, Mahmood; Mohammadabadi, Mohammadreza

2012-04-01

Data and pedigree information used in the present study were 3,022 records of kids obtained from the breeding station of Raini goat. The studied traits were birth weight (BW), weaning weight (WW), average daily gain from birth to weaning (ADG) and Kleiber ratio at weaning (KR). The model included the fixed effects of sex of kid, type of birth, age of dam, year of birth, month of birth, and age of kid (days) as covariate that had significant effects, and random effects direct additive genetic, maternal additive genetic, maternal permanent environmental effects and residual. (Co) variance components were estimated using univariate and multivariate analysis by WOMBAT software applying four animal models including and ignoring maternal effects. Likelihood ratio test used to determine the most appropriate models. Heritability (h(a)(2)) estimates for BW, WW, ADG, and KR according to suitable model were 0.12 ± 0.05, 0.08 ± 0.06, 0.10 ± 0.06, and 0.06 ± 0.05, respectively. Estimates of the proportion of maternal permanent environmental effect to phenotypic variance (c(2)) were 0.17 ± 0.03, 0.07 ± 0.03, and 0.07 ± 0.03 for BW, WW, and ADG, respectively. Genetic correlations among traits were positive and ranged from 0.53 (BW-ADG) to 1.00 (WW-ADG, WW-KR, and ADG-KR). The maternal permanent environmental correlations between BW-WW, BW-ADG, and WW-ADG were 0.54, 0.48, and 0.99, respectively. Results indicated that maternal effects, especially maternal permanent environmental effects are an important source of variation in pre-weaning growth trait and ignoring those in the model redound incorrect genetic evaluation of kids.

Genetic diversity, population structure and marker-trait associations for agronomic and grain traits in wild diploid wheat Triticum urartu.

Science.gov (United States)

Wang, Xin; Luo, Guangbin; Yang, Wenlong; Li, Yiwen; Sun, Jiazhu; Zhan, Kehui; Liu, Dongcheng; Zhang, Aimin

2017-07-01

Wild diploid wheat, Triticum urartu (T. urartu) is the progenitor of bread wheat, and understanding its genetic diversity and genome function will provide considerable reference for dissecting genomic information of common wheat. In this study, we investigated the morphological and genetic diversity and population structure of 238 T. urartu accessions collected from different geographic regions. This collection had 19.37 alleles per SSR locus and its polymorphic information content (PIC) value was 0.76, and the PIC and Nei's gene diversity (GD) of high-molecular-weight glutenin subunits (HMW-GSs) were 0.86 and 0.88, respectively. UPGMA clustering analysis indicated that the 238 T. urartu accessions could be classified into two subpopulations, of which Cluster I contained accessions from Eastern Mediterranean coast and those from Mesopotamia and Transcaucasia belonged to Cluster II. The wide range of genetic diversity along with the manageable number of accessions makes it one of the best collections for mining valuable genes based on marker-trait association. Significant associations were observed between simple sequence repeats (SSR) or HMW-GSs and six morphological traits: heading date (HD), plant height (PH), spike length (SPL), spikelet number per spike (SPLN), tiller angle (TA) and grain length (GL). Our data demonstrated that SSRs and HMW-GSs were useful markers for identification of beneficial genes controlling important traits in T. urartu, and subsequently for their conservation and future utilization, which may be useful for genetic improvement of the cultivated hexaploid wheat.

Genetic diversity in radish germplasm for morphological traits and seed storage proteins

International Nuclear Information System (INIS)

Jatoi, S.A.; Siddiqui, S.U.; Masood, M.S.; Javaid, A.; Iqbal, M.; Sayal, O.U.

2011-01-01

Genetic variation of forty-nine local and exotic radish genotypes including two checks was studied for morphological traits and seed storage protein electrophoresis using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) markers. A high variation in germplasm for root shape, root length, root colour (internal and external), flesh texture and root type was observed. Among these genotypes, the genetic variation was apparent for most of the characters like plant biomass, root weight, leaf length, root length and root diameter that indicated the potential for crop improvement in these traits through simple selection. Exotic germplasm exhibited higher variation for plant biomass, root weight and root length which could be utilized through breeding programme. Cluster analysis on the basis of genetic diversity for seven quantitative traits resulted into four clusters. No clustering was found on the basis of origin. Low level of variance was observed for SDS-PAGE electrophoresis that suggested acquisition of more germplasm. On the basis of high yield and crispy root texture some genotypes (10076, 10362, 10429, 10658, 10662 and 10667) were identified for further testing under wide range of agro-ecological conditions. (author)

"Are we there yet?": Deciding when one has demonstrated specific genetic causation in complex diseases and quantitative traits.

Science.gov (United States)

Page, Grier P; George, Varghese; Go, Rodney C; Page, Patricia Z; Allison, David B

2003-10-01

Although mathematical relationships can be proven by deductive logic, biological relationships can only be inferred from empirical observations. This is a distinct disadvantage for those of us who strive to identify the genes involved in complex diseases and quantitative traits. If causation cannot be proven, however, what does constitute sufficient evidence for causation? The philosopher Karl Popper said, "Our belief in a hypothesis can have no stronger basis than our repeated unsuccessful critical attempts to refute it." We believe that to establish causation, as scientists, we must make a serious attempt to refute our own hypotheses and to eliminate all known sources of bias before association becomes causation. In addition, we suggest that investigators must provide sufficient data and evidence of their unsuccessful efforts to find any confounding biases. In this editorial, we discuss what "causation" means in the context of complex diseases and quantitative traits, and we suggest guidelines for steps that may be taken to address possible confounders of association before polymorphisms may be called "causative."

Novel applications of multitask learning and multiple output regression to multiple genetic trait prediction.

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He, Dan; Kuhn, David; Parida, Laxmi

2016-06-15

Given a set of biallelic molecular markers, such as SNPs, with genotype values encoded numerically on a collection of plant, animal or human samples, the goal of genetic trait prediction is to predict the quantitative trait values by simultaneously modeling all marker effects. Genetic trait prediction is usually represented as linear regression models. In many cases, for the same set of samples and markers, multiple traits are observed. Some of these traits might be correlated with each other. Therefore, modeling all the multiple traits together may improve the prediction accuracy. In this work, we view the multitrait prediction problem from a machine learning angle: as either a multitask learning problem or a multiple output regression problem, depending on whether different traits share the same genotype matrix or not. We then adapted multitask learning algorithms and multiple output regression algorithms to solve the multitrait prediction problem. We proposed a few strategies to improve the least square error of the prediction from these algorithms. Our experiments show that modeling multiple traits together could improve the prediction accuracy for correlated traits. The programs we used are either public or directly from the referred authors, such as MALSAR (http://www.public.asu.edu/~jye02/Software/MALSAR/) package. The Avocado data set has not been published yet and is available upon request. dhe@us.ibm.com. © The Author 2016. Published by Oxford University Press.

Population-genetic analysis of seven qualitative traits in the population of the municipality Maglaj (Bosnia and Herzegovina

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Mrehić Elma

2015-01-01

Full Text Available On the basis of the complex seven monogenic qualitative characteristics (shape of the earlobes, hairiness of middle phalange, flexibility of lateral tongue edges, the extensiveness of the distal and proximal joint of the thumb and the flexibility of the distal phalanx of the little finger and one sexually conditioned property (digital index we analyzed the genetic structure of four populations of rural municipality Maglaj: Kosova, Novi Šeher, Jablanica, Moševac, then one isolated local population Ravna and one urban population area called Maglaj. The survey covered a total of 440 students (213 girls and 227 boys aged 11-18 years. According to the degree of genetic heterogeneity, values of Wahlund variance that are obtained for each trait belong in the category of low genetic differentiation. The maximum value of Wahlund variance was identified for the property shape of the earlobes (by Cavalli - Sforza, Bodmer = 0.0452, and the lowest for phenotypic system flexibility of lateral tongue edges (by Cavalli - Sforza, Bodmer = 0.0000. Studied set of population is the most heterogeneous according to the frequency of recessive allelogene for phenotypic characteristic shape of the earlobes, and the most homogeneous for the phenotypic trait flexibility of lateral tongue edge. Based on the analysis of genetic distance for seven phenotypic traits in populations of municipality Maglaj we established the minimum genetic distance between populations of Kosova and Maglaj (fθ = 0.0007, and the largest genetic distance between populations of Jablanica and Moševac (fθ = 0.0144. It was noted that the lowest average coefficient of kinship has a local population of Kosova (fθ = 0.0028, while the highest average coefficient of kinship has a population Moševac (fθ = 0.0081. The greatest characteristic has a population of Moševac (fθs = 0.7556, and the lowest characteristic has a population of Novi Šeher (fθs = -0.0795. Based on the obtained values of

Genetic gain and economic values of selection strategies including semen traits in three- and four-way crossbreeding systems for swine production.

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González-Peña, D; Knox, R V; MacNeil, M D; Rodriguez-Zas, S L

2015-03-01

Four semen traits: volume (VOL), concentration (CON), progressive motility of spermatozoa (MOT), and abnormal spermatozoa (ABN) provide complementary information on boar fertility. Assessment of the impact of selection for semen traits is hindered by limited information on economic parameters. Objectives of this study were to estimate economic values for semen traits and to evaluate the genetic gain when these traits are incorporated into traditional selection strategies in a 3-tier system of swine production. Three-way (maternal nucleus lines A and B and paternal nucleus line C) and 4-way (additional paternal nucleus line D) crossbreeding schemes were compared. A novel population structure that accommodated selection for semen traits was developed. Three selection strategies were simulated. Selection Strategy I (baseline) encompassed selection for maternal traits: number of pigs born alive (NBA), litter birth weight (LBW), adjusted 21-d litter weight (A21), and number of pigs at 21 d (N21); and paternal traits: number of days to 113.5 kg (D113), backfat (BF), ADG, feed efficiency (FE), and carcass lean % (LEAN). Selection Strategy II included Strategy I and the number of usable semen doses per collection (DOSES), a function of the 4 semen traits. Selection Strategy III included Strategy I and the 4 semen traits individually. The estimated economic values of VOL, CON, MOT, ABN, and DOSES for 7 to 1 collections/wk ranged from $0.21 to $1.44/mL, $0.12 to $0.83/10 spermatozoa/mm, $0.61 to $12.66/%, -$0.53 to -$10.88/%, and $2.01 to $41.43/%, respectively. The decrease in the relative economic values of semen traits and DOSES with higher number of collections per wk was sharper between 1 and 2.33 collections/wk than between 2.33 and 7 collections/wk. The higher economic value of MOT and ABN relative to VOL and CON could be linked to the genetic variances and covariances of these traits. Average genetic gains for the maternal traits were comparable across strategies

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

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

2016-01-01

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

Dose response behaviour of water scarcity towards genetical and morphological traits in spring wheat

International Nuclear Information System (INIS)

Noorkha, I.R.; Tabasum, S.

2015-01-01

Combining ability was studied in a Line * Tester mating fashion in wheat (Tricticum aestivum L.). Significant differences were observed for all the yield and yield contributing traits. GCA and SCA components of variation were found significant for most of the traits. Under water stressed conditions among lines the genotype Kohistan-97 revealed significant GCA effects for all the traits except spike length. Among testers, the genotype V08172 showed significant effects for the traits spike length, 1000-grain weight and flag leaf area. Based on desirable SCA effects and mean performance the cross combinations Kohistan-97 * V08172, Chakwal-86 * Punjab-81, Fsd-2008 * Punjab-81, Sehar-2006 * V08172 and Chakwal-86 * V08172 behaved best combiner to tolerate the water stress. Results of genetic analysis offered over dominance type of gene action that remained unchanged with the change in water provision for the traits like 1000 grain weight and economic yield. Similarly additive gene action was observed for the trait plant height under both normal irrigation and water stress conditions. However the cumulative genetic effects to control the expression of yield and yield components was shifted due to the changed environments. The study was concluded that due to presence of additive variance, selection could be practiced in early generation whereas in the presence of recessiveness the selection may be delayed up to the later generations. Plant traits associated with water stress tolerance having high heritability and with additive gene action may be used as indirect selection criteria for early selection of water stress tolerant genotypes. The information generated as a result of this study on genetic analysis of important economic traits of wheat under contrasting water availability positions will be of great value to the wheat breeders to design future breeding programmes. (author)

From observational to dynamic genetics

Directory of Open Access Journals (Sweden)

Claire M. A. Haworth

2014-01-01

Full Text Available Twin and family studies have shown that most traits are at least moderately heritable. But what are the implications of finding genetic influence for the design of intervention and prevention programs? For complex traits, heritability does not mean immutability, and research has shown that genetic influences can change with age, context and in response to behavioural and drug interventions. The most significant implications for intervention will come when we move from observational genetics to investigating dynamic genetics, including genetically sensitive interventions. Future interventions should be designed to overcome genetic risk and draw upon genetic strengths by changing the environment.

Analyses of genetic relationships between linear type traits, fat-to-protein ratio, milk production traits, and somatic cell count in first-parity Czech Holstein cows

DEFF Research Database (Denmark)

Zink, V; Zavadilová, L; Lassen, Jan

2014-01-01

. The number of animals for each linear type trait was 59 454, except for locomotion, for which 53 424 animals were recorded. The numbers of animals with records of milk production data were 43 992 for milk yield, fat percentage, protein percentage, and fat-to-protein percentage ratio and 43 978 for fat yield...... and protein yield. In total, 27 098 somatic cell score records were available. The strongest positive genetic correlation between production traits and linear type traits was estimated between udder width and fat yield (0.51 ± 0.04), while the strongest negative correlation estimated was between body......Genetic and phenotypic correlations between production traits, selected linear type traits, and somatic cell score were estimated. The results could be useful for breeding programs involving Czech Holstein dairy cows or other populations. A series of bivariate analyses was applied whereby (co...

Genetic correlations between methane production and fertility, health, and body type traits in Danish Holstein cows.

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Zetouni, L; Kargo, M; Norberg, E; Lassen, J

2018-03-01

Our aim was to investigate the genetic correlations between CH 4 production and body conformation, fertility, and health traits in dairy cows. Data were collected from 10 commercial Holstein herds in Denmark, including 5,758 cows with records for body conformation traits, 7,390 for fertility traits, 7,439 for health traits, and 1,397 with individual CH 4 measurements. Methane production was measured during milking in automatic milking systems, using a sniffer approach. Correlations between CH 4 and several different traits were estimated. These traits were interval between calving and first insemination, interval between first and last insemination, number of inseminations, udder diseases, other diseases, height, body depth, chest width, dairy character, top line, and body condition score. Bivariate linear models were used to estimate the genetic parameters within and between CH 4 and the other traits. In general, the genetic correlations between CH 4 and the traits investigated were low. The heritability of CH 4 was 0.25, and ranged from 0.02 to 0.07 for fertility and health traits, and from 0.17 to 0.74 for body conformation traits. Further research with a larger data set should be performed to more accurately establish how CH 4 relates to fertility, health, and body conformation traits in dairy cattle. This will be useful in the design of future breeding goals that consider the production of CH 4 . The Authors. Published by the Federation of Animal Science Societies and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

In situ genetic association for serotiny, a fire-related trait, in Mediterranean maritime pine (Pinus pinaster).

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Budde, Katharina B; Heuertz, Myriam; Hernández-Serrano, Ana; Pausas, Juli G; Vendramin, Giovanni G; Verdú, Miguel; González-Martínez, Santiago C

2014-01-01

Wildfire is a major ecological driver of plant evolution. Understanding the genetic basis of plant adaptation to wildfire is crucial, because impending climate change will involve fire regime changes worldwide. We studied the molecular genetic basis of serotiny, a fire-related trait, in Mediterranean maritime pine using association genetics. A single nucleotide polymorphism (SNP) set was used to identify genotype : phenotype associations in situ in an unstructured natural population of maritime pine (eastern Iberian Peninsula) under a mixed-effects model framework. RR-BLUP was used to build predictive models for serotiny in this region. Model prediction power outside the focal region was tested using independent range-wide serotiny data. Seventeen SNPs were potentially associated with serotiny, explaining approximately 29% of the trait phenotypic variation in the eastern Iberian Peninsula. Similar prediction power was found for nearby geographical regions from the same maternal lineage, but not for other genetic lineages. Association genetics for ecologically relevant traits evaluated in situ is an attractive approach for forest trees provided that traits are under strong genetic control and populations are unstructured, with large phenotypic variability. This will help to extend the research focus to ecological keystone non-model species in their natural environments, where polymorphisms acquired their adaptive value. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Arms race between selfishness and policing: two-trait quantitative genetic model for caste fate conflict in eusocial Hymenoptera.

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Dobata, Shigeto

2012-12-01

Policing against selfishness is now regarded as the main force maintaining cooperation, by reducing costly conflict in complex social systems. Although policing has been studied extensively in social insect colonies, its coevolution against selfishness has not been fully captured by previous theories. In this study, I developed a two-trait quantitative genetic model of the conflict between selfish immature females (usually larvae) and policing workers in eusocial Hymenoptera over the immatures' propensity to develop into new queens. This model allows for the analysis of coevolution between genomes expressed in immatures and workers that collectively determine the immatures' queen caste fate. The main prediction of the model is that a higher level of polyandry leads to a smaller fraction of queens produced among new females through caste fate policing. The other main prediction of the present model is that, as a result of arms race, caste fate policing by workers coevolves with exaggerated selfishness of the immatures achieving maximum potential to develop into queens. Moreover, the model can incorporate genetic correlation between traits, which has been largely unexplored in social evolution theory. This study highlights the importance of understanding social traits as influenced by the coevolution of conflicting genomes. © 2012 The Author. Evolution© 2012 The Society for the Study of Evolution.

Genetic disparity and relationship among quantitatively inherited yield related traits in diallel crosses of upland cotton

International Nuclear Information System (INIS)

Bibi, M.; Khan, N.U.; Mohammad, F.; Gul, R.; Idrees, M.; Sayal, O.U.; Khakwani, A.A.; Khan, I.A.

2011-01-01

In quantitative genetics, development of high yielding genotypes from parental cultivars of same ancestry is some what confusing as compared to genetically diverse parents. However, sufficient recombinations through allelic variations in mating of closely-related populations result in superior agronomic performance. Development of improved cotton genotypes is one of the prime objectives of any cotton breeding programmes. Genetic divergence and yield potential of parental cotton genotypes versus their diallel hybrids, relationship of yield with various morpho-yield traits and their heritability were studied in 8 X 8 F/sub 1/ diallel hybrids and their parental cultivars in Gossypium hirsutum L. during 2008-09 at Khyber Pakhtunkhwa Agricultural University, Peshawar, Pakistan. Highly significant (p less than or equal to 0.01) differences were observed among parental genotypes and F/sub 1/ populations for all the traits. Results revealed that F/sub 1/ hybrids i.e., CIM-506 X CIM-554, CIM-473 X CIM-554, CIM-446 X CIM-496 and CIM-446 X CIM-554 produced significantly higher number of sympodia, bolls per populations showed incredible performance for plant height, locules per boll and seeds plant and seed cotton yield. Some F/sub 1/ per locule. Seed cotton yield manifested positive association with morpho-yield traits which also accounted for greater genetic variations to yield being dependent trait. Heritabilities (broad sense) were moderate to high in magnitude for all populations with larger genetic potential, positive relationship between yield and yield traits. Results revealed that F1 contributing traits and moderate to high heritability can guide intensive selection and improvement per se in segregating populations. (author)

Genetic and Phenotypic Correlations between Performance Traits with Meat Quality and Carcass Characteristics in Commercial Crossbred Pigs

Science.gov (United States)

Miar, Younes; Plastow, Graham; Bruce, Heather; Moore, Stephen; Manafiazar, Ghader; Kemp, Robert; Charagu, Patrick; Huisman, Abe; van Haandel, Benny; Zhang, Chunyan; McKay, Robert; Wang, Zhiquan

2014-01-01

Genetic correlations between performance traits with meat quality and carcass traits were estimated on 6,408 commercial crossbred pigs with performance traits recorded in production systems with 2,100 of them having meat quality and carcass measurements. Significant fixed effects (company, sex and batch), covariates (birth weight, cold carcass weight, and age), random effects (additive, litter and maternal) were fitted in the statistical models. A series of pairwise bivariate analyses were implemented in ASREML to estimate heritability, phenotypic, and genetic correlations between performance traits (n = 9) with meat quality (n = 25) and carcass (n = 19) traits. The animals had a pedigree compromised of 9,439 animals over 15 generations. Performance traits had low-to-moderate heritabilities (±SE), ranged from 0.07±0.13 to 0.45±0.07 for weaning weight, and ultrasound backfat depth, respectively. Genetic correlations between performance and carcass traits were moderate to high. The results indicate that: (a) selection for birth weight may increase drip loss, lightness of longissimus dorsi, and gluteus medius muscles but may reduce fat depth; (b) selection for nursery weight can be valuable for increasing both quantity and quality traits; (c) selection for increased daily gain may increase the carcass weight and most of the primal cuts. These findings suggest that deterioration of pork quality may have occurred over many generations through the selection for less backfat thickness, and feed efficiency, but selection for growth had no adverse effects on pork quality. Low-to-moderate heritabilities for performance traits indicate that they could be improved using traditional selection or genomic selection. The estimated genetic parameters for performance, carcass and meat quality traits may be incorporated into the breeding programs that emphasize product quality in these Canadian swine populations. PMID:25350845

Genetic relationships between body condition score and reproduction traits in Canadian Holstein and Ayrshire first-parity cows.

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Bastin, C; Loker, S; Gengler, N; Sewalem, A; Miglior, F

2010-05-01

The objective of this study was to investigate the genetic relationship between body condition score (BCS) and reproduction traits for first-parity Canadian Ayrshire and Holstein cows. Body condition scores were collected by field staff several times over the lactation in herds from Québec, and reproduction records (including both fertility and calving traits) were extracted from the official database used for the Canadian genetic evaluation of those herds. For each breed, six 2-trait animal models were run; they included random regressions that allowed the estimation of genetic correlations between BCS over the lactation and reproduction traits that are measured as a single lactation record. Analyses were undertaken on data from 108 Ayrshire herds and 342 Holstein herds. Average daily heritabilities of BCS were close to 0.13 for both breeds; these relatively low estimates might be explained by the high variability among herds and BCS evaluators. Genetic correlations between BCS and interval fertility traits (days from calving to first service, days from first service to conception, and days open) were negative and ranged between -0.77 and -0.58 for Ayrshire and between -0.31 and -0.03 for Holstein. Genetic correlations between BCS and 56-d nonreturn rate at first insemination were positive and moderate. The trends of these genetic correlations over the lactation suggest that a genetically low BCS in early lactation would increase the number of days that the primiparous cow was not pregnant and would decrease the chances of the primiparous cow to conceive at first service. Genetic correlations between BCS and calving traits were generally the strongest at calving and decreased with increasing days in milk. The correlation between BCS at calving and maternal calving ease was 0.21 for Holstein and 0.31 for Ayrshire and emphasized the relationship between fat cows around calving and dystocia. Genetic correlations between calving traits and BCS during the subsequent

Genetic parameters for carcass and ultrasound traits in Hereford and admixed Simmental beef cattle: Accuracy of evaluating carcass traits.

Science.gov (United States)

Su, H; Golden, B; Hyde, L; Sanders, S; Garrick, D

2017-11-01

Genetic parameters are required to evaluate carcass merit using correlated real-time ultrasound (RTU) measurements. Many registered bulls and heifers are measured using RTU before consideration for selection as parents, whereas few animals are recorded for carcass traits and those are often crossbred steers. The objective of this study was to estimate genetic parameters required for evaluating carcass merit in the American Hereford Association (AHA) and the American Simmental Association (ASA) using multivariate models and to assess accuracy of carcass trait estimated breeding values (EBV) for selection candidates. All available carcass data including carcass weight (CWT), fat thickness (FAT), longissimus muscle area (LMA), and marbling score (MRB) were provided by the AHA and the ASA along with RTU data including fat thickness (UFAT), longissimus muscle area (ULMA), and percentage of intramuscular fat (UIMF). Carcass data comprised 6,054 AHA and 9,056 ASA cattle, while RTU data in comparable numbers from close relatives comprised 6,074 AHA and 7,753 ASA cattle. Pedigrees included 33,226 AHA and 37,665 ASA animals. Fixed effects for carcass and RTU data included contemporary group, age at scan/slaughter, and major breed percentages. Restricted maximum likelihood procedures were applied to all the carcass and RTU measurements, along with birth weight to account for selection, fitting 8-trait multivariate models separately for each breed association. Heritability estimates for AHA and ASA carcass traits were 0.41 ± 0.04 and 0.25 ± 0.03 for FAT, 0.47 ± 0.04 and 0.32 ± 0.03 for LMA, 0.48 ± 0.04 and 0.43 ± 0.04 for MRB, 0.51 ± 0.04 and 0.34 ± 0.03 for CWT, and for RTU traits were 0.29 ± 0.04 and 0.37 ± 0.03 for UFAT, 0.31 ± 0.04 and 0.44 ± 0.03 for ULMA, and 0.45 ± 0.04 and 0.42 ± 0.03 for UIMF. Genetic correlations for AHA and ASA analyses between FAT and UFAT were 0.74 ± 0.08 and 0.28 ± 0.13, between LMA and ULMA were 0.81 ± 0.07 and 0.57 ± 0.10, and

Estimation of genetic parameters for milk traits in Romanian local sheep breed

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Pelmus RS

2014-03-01

Full Text Available Objective. Estimate the genetic parameters for milk traits in a Romanian local sheep population Teleorman Black Head. Material and methods. Records of 262 sheep belonging to 17 rams and 139 ewes were used in the study. The following traits were investigated: milk yield, fat yield, protein yield, fat percentage and protein percentage. The genetic parameters were estimated using the Restricted Maximum Likelihood method, with a model including maternal effects. Results. The results from our study revealed that direct heritability estimates were moderate for milk yield (0.449, fat yield (0.442, protein yield (0.386 while for protein percentage (0.708 and fat percentage (0.924 were high. The high direct and maternal genetic correlation was between milk yield and protein yield (0.979, 0.973 and between protein yield and fat yield (0.952, 0.913 while the phenotypic correlation between the milk yield and fat yield (0.968, the milk yield and protein yield (0.967, fat yield and protein yield (0.936 was high and positive. Conclusions. The genetic parameters are important in selection program on this breed for genetic improvement.

Genetic characterisation of seed yield and fertility traits in perennial ryegrass (Lolium perenne L.)

DEFF Research Database (Denmark)

Studer, Bruno; Jensen, Louise Bach; Hentrup, Stephan

2008-01-01

A population. Path analysis partitioned the direct and indirect effects of seed yield components on seed yield per plant. Seed yield per panicle showed the highest effect on total seed yield. The adjusted mean values of each trait and a genetic linkage map consisting of 97 anonymous and 85 gene associated DNA......Seed yield is a trait of major interest for the key grassland species Lolium perenne L. An F2 mapping population of perennial ryegrass (VrnA), recently characterised for vernalisation response, was assessed in a glasshouse for traits related to seed yield based on a lattice design with four...... replications over 2 years. The traits heading date, plant height, length of panicles, number of panicles per plant, seed yield per panicle, flag leaf length, flag leaf width and seed yield per plant revealed repeatabilities ranging from 41 to 76% and a considerable amount of genetic variation in the Vrn...

Population genetics of non-genetic traits: Evolutionary roles of stochasticity in gene expression

KAUST Repository

Mineta, Katsuhiko

2015-05-01

The role of stochasticity in evolutionary genetics has long been debated. To date, however, the potential roles of non-genetic traits in evolutionary processes have been largely neglected. In molecular biology, growing evidence suggests that stochasticity in gene expression (SGE) is common and that SGE has major impacts on phenotypes and fitness. Here, we provide a general overview of the potential effects of SGE on population genetic parameters, arguing that SGE can indeed have a profound effect on evolutionary processes. Our analyses suggest that SGE potentially alters the fate of mutations by influencing effective population size and fixation probability. In addition, a genetic control of SGE magnitude could evolve under certain conditions, if the fitness of the less-fit individual increases due to SGE and environmental fluctuation. Although empirical evidence for our arguments is yet to come, methodological developments for precisely measuring SGE in living organisms will further advance our understanding of SGE-driven evolution.

Population genetics of non-genetic traits: Evolutionary roles of stochasticity in gene expression

KAUST Repository

Mineta, Katsuhiko; Matsumoto, Tomotaka; Osada, Naoki; Araki, Hitoshi

2015-01-01

The role of stochasticity in evolutionary genetics has long been debated. To date, however, the potential roles of non-genetic traits in evolutionary processes have been largely neglected. In molecular biology, growing evidence suggests that stochasticity in gene expression (SGE) is common and that SGE has major impacts on phenotypes and fitness. Here, we provide a general overview of the potential effects of SGE on population genetic parameters, arguing that SGE can indeed have a profound effect on evolutionary processes. Our analyses suggest that SGE potentially alters the fate of mutations by influencing effective population size and fixation probability. In addition, a genetic control of SGE magnitude could evolve under certain conditions, if the fitness of the less-fit individual increases due to SGE and environmental fluctuation. Although empirical evidence for our arguments is yet to come, methodological developments for precisely measuring SGE in living organisms will further advance our understanding of SGE-driven evolution.

Genetic and phenotypic variance and covariance components for methane emission and postweaning traits in Angus cattle.

Science.gov (United States)

Donoghue, K A; Bird-Gardiner, T; Arthur, P F; Herd, R M; Hegarty, R F

2016-04-01

Ruminants contribute 80% of the global livestock greenhouse gas (GHG) emissions mainly through the production of methane, a byproduct of enteric microbial fermentation primarily in the rumen. Hence, reducing enteric methane production is essential in any GHG emissions reduction strategy in livestock. Data on 1,046 young bulls and heifers from 2 performance-recording research herds of Angus cattle were analyzed to provide genetic and phenotypic variance and covariance estimates for methane emissions and production traits and to examine the interrelationships among these traits. The cattle were fed a roughage diet at 1.2 times their estimated maintenance energy requirements and measured for methane production rate (MPR) in open circuit respiration chambers for 48 h. Traits studied included DMI during the methane measurement period, MPR, and methane yield (MY; MPR/DMI), with means of 6.1 kg/d (SD 1.3), 132 g/d (SD 25), and 22.0 g/kg (SD 2.3) DMI, respectively. Four forms of residual methane production (RMP), which is a measure of actual minus predicted MPR, were evaluated. For the first 3 forms, predicted MPR was calculated using published equations. For the fourth (RMP), predicted MPR was obtained by regression of MPR on DMI. Growth and body composition traits evaluated were birth weight (BWT), weaning weight (WWT), yearling weight (YWT), final weight (FWT), and ultrasound measures of eye muscle area, rump fat depth, rib fat depth, and intramuscular fat. Heritability estimates were moderate for MPR (0.27 [SE 0.07]), MY (0.22 [SE 0.06]), and the RMP traits (0.19 [SE 0.06] for each), indicating that genetic improvement to reduce methane emissions is possible. The RMP traits and MY were strongly genetically correlated with each other (0.99 ± 0.01). The genetic correlation of MPR with MY as well as with the RMP traits was moderate (0.32 to 0.63). The genetic correlation between MPR and the growth traits (except BWT) was strong (0.79 to 0.86). These results indicate that

Litter size, fur quality and genetic analyses of American mink

DEFF Research Database (Denmark)

Thirstrup, Janne Pia

of the skin, have been analyzed. Both fur quality traits and litter size are complex traits underlying quantitative genetic variation. Methods for estimating genetic variance, spanning from pedigree information to the use of different genetic markers, have been utilized in order to gain knowledge about...

Makeup of the genetic correlation between milk production traits using genome-wide single nucleotide polymorphism information.

Science.gov (United States)

van Binsbergen, R; Veerkamp, R F; Calus, M P L

2012-04-01

The correlated responses between traits may differ depending on the makeup of genetic covariances, and may differ from the predictions of polygenic covariances. Therefore, the objective of the present study was to investigate the makeup of the genetic covariances between the well-studied traits: milk yield, fat yield, protein yield, and their percentages in more detail. Phenotypic records of 1,737 heifers of research farms in 4 different countries were used after homogenizing and adjusting for management effects. All cows had a genotype for 37,590 single nucleotide polymorphisms (SNP). A bayesian stochastic search variable selection model was used to estimate the SNP effects for each trait. About 0.5 to 1.0% of the SNP had a significant effect on 1 or more traits; however, the SNP without a significant effect explained most of the genetic variances and covariances of the traits. Single nucleotide polymorphism correlations differed from the polygenic correlations, but only 10 regions were found with an effect on multiple traits; in 1 of these regions the DGAT1 gene was previously reported with an effect on multiple traits. This region explained up to 41% of the variances of 4 traits and explained a major part of the correlation between fat yield and fat percentage and contributes to asymmetry in correlated response between fat yield and fat percentage. Overall, for the traits in this study, the infinitesimal model is expected to be sufficient for the estimation of the variances and covariances. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Heritability, genetic advance and correlation studies of some important traits in rice

International Nuclear Information System (INIS)

Bughio, H.R.; Asad, M.A.; Arain, M.A.; Bughio, M.S.

2009-01-01

Genetic variability, estimates of broad sense heritability, genetic advance as percent of mean and genotypic and phenotypic correlation coefficients were observed in eight rice genotypes at Nuclear Institute of Agriculture, Tando Jam in 2005. High heritability coupled with high genetic advance was exhibited for number of fertile grains per panicle, number of productive tillers per plant and grain yield per plant, indicating additive gene action and possibility of improving these traits by simple selection. High heritability with moderate genetic advance was exhibited for plant height, 1000-grain weight and panicle length indicating the involvement of additive and non-additive type of gene action and postponement of selection programs for the improvement of these traits. The characters productive tillers per plant, panicle length, number of fertile grains per panicle, panicle fertility percentage and 1000-grain weight showed significant positive correlation with grain yield per plant. While plant height and days to 50% flowering were observed non-significant and negatively correlated with grain yield per plant. Fertile grain had significant and positive correlation with panicle fertility percentage. (author)

Genetic parameters for female fertility, locomotion, body condition score, and linear type traits in Czech Holstein cattle

DEFF Research Database (Denmark)

Zink, Vojtech; Stipkova, M; Lassen, Jan

2011-01-01

The aim of this study was to estimate genetic parameters for fertility traits and linear type traits in the Czech Holstein dairy cattle population. Phenotypic data regarding 12 linear type traits, measured in first lactation, and 3 fertility traits, measured in each of first and second lactation,...

A Simple Test of Class-Level Genetic Association Can Reveal Novel Cardiometabolic Trait Loci.

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Jing Qian

Full Text Available Characterizing the genetic determinants of complex diseases can be further augmented by incorporating knowledge of underlying structure or classifications of the genome, such as newly developed mappings of protein-coding genes, epigenetic marks, enhancer elements and non-coding RNAs.We apply a simple class-level testing framework, termed Genetic Class Association Testing (GenCAT, to identify protein-coding gene association with 14 cardiometabolic (CMD related traits across 6 publicly available genome wide association (GWA meta-analysis data resources. GenCAT uses SNP-level meta-analysis test statistics across all SNPs within a class of elements, as well as the size of the class and its unique correlation structure, to determine if the class is statistically meaningful. The novelty of findings is evaluated through investigation of regional signals. A subset of findings are validated using recently updated, larger meta-analysis resources. A simulation study is presented to characterize overall performance with respect to power, control of family-wise error and computational efficiency. All analysis is performed using the GenCAT package, R version 3.2.1.We demonstrate that class-level testing complements the common first stage minP approach that involves individual SNP-level testing followed by post-hoc ascribing of statistically significant SNPs to genes and loci. GenCAT suggests 54 protein-coding genes at 41 distinct loci for the 13 CMD traits investigated in the discovery analysis, that are beyond the discoveries of minP alone. An additional application to biological pathways demonstrates flexibility in defining genetic classes.We conclude that it would be prudent to include class-level testing as standard practice in GWA analysis. GenCAT, for example, can be used as a simple, complementary and efficient strategy for class-level testing that leverages existing data resources, requires only summary level data in the form of test statistics, and

Genetic parameter estimates for carcass traits and visual scores including or not genomic information.

Science.gov (United States)

Gordo, D G M; Espigolan, R; Tonussi, R L; Júnior, G A F; Bresolin, T; Magalhães, A F Braga; Feitosa, F L; Baldi, F; Carvalheiro, R; Tonhati, H; de Oliveira, H N; Chardulo, L A L; de Albuquerque, L G

2016-05-01

The objective of this study was to determine whether visual scores used as selection criteria in Nellore breeding programs are effective indicators of carcass traits measured after slaughter. Additionally, this study evaluated the effect of different structures of the relationship matrix ( and ) on the estimation of genetic parameters and on the prediction accuracy of breeding values. There were 13,524 animals for visual scores of conformation (CS), finishing precocity (FP), and muscling (MS) and 1,753, 1,747, and 1,564 for LM area (LMA), backfat thickness (BF), and HCW, respectively. Of these, 1,566 animals were genotyped using a high-density panel containing 777,962 SNP. Six analyses were performed using multitrait animal models, each including the 3 visual scores and 1 carcass trait. For the visual scores, the model included direct additive genetic and residual random effects and the fixed effects of contemporary group (defined by year of birth, management group at yearling, and farm) and the linear effect of age of animal at yearling. The same model was used for the carcass traits, replacing the effect of age of animal at yearling with the linear effect of age of animal at slaughter. The variance and covariance components were estimated by the REML method in analyses using the numerator relationship matrix () or combining the genomic and the numerator relationship matrices (). The heritability estimates for the visual scores obtained with the 2 methods were similar and of moderate magnitude (0.23-0.34), indicating that these traits should response to direct selection. The heritabilities for LMA, BF, and HCW were 0.13, 0.07, and 0.17, respectively, using matrix and 0.29, 0.16, and 0.23, respectively, using matrix . The genetic correlations between the visual scores and carcass traits were positive, and higher correlations were generally obtained when matrix was used. Considering the difficulties and cost of measuring carcass traits postmortem, visual scores of

Impacts of population structure and analytical models in genome-wide association studies of complex traits in forest trees: a case study in Eucalyptus globulus.

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Eduardo P Cappa

Full Text Available The promise of association genetics to identify genes or genomic regions controlling complex traits has generated a flurry of interest. Such phenotype-genotype associations could be useful to accelerate tree breeding cycles, increase precision and selection intensity for late expressing, low heritability traits. However, the prospects of association genetics in highly heterozygous undomesticated forest trees can be severely impacted by the presence of cryptic population and pedigree structure. To investigate how to better account for this, we compared the GLM and five combinations of the Unified Mixed Model ( UMM on data of a low-density genome-wide association study for growth and wood property traits carried out in a Eucalyptus globulus population (n = 303 with 7,680 Diversity Array Technology (DArT markers. Model comparisons were based on the degree of deviation from the uniform distribution and estimates of the mean square differences between the observed and expected p-values of all significant marker-trait associations detected. Our analysis revealed the presence of population and family structure. There was not a single best model for all traits. Striking differences in detection power and accuracy were observed among the different models especially when population structure was not accounted for. The UMM method was the best and produced superior results when compared to GLM for all traits. Following stringent correction for false discoveries, 18 marker-trait associations were detected, 16 for tree diameter growth and two for lignin monomer composition (S:G ratio, a key wood property trait. The two DArT markers associated with S:G ratio on chromosome 10, physically map within 1 Mbp of the ferulate 5-hydroxylase (F5H gene, providing a putative independent validation of this marker-trait association. This study details the merit of collectively integrate population structure and relatedness in association analyses in undomesticated, highly

Impacts of Population Structure and Analytical Models in Genome-Wide Association Studies of Complex Traits in Forest Trees: A Case Study in Eucalyptus globulus

Science.gov (United States)

Garcia, Martín N.; Acuña, Cintia; Borralho, Nuno M. G.; Grattapaglia, Dario; Marcucci Poltri, Susana N.

2013-01-01

The promise of association genetics to identify genes or genomic regions controlling complex traits has generated a flurry of interest. Such phenotype-genotype associations could be useful to accelerate tree breeding cycles, increase precision and selection intensity for late expressing, low heritability traits. However, the prospects of association genetics in highly heterozygous undomesticated forest trees can be severely impacted by the presence of cryptic population and pedigree structure. To investigate how to better account for this, we compared the GLM and five combinations of the Unified Mixed Model (UMM) on data of a low-density genome-wide association study for growth and wood property traits carried out in a Eucalyptus globulus population (n = 303) with 7,680 Diversity Array Technology (DArT) markers. Model comparisons were based on the degree of deviation from the uniform distribution and estimates of the mean square differences between the observed and expected p-values of all significant marker-trait associations detected. Our analysis revealed the presence of population and family structure. There was not a single best model for all traits. Striking differences in detection power and accuracy were observed among the different models especially when population structure was not accounted for. The UMM method was the best and produced superior results when compared to GLM for all traits. Following stringent correction for false discoveries, 18 marker-trait associations were detected, 16 for tree diameter growth and two for lignin monomer composition (S∶G ratio), a key wood property trait. The two DArT markers associated with S∶G ratio on chromosome 10, physically map within 1 Mbp of the ferulate 5-hydroxylase (F5H) gene, providing a putative independent validation of this marker-trait association. This study details the merit of collectively integrate population structure and relatedness in association analyses in undomesticated, highly

Genetic correlations between conformation traits and radiographic findings in the limbs of German Warmblood riding horses

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Distl Ottmar

2006-11-01

Full Text Available Abstract Studbook inspection (SBI data of 20 768 German Warmblood mares and radiography results (RR data of 5102 Hanoverian Warmblood horses were used for genetic correlation analyses. The scores on a scale from 0 to 10 were given for conformation and basic quality of gaits, resulting in 14 SBI traits which were used for the correlation analyses. The radiographic findings considered included osseous fragments in fetlock (OFF and hock joints (OFH, deforming arthropathy in hock joints (DAH and distinct radiographic findings in the navicular bones (DNB which were analyzed as binary traits, and radiographic appearance of the navicular bones (RNB which was analyzed as a quasi-linear trait. Genetic parameters were estimated multivariately in linear animal models with REML using information on 24 448 horses with SBI and/or RR records. The ranges of heritability estimates were h2 = 0.14–0.34 for the RR traits and h2 = 0.09–0.50 for the SBI traits. Negative additive genetic correlations of rg = -0.19 to -0.56 were estimated between OFF and conformation of front and hind limbs and walk at hand, and between DNB and hind limb conformation. There were indications of negative additive genetic correlations between DAH and all SBI traits, but because of low prevalence and low heritability of DAH, these results require further scrutiny. Positive additive genetic correlations of rg = 0.37–0.52 were estimated between OFF and withers height and between OFH and withers height, indicating that selection for taller horses will increase disposition to develop OFF and OFH. Selection of broodmares with regards to functional conformation will assist, but cannot replace possible selection against radiographic findings in the limbs of young Warmblood riding horses, particularly with regards to OFF.

Genetic Analysis for Some of Morphological Traits in Bread Wheat under Drought Stress Condition Using Generations Mean Analysis

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Jamileh Abedi

2015-06-01

Full Text Available Perception of genes action controlling of quantitative traits is very important in genetic breeding methods the plant populations. to study and estimate the parameters of genetic and appointment the best genetically model for justification the genetic changing some of traits the bread wheat under drought stress condition, parents (P1 & P2 and F3, F4, F5 generations together the four control cultivars (Kharchia, Gaspard, Moghan and Mahuti were evaluated by generation mean analysis using a agoment design including six blocks. Generation mean analysis was performed for all traits with Mather and Jinks model using joint scaling test. Three parameter model [m d h] provided the best fit for all traits expect harvest index, main spike grain weight, number of grain per plant, Total spike weight of plant with significant at 5% and 1% levels . Though additive and dominance effect both had interfered in controlling often the traits but with attention to difference effects and variety component was determined that dominance is more impressive than additive effect for traits of number of tiller, main spike weight, grain yield and grain number of main spike. Therefore will benefit using of these traits in the collection and to improve these traits hybridization would be much efficient than the selection strategies. In this study additive Ч additive epistasis effect only observed for traits of Total spike weight of plant, number of grain per plant, main spike grain weight and harvest index and other traits hadn’t any epistasis effect that it was demonstration lack of existence the genes reciprocal effect in the inheritance studied traits. Therefore we can suggest that the selection strategies perform in terminal generations and additive Ч additive epistasis effect would be confirmed in selection under self-pollination condition.

Genetic variation of seedling traits in a random mating population of sunflower

International Nuclear Information System (INIS)

Habib, S.

2004-01-01

Forty S/sub 1/ families obtained from a random mating population of sunflower were evaluated in the laboratory for various seedling traits. The objectives of this study were to investigate the extent and nature of genetic variability and to determine the estimates of genotypic and phenotypic correlations among ten seedling traits prevailing in a random mating population of sunflower. The results indicated that significant differences existed among the 40 S/sub 1/ families for all the traits evaluated. Genotypic and phenotypic coefficients of variation were comparatively high for emergence rate index, root/shoot ratio, dry root weight, fresh root weight and fresh shoot weight. The estimates of broad-sense heritability were high and significant for all the traits. The study of genotypic and phenotypic correlations among these traits revealed that generally, the seedlings which took more time to emerge were vigorous for most of the traits except fresh shoot length. However, rapidly emerging seedlings had higher emergence percentage. The root traits appeared to be better indicators of seedling vigour compared to other traits as these traits exhibited strong and positive genotypic and phenotypic correlations among them. (author)

A genetic deconstruction of neurocognitive traits in schizophrenia and bipolar disorder

NARCIS (Netherlands)

C.P.D. Fernandes (Carla P.); A. Christoforou (Andrea); S. Giddaluru (Sudheer); K.M. Ersland (Kari); S. Djurovic (Srdjan); M. Mattheisen (Manuel); A.J. Lundervold (Astri); I. Reinvang (Ivar); M.M. Nöthen (Markus); M. Rietschel (Marcella); R.A. Ophoff (Roel); A. Hofman (Albert); A.G. Uitterlinden (André); T.M. Werge (Thomas); S. Cichon (Sven); T. Espeseth (Thomas); O.A. Andreassen (Ole); V.M. Steen (Vidar); S. Le Hellard (Stephanie)

2013-01-01

textabstractBackground: Impairments in cognitive functions are common in patients suffering from psychiatric disorders, such as schizophrenia and bipolar disorder. Cognitive traits have been proposed as useful for understanding the biological and genetic mechanisms implicated in cognitive function

Genetic analyses of herding traits in the Border Collie using sheepdog trial data.

Science.gov (United States)

Storteig Horn, S; Steinheim, G; Fjerdingby Olsen, H; Gjerjordet, H F; Klemetsdal, G

2017-04-01

The aim of this study was to evaluate the quality of the data provided from sheepdog trials in Norway, estimate heritabilities, repeatabilities and genetic correlations for the traits included in the trial and make recommendations on how sheepdog trials best can be utilized in the breeding of Border Collies in Norway. The analyses were based on test results from sheepdog trials carried out in Norway from 1993 to 2012. A total of 45 732 records from 3841 Border Collies were available, but after quality assurance only a third was left. The results demonstrated little information in the data. Heritabilities varied between 0.010 and 0.056 with standard errors ranging from 0.010 to 0.023, while repeatabilities ranged from 0.041 to 0.286. There is a need to assure the quality of data to improve the information in the test results. We recommend adding new traits based on the Herding Trait Characterization scheme evaluated in Sweden, and on traits from the predatory motor pattern, regarded as common for all dogs. These new traits may be scored across the elements that make up the current trial system, which should be kept in place to stimulate participation in the genetic evaluation scheme. © 2016 Blackwell Verlag GmbH.

Bayesian analyses of genetic parameters for growth traits in Nellore cattle raised on pasture.

Science.gov (United States)

Lopes, F B; Ferreira, J L; Lobo, R B; Rosa, G J M

2017-07-06

This study was carried out to investigate (co)variance components and genetic parameters for growth traits in beef cattle using a multi-trait model by Bayesian methods. Genetic and residual (co)variances and parameters were estimated for weights at standard ages of 120 (W120), 210 (W210), 365 (W365), and 450 days (W450), and for pre- and post-weaning daily weight gain (preWWG and postWWG) in Nellore cattle. Data were collected over 16 years (1993-2009), and all animals were raised on pasture in eight farms in the North of Brazil that participate in the National Association of Breeders and Researchers. Analyses were run by the Bayesian approach using Gibbs sampler. Additive direct heritabilities for W120, W210, W365, and W450 and for preWWG and postWWG were 0.28 ± 0.013, 0.32 ± 0.002, 0.31 ± 0.002, 0.50 ± 0.026, 0.61 ± 0.047, and 0.79 ± 0.055, respectively. The estimates of maternal heritability were 0.32 ± 0.012, 0.29 ± 0.004, 0.30 ± 0.005, 0.25 ± 0.015, 0.23 ± 0.017, and 0.22 ± 0.016, respectively, for W120, W210, W365, and W450 and for preWWG and postWWG. The estimates of genetic direct additive correlation among all traits were positive and ranged from 0.25 ± 0.03 (preWWG and postWWG) to 0.99 ± 0.00 (W210 and preWWG). The moderate to high estimates of heritability and genetic correlation for weights and daily weight gains at different ages is suggestive of genetic improvement in these traits by selection at an appropriate age. Maternal genetic effects seemed to be significant across the traits. When the focus is on direct and maternal effects, W210 seems to be a good criterium for the selection of Nellore cattle considering the importance of this breed as a major breed of beef cattle not only in Northern Brazil but all regions covered by tropical pastures. As in this study the genetic correlations among all traits were high, the selection based on weaning weight might be a good choice because at this age there are two important effects (maternal

Estimation of genetic parameters for test day records of dairy traits in the first three lactations

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Ducrocq Vincent

2005-05-01

Full Text Available Abstract Application of test-day models for the genetic evaluation of dairy populations requires the solution of large mixed model equations. The size of the (covariance matrices required with such models can be reduced through the use of its first eigenvectors. Here, the first two eigenvectors of (covariance matrices estimated for dairy traits in first lactation were used as covariables to jointly estimate genetic parameters of the first three lactations. These eigenvectors appear to be similar across traits and have a biological interpretation, one being related to the level of production and the other to persistency. Furthermore, they explain more than 95% of the total genetic variation. Variances and heritabilities obtained with this model were consistent with previous studies. High correlations were found among production levels in different lactations. Persistency measures were less correlated. Genetic correlations between second and third lactations were close to one, indicating that these can be considered as the same trait. Genetic correlations within lactation were high except between extreme parts of the lactation. This study shows that the use of eigenvectors can reduce the rank of (covariance matrices for the test-day model and can provide consistent genetic parameters.

Genetic relationship between methane emissions and conformation traits in Danish Holstein cattle

DEFF Research Database (Denmark)

Zetouni, Larissa; Kargo, Morten; Lassen, Jan

2016-01-01

Conformation traits have been widely explored in dairy cattle evaluation, being a part of the total merit index for Holstein cows in different countries. They have been used as a way to access the cow’s condition in general, based on its body features. Lots of studies have analyzed the relationship...... traits in Holstein cows: height (H), body depth (BD), chest width (CW), dairy character (DC) and body condition score (BCS). Data was collected on 1114 Holstein cows from 11 commercial herds in Denmark. Methane emission was measured during milking in milking robots, and then quantifed using information...... between conformation traits and other traits of interest in dairy cattle, such as fertility, longevity and feed effciency, but little is known about how methane emissions correlate with conformation traits. Therefore, our goal was to evaluate the genetic correlations between methane and six conformation...

Genetic Properties of Some Economic Traits in Isfahan Native Fowl Using Bayesian and REML Methods

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Salehinasab M

2015-12-01

Full Text Available The objective of the present study was to estimate heritability values for some performance and egg quality traits of native fowl in Isfahan breeding center using REML and Bayesian approaches. The records were about 51521 and 975 for performance and egg quality traits, respectively. At the first step, variance components were estimated for body weight at hatch (BW0, body weight at 8 weeks of age (BW8, weight at sexual maturity (WSM, egg yolk weight (YW, egg Haugh unit and eggshell thickness, via REML approach using ASREML software. At the second step, the same traits were analyzed via Bayesian approach using Gibbs3f90 software. In both approaches six different animal models were applied and the best model was determined using likelihood ratio test (LRT and deviance information criterion (DIC for REML and Bayesian approaches, respectively. Heritability estimates for BW0, WSM and ST were the same in both approaches. For BW0, LRT and DIC indexes confirmed that the model consisting maternal genetic, permanent environmental and direct genetic effects was significantly better than other models. For WSM, a model consisting of maternal permanent environmental effect in addition to direct genetic effect was the best. For shell thickness, the basic model consisting direct genetic effect was the best. The results for BW8, YW and Haugh unit, were different between the two approaches. The reason behind this tiny differences was that the convergence could not be achieved for some models in REML approach and thus for these traits the Bayesian approach estimated the variance components more accurately. The results indicated that ignoring maternal effects, overestimates the direct genetic variance and heritability for most of the traits. Also, the Bayesian-based software could take more variance components into account.

Genetic variation and heritability for cotton seed, fiber and oil traits in gossypium hirsutum

International Nuclear Information System (INIS)

Khan, N.U.; Farhatullah; Batool, S.; Makhdoom, K.; Marwat, K.B.; Hassan, G.; Ahmad, W.; Khan, H.U.

2010-01-01

The research work pertaining to the study of genetic variability, heritability, genetic gain and correlation for cottonseed, fiber and cottonseed oil % in Gossypium hirsutum cultivars was conducted during 2005 at NWFP Agricultural University Peshawar, Pakistan. Analysis of variance manifested highly significant differences among the genotypes for all the traits except seeds per locule. Genetic potential range of eight cotton cultivars for different parameters was recorded i.e. seeds locule-1 (6.33 to 6.60), seeds boll-1 (26.10 to 28.47), seed index (8.61 to 9.69 g), lint index (5.35 to 6.05 g), lint % (35.17 to 38.13 %), seed cotton yield (1200 to 2450 kg ha/sup -1/) and cottonseed oil % (27.52 to 30.15%). Genetic variances were found almost greater than the environmental variances for all the traits except seeds locule-1 and seed index. High broad sense heritability and selection response were also formulated for seeds boll-1 (0.67, 0.84), seed index (0.77, 0.47 g), lint index (0.96, 0.33 g), lint % (0.96, 1.66 %), seed cotton yield (0.98, 643.16 kg) and cottonseed oil % (0.87, 1.28 %), respectively. Correlation of yield with other traits was found positive for majority of traits except seeds locule-1 and cotton seed oil %. Seed cotton yield is our ultimate goal in growing cotton besides lint %. Highest seed cotton yield was recorded in CIM-499 followed by CIM-473, CIM-496 and CIM-506 and were also found as the second and third top scoring genotypes for seeds per boll, seed index, lint % and cottonseed oil %. Cultivar SLH-279 performed better for lint index, lint % and oil %. This type of correlation is rarely found and ultra desirable by the cotton breeders and a little genetic gain in seed and lint traits, and oil content is a great accomplishment. (author)

A genetic deconstruction of neurocognitive traits in schizophrenia and bipolar disorder

DEFF Research Database (Denmark)

Fernandes, Carla P D; Christoforou, Andrea; Giddaluru, Sudheer

2013-01-01

Impairments in cognitive functions are common in patients suffering from psychiatric disorders, such as schizophrenia and bipolar disorder. Cognitive traits have been proposed as useful for understanding the biological and genetic mechanisms implicated in cognitive function in healthy individuals...

A Genetic Deconstruction of Neurocognitive Traits in Schizophrenia and Bipolar Disorder

NARCIS (Netherlands)

Fernandes, Carla P. D.; Christoforou, Andrea; Giddaluru, Sudheer; Ersland, Kari M.; Djurovic, Srdjan; Mattheisen, Manuel; Lundervold, Astri J.; Reinvang, Ivar; Nöthen, Markus M.; Rietschel, Marcella; Ophoff, Roel A.; Hofman, Albert; Uitterlinden, André G.; Werge, Thomas; Cichon, Sven; Espeseth, Thomas; Andreassen, Ole A.; Steen, Vidar M.; Le Hellard, Stephanie; Kahn, René S.; Linszen, Don H.; van Os, Jim; Wiersma, Durk; Bruggeman, Richard; Cahn, Wiepke; de Haan, Lieuwe; Krabbendam, Lydia; Myin-Germeys, Inez

2013-01-01

Background: Impairments in cognitive functions are common in patients suffering from psychiatric disorders, such as schizophrenia and bipolar disorder. Cognitive traits have been proposed as useful for understanding the biological and genetic mechanisms implicated in cognitive function in healthy

Genetic Variation in Functional Traits Influences Arthropod Community Composition in Aspen (Populus tremula L.)

Science.gov (United States)

Robinson, Kathryn M.; Ingvarsson, Pär K.; Jansson, Stefan; Albrectsen, Benedicte R.

2012-01-01

We conducted a study of natural variation in functional leaf traits and herbivory in 116 clones of European aspen, Populus tremula L., the Swedish Aspen (SwAsp) collection, originating from ten degrees of latitude across Sweden and grown in a common garden. In surveys of phytophagous arthropods over two years, we found the aspen canopy supports nearly 100 morphospecies. We identified significant broad-sense heritability of plant functional traits, basic plant defence chemistry, and arthropod community traits. The majority of arthropods were specialists, those coevolved with P. tremula to tolerate and even utilize leaf defence compounds. Arthropod abundance and richness were more closely related to plant growth rates than general chemical defences and relationships were identified between the arthropod community and stem growth, leaf and petiole morphology, anthocyanins, and condensed tannins. Heritable genetic variation in plant traits in young aspen was found to structure arthropod community; however no single trait drives the preferences of arthropod folivores among young aspen genotypes. The influence of natural variation in plant traits on the arthropod community indicates the importance of maintaining genetic variation in wild trees as keystone species for biodiversity. It further suggests that aspen can be a resource for the study of mechanisms of natural resistance to herbivores. PMID:22662190

Genetic variation in functional traits influences arthropod community composition in aspen (Populus tremula L..

Directory of Open Access Journals (Sweden)

Kathryn M Robinson

Full Text Available We conducted a study of natural variation in functional leaf traits and herbivory in 116 clones of European aspen, Populus tremula L., the Swedish Aspen (SwAsp collection, originating from ten degrees of latitude across Sweden and grown in a common garden. In surveys of phytophagous arthropods over two years, we found the aspen canopy supports nearly 100 morphospecies. We identified significant broad-sense heritability of plant functional traits, basic plant defence chemistry, and arthropod community traits. The majority of arthropods were specialists, those coevolved with P. tremula to tolerate and even utilize leaf defence compounds. Arthropod abundance and richness were more closely related to plant growth rates than general chemical defences and relationships were identified between the arthropod community and stem growth, leaf and petiole morphology, anthocyanins, and condensed tannins. Heritable genetic variation in plant traits in young aspen was found to structure arthropod community; however no single trait drives the preferences of arthropod folivores among young aspen genotypes. The influence of natural variation in plant traits on the arthropod community indicates the importance of maintaining genetic variation in wild trees as keystone species for biodiversity. It further suggests that aspen can be a resource for the study of mechanisms of natural resistance to herbivores.

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

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Pengyuan Liu

2007-07-01

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

Fruit self-thinning: a trait to consider for genetic improvement of apple tree.

Science.gov (United States)

Celton, Jean-Marc; Kelner, Jean-Jacques; Martinez, Sébastien; Bechti, Abdel; Khelifi Touhami, Amina; James, Marie José; Durel, Charles-Eric; Laurens, François; Costes, Evelyne

2014-01-01

In apple (Malus×domestica Borkh), as in many fruiting crops, fruit maintenance vs abscission is a major criteria for production profitability. Growers routinely make use of chemical thinning agents to control total fruit load. However, serious threats for the environment lead to the demand for new apple cultivars with self-thinning properties. In this project, we studied the genetic determinism of this trait using a F1 progeny derived from the cross between the hybrid INRA X3263, assumed to possess the self-thinning trait, and the cultivar 'Belrène'. Both counting and percentage variables were considered to capture the fruiting behaviour on different shoot types and over three consecutive years. Besides low to moderate but significant genetic effects, mixed models showed considerable effects of the year and the shoot type, as well as an interaction effect. Year effect resulted mainly from biennial fruiting. Eight Quantitative Trait Locus (QTL) were detected on several linkage groups (LG), either independent or specific of the year of observation or the shoot type. The QTL with highest LOD value was located on the top third of LG10. The screening of three QTL zones for candidate genes revealed a list of transcription factors and genes involved in fruit nutrition, xylem differentiation, plant responses to starvation and organ abscission that open new avenues for further molecular investigations. The detailed phenotyping performed revealed the dependency between the self-thinning trait and the fruiting status of the trees. Despite a moderate genetic control of the self-thinning trait, QTL and candidate genes were identified which will need further analyses involving other progenies and molecular investigations.

Genetics of serum carotenoid concentrations and their correlation with obesity-related traits in Mexican American children.

Science.gov (United States)

Farook, Vidya S; Reddivari, Lavanya; Mummidi, Srinivas; Puppala, Sobha; Arya, Rector; Lopez-Alvarenga, Juan Carlos; Fowler, Sharon P; Chittoor, Geetha; Resendez, Roy G; Kumar, Birunda Mohan; Comuzzie, Anthony G; Curran, Joanne E; Lehman, Donna M; Jenkinson, Christopher P; Lynch, Jane L; DeFronzo, Ralph A; Blangero, John; Hale, Daniel E; Duggirala, Ravindranath; Vanamala, Jairam Kp

2017-07-01

Background: Dietary intake of phytonutrients present in fruits and vegetables, such as carotenoids, is associated with a lower risk of obesity and related traits, but the impact of genetic variation on these associations is poorly understood, especially in children. Objective: We estimated common genetic influences on serum carotenoid concentrations and obesity-related traits in Mexican American (MA) children. Design: Obesity-related data were obtained from 670 nondiabetic MA children, aged 6-17 y. Serum α- and β-carotenoid concentrations were measured in ∼570 (α-carotene in 565 and β-carotene in 572) of these children with the use of an ultraperformance liquid chromatography-photodiode array. We determined heritabilities for both carotenoids and examined their genetic relation with 10 obesity-related traits [body mass index (BMI), waist circumference (WC), high-density lipoprotein (HDL) cholesterol, triglycerides, fat mass (FM), systolic and diastolic blood pressure, fasting insulin and glucose, and homeostasis model assessment of insulin resistance] by using family data and a variance components approach. For these analyses, carotenoid values were inverse normalized, and all traits were adjusted for significant covariate effects of age and sex. Results: Carotenoid concentrations were highly heritable and significant [α-carotene: heritability ( h 2 ) = 0.81, P = 6.7 × 10 -11 ; β-carotene: h 2 = 0.90, P = 3.5 × 10 -15 ]. After adjusting for multiple comparisons, we found significant ( P ≤ 0.05) negative phenotypic correlations between carotenoid concentrations and the following traits: BMI, WC, FM, and triglycerides (range: α-carotene = -0.19 to -0.12; β-carotene = -0.24 to -0.13) and positive correlations with HDL cholesterol (α-carotene = 0.17; β-carotene = 0.24). However, when the phenotypic correlations were partitioned into genetic and environmental correlations, we found marginally significant ( P = 0.051) genetic correlations only between �

Phenotypic Characterization and Genetic Dissection of Growth Period Traits in Soybean (Glycine max Using Association Mapping.

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Zhangxiong Liu

Full Text Available The growth period traits are important traits that affect soybean yield. The insights into the genetic basis of growth period traits can provide theoretical basis for cultivated area division, rational distribution, and molecular breeding for soybean varieties. In this study, genome-wide association analysis (GWAS was exploited to detect the quantitative trait loci (QTL for number of days to flowering (ETF, number of days from flowering to maturity (FTM, and number of days to maturity (ETM using 4032 single nucleotide polymorphism (SNP markers with 146 cultivars mainly from Northeast China. Results showed that abundant phenotypic variation was presented in the population, and variation explained by genotype, environment, and genotype by environment interaction were all significant for each trait. The whole accessions could be clearly clustered into two subpopulations based on their genetic relatedness, and accessions in the same group were almost from the same province. GWAS based on the unified mixed model identified 19 significant SNPs distributed on 11 soybean chromosomes, 12 of which can be consistently detected in both planting densities, and 5 of which were pleotropic QTL. Of 19 SNPs, 7 SNPs located in or close to the previously reported QTL or genes controlling growth period traits. The QTL identified with high resolution in this study will enrich our genomic understanding of growth period traits and could then be explored as genetic markers to be used in genomic applications in soybean breeding.

Seedling vigor and genetic variability for rice seed, seedling emergence and seedling traits

International Nuclear Information System (INIS)

Ali, S.S.; Jafri, S.J.H.; Jamil, M.; Ijaz, M.

1994-01-01

Eleven local rice cultivars including Basmati 370 were evaluated for seedling vigor. Three groups of traits were evaluated viz; seed traits (Seed density, seed volume see weight, paddy length and grain length), seed emergence traits (emergence %, emergence index and emergence rate index), and seedling traits (fresh root length, dry root weight, emergence percentage, root length, dry root weight, seed weight and relative root weight were observed significant, respectively. Seed density, relative root weight, emergence rate index and root to shoot ratio were relatively more amenable to improvement. Relative expected genetic advance was the function of heritability and coefficient of phenotypic variability, latter being more important. (author)

Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years.

Science.gov (United States)

Berlin, Sofia; Hallingbäck, Henrik R; Beyer, Friderike; Nordh, Nils-Erik; Weih, Martin; Rönnberg-Wästljung, Ann-Christin

2017-07-01

Phenotypic plasticity can affect the geographical distribution of taxa and greatly impact the productivity of crops across contrasting and variable environments. The main objectives of this study were to identify genotype-phenotype associations in key biomass and phenology traits and the strength of phenotypic plasticity of these traits in a short-rotation coppice willow population across multiple years and contrasting environments to facilitate marker-assisted selection for these traits. A hybrid Salix viminalis  × ( S. viminalis × Salix schwerinii ) population with 463 individuals was clonally propagated and planted in three common garden experiments comprising one climatic contrast between Sweden and Italy and one water availability contrast in Italy. Several key phenotypic traits were measured and phenotypic plasticity was estimated as the trait value difference between experiments. Quantitative trait locus (QTL) mapping analyses were conducted using a dense linkage map and phenotypic effects of S. schwerinii haplotypes derived from detected QTL were assessed. Across the climatic contrast, clone predictor correlations for biomass traits were low and few common biomass QTL were detected. This indicates that the genetic regulation of biomass traits was sensitive to environmental variation. Biomass QTL were, however, frequently shared across years and across the water availability contrast. Phenology QTL were generally shared between all experiments. Substantial phenotypic plasticity was found among the hybrid offspring, that to a large extent had a genetic origin. Individuals carrying influential S. schwerinii haplotypes generally performed well in Sweden but less well in Italy in terms of biomass production. The results indicate that specific genetic elements of S. schwerinii are more suited to Swedish conditions than to those of Italy. Therefore, selection should preferably be conducted separately for such environments in order to maximize biomass

Estimation of Genetic Parameters for Direct and Maternal Effects in Growth Traits of Sangsari Sheep Using Gibbs Sampling

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Zohreh Yousefi

2016-11-01

Full Text Available Introduction Small ruminants, especially native breed types, play an important role in livelihoods of a considerable part of human population in the tropics from socio-economic aspects. Therefore, integrated attempt in terms of management and genetic improvement to enhance production is of crucial importance. Knowledge of genetic variation and co-variation among traits is required for both the design of effective sheep breeding programs and the accurate prediction of genetic progress from these programs. Body weight and growth traits are one of the economically important traits in sheep production, especially in Iran where lamb sale is the main source of income for sheep breeders while other products are in secondary importance. Although mutton is the most important source of protein in Iran, meat production from the sheep does not cover the increasing consumer demand. On the other hand, increase in sheep number to increase meat production has been limited by low quality and quantity of forage range. Therefore, enhancing meat production should be achieved by selecting the animals that have maximum genetic merit as next generation parents. To design an efficient improvement program and genetic evaluation system for maximization response to selection for economically important traits, accurate estimates of the genetic parameters and the genetic relationships between the traits are necessary. Studies of various sheep breeds have shown that both direct and maternal genetic influences are of importance for lamb growth. When growth traits are included in the breeding goal, both direct and maternal genetic effects should be taken into account in order to achieve optimum genetic progress. The objective of this study was to estimate the variance components and heritability, for growth traits, by fitting six animal models in the Sangsari sheep using Gibbs sampling. Material and Method Sangsari is a fat-tailed and relatively small sized breed of sheep

Environmental sensitivity in dairy cattle with focus on fertility traits

DEFF Research Database (Denmark)

Ismael, Ahmed; Løvendahl, Peter; Strandberg, Erling

2012-01-01

Dairy cattle differ in production, fertility, health, and other important traits in the different environment as both the phenopypic and genetic level (Winding et la., 2005 and Calus et al., 2005). Fertility of Nordic dairy cattle breeds (Holstein, Red, Jersey) is a complex trait and the heritabi...

Genetic evaluation with major genes and polygenic inheritance when some animals are not genotyped using gene content multiple-trait BLUP.

Science.gov (United States)

Legarra, Andrés; Vitezica, Zulma G

2015-11-17

In pedigreed populations with a major gene segregating for a quantitative trait, it is not clear how to use pedigree, genotype and phenotype information when some individuals are not genotyped. We propose to consider gene content at the major gene as a second trait correlated to the quantitative trait, in a gene content multiple-trait best linear unbiased prediction (GCMTBLUP) method. The genetic covariance between the trait and gene content at the major gene is a function of the substitution effect of the gene. This genetic covariance can be written in a multiple-trait form that accommodates any pattern of missing values for either genotype or phenotype data. Effects of major gene alleles and the genetic covariance between genotype at the major gene and the phenotype can be estimated using standard EM-REML or Gibbs sampling. Prediction of breeding values with genotypes at the major gene can use multiple-trait BLUP software. Major genes with more than two alleles can be considered by including negative covariances between gene contents at each different allele. We simulated two scenarios: a selected and an unselected trait with heritabilities of 0.05 and 0.5, respectively. In both cases, the major gene explained half the genetic variation. Competing methods used imputed gene contents derived by the method of Gengler et al. or by iterative peeling. Imputed gene contents, in contrast to GCMTBLUP, do not consider information on the quantitative trait for genotype prediction. GCMTBLUP gave unbiased estimates of the gene effect, in contrast to the other methods, with less bias and better or equal accuracy of prediction. GCMTBLUP improved estimation of genotypes in non-genotyped individuals, in particular if these individuals had own phenotype records and the trait had a high heritability. Ignoring the major gene in genetic evaluation led to serious biases and decreased prediction accuracy. CGMTBLUP is the best linear predictor of additive genetic merit including

Heritability of rectal temperature and genetic correlations with production and reproduction traits in dairy cattle.

Science.gov (United States)

Dikmen, S; Cole, J B; Null, D J; Hansen, P J

2012-06-01

Genetic selection for body temperature during heat stress might be a useful approach to reduce the magnitude of heat stress effects on production and reproduction. Objectives of the study were to estimate the genetic parameters of rectal temperature (RT) in dairy cows in freestall barns under heat stress conditions and to determine the genetic and phenotypic correlations of rectal temperature with other traits. Afternoon RT were measured in a total of 1,695 lactating Holstein cows sired by 509 bulls during the summer in North Florida. Genetic parameters were estimated with Gibbs sampling, and best linear unbiased predictions of breeding values were predicted using an animal model. The heritability of RT was estimated to be 0.17 ± 0.13. Predicted transmitting abilities for rectal temperature changed 0.0068 ± 0.0020°C/yr from (birth year) 2002 to 2008. Approximate genetic correlations between RT and 305-d milk, fat, and protein yields, productive life, and net merit were significant and positive, whereas approximate genetic correlations between RT and somatic cell count score and daughter pregnancy rate were significant and negative. Rectal temperature during heat stress has moderate heritability, but genetic correlations with economically important traits mean that selection for RT could lead to lower productivity unless methods are used to identify genes affecting RT that do not adversely affect other traits of economic importance. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genetic Evidence for Causal Relationships Between Maternal Obesity-Related Traits and Birth Weight

DEFF Research Database (Denmark)

Tyrrell, Jessica; Richmond, Rebecca C; Palmer, Tom M

2016-01-01

IMPORTANCE: Neonates born to overweight or obese women are larger and at higher risk of birth complications. Many maternal obesity-related traits are observationally associated with birth weight, but the causal nature of these associations is uncertain. OBJECTIVE: To test for genetic evidence...... of causal associations of maternal body mass index (BMI) and related traits with birth weight. DESIGN, SETTING, AND PARTICIPANTS: Mendelian randomization to test whether maternal BMI and obesity-related traits are potentially causally related to offspring birth weight. Data from 30,487 women in 18 studies...

Genetic parameters for body weight ratio, fertility and growth traits in Canchim breed females

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Silvio de Paula Mello

2013-03-01

Full Text Available The objective of this study was to estimate the heritability of age at first calving (AFC, body condition score at first calving (BCF, body condition score at calving (BCC, weaning weight (WW, yearling weight (W12, weaning weight of calf/weight of cow at calving (RCC and weaning weight of first calf/weight of cow at first calving (RCCF ratios, and genetic correlations of AFC, BCF, WW and W12 with RCCF, in a Canchim beef cattle herd. The variance and covariance components were obtained by bayesian inference with single and two-trait analyses. The statistical models included the additive direct and maternal, the permanent environmental and the residual random effects, and the fixed effects of year and month of birth or of calving, age of cow at calving and sex of calf, depending on the trait. The posterior means of heritability, obtained by single-trait analyses, were 0.12 (AFC, 0.36 (BCF, 0.18 (BCC, 0.50 (WW, 0.46 (W12, 0.16 (RCC and 0.40 (RCCF indicating that these traits have enough genetic variability to  show response to mass selection with the exception of AFC. The genetic correlations of AFC (-0.61, BCF (-0.36, WW (-0.20 and W12 (-0.05 with RCCF suggest that selection to reduce age and body condition score at first calving should improve the productivity trait of females at first calving, while selection for heavier females at young ages would not promote any change in the productivity of dams.

Complex pedigree analysis to detect quantitative trait loci in dairy cattle

NARCIS (Netherlands)

Bink, M.C.A.M.

1998-01-01

In dairy cattle, many quantitative traits of economic importance show phenotypic variation. For breeding purposes the analysis of this phenotypic variation and uncovering the contribution of genetic factors is very important. Usually, the individual gene effects contributing to the

Genetic Relationship between Culling, Milk Production, Fertility, and Health Traits in Norwegian Red Cows

DEFF Research Database (Denmark)

Holtsmark, M; Heringstad, B; Madsen, P

2008-01-01

First-lactation records on 836,452 daughters of 3,064 Norwegian Red sires were used to examine associations between culling in first lactation and 305-d protein yield, susceptibility to clinical mastitis, lactation mean somatic cell score (SCS), nonreturn rate within 56 d in heifers and primiparous......, including functional traits such as health and fertility, most of the genetic variation in culling will probably be covered by other traits in the breeding goal. However, in populations where data on health and fertility is scarce or not available at all, selection against early culling may be useful...... cows, and interval from calving to first insemination. A Bayesian multivariate threshold-linear model was used for analysis. Posterior mean of heritability of liability to culling of primiparous cows was 0.04. The posterior means of the genetic correlations between culling and the other traits were -0...

Genetic analysis of agro-morphological traits in promising hybrids of sunflower (Helianthus annuus L.

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Maryam GOLABADI

2015-11-01

Full Text Available The main objective underlying sunflower breeding programs is to develop high-yielding productive F1 hybrid cultivars. This study was conducted to investigate the genetic control of some agro-morphological traits of new sunflower F1 hybrids. For this purpose, fourteen inbred lines of sunflower were crossed with three male sterile inbred lines. Their hybrids (14 hybrids were then evaluated against three control cultivars. The data thus obtained were analyzed using the nested model (North Carolina Design І as a completely randomized block design (CRBD with four replications. Analysis of variance showed that the hybrids were significantly different in all the traits studied, except for head and stem diameters. From among the hybrids evaluated, Cms19 × Rn1-81 was found to have the highest seed yield and oil content. Cluster analysis classified the hybrids into four different groups. Genetic analysis showed that days to maturity, seed weight, and oil content (% were under the additive gene action. Breeding strategies based on selection could be suggested for the improvement of these traits. Head angle, head diameter, seed yield, and oil yield were under the dominance gene action; breeding based on hybridization methods is, therefore, proposed for these traits. Finally, both additive and dominance gene actions were observed to play important roles in the genetic control of plant height and stem diameter.

Phenotypic and genetic effects of contrasting ethanol environments on physiological and developmental traits in Drosophila melanogaster.

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Luis E Castañeda

Full Text Available A central problem in evolutionary physiology is to understand the relationship between energy metabolism and fitness-related traits. Most attempts to do so have been based on phenotypic correlations that are not informative for the evolutionary potential of natural populations. Here, we explored the effect of contrasting ethanol environments on physiological and developmental traits, their genetic (covariances and genetic architecture in Drosophila melanogaster. Phenotypic and genetic parameters were estimated in two populations (San Fernando and Valdivia, Chile, using a half-sib family design where broods were split into ethanol-free and ethanol-supplemented conditions. Our findings show that metabolic rate, body mass and development times were sensitive (i.e., phenotypic plasticity to ethanol conditions and dependent on population origin. Significant heritabilities were found for all traits, while significant genetic correlations were only found between larval and total development time and between development time and metabolic rate for flies of the San Fernando population developed in ethanol-free conditions. Posterior analyses indicated that the G matrices differed between ethanol conditions for the San Fernando population (mainly explained by differences in genetic (covariances of developmental traits, whereas the Valdivia population exhibited similar G matrices between ethanol conditions. Our findings suggest that ethanol-free environment increases the energy available to reduce development time. Therefore, our results indicate that environmental ethanol could modify the process of energy allocation, which could have consequences on the evolutionary response of natural populations of D. melanogaster.

Phenotypic and Genetic Effects of Contrasting Ethanol Environments on Physiological and Developmental Traits in Drosophila melanogaster

Science.gov (United States)

Castañeda, Luis E.; Nespolo, Roberto F.

2013-01-01

A central problem in evolutionary physiology is to understand the relationship between energy metabolism and fitness-related traits. Most attempts to do so have been based on phenotypic correlations that are not informative for the evolutionary potential of natural populations. Here, we explored the effect of contrasting ethanol environments on physiological and developmental traits, their genetic (co)variances and genetic architecture in Drosophila melanogaster. Phenotypic and genetic parameters were estimated in two populations (San Fernando and Valdivia, Chile), using a half-sib family design where broods were split into ethanol-free and ethanol-supplemented conditions. Our findings show that metabolic rate, body mass and development times were sensitive (i.e., phenotypic plasticity) to ethanol conditions and dependent on population origin. Significant heritabilities were found for all traits, while significant genetic correlations were only found between larval and total development time and between development time and metabolic rate for flies of the San Fernando population developed in ethanol-free conditions. Posterior analyses indicated that the G matrices differed between ethanol conditions for the San Fernando population (mainly explained by differences in genetic (co)variances of developmental traits), whereas the Valdivia population exhibited similar G matrices between ethanol conditions. Our findings suggest that ethanol-free environment increases the energy available to reduce development time. Therefore, our results indicate that environmental ethanol could modify the process of energy allocation, which could have consequences on the evolutionary response of natural populations of D. melanogaster. PMID:23505567

On the Genetic and Environmental Correlations between Trait Emotional Intelligence and Vocational Interest Factors.

Science.gov (United States)

Schermer, Julie Aitken; Petrides, Konstantinos V; Vernon, Philip A

2015-04-01

The phenotypic (observed), genetic, and environmental correlations were examined in a sample of adult twins between the four factors and global score of the trait emotional intelligence questionnaire (TEIQue) and the seven vocational interest factors of the Jackson Career Explorer (JCE). Multiple significant correlations were found involving the work style vocational interest factor (consisting of job security, stamina, accountability, planfulness, and interpersonal confidence) and the social vocational interest factor (which included interests in the social sciences, personal services, teaching, social services, and elementary education), both of which correlated significantly with all of the TEIQue variables (well-being, self-control, emotionality, sociability, and global trait EI). Following bivariate genetic analyses, most of the significant phenotypic correlations were found to also have significant genetic correlations as well as significant non-shared (unique) environmental correlations.

Genetic diversity among Juglans regia L. genotypes assessed by morphological traits and microsatellite markers

Energy Technology Data Exchange (ETDEWEB)

Mahmoodi, R.; Rahmani, F.; Rezaee, R.

2013-06-01

In this study, genetic diversity was assayed among 16 accessions and five cultivars of Persian walnut (Juglans regia L.) using morphological traits and nine simple sequence repeat (SSR) markers. Samples were collected from Agriculture Research Center of Urmia city (North West Iran). Study on important morphological traits revealed genetic similarity of -0.6 to 0.99 based on CORR coefficient. The microsatellite marker system produced 34 alleles in range of 160-290 bp. The minimum (2) and maximum (7) number of alleles were obtained from WGA71 and WGA202 genetic loci, respectively. The mean number of alleles per locus was 4.25. Jaccards similarity coefficient ranged from 0.13 to 0.76. The results of this paper indicate high diversity among these genotypes which could be used for breeding management. (Author) 28 refs.

Evaluation of mature cow weight: genetic correlations with traits used in selection indices, correlated responses, and genetic trends in Nelore cattle.

Science.gov (United States)

Boligon, A A; Carvalheiro, R; Albuquerque, L G

2013-01-01

Genetic correlations of selection indices and the traits considered in these indices with mature weight (MW) of Nelore females and correlated responses were estimated to determine whether current selection practices will result in an undesired correlated response in MW. Genetic trends for weaning and yearling indices and MW were also estimated. Data from 612,244 Nelore animals born between 1984 and 2010, belonging to different beef cattle evaluation programs from Brazil and Paraguay, were used. The following traits were studied: weaning conformation (WC), weaning precocity (WP), weaning muscling (WM), yearling conformation (YC), yearling precocity (YP), yearling muscling (YM), weaning and yearling indices, BW gain from birth to weaning (BWG), postweaning BW gain (PWG), scrotal circumference (SC), and MW. The variance and covariance components were estimated by Bayesian inference in a multitrait analysis, including all traits in the same analysis, using a nonlinear (threshold) animal model for visual scores and a linear animal model for the other traits. The mean direct heritabilities were 0.21±0.007 (WC), 0.22±0.007 (WP), 0.20±0.007 (WM), 0.43±0.005 (YC), 0.40±0.005 (YP), 0.40±0.005 (YM), 0.17±0.003 (BWG), 0.21±0.004 (PWG), 0.32±0.001 (SC), and 0.44±0.018 (MW). The genetic correlations between MW and weaning and yearling indices were positive and of medium magnitude (0.30±0.01 and 0.31±0.01, respectively). The genetic changes in weaning index, yearling index, and MW, expressed as units of genetic SD per year, were 0.26, 0.27, and 0.01, respectively. The genetic trend for MW was nonsignificant, suggesting no negative correlated response. The selection practice based on the use of sires with high final index giving preference for those better ranked for yearling precocity and muscling than for conformation generates only a minimal correlated response in MW.

Analysis of Non-Genetic Factors Influencing Reproductive Traits of Japanese Black Heifer

Science.gov (United States)

Setiaji, A.; Oikawa, T.

2018-02-01

This study aimed was to identify non-genetic factors strongly associated with reproductive traits on Japanese Black heifer. Artificial insemination and calving records were analyzed to investigate non-genetic effect on reproductive performances. A total of 2220 records of heifer raised between 2005 and 2016 were utilized in this study. Studied traits were first service non return rate to 56 days (NRR), first service pregnancy rate (FPR), days from first to successful insemination (FSI), number of services per conception (NSC), age at first calving (AFC), and gestation length (GL). Test of significance for effects in the statistical model was performed using GLM procedure of SAS 9.3. The yearling trend was plotted on the adjusted mean of parameters, by the least square mean procedure. Means of NRR, FPR, FSI, NSC, AFC and GL were 72%, 53%, 52.71 days, 1.76, 760.71 days and 288.26 days, respectively. The effect of farm was significant (Page of heifer at first insemination was significant (P<0.001) for AFC. Month of insemination and sex of calf were significant (P<0.001) for GL. Compared with average value of reproductive traits, NSC and GL were generally within standard values for Japanese Black cattle, while AFC was slightly earlier. The result indicated that different management of farms strongly influenced reproductive traits of Japanese Black heifer.

Phenotypic and Genetic Correlations of Feed Efficiency Traits with Growth and Carcass Traits in Nellore Cattle Selected for Postweaning Weight

Science.gov (United States)

Ceacero, Thais Matos; Mercadante, Maria Eugênia Zerlotti; Cyrillo, Joslaine Noely dos Santos Gonçalves; Canesin, Roberta Carrilho; Bonilha, Sarah Figueiredo Martins; de Albuquerque, Lucia Galvão

2016-01-01

This study evaluated phenotypic (rph) and genetic correlations (rg) between 8 feed efficiency traits and other traits of economic interest including weight at selection (WS), loin-eye area (LEA), backfat thickness (BF), and rump fat thickness (RF) in Nellore cattle. Feed efficiency traits were gain:feed, residual feed intake (RFI), residual feed intake adjusted for backfat thickness (RFIb) and for backfat and rump fat thickness (RFIsf), residual body weight gain (RG), residual intake and body weight gain (RIG), and residual intake and body weight gain using RFIb (RIGb) and RFIsf (RIGsf). The variance components were estimated by the restricted maximum likelihood method using a two-trait animal model. The heritability estimates (h2) were 0.14, 0.24, 0.20, 0.22, 0.19, 0.15, 0.11 and 0.11 for gain:feed, RFI, RFIb, RFIsf, RG, RIG, RIGb and RIGsf, respectively. All rph values between traits were close to zero, except for the correlation of feed efficiency traits with dry matter intake and average daily gain. High rg values were observed for the correlation of dry matter intake, average daily gain and metabolic weight with WS and hip height (>0.61) and low to medium values (0.15 to 0.48) with the carcass traits (LEA, BF, RF). Among the feed efficiency traits, RG showed the highest rg with WS and hip height (0.34 and 0.25) and the lowest rg with subcutaneous fat thickness (-0.17 to 0.18). The rg values of RFI, RFIb and RFIsf with WS (0.17, 0.23 and 0.22), BF (0.37, 0.33 and 0.33) and RF (0.30, 0.31 and 0.32) were unfavorable. The rg values of gain:feed, RIG, RIGb and RIGsf with WS were low and favorable (0.07 to 0.22), while medium and unfavorable (-0.22 to -0.45) correlations were observed with fat thickness. The inclusion of subcutaneous fat thickness in the models used to calculate RFI did not reduce the rg between these traits. Selecting animals for higher feed efficiency will result in little or no genetic change in growth and will decrease subcutaneous fat thickness

Mapping epistasis and environment × QTX interaction based on four -omics genotypes for the detected QTX loci controlling complex traits in tobacco

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Liyuan Zhou

2013-12-01

Full Text Available Using newly developed methods and software, association mapping was conducted for chromium content and total sugar in tobacco leaf, based on four -omics datasets. Our objective was to collect data on genotype and phenotype for 60 leaf samples at four developmental stages, from three plant architectural positions and for three cultivars that were grown in two locations. Association mapping was conducted to detect genetic variants at quantitative trait SNP (QTS loci, quantitative trait transcript (QTT differences, quantitative trait protein (QTP variability, and quantitative trait metabolite (QTM changes, which can be summarized as QTX locus variation. The total heritabilities of the four -omics loci for both traits tested were 23.60% for epistasis and 15.26% for treatment interaction. Epistasis and environment × treatment interaction had important impacts on complex traits at all -omics levels. For decreasing chromium content and increasing total sugar in tobacco leaf, six methylated loci can be directly used for marker-assisted selection, and expression of ten QTTs, seven QTPs and six QTMs can be modified by selection or cultivation.

A power set-based statistical selection procedure to locate susceptible rare variants associated with complex traits with sequencing data.

Science.gov (United States)

Sun, Hokeun; Wang, Shuang

2014-08-15

Existing association methods for rare variants from sequencing data have focused on aggregating variants in a gene or a genetic region because of the fact that analysing individual rare variants is underpowered. However, these existing rare variant detection methods are not able to identify which rare variants in a gene or a genetic region of all variants are associated with the complex diseases or traits. Once phenotypic associations of a gene or a genetic region are identified, the natural next step in the association study with sequencing data is to locate the susceptible rare variants within the gene or the genetic region. In this article, we propose a power set-based statistical selection procedure that is able to identify the locations of the potentially susceptible rare variants within a disease-related gene or a genetic region. The selection performance of the proposed selection procedure was evaluated through simulation studies, where we demonstrated the feasibility and superior power over several comparable existing methods. In particular, the proposed method is able to handle the mixed effects when both risk and protective variants are present in a gene or a genetic region. The proposed selection procedure was also applied to the sequence data on the ANGPTL gene family from the Dallas Heart Study to identify potentially susceptible rare variants within the trait-related genes. An R package 'rvsel' can be downloaded from http://www.columbia.edu/∼sw2206/ and http://statsun.pusan.ac.kr. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Genome-wide association study of swine farrowing traits. Part I: genetic and genomic parameter estimates.

Science.gov (United States)

Schneider, J F; Rempel, L A; Rohrer, G A

2012-10-01

The primary objective of this study was to determine genetic and genomic parameters among swine (Sus scrofa) farrowing traits. Genetic parameters were obtained using MTDFREML. Genomic parameters were obtained using GENSEL. Genetic and residual variances obtained from MTDFREML were used as priors for the Bayes C analysis of GENSEL. Farrowing traits included total number born (TNB), number born alive (NBA), number born dead (NBD), number stillborn (NSB), number of mummies (MUM), litter birth weight (LBW), and average piglet birth weight (ABW). Statistically significant heritabilities included TNB (0.09, P = 0.048), NBA (0.09, P = 0.041), LBW (0.20, P = 0.002), and ABW (0.26, P NBA (0.97, P NBA-LBW (0.56, P NBA (0.06), NBD (0.00), NSB (0.01), MUM (0.00), LBW (0.11), and ABW (0.31). Limited information is available in the literature about genomic parameters. Only the GP estimate for NSB is significantly lower than what has been published. The GP estimate for ABW is greater than the estimate for heritability found in this study. Other traits with significant heritability had GP estimates half the value of heritability. This research indicates that significant genetic markers will be found for TNB, NBA, LBW, and ABW that will have either immediate use in industry or provide a roadmap to further research with fine mapping or sequencing of areas of significance. Furthermore, these results indicate that genomic selection implemented at an early age would have similar annual progress as traditional selection, and could be incorporated along with traditional selection procedures to improve genetic progress of litter traits.

Genetic Linkage Map Construction and QTL Analysis of Two Interspecific Reproductive Isolation Traits in Sponge Gourd

OpenAIRE

Wu, Haibin; He, Xiaoli; Gong, Hao; Luo, Shaobo; Li, Mingzhu; Chen, Junqiu; Zhang, Changyuan; Yu, Ting; Huang, Wangping; Luo, Jianning

2016-01-01

The hybrids between Luffa acutangula (L.) Roxb. and L.cylindrica (L.) Roem. have strong heterosis effects. However, some reproductive isolation traits hindered their normal hybridization and fructification, which was mainly caused by the flowering time and hybrid pollen sterility. In order to study the genetic basis of two interspecific reproductive isolation traits, we constructed a genetic linkage map using an F2 population derived from a cross between S1174 [L. acutangula (L.) Roxb.] and 9...

Genetic parameters of Visual Image Analysis primal cut carcass traits of commercial prime beef slaughter animals.

Science.gov (United States)

Moore, K L; Mrode, R; Coffey, M P

2017-10-01

Visual Image analysis (VIA) of carcass traits provides the opportunity to estimate carcass primal cut yields on large numbers of slaughter animals. This allows carcases to be better differentiated and farmers to be paid based on the primal cut yields. It also creates more accurate genetic selection due to high volumes of data which enables breeders to breed cattle that better meet the abattoir specifications and market requirements. In order to implement genetic evaluations for VIA primal cut yields, genetic parameters must first be estimated and that was the aim of this study. Slaughter records from the UK prime slaughter population for VIA carcass traits was available from two processing plants. After edits, there were 17 765 VIA carcass records for six primal cut traits, carcass weight as well as the EUROP conformation and fat class grades. Heritability estimates after traits were adjusted for age ranged from 0.32 (0.03) for EUROP fat to 0.46 (0.03) for VIA Topside primal cut yield. Adjusting the VIA primal cut yields for carcass weight reduced the heritability estimates, with estimates of primal cut yields ranging from 0.23 (0.03) for Fillet to 0.29 (0.03) for Knuckle. Genetic correlations between VIA primal cut yields adjusted for carcass weight were very strong, ranging from 0.40 (0.06) between Fillet and Striploin to 0.92 (0.02) between Topside and Silverside. EUROP conformation was also positively correlated with the VIA primal cuts with genetic correlation estimates ranging from 0.59 to 0.84, whereas EUROP fat was estimated to have moderate negative correlations with primal cut yields, estimates ranged from -0.11 to -0.46. Based on these genetic parameter estimates, genetic evaluation of VIA primal cut yields can be undertaken to allow the UK beef industry to select carcases that better meet abattoir specification and market requirements.

Genetic control of environmental variation of two quantitative traits of Drosophila melanogaster revealed by whole-genome sequencing

DEFF Research Database (Denmark)

Sørensen, Peter; de los Campos, Gustavo; Morgante, Fabio

2015-01-01

and others more volatile performance. Understanding the mechanisms responsible for environmental variability not only informs medical questions but is relevant in evolution and in agricultural science. In this work fully sequenced inbred lines of Drosophila melanogaster were analyzed to study the nature...... of genetic control of environmental variance for two quantitative traits: starvation resistance (SR) and startle response (SL). The evidence for genetic control of environmental variance is compelling for both traits. Sequence information is incorporated in random regression models to study the underlying...... genetic signals, which are shown to be different in the two traits. Genomic variance in sexual dimorphism was found for SR but not for SL. Indeed, the proportion of variance captured by sequence information and the contribution to this variance from four chromosome segments differ between sexes in SR...

On coding genotypes for genetic markers with multiple alleles in genetic association study of quantitative traits

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Wang Tao

2011-09-01

Full Text Available Abstract Background In genetic association study of quantitative traits using F∞ models, how to code the marker genotypes and interpret the model parameters appropriately is important for constructing hypothesis tests and making statistical inferences. Currently, the coding of marker genotypes in building F∞ models has mainly focused on the biallelic case. A thorough work on the coding of marker genotypes and interpretation of model parameters for F∞ models is needed especially for genetic markers with multiple alleles. Results In this study, we will formulate F∞ genetic models under various regression model frameworks and introduce three genotype coding schemes for genetic markers with multiple alleles. Starting from an allele-based modeling strategy, we first describe a regression framework to model the expected genotypic values at given markers. Then, as extension from the biallelic case, we introduce three coding schemes for constructing fully parameterized one-locus F∞ models and discuss the relationships between the model parameters and the expected genotypic values. Next, under a simplified modeling framework for the expected genotypic values, we consider several reduced one-locus F∞ models from the three coding schemes on the estimability and interpretation of their model parameters. Finally, we explore some extensions of the one-locus F∞ models to two loci. Several fully parameterized as well as reduced two-locus F∞ models are addressed. Conclusions The genotype coding schemes provide different ways to construct F∞ models for association testing of multi-allele genetic markers with quantitative traits. Which coding scheme should be applied depends on how convenient it can provide the statistical inferences on the parameters of our research interests. Based on these F∞ models, the standard regression model fitting tools can be used to estimate and test for various genetic effects through statistical contrasts with the

Genetic by environment interaction for post weaning growth traits in tropical cattle

OpenAIRE

Navès, Michel; Menendez Buxadera, Alberto; Farant, Alain; Mandonnet, Nathalie

2006-01-01

Genetic by environment interactions for post weaning traits were studied in a local breed of cattle, well adapted to tropical conditions. After weaning, 444 beef calves of both sexes were separated within two management systems, either in intensive fattening or at pasture. The traits analysed included weights at standard age, of 365 days (W12), 455 days (W15) and 545 days (W18), and post weaning growth rates from weaning until 15 months (PWG15) or 18 months (PWG18). (Co)varianc...

Genetic trends of selection for pelt traits in Karakul sheep I. Direct ...

African Journals Online (AJOL)

Genetic trends of selection for pelt traits in Karakul sheep. I. Direct ... development in the Karakul Wereestimated with the Animal Model in four selection lines and in a control flock over ..... Selection experiments in laboratory and domestic.

Common Genetic Components of Obesity Traits and Serum Leptin

DEFF Research Database (Denmark)

Hasselbalch, Ann L; Benyamin, Beben; Visscher, Peter M

2008-01-01

To estimate common and distinct genetic influences on a panel of obesity-related traits and serum leptin level in adults. In a cross-sectional study of 625 Danish, adult, healthy, monozygotic, and same-sex dizygotic twin pairs of both genders, we carried out detailed anthropometry (height, weight...... components, which suggests that it is important to distinguish between the different phenotypes in the search for genes involved in the development of obesity.Obesity (2008) doi:10.1038/oby.2008.440........ For leptin vs. the various measures of overall and local fatness the correlations ranged from 0.54 to 0.74 in men and from 0.48 to 0.75 in women. All correlations were significantly different genetic...

Limnephilid taxa revised by speciation traits: Rhadicoleptus, Isogamus, Melampophylax genera, Chaetopteryx rugulosa, Psilopteryx psorosa species groups, Drusus bolivari, Annitella kosciuszkii species complexes (Trichoptera: Limnephilidae

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Oláh, J.

2015-06-01

Full Text Available Speciation traits of paramere, paraproct and aedeagus were applied to find initial split criteria with fine structure analysis in order to prepare diverged trait matrices for delimiting phylogenetic incipient species of unsettled limnephilid taxa in the early stages of reproductive isolation. A brief history is presented how this phenotypic taxonomic tool of the speciation traits was discovered and applied in caddisfly taxonomy. The theoretical basis was elaborated for the phenotypic speciation trait by reviewing several relevant topics in the sciences of taxonomy, molecular genetics and phylogenetics. Perspectives of integrative taxonomy is discussed in context of phenotype versus genotype, immensely complex phenotype versus phenomic challenge, taxonomic impediment versus genetic expedient, taxonomic adaptation of genetic vocabulary versus genetic sophistication and virtualization, New Systematics of Huxley and Mayr versus New Taxonomy of Wheeler. Debates on magic trait, speciation phenotype, speciation trait and super traits are discussed concluding that evolution works with phenotype and why the cryptic species concept is irrelevant. Briefly summarized how speciation traits evolve in sexual selection, through accelerated reproductive isolation with genital evolution through sex-limited speciation traits, including minor sex chromosomes. Why neutral molecular markers are blind compared to the adaptive speciation traits sensitized by fine structure analysis and backed by the potential of high-tech and high-throughput phenotyping and cyber-infrastructure broadly accessible and fed by computable phenotype descriptions. What sort of genetics could really help taxonomy to describe biodiversity of the over 100 million unknown taxa? Collecting new and re-examining old type materials deposited in various collections, the following taxonomic actions were elaborated by speciation traits. Drusus bolivari new species complex has been erected with

Genetic parameter estimation of reproductive traits of Litopenaeus vannamei

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Tan, Jian; Kong, Jie; Cao, Baoxiang; Luo, Kun; Liu, Ning; Meng, Xianhong; Xu, Shengyu; Guo, Zhaojia; Chen, Guoliang; Luan, Sheng

2017-02-01

In this study, the heritability, repeatability, phenotypic correlation, and genetic correlation of the reproductive and growth traits of L. vannamei were investigated and estimated. Eight traits of 385 shrimps from forty-two families, including the number of eggs (EN), number of nauplii (NN), egg diameter (ED), spawning frequency (SF), spawning success (SS), female body weight (BW) and body length (BL) at insemination, and condition factor (K), were measured,. A total of 519 spawning records including multiple spawning and 91 no spawning records were collected. The genetic parameters were estimated using an animal model, a multinomial logit model (for SF), and a sire-dam and probit model (for SS). Because there were repeated records, permanent environmental effects were included in the models. The heritability estimates for BW, BL, EN, NN, ED, SF, SS, and K were 0.49 ± 0.14, 0.51 ± 0.14, 0.12 ± 0.08, 0, 0.01 ± 0.04, 0.06 ± 0.06, 0.18 ± 0.07, and 0.10 ± 0.06, respectively. The genetic correlation was 0.99 ± 0.01 between BW and BL, 0.90 ± 0.19 between BW and EN, 0.22 ± 0.97 between BW and ED, -0.77 ± 1.14 between EN and ED, and -0.27 ± 0.36 between BW and K. The heritability of EN estimated without a covariate was 0.12 ± 0.08, and the genetic correlation was 0.90 ± 0.19 between BW and EN, indicating that improving BW may be used in selection programs to genetically improve the reproductive output of L. vannamei during the breeding. For EN, the data were also analyzed using body weight as a covariate (EN-2). The heritability of EN-2 was 0.03 ± 0.05, indicating that it is difficult to improve the reproductive output by genetic improvement. Furthermore, excessive pursuit of this selection is often at the expense of growth speed. Therefore, the selection of high-performance spawners using BW and SS may be an important strategy to improve nauplii production.

“Are We There Yet?”: Deciding When One Has Demonstrated Specific Genetic Causation in Complex Diseases and Quantitative Traits

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Page, Grier P.; George, Varghese; Go, Rodney C.; Page, Patricia Z.; Allison, David B.

2003-01-01

Although mathematical relationships can be proven by deductive logic, biological relationships can only be inferred from empirical observations. This is a distinct disadvantage for those of us who strive to identify the genes involved in complex diseases and quantitative traits. If causation cannot be proven, however, what does constitute sufficient evidence for causation? The philosopher Karl Popper said, “Our belief in a hypothesis can have no stronger basis than our repeated unsuccessful critical attempts to refute it.” We believe that to establish causation, as scientists, we must make a serious attempt to refute our own hypotheses and to eliminate all known sources of bias before association becomes causation. In addition, we suggest that investigators must provide sufficient data and evidence of their unsuccessful efforts to find any confounding biases. In this editorial, we discuss what “causation” means in the context of complex diseases and quantitative traits, and we suggest guidelines for steps that may be taken to address possible confounders of association before polymorphisms may be called “causative.” PMID:13680525

Genetic basis of yield and some yield related traits in basmati rice

International Nuclear Information System (INIS)

Saleem, M.Y.; Haq, M.A.; Mirza, J.I.

2010-01-01

Additive, dominance and epistasis components of genetic variation for yield and some yield related traits were assessed through modified triple test cross technique in Basmati rice. Epistasis was found an important part of genetic variation for plant height, tillers per plant, secondary branches per panicle, grains per panicle, 1000-grain weight and yield per plant except primary branches per panicle and panicle length. Bifurcation of epistasis showed that additive x additive (i) type and additive x dominance + dominance x dominance (j + l) types of non-allelic interactions were involved in the expression of these traits. Additive and dominance type of gene action influenced the expression of primary branches per panicle and panicle length. No evidence of directional dominance was observed for these two traits. For plant height, tillers per plant, secondary branches per panicle, grains per panicle, 1000-grain weight and yield per plant, recurrent selection or bi parental mating may be exercised in F2 and following generations however, selection of desired plants may be postponed till F5 or F6 generations to permit maximum obsession of epistatic effects to develop desired cultivar(s) in Basmati rice.(author)

A genetic basis for mechanosensory traits in humans.

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Henning Frenzel

Full Text Available In all vertebrates hearing and touch represent two distinct sensory systems that both rely on the transformation of mechanical force into electrical signals. There is an extensive literature describing single gene mutations in humans that cause hearing impairment, but there are essentially none for touch. Here we first asked if touch sensitivity is a heritable trait and second whether there are common genes that influence different mechanosensory senses like hearing and touch in humans. Using a classical twin study design we demonstrate that touch sensitivity and touch acuity are highly heritable traits. Quantitative phenotypic measures of different mechanosensory systems revealed significant correlations between touch and hearing acuity in a healthy human population. Thus mutations in genes causing deafness genes could conceivably negatively influence touch sensitivity. In agreement with this hypothesis we found that a proportion of a cohort of congenitally deaf young adults display significantly impaired measures of touch sensitivity compared to controls. In contrast, blind individuals showed enhanced, not diminished touch acuity. Finally, by examining a cohort of patients with Usher syndrome, a genetically well-characterized deaf-blindness syndrome, we could show that recessive pathogenic mutations in the USH2A gene influence touch acuity. Control Usher syndrome cohorts lacking demonstrable pathogenic USH2A mutations showed no impairment in touch acuity. Our study thus provides comprehensive evidence that there are common genetic elements that contribute to touch and hearing and has identified one of these genes as USH2A.

Little genetic variability in resilience among cattle exists for a range of performance traits across herds in Ireland differing in Fasciola hepatica prevalence.

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Twomey, Alan J; Graham, David A; Doherty, Michael L; Blom, Astrid; Berry, Donagh P

2018-06-04

It is anticipated that in the future, livestock will be exposed to a greater risk of infection from parasitic diseases. Therefore, future breeding strategies for livestock, which are generally long-term strategies for change, should target animals adaptable to environments with a high parasitic load. Covariance components were estimated in the present study for a selection of dairy and beef performance traits over herd-years differing in Fasciola hepatica load using random regression sire models. Herd-year prevalence of F. hepatica was determined by using F. hepatica-damaged liver phenotypes which were recorded in abattoirs nationally. The data analyzed consisted up to 83,821 lactation records from dairy cows for a range of milk production and fertility traits, as well as 105,054 young animals with carcass-related information obtained at slaughter. Reaction norms for individual sires were derived from the random regression coefficients. The heritability and additive genetic standard deviations for all traits analyzed remained relatively constant as herd-year F. hepatica prevalence gradient increased up to a prevalence level of 0.7; although there was a large increase in heritability and additive genetic standard deviation for milk and fertility traits in the observed F. hepatica prevalence levels >0.7, only 5% of the data existed in herd-year prevalence levels >0.7. Very little rescaling, therefore, exists across differing herd-year F. hepatica prevalence levels. Within-trait genetic correlations among the performance traits across different herd-year F. hepatica prevalence levels were less than unity for all traits. Nevertheless, within-trait genetic correlations for milk production and carcass traits were all >0.8 for F. hepatica prevalence levels between 0.2 and 0.8. The lowest estimate of within-trait genetic correlations for the different fertility traits ranged from -0.03 (SE = 1.09) in age of first calving to 0.54 (SE = 0.22) for calving to first service

Prediction of Complex Human Traits Using the Genomic Best Linear Unbiased Predictor

DEFF Research Database (Denmark)

de los Campos, Gustavo; Vazquez, Ana I; Fernando, Rohan

2013-01-01

Despite important advances from Genome Wide Association Studies (GWAS), for most complex human traits and diseases, a sizable proportion of genetic variance remains unexplained and prediction accuracy (PA) is usually low. Evidence suggests that PA can be improved using Whole-Genome Regression (WGR......) models where phenotypes are regressed on hundreds of thousands of variants simultaneously. The Genomic Best Linear Unbiased Prediction G-BLUP, a ridge-regression type method) is a commonly used WGR method and has shown good predictive performance when applied to plant and animal breeding populations....... However, breeding and human populations differ greatly in a number of factors that can affect the predictive performance of G-BLUP. Using theory, simulations, and real data analysis, we study the erformance of G-BLUP when applied to data from related and unrelated human subjects. Under perfect linkage...

Effect of captivity on genetic variance for five traits in the large milkweed bug (Oncopeltus fasciatus).

Science.gov (United States)

Rodríguez-Clark, K M

2004-07-01

Understanding the changes in genetic variance which may occur as populations move from nature into captivity has been considered important when populations in captivity are used as models of wild ones. However, the inherent significance of these changes has not previously been appreciated in a conservation context: are the methods aimed at founding captive populations with gene diversity representative of natural populations likely also to capture representative quantitative genetic variation? Here, I investigate changes in heritability and a less traditional measure, evolvability, between nature and captivity for the large milkweed bug, Oncopeltus fasciatus, to address this question. Founders were collected from a 100-km transect across the north-eastern US, and five traits (wing colour, pronotum colour, wing length, early fecundity and later fecundity) were recorded for founders and for their offspring during two generations in captivity. Analyses reveal significant heritable variation for some life history and morphological traits in both environments, with comparable absolute levels of evolvability across all traits (0-30%). Randomization tests show that while changes in heritability and total phenotypic variance were highly variable, additive genetic variance and evolvability remained stable across the environmental transition in the three morphological traits (changing 1-2% or less), while they declined significantly in the two life-history traits (5-8%). Although it is unclear whether the declines were due to selection or gene-by-environment interactions (or both), such declines do not appear inevitable: captive populations with small numbers of founders may contain substantial amounts of the evolvability found in nature, at least for some traits.

Personality traits as an endophenotype in genetic studies on suicidality in bipolar disorder.

Science.gov (United States)

Pawlak, J; Dmitrzak-Węglarz, M; Maciukiewicz, M; Kapelski, P; Czerski, P; Leszczyńska-Rodziewicz, A; Zaremba, D; Hauser, J

2017-04-01

Introduction The influence of personality traits on suicidal behaviour risk has been well documented. Personality traits and suicidal behaviour are partially genetically determined and personality has been described as an endophenotype of suicidal behaviour. The aim of this study was to investigate a possible association between personality traits with suicidal behaviour and selected serotonergic gene polymorphisms. In the study we included 156 patients meeting DSM-IV criteria for bipolar disorder (BP) and 93 healthy controls. The personality dimensions were assessed using the Temperament and Character Inventory (TCI). We genotyped two selected polymorphisms of the tryptophan hydroxylase 1 (TPH1) gene (rs1800532 218A>C and rs1799913 779A>C) and polymorphism in the promoter region of serotonin transporter gene (5-HTTLPR, rs25531) related to serotoninergic neurotransmission. Multiple poisson regression, logistic regression and Kruskal-Wallis tests were applied. We found numerous differences between the BP patients and the control group in terms of their TCI dimensions/subdimensions. Significant differences were found between patients with, and without, suicidal attempts in fatigability and asthenia (Ha4), as well as in harm avoidance (Ha). We also found that the interactions between TCI subdimensions (the interaction of disordiness (Ns4) and spiritual acceptance (St3), disordiness (Ns4) and integrated conscience (C5), extravagance (Ns3) and resourcefulness (Sd3)) were significantly contributing for suicidal behaviour risk. We found association between all studied genetic polymorphisms and several TCI dimensions and subdimensions. Our results confirm that personality traits are partially determined by genes. Both personality traits and the interactions between temperament and character traits, may be helpful in predicting suicidal behaviour.

Short communication: Genetic parameters for post-weaning visual scores and reproductive traits in Suffolk sheep

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Juliana V. Portes

2018-04-01

Full Text Available The aim of this study was to estimate the coefficients of heritability and genetic correlations among visual scores (conformation, CPW; precocity, PPW; musculature, MPW and reproductive traits: age at first lambing (AFL and scrotal circumference (SC evaluated at 180 days of age in Suffolk lambs. In the statistical model only the additive genetic effect was considered as random effect. The heritability estimates by univariate analyses for CPW, PPW, MPW, AFL and SC were 0.08, 0.12, 0.09, 0.20 and 0.22, respectively. The genetic correlations among AFL and CPW, PPW, MPW were -0.26, 0.19, and 0.08, respectively. The genetic correlation among SC and CPW, PPW, MPW were, respectively, 0.54, 0.88 and 0.86, and between AFL and SC was 0.26. The direct selection for conformation, precocity and musculature at 180 days of age and age at first lambing will provide slow genetic progress due to low heritability estimates. It is possible to obtain genetic gain in sexual precocity through selection on scrotal circumference in Suffolk rams. The favorable genetic correlation among visual scores and SC and between CPW and AFL, indicated the possibility to gain in genetic progress for reproductive traits through indirect selection of the visual scores in Suffolk sheep.

Genetic Evidence for Causal Relationships Between Maternal Obesity-Related Traits and Birth Weight.

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Tyrrell, Jessica; Richmond, Rebecca C; Palmer, Tom M; Feenstra, Bjarke; Rangarajan, Janani; Metrustry, Sarah; Cavadino, Alana; Paternoster, Lavinia; Armstrong, Loren L; De Silva, N Maneka G; Wood, Andrew R; Horikoshi, Momoko; Geller, Frank; Myhre, Ronny; Bradfield, Jonathan P; Kreiner-Møller, Eskil; Huikari, Ville; Painter, Jodie N; Hottenga, Jouke-Jan; Allard, Catherine; Berry, Diane J; Bouchard, Luigi; Das, Shikta; Evans, David M; Hakonarson, Hakon; Hayes, M Geoffrey; Heikkinen, Jani; Hofman, Albert; Knight, Bridget; Lind, Penelope A; McCarthy, Mark I; McMahon, George; Medland, Sarah E; Melbye, Mads; Morris, Andrew P; Nodzenski, Michael; Reichetzeder, Christoph; Ring, Susan M; Sebert, Sylvain; Sengpiel, Verena; Sørensen, Thorkild I A; Willemsen, Gonneke; de Geus, Eco J C; Martin, Nicholas G; Spector, Tim D; Power, Christine; Järvelin, Marjo-Riitta; Bisgaard, Hans; Grant, Struan F A; Nohr, Ellen A; Jaddoe, Vincent W; Jacobsson, Bo; Murray, Jeffrey C; Hocher, Berthold; Hattersley, Andrew T; Scholtens, Denise M; Davey Smith, George; Hivert, Marie-France; Felix, Janine F; Hyppönen, Elina; Lowe, William L; Frayling, Timothy M; Lawlor, Debbie A; Freathy, Rachel M

2016-03-15

Neonates born to overweight or obese women are larger and at higher risk of birth complications. Many maternal obesity-related traits are observationally associated with birth weight, but the causal nature of these associations is uncertain. To test for genetic evidence of causal associations of maternal body mass index (BMI) and related traits with birth weight. Mendelian randomization to test whether maternal BMI and obesity-related traits are potentially causally related to offspring birth weight. Data from 30,487 women in 18 studies were analyzed. Participants were of European ancestry from population- or community-based studies in Europe, North America, or Australia and were part of the Early Growth Genetics Consortium. Live, term, singleton offspring born between 1929 and 2013 were included. Genetic scores for BMI, fasting glucose level, type 2 diabetes, systolic blood pressure (SBP), triglyceride level, high-density lipoprotein cholesterol (HDL-C) level, vitamin D status, and adiponectin level. Offspring birth weight from 18 studies. Among the 30,487 newborns the mean birth weight in the various cohorts ranged from 3325 g to 3679 g. The maternal genetic score for BMI was associated with a 2-g (95% CI, 0 to 3 g) higher offspring birth weight per maternal BMI-raising allele (P = .008). The maternal genetic scores for fasting glucose and SBP were also associated with birth weight with effect sizes of 8 g (95% CI, 6 to 10 g) per glucose-raising allele (P = 7 × 10(-14)) and -4 g (95% CI, -6 to -2 g) per SBP-raising allele (P = 1×10(-5)), respectively. A 1-SD ( ≈ 4 points) genetically higher maternal BMI was associated with a 55-g higher offspring birth weight (95% CI, 17 to 93 g). A 1-SD ( ≈ 7.2 mg/dL) genetically higher maternal fasting glucose concentration was associated with 114-g higher offspring birth weight (95% CI, 80 to 147 g). However, a 1-SD ( ≈ 10 mm Hg) genetically higher maternal SBP was associated with a 208-g

Estimation of genetic parameters for reproductive traits in Shall sheep.

Science.gov (United States)

Amou Posht-e-Masari, Hesam; Shadparvar, Abdol Ahad; Ghavi Hossein-Zadeh, Navid; Hadi Tavatori, Mohammad Hossein

2013-06-01

The objective of this study was to estimate genetic parameters for reproductive traits in Shall sheep. Data included 1,316 records on reproductive performances of 395 Shall ewes from 41 sires and 136 dams which were collected from 2001 to 2007 in Shall breeding station in Qazvin province at the Northwest of Iran. Studied traits were litter size at birth (LSB), litter size at weaning (LSW), litter mean weight per lamb born (LMWLB), litter mean weight per lamb weaned (LMWLW), total litter weight at birth (TLWB), and total litter weight at weaning (TLWW). Test of significance to include fixed effects in the statistical model was performed using the general linear model procedure of SAS. The effects of lambing year and ewe age at lambing were significant (Psheep.

Genetic linkage map and QTL identification for adventitious rooting traits in red gum eucalypts.

Science.gov (United States)

Sumathi, Murugan; Bachpai, Vijaya Kumar Waman; Mayavel, A; Dasgupta, Modhumita Ghosh; Nagarajan, Binai; Rajasugunasekar, D; Sivakumar, Veerasamy; Yasodha, Ramasamy

2018-05-01

The eucalypt species, Eucalyptus tereticornis and Eucalyptus camaldulensis , show tolerance to drought and salinity conditions, respectively, and are widely cultivated in arid and semiarid regions of tropical countries. In this study, genetic linkage map was developed for interspecific cross E. tereticornis  ×  E. camaldulensis using pseudo-testcross strategy with simple sequence repeats (SSRs), intersimple sequence repeats (ISSRs), and sequence-related amplified polymorphism (SRAP) markers. The consensus genetic map comprised totally 283 markers with 84 SSRs, 94 ISSRs, and 105 SRAP markers on 11 linkage groups spanning 1163.4 cM genetic distance. Blasting the SSR sequences against E. grandis sequences allowed an alignment of 64% and the average ratio of genetic-to-physical distance was 1.7 Mbp/cM, which strengths the evidence that high amount of synteny and colinearity exists among eucalypts genome. Blast searches also revealed that 37% of SSRs had homologies with genes, which could potentially be used in the variety of downstream applications including candidate gene polymorphism. Quantitative trait loci (QTL) analysis for adventitious rooting traits revealed six QTL for rooting percent and root length on five chromosomes with interval and composite interval mapping. All the QTL explained 12.0-14.7% of the phenotypic variance, showing the involvement of major effect QTL on adventitious rooting traits. Increasing the density of markers would facilitate the detection of more number of small-effect QTL and also underpinning the genes involved in rooting process.

Neutral mutation as the source of genetic variation in life history traits.

Science.gov (United States)

Brcić-Kostić, Krunoslav

2005-08-01

The mechanism underlying the maintenance of adaptive genetic variation is a long-standing question in evolutionary genetics. There are two concepts (mutation-selection balance and balancing selection) which are based on the phenotypic differences between alleles. Mutation - selection balance and balancing selection cannot properly explain the process of gene substitution, i.e. the molecular evolution of quantitative trait loci affecting fitness. I assume that such loci have non-essential functions (small effects on fitness), and that they have the potential to evolve into new functions and acquire new adaptations. Here I show that a high amount of neutral polymorphism at these loci can exist in real populations. Consistent with this, I propose a hypothesis for the maintenance of genetic variation in life history traits which can be efficient for the fixation of alleles with very small selective advantage. The hypothesis is based on neutral polymorphism at quantitative trait loci and both neutral and adaptive gene substitutions. The model of neutral - adaptive conversion (NAC) assumes that neutral alleles are not neutral indefinitely, and that in specific and very rare situations phenotypic (relative fitness) differences between them can appear. In this paper I focus on NAC due to phenotypic plasticity of neutral alleles. The important evolutionary consequence of NAC could be the increased adaptive potential of a population. Loci responsible for adaptation should be fast evolving genes with minimally discernible phenotypic effects, and the recent discovery of genes with such characteristics implicates them as suitable candidates for loci involved in adaptation.

Advances in the genetically complex autoinflammatory diseases.

Science.gov (United States)

Ombrello, Michael J

2015-07-01

Monogenic diseases usually demonstrate Mendelian inheritance and are caused by highly penetrant genetic variants of a single gene. In contrast, genetically complex diseases arise from a combination of multiple genetic and environmental factors. The concept of autoinflammation originally emerged from the identification of individual, activating lesions of the innate immune system as the molecular basis of the hereditary periodic fever syndromes. In addition to these rare, monogenic forms of autoinflammation, genetically complex autoinflammatory diseases like the periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) syndrome, chronic recurrent multifocal osteomyelitis (CRMO), Behçet's disease, and systemic arthritis also fulfill the definition of autoinflammatory diseases-namely, the development of apparently unprovoked episodes of inflammation without identifiable exogenous triggers and in the absence of autoimmunity. Interestingly, investigations of these genetically complex autoinflammatory diseases have implicated both innate and adaptive immune abnormalities, blurring the line between autoinflammation and autoimmunity. This reinforces the paradigm of concerted innate and adaptive immune dysfunction leading to genetically complex autoinflammatory phenotypes.

Plant traits correlated with generation time directly affect inbreeding depression and mating system and indirectly genetic structure

Directory of Open Access Journals (Sweden)

Hardy Olivier J

2009-07-01

Full Text Available Abstract Background Understanding the mechanisms that control species genetic structure has always been a major objective in evolutionary studies. The association between genetic structure and species attributes has received special attention. As species attributes are highly taxonomically constrained, phylogenetically controlled methods are necessary to infer causal relationships. In plants, a previous study controlling for phylogenetic signal has demonstrated that Wright's FST, a measure of genetic differentiation among populations, is best predicted by the mating system (outcrossing, mixed-mating or selfing and that plant traits such as perenniality and growth form have only an indirect influence on FST via their association with the mating system. The objective of this study is to further outline the determinants of plant genetic structure by distinguishing the effects of mating system on gene flow and on genetic drift. The association of biparental inbreeding and inbreeding depression with population genetic structure, mating system and plant traits are also investigated. Results Based on data from 263 plant species for which estimates of FST, inbreeding (FIS and outcrossing rate (tm are available, we confirm that mating system is the main influencing factor of FST. Moreover, using an alternative measure of FST unaffected by the impact of inbreeding on effective population size, we show that the influence of tm on FST is due to its impact on gene flow (reduced pollen flow under selfing and on genetic drift (higher drift under selfing due to inbreeding. Plant traits, in particular perenniality, influence FST mostly via their effect on the mating system but also via their association with the magnitude of selection against inbred individuals: the mean inbreeding depression increases from short-lived herbaceous to long-lived herbaceous and then to woody species. The influence of perenniality on mating system does not seem to be related to

Comparison of statistical tests for association between rare variants and binary traits.

OpenAIRE

Bacanu, SA; Nelson, MR; Whittaker, JC

2012-01-01

: Genome-wide association studies have found thousands of common genetic variants associated with a wide variety of diseases and other complex traits. However, a large portion of the predicted genetic contribution to many traits remains unknown. One plausible explanation is that some of the missing variation is due to the effects of rare variants. Nonetheless, the statistical analysis of rare variants is challenging. A commonly used method is to contrast, within the same region (gene), the fr...

Genetic Parameter Estimates of Carcass Traits under National Scale Breeding Scheme for Beef Cattle

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ChangHee Do

2016-08-01

Full Text Available Carcass and price traits of 72,969 Hanwoo cows, bulls and steers aged 16 to 80 months at slaughter collected from 2002 to 2013 at 75 beef packing plants in Korea were analyzed to determine heritability, correlation and breeding value using the Multi-Trait restricted maximum likelihood (REML animal model procedure. The traits included carcass measurements, scores and grades at 24 h postmortem and bid prices at auction. Relatively high heritability was found for maturity (0.41±0.031, while moderate heritability estimates were obtained for backfat thickness (0.20±0.018, longissimus muscle (LM area (0.23±0.020, carcass weight (0.28±0.019, yield index (0.20±0.018, yield grade (0.16±0.017, marbling (0.28±0.021, texture (0.14±0.016, quality grade (0.26±0.016 and price/kg (0.24±0.025. Relatively low heritability estimates were observed for meat color (0.06±0.013 and fat color (0.06±0.012. Heritability estimates for most traits were lower than those in the literature. Genetic correlations of carcass measurements with characteristic scores or quality grade of carcass ranged from −0.27 to +0.21. Genetic correlations of yield grade with backfat thickness, LM area and carcass weight were 0.91, −0.43, and −0.09, respectively. Genetic correlations of quality grade with scores of marbling, meat color, fat color and texture were −0.99, 0.48, 0.47, and 0.98, respectively. Genetic correlations of price/kg with LM area, carcass weight, marbling, meat color, texture and maturity were 0.57, 0.64, 0.76, −0.41, −0.79, and −0.42, respectively. Genetic correlations of carcass price with LM area, carcass weight, marbling and texture were 0.61, 0.57, 0.64, and −0.73, respectively, with standard errors ranging from ±0.047 to ±0.058. The mean carcass weight breeding values increased by more than 8 kg, whereas the mean marbling scores decreased by approximately 0.2 from 2000 through 2009. Overall, the results suggest that genetic improvement of

Genetic parameters for canalisation analysis of litter size and litter weight traits at birth in mice

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Salgado Concepción

2006-09-01

Full Text Available Abstract The aim of this research was to explore the genetic parameters associated with environmental variability for litter size (LS, litter weight (LW and mean individual birth weight (IW in mice before canalisation. The analyses were conducted on an experimental mice population designed to reduce environmental variability for LS. The analysed database included 1976 records for LW and IW and 4129 records for LS. The total number of individuals included in the analysed pedigree was 3997. Heritabilities estimated for the traits under an initial exploratory approach varied from 0.099 to 0.101 for LS, from 0.112 to 0.148 for LW and from 0.028 to 0.033 for IW. The means of the posterior distribution of the heritability under a Bayesian approach were the following: 0.10 (LS, 0.13 (LW and 0.03 (IW. In general, the heritabilities estimated under the initial exploratory approach for the environmental variability of the analysed traits were low. Genetic correlations estimated between the trait and its variability reached values of -0.929 (LS, -0.815 (LW and 0.969 (IW. The results presented here for the first time in mice may suggest a genetic basis for variability of the evaluated traits, thus opening the possibility to be implemented in selection schemes.

Genetic polymorphism of beta-casein gene and its associations with milk traits in Holstein-Friesian cows

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Teodor Bugeac

2015-05-01

Full Text Available In animal breeding finding and using effective genetic markers for improving important traits it is a continuous challenge. In this respect, several genetic markers were associated in cattle with increased milk production or a better milk quality. This proved to be a useful tool for improving certain traits by selecting individuals carriers of allelic variants that have an effect on a desirable trait. In particular, positive associations between certain alleles found at the milk protein loci with some milk production traits convincingly demonstrated in several cattle breeds. Although, in some cases the results obtained in various studies were not in agreement and varied between breeds or populations. Therefore the objective of this study was to establish associations (if any between alleles found at the beta-casein (CSN2 locus and some milk production traits (milk yield and fat, protein, casein and lactose content in a Holstein-Friesian population reared in Romania. Genetic variants at CSN2 locus were identified by isoelectric focusing (IEF of milk samples. In order to determine milk composition the samples were analysed with MilkoScan FT 6000. For the statistical analysis of data SPSS v.19 for Windows was used. At the CSN2 locus four alleles and seven genotypes were identified in the analyzed cattle population. The cows carriers of CSN2 A2 allele produced the highest milk yield and the highest milk protein content, this result being in agreement with other previous studies.

A high density genetic map and QTL for agronomic and yield traits in Foxtail millet [Setaria italica (L.) P. Beauv].

Science.gov (United States)

Fang, Xiaomei; Dong, Kongjun; Wang, Xiaoqin; Liu, Tianpeng; He, Jihong; Ren, Ruiyu; Zhang, Lei; Liu, Rui; Liu, Xueying; Li, Man; Huang, Mengzhu; Zhang, Zhengsheng; Yang, Tianyu

2016-05-04

Foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China, has been adopted as a model crop for studying C-4 photosynthesis, stress biology and biofuel traits. Construction of a high density genetic map and identification of stable quantitative trait loci (QTL) lay the foundation for marker-assisted selection for agronomic traits and yield improvement. A total of 10598 SSR markers were developed according to the reference genome sequence of foxtail millet cultivar 'Yugu1'. A total of 1013 SSR markers showing polymorphism between Yugu1 and Longgu7 were used to genotype 167 individuals from a Yugu1 × Longgu7 F2 population, and a high density genetic map was constructed. The genetic map contained 1035 loci and spanned 1318.8 cM with an average distance of 1.27 cM between adjacent markers. Based on agronomic and yield traits identified in 2 years, 29 QTL were identified for 11 traits with combined analysis and single environment analysis. These QTL explained from 7.0 to 14.3 % of phenotypic variation. Favorable QTL alleles for peduncle length originated from Longgu7 whereas favorable alleles for the other traits originated from Yugu1 except for qLMS6.1. New SSR markers, a high density genetic map and QTL identified for agronomic and yield traits lay the ground work for functional gene mapping, map-based cloning and marker-assisted selection in foxtail millet.

Genetic control and combining ability of flag leaf area and relative water content traits of bread wheat cultivars under drought stress condition

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Golparvar Ahmad Reza

2013-01-01

Full Text Available In order to compare mode of inheritance, combining ability, heterosis and gene action in genetic control of traits flag leaf area, relative water content and grain filling rate of bread wheat under drought stress, a study was conducted on 8 cultivars using of Griffing’s method2 in fixed model. Mean square of general combining ability was significant also for all traits and mean square of specific combining ability was significant also for all traits except relative water content of leaf which show importance of both additive and dominant effects of genes in heredity of these traits under stress. GCA to SCA mean square ratio was significant for none of traits. Results of this study showed that non additive effects of genes were more important than additive effect for all traits. According to results we can understand that genetic improvement of mentioned traits will have low genetic efficiency by selection from the best crosses of early generations. Then it is better to delay selection until advanced generations and increase in heritability of these traits.

The Genetic and Environmental Covariation among Psychopathic Personality Traits, and Reactive and Proactive Aggression in Childhood

Science.gov (United States)

Bezdjian, Serena; Tuvblad, Catherine; Raine, Adrian; Baker, Laura A.

2011-01-01

The present study investigated the genetic and environmental covariance between psychopathic personality traits with reactive and proactive aggression in 9- to 10-year-old twins (N = 1,219). Psychopathic personality traits were assessed with the Child Psychopathy Scale (D. R. Lynam, 1997), while aggressive behaviors were assessed using the…

Quantitative genetic analysis of life-history traits of Caenorhabditis elegans in stressful environments

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Shorto Alison

2008-01-01

Full Text Available Abstract Background Organisms live in environments that vary. For life-history traits that vary across environments, fitness will be maximised when the phenotype is appropriately matched to the environmental conditions. For the free-living nematode Caenorhabditis elegans, we have investigated how two major life-history traits, (i the development of environmentally resistant dauer larvae and (ii reproduction, respond to environmental stress (high population density and low food availability, and how these traits vary between lines and the genetic basis of this variation. Results We found that lines of C. elegans vary in their phenotypic plasticity of dauer larva development, i.e. there is variation in the likelihood of developing into a dauer larva for the same environmental change. There was also variation in how lifetime fecundity and the rate of reproduction changed under conditions of environmental stress. These traits were related, such that lines that are highly plastic for dauer larva development also maintain a high population growth rate when stressed. We identified quantitative trait loci (QTL on two chromosomes that control the dauer larva development and population size phenotypes. The QTLs affecting the dauer larva development and population size phenotypes on chromosome II are closely linked, but are genetically separable. This chromosome II QTL controlling dauer larva development does not encompass any loci previously identified to control dauer larva development. This chromosome II region contains many predicted 7-transmembrane receptors. Such proteins are often involved in information transduction, which is clearly relevant to the control of dauer larva development. Conclusion C. elegans alters both its larval development and adult reproductive strategy in response to environmental stress. Together the phenotypic and genotypic data suggest that these two major life-history traits are co-ordinated responses to environmental stress

A power study of bivariate LOD score analysis of a complex trait and fear/discomfort with strangers.

Science.gov (United States)

Ji, Fei; Lee, Dayoung; Mendell, Nancy Role

2005-12-30

Complex diseases are often reported along with disease-related traits (DRT). Sometimes investigators consider both disease and DRT phenotypes separately and sometimes they consider individuals as affected if they have either the disease or the DRT, or both. We propose instead to consider the joint distribution of the disease and the DRT and do a linkage analysis assuming a pleiotropic model. We evaluated our results through analysis of the simulated datasets provided by Genetic Analysis Workshop 14. We first conducted univariate linkage analysis of the simulated disease, Kofendrerd Personality Disorder and one of its simulated associated traits, phenotype b (fear/discomfort with strangers). Subsequently, we considered the bivariate phenotype, which combined the information on Kofendrerd Personality Disorder and fear/discomfort with strangers. We developed a program to perform bivariate linkage analysis using an extension to the Elston-Stewart peeling method of likelihood calculation. Using this program we considered the microsatellites within 30 cM of the gene pleiotropic for this simulated disease and DRT. Based on 100 simulations of 300 families we observed excellent power to detect linkage within 10 cM of the disease locus using the DRT and the bivariate trait.

Association analysis of three diverse rice (Oryza sativa L.) germplasm collections for loci regulating grain quality traits

Science.gov (United States)

In rice (Oryza sativa L.), end-use/cooking quality is vital for producers and millions of consumers worldwide. Grain quality is a complex trait with interacting genetic and environmental factors. Deciphering the complex genetic architecture associated with grain quality, will provide vital informati...

Genetic insight into yield-associated traits of wheat grown in multiple rain-fed environments.

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Xianshan Wu

Full Text Available BACKGROUND: Grain yield is a key economic driver of successful wheat production. Due to its complex nature, little is known regarding its genetic control. The goal of this study was to identify important quantitative trait loci (QTL directly and indirectly affecting grain yield using doubled haploid lines derived from a cross between Hanxuan 10 and Lumai 14. METHODOLOGY/PRINCIPAL FINDINGS: Ten yield-associated traits, including yield per plant (YP, number of spikes per plant (NSP, number of grains per spike (NGS, one-thousand grain weight (TGW, total number of spikelets per spike (TNSS, number of sterile spikelets per spike (NSSS, proportion of fertile spikelets per spike (PFSS, spike length (SL, density of spikelets per spike (DSS and plant height (PH, were assessed across 14 (for YP to 23 (for TGW year × location × water regime environments in China. Then, the genetic effects were partitioned into additive main effects (a, epistatic main effects (aa and their environment interaction effects (ae and aae by using composite interval mapping in a mixed linear model. CONCLUSIONS/SIGNIFICANCE: Twelve (YP to 33 (PH QTLs were identified on all 21 chromosomes except 6D. QTLs were more frequently observed on chromosomes 1B, 2B, 2D, 5A and 6B, and were concentrated in a few regions on individual chromosomes, exemplified by three striking yield-related QTL clusters on chromosomes 2B, 1B and 4B that explained the correlations between YP and other traits. The additive main-effect QTLs contributed more phenotypic variation than the epistasis and environmental interaction. Consistent with agronomic analyses, a group of progeny derived by selecting TGW and NGS, with higher grain yield, had an increased frequency of QTL for high YP, NGS, TGW, TNSS, PFSS, SL, PH and fewer NSSS, when compared to low yielding progeny. This indicated that it is feasible by marker-assisted selection to facilitate wheat production.

Multivariate Survival Mixed Models for Genetic Analysis of Longevity Traits

DEFF Research Database (Denmark)

Pimentel Maia, Rafael; Madsen, Per; Labouriau, Rodrigo

2014-01-01

A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented co...... applications. The methods presented are implemented in such a way that large and complex quantitative genetic data can be analyzed......A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented...... concentrates on longevity studies. The framework presented allows to combine models based on continuous time with models based on discrete time in a joint analysis. The continuous time models are approximations of the frailty model in which the hazard function will be assumed to be piece-wise constant...

Multivariate Survival Mixed Models for Genetic Analysis of Longevity Traits

DEFF Research Database (Denmark)

Pimentel Maia, Rafael; Madsen, Per; Labouriau, Rodrigo

2013-01-01

A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented co...... applications. The methods presented are implemented in such a way that large and complex quantitative genetic data can be analyzed......A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented...... concentrates on longevity studies. The framework presented allows to combine models based on continuous time with models based on discrete time in a joint analysis. The continuous time models are approximations of the frailty model in which the hazard function will be assumed to be piece-wise constant...

Heritability and genetic advance studies for biochemical traits in F2-3 introgressed families of Brassica

International Nuclear Information System (INIS)

Farhatullah, N.K.; Khalil, I.H.; Nahed, H.

2015-01-01

Higher heritability estimates along with high genetic advance values are effective in envisaging gain under selection in developing genotypes. The objective of the present study was to evaluate variability, heritability and genetic advance in 10 interspecific F2-3 families of Brassica species (B. napus * B. juncea, B. napus * B. rapa). These families were studied for heterospecific introgression of biochemical traits. Low to high heritability estimates were recorded for seed quality traits. Considerable variations within F2-3 families were observed for biochemical traits. Most of the F2-3 families for oil content and erucic showed moderate to high heritability indicating the slightest influence of environment thus modification of trait by selection would be more effective. Among F2-3 introgressed families Bn-510 x Bj-109 produced high oil i.e., 49.5% while Bn-532 x Br-118 (24.4%), Bn-533 x Bj-109 (24.1%) and high protein percentage in terms of mean performance. In the present research, individual segregating progenies of interspecific cross populations i.e., which possessed combination of desirable traits, were identified which could be incorporated in the future Breeding programs and it may facilitate varietal development. (author)

Genetic variability and heritability estimates of some polygenic traits in upland cotton

International Nuclear Information System (INIS)

Baloch, M.J.

2004-01-01

Plant breeders are more interested in genetic variance rather than phenotypic variance because it is amenable to selection and bring further improvement in the character. Twenty-eight F/sub 2/ progenies were tested in two environments so as to predict genetic variances, heritability estimates and genetic gains. Mean squares for locations were significant for all the five traits suggesting that genotypes performed differently under varying environments. Genetic variances, in most cases, however, were about equal to that of phenotypic variances consequently giving high heritability estimates and significant genetic gains. The broad sense heritability estimates were; 94.2, 92.9, 33.6, 81.9 and 86.9% and genetic gains were; 30.19, 10.55,0.20,0.89 and 1.76 in seed cotton yield, bolls per plant, lint %, fibre length and fibre uniformity ratio, respectively. Substantial genetic variances and high heritability estimates implied that these characters could be improved through selection from segregating populations. (author)

Estimation of genetic parameters for morphological and functional traits in a Menorca horse population

Energy Technology Data Exchange (ETDEWEB)

Sole, M.; Cervantes, I.; Gutierrez, J. P.; Gomez, M. D.; Valera, M.

2014-06-01

Functional conformation and performance in Classic and Menorca Dressage are the main selection criteria in the Menorca Horse breeding program. Menorca Dressage is an alternative Classical Dressage discipline which is exclusive of the Menorca Island, but including a series of movements that the animals perform in the traditional festivities called Jaleo Menorquin. One of these movements involves the horse raising its forelimbs and standing or walking on its hindlimbs, which is called el bot. To make the Menorca horse breed more competitive in the equestrian market, it is necessary to understand the genetic background that characterizes the aptitude for Menorca Dressage and its relationship with conformation traits. The analysed data consisted of 15 conformation traits from 347 Menorca horses (200 males and 147 females), with 1,550 performance records in Menorca Dressage competitions. Genetic parameters were estimated using linear and threshold animal models. The heritabilities for heights and lengths were high (0.45-0.76), those for angulations and binary conformation traits were low to moderate (0.10-0.36) as were the scores for dressage performance (0.13-0.21). The results suggest that the analyzed traits could be used as an efficient tool for selecting breeding horses. (Author)

Estimation of genetic parameters for morphological and functional traits in a Menorca horse population

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Marina Solé

2014-01-01

Full Text Available Functional conformation and performance in Classic and Menorca Dressage are the main selection criteria in the Menorca Horse breeding program. Menorca Dressage is an alternative Classical Dressage discipline which is exclusive of the Menorca Island, but including a series of movements that the animals perform in the traditional festivities called “Jaleo Menorquín”. One of these movements involves the horse raising its forelimbs and standing or walking on its hindlimbs, which is called “el bot”. To make the Menorca horse breed more competitive in the equestrian market, it is necessary to understand the genetic background that characterizes the aptitude for Menorca Dressage and its relationship with conformation traits. The analysed data consisted of 15 conformation traits from 347 Menorca horses (200 males and 147 females, with 1,550 performance records in Menorca Dressage competitions. Genetic parameters were estimated using linear and threshold animal models. The heritabilities for heights and lengths were high (0.45-0.76, those for angulations and binary conformation traits were low to moderate (0.10-0.36 as were the scores for dressage performance (0.13-0.21. The results suggest that the analyzed traits could be used as an efficient tool for selecting breeding horses.

Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium

NARCIS (Netherlands)

Kazmi, R.H.; Khan, N.; Willems, L.A.J.; Heusden, van A.W.; Ligterink, J.W.; Hilhorst, H.W.M.

2012-01-01

Seed quality in tomato is associated with many complex physiological and genetic traits. While plant processes are frequently controlled by the action of small- to large-effect genes that follow classic Mendelian inheritance, our study suggests that seed quality is primarily quantitative and

Genetic and phenotypic parameter estimates for growth traits of Hainan Black goat in southern China

NARCIS (Netherlands)

Zhou, Han Lin; Gu, Li Hong; Sun, Yanyan; Xu, Tie Shan; Rong, Guang

2015-01-01

Genetic improvement of the growth of Hainan Black goats is a major concern as the breed is an important meat-type goat raised in southern China. To estimate genetic and phenotypic parameters for growth traits for this breed, a population of 1354 Hainan Black goats born and maintained at the

Expression quantitative trait loci and genetic regulatory network analysis reveals that Gabra2 is involved in stress responses in the mouse.

Science.gov (United States)

Dai, Jiajuan; Wang, Xusheng; Chen, Ying; Wang, Xiaodong; Zhu, Jun; Lu, Lu

2009-11-01

Previous studies have revealed that the subunit alpha 2 (Gabra2) of the gamma-aminobutyric acid receptor plays a critical role in the stress response. However, little is known about the gentetic regulatory network for Gabra2 and the stress response. We combined gene expression microarray analysis and quantitative trait loci (QTL) mapping to characterize the genetic regulatory network for Gabra2 expression in the hippocampus of BXD recombinant inbred (RI) mice. Our analysis found that the expression level of Gabra2 exhibited much variation in the hippocampus across the BXD RI strains and between the parental strains, C57BL/6J, and DBA/2J. Expression QTL (eQTL) mapping showed three microarray probe sets of Gabra2 to have highly significant linkage likelihood ratio statistic (LRS) scores. Gene co-regulatory network analysis showed that 10 genes, including Gria3, Chka, Drd3, Homer1, Grik2, Odz4, Prkag2, Grm5, Gabrb1, and Nlgn1 are directly or indirectly associated with stress responses. Eleven genes were implicated as Gabra2 downstream genes through mapping joint modulation. The genetical genomics approach demonstrates the importance and the potential power of the eQTL studies in identifying genetic regulatory networks that contribute to complex traits, such as stress responses.

A tight association in two genetically unlinked dispersal related traits in sympatric and allopatric salt marsh beetle populations.

Science.gov (United States)

Van Belleghem, Steven M; Hendrickx, Frederik

2014-02-01

Local adaptation likely involves selection on multiple, genetically unlinked traits to increase fitness in divergent habitats. Conversely, recombination is expected to counteract local adaptation under gene flow by breaking down adaptive gene combinations. Western European populations of the salt marsh beetle Pogonus chalceus are characterized by large interpopulation variation at various geographical ranges in two traits related to dispersal ability, i.e. wing size and different allozymes of the mitochondrial NADP(+)-dependent isocitrate dehydrogenase (mtIdh) gene. In this study, we tested whether variation in wing length was as strongly genetically determined in locally adapted populations in a sympatric mosaic compared to allopatric populations, and if variation in mtIDH and wing size was genetically unlinked. We demonstrate that the genetic determination of wing size is very high (h (2) = 0.90) in sympatry and of comparable magnitude as geographically separated populations. Second, we show that, although frequencies of mtIDH allozymes are tightly associated with mean population wing size across Western European populations, the correlation is strongly reduced within some of the populations. These findings demonstrate that the divergence involves at least two traits under independent genetic control and that the genetically distinct ecotypes are retained at geographical distances with ample opportunity for gene flow.

Estimation of Genetic Parameters for Fat Deposition and Carcass Traits in Broilers

NARCIS (Netherlands)

Zerehdaran, S.; Vereijken, A.L.J.; Arendonk, van J.A.M.; Waaij, van der E.H.

2004-01-01

Abdominal and subcutaneous fat are regarded as the main sources of waste in the slaughterhouse. Fat stored intramuscularly is regarded a favorite trait related to meat quality. The objective of current study was to estimate genetic parameters for fat deposition in the 3 different parts of body and

The Genetics of Biofuel Traits in Panicum Grasses: Developing a Model System with Diploid Panicum Hallii

Energy Technology Data Exchange (ETDEWEB)

Juenger, Thomas [Univ. of Texas, Austin, TX (United States). Dept. of Integrative Biology; Wolfrum, Ed [National Renewable Energy Lab. (NREL), Golden, CO (United States)

2016-07-31

Our DOE funded project focused on characterizing natural variation in C4 perennial grasses including switchgrass (Panicum virgatum) and Hall’s panicgrass (Panicum hallii). The main theme of our project was to better understand traits linked with plant performance and that impact the utility of plant biomass as a biofuel feedstock. In addition, our project developed tools and resources for studying genetic variation in Panicum hallii. Our project successfully screened both Panicum virgatum and Panicum hallii diverse natural collections for a host of phenotypes, developed genetic mapping populations for both species, completed genetic mapping for biofuel related traits, and helped in the development of genomic resources of Panicum hallii. Together, these studies have improved our understanding of the role of genetic and environmental factors in impacting plant performance. This information, along with new tools, will help foster the improvement of perennial grasses for feedstock applications.

Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower.

Science.gov (United States)

Thorwarth, Patrick; Yousef, Eltohamy A A; Schmid, Karl J

2018-02-02

Genetic resources are an important source of genetic variation for plant breeding. Genome-wide association studies (GWAS) and genomic prediction greatly facilitate the analysis and utilization of useful genetic diversity for improving complex phenotypic traits in crop plants. We explored the potential of GWAS and genomic prediction for improving curd-related traits in cauliflower ( Brassica oleracea var. botrytis ) by combining 174 randomly selected cauliflower gene bank accessions from two different gene banks. The collection was genotyped with genotyping-by-sequencing (GBS) and phenotyped for six curd-related traits at two locations and three growing seasons. A GWAS analysis based on 120,693 single-nucleotide polymorphisms identified a total of 24 significant associations for curd-related traits. The potential for genomic prediction was assessed with a genomic best linear unbiased prediction model and BayesB. Prediction abilities ranged from 0.10 to 0.66 for different traits and did not differ between prediction methods. Imputation of missing genotypes only slightly improved prediction ability. Our results demonstrate that GWAS and genomic prediction in combination with GBS and phenotyping of highly heritable traits can be used to identify useful quantitative trait loci and genotypes among genetically diverse gene bank material for subsequent utilization as genetic resources in cauliflower breeding. Copyright © 2018 Thorwarth et al.

Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower

Directory of Open Access Journals (Sweden)

Patrick Thorwarth

2018-02-01

Full Text Available Genetic resources are an important source of genetic variation for plant breeding. Genome-wide association studies (GWAS and genomic prediction greatly facilitate the analysis and utilization of useful genetic diversity for improving complex phenotypic traits in crop plants. We explored the potential of GWAS and genomic prediction for improving curd-related traits in cauliflower (Brassica oleracea var. botrytis by combining 174 randomly selected cauliflower gene bank accessions from two different gene banks. The collection was genotyped with genotyping-by-sequencing (GBS and phenotyped for six curd-related traits at two locations and three growing seasons. A GWAS analysis based on 120,693 single-nucleotide polymorphisms identified a total of 24 significant associations for curd-related traits. The potential for genomic prediction was assessed with a genomic best linear unbiased prediction model and BayesB. Prediction abilities ranged from 0.10 to 0.66 for different traits and did not differ between prediction methods. Imputation of missing genotypes only slightly improved prediction ability. Our results demonstrate that GWAS and genomic prediction in combination with GBS and phenotyping of highly heritable traits can be used to identify useful quantitative trait loci and genotypes among genetically diverse gene bank material for subsequent utilization as genetic resources in cauliflower breeding.

Psoriasis and cardiometabolic traits: modest association but distinct genetic architectures

Science.gov (United States)

Koch, Manja; Baurecht, Hansjörg; Ried, Janina S.; Rodriguez, Elke; Schlesinger, Sabrina; Volks, Natalie; Gieger, Christian; Rückert, Ina-Maria; Heinrich, Luise; Willenborg, Christina; Smith, Catherine; Peters, Annette; Thorand, Barbara; Koenig, Wolfgang; Lamina, Claudia; Jansen, Henning; Kronenberg, Florian; Seissler, Jochen; Thiery, Joachim; Rathmann, Wolfgang; Schunkert, Heribert; Erdmann, Jeanette; Barker, Jonathan; Nair, Rajan P; Tsoi, Lam C; Elder, James T; Mrowietz, Ulrich; Weichenthal, Michael; Mucha, Sören; Schreiber, Stefan; Franke, Andre; Schmitt, Jochen; Lieb, Wolfgang; Weidinger, Stephan

2015-01-01

Psoriasis has been linked to cardiometabolic diseases, but epidemiological findings are inconsistent. We investigated the association between psoriasis and cardiometabolic outcomes in a German cross-sectional study (n=4.185) and a prospective cohort of German Health Insurance beneficiaries (n=1.811.098). A potential genetic overlap was explored using genome-wide data from >22.000 coronary artery disease (CAD) and >4.000 psoriasis cases, and with a dense genotyping study of cardiometabolic risk loci on 927 psoriasis cases and 3.717 controls. Controlling for major confounders, in the cross-sectional analysis psoriasis was significantly associated with type 2 diabetes (T2D, adjusted odd’s ratio OR=2.36; 95% confidence interval CI=1.26–4.41) and myocardial infarction (MI, OR=2.26, 95% CI=1.03–4.96). In the longitudinal study, psoriasis slightly increased the risk for incident T2D (adjusted relative risk RR=1.11; 95%CI=1.08–1.14) and MI (RR=1.14; 95%CI=1.06–1.22), with highest risk increments in systemically treated psoriasis, which accounted for 11 and 17 excess cases of T2D and MI per 10,000 person-years. Except for weak signals from within the MHC, there was no evidence for genetic risk loci shared between psoriasis and cardiometabolic traits. Our findings suggest that psoriasis, in particular severe psoriasis, increases risk for T2D and MI, and that the genetic architecture of psoriasis and cardiometabolic traits is largely distinct. PMID:25599394

Genetic and environmental sources of individual religiousness: the roles of individual personality traits and perceived environmental religiousness.

Science.gov (United States)

Kandler, Christian; Riemann, Rainer

2013-07-01

In the current study, we examined the genetic and environmental sources of the links between individual religiousness and individual personality traits, perceived parental religiousness, and perceived peer religiousness. Data from 870 individuals (incl. 394 twin pairs) were analyzed. Variance in individual religiousness was significantly influenced by genetic effects, environmental influences shared by twins reared together, and individual-specific environmental influences. Individual religiousness showed significant associations with age, sex, specific personality traits (e.g., agreeableness, openness to values), and perceived religiousness of important social interaction partners, such as parents, best friends, and spouses. The links to personality traits were relatively small and primarily genetically mediated. The associations between individual religiousness and parental religiousness were substantial and mediated by shared environmental effects. These links significantly decreased across age accompanying a significant decrease of shared environmental influences on individual religiousness. The correlations between individual religiousness and perceived religiousness of spouses and best friends were relatively moderate but increased with age. These associations were mediated by genetic as well as nonshared environmental sources accompanying an increase of nonshared environmental influences on individual religiousness with age. The results suggest that inter-individual differences in religiousness are due to multiple sources.

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

Science.gov (United States)

Wang, Hai-yan

2015-08-01

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

Quantitative magnetic resonance imaging traits as endophenotypes for genetic mapping in epilepsy

Directory of Open Access Journals (Sweden)

Saud Alhusaini

2016-01-01

Full Text Available Over the last decade, the field of imaging genomics has combined high-throughput genotype data with quantitative magnetic resonance imaging (QMRI measures to identify genes associated with brain structure, cognition, and several brain-related disorders. Despite its successful application in different psychiatric and neurological disorders, the field has yet to be advanced in epilepsy. In this article we examine the relevance of imaging genomics for future genetic studies in epilepsy from three perspectives. First, we discuss prior genome-wide genetic mapping efforts in epilepsy, considering the possibility that some studies may have been constrained by inherent theoretical and methodological limitations of the genome-wide association study (GWAS method. Second, we offer a brief overview of the imaging genomics paradigm, from its original inception, to its role in the discovery of important risk genes in a number of brain-related disorders, and its successful application in large-scale multinational research networks. Third, we provide a comprehensive review of past studies that have explored the eligibility of brain QMRI traits as endophenotypes for epilepsy. While the breadth of studies exploring QMRI-derived endophenotypes in epilepsy remains narrow, robust syndrome-specific neuroanatomical QMRI traits have the potential to serve as accessible and relevant intermediate phenotypes for future genetic mapping efforts in epilepsy.

Plasticity Regulators Modulate Specific Root Traits in Discrete Nitrogen Environments

Science.gov (United States)

Gifford, Miriam L.; Banta, Joshua A.; Katari, Manpreet S.; Hulsmans, Jo; Chen, Lisa; Ristova, Daniela; Tranchina, Daniel; Purugganan, Michael D.; Coruzzi, Gloria M.; Birnbaum, Kenneth D.

2013-01-01

Plant development is remarkably plastic but how precisely can the plant customize its form to specific environments? When the plant adjusts its development to different environments, related traits can change in a coordinated fashion, such that two traits co-vary across many genotypes. Alternatively, traits can vary independently, such that a change in one trait has little predictive value for the change in a second trait. To characterize such “tunability” in developmental plasticity, we carried out a detailed phenotypic characterization of complex root traits among 96 accessions of the model Arabidopsis thaliana in two nitrogen environments. The results revealed a surprising level of independence in the control of traits to environment – a highly tunable form of plasticity. We mapped genetic architecture of plasticity using genome-wide association studies and further used gene expression analysis to narrow down gene candidates in mapped regions. Mutants in genes implicated by association and expression analysis showed precise defects in the predicted traits in the predicted environment, corroborating the independent control of plasticity traits. The overall results suggest that there is a pool of genetic variability in plants that controls traits in specific environments, with opportunity to tune crop plants to a given environment. PMID:24039603

Genetic markers of inflammation may not contribute to metabolic traits in Mexican children

Directory of Open Access Journals (Sweden)

Neeti Vashi

2016-06-01

Full Text Available Background: Low-grade chronic inflammation is a common feature of obesity and its cardio-metabolic complications. However, little is known about a possible causal role of inflammation in metabolic disorders. Mexico is among the countries with the highest obesity rates in the world and the admixed Mexican population is a relevant sample due to high levels of genetic diversity. Methods: Here, we studied 1,462 Mexican children recruited from Mexico City. Six genetic variants in five inflammation-related genes were genotyped: rs1137101 (leptin receptor (LEPR, rs7305618 (hepatocyte nuclear factor 1 alpha (HNF1A, rs1800629 (tumor necrosis factor alpha (TNFA, rs1800896, rs1800871 (interleukin-10 (IL-10, rs1862513 (resistin (RETN. Ten continuous and eight binary traits were assessed. Linear and logistic regression models were used adjusting for age, sex, and recruitment centre. Results: We found that one SNP displayed a nominal evidence of association with a continuous trait: rs1800871 (IL-10 with LDL (beta = −0.068 ± 1.006, P = 0.01. Subsequently, we found one nominal association with a binary trait: rs7305618 (HNF1A with family history of hypertension (odds-ratio = 1.389 [1.054–1.829], P = 0.02. However, no P-value passed the Bonferroni correction for multiple testing. Discussion: Our data in a Mexican children population are consistent with previous reports in European adults in failing to demonstrate an association between inflammation-associated single nucleotide polymorphisms (SNPs and metabolic traits.

GENETIC CHANGES FOR PERFORMANCE TRAITS IN SLOVENIAN PIG NUCLEUS HERDS

Directory of Open Access Journals (Sweden)

Špela Malovrh

2000-06-01

Full Text Available In Slovenian pig nucleus herds, the genetic trends for performance traits in boars were investigated using mixed model methodology. Altogether, data sets from four farms with test stations consisted of 60709 records for five breeds: Swedish Landrace (SL, Large White (LW, Duroc (D, Pietrain (P, and German Landrace (GL boars from years 1975 to 1999. Separate analyses were performed for each farm using the PEST package. Breed, season, and weight on test within breed were fixed effects, while common litter environment and additive genetic effect were treated as random. Genetic trends for days on test from 30 to 100 kg (DoT30100, feed conversion efficiency from 30 to 100 kg (FCE30100, and ultrasonically measured backfat thickness (BF100 were expressed as linear regression of the averages of predicted breeding values on the year of birth. Estimates for genetic changes varied between farms and breeds from +0.0046 to –0.374 day, +0.0019 to – 0.013, and +0.262 to –0.221 mm per year for DoT30100, FCE30100, and BF100, respectively.

A Genome-Wide mQTL Analysis in Human Adipose Tissue Identifies Genetic Variants Associated with DNA Methylation, Gene Expression and Metabolic Traits.

Directory of Open Access Journals (Sweden)

Petr Volkov

Full Text Available Little is known about the extent to which interactions between genetics and epigenetics may affect the risk of complex metabolic diseases and/or their intermediary phenotypes. We performed a genome-wide DNA methylation quantitative trait locus (mQTL analysis in human adipose tissue of 119 men, where 592,794 single nucleotide polymorphisms (SNPs were related to DNA methylation of 477,891 CpG sites, covering 99% of RefSeq genes. SNPs in significant mQTLs were further related to gene expression in adipose tissue and obesity related traits. We found 101,911 SNP-CpG pairs (mQTLs in cis and 5,342 SNP-CpG pairs in trans showing significant associations between genotype and DNA methylation in adipose tissue after correction for multiple testing, where cis is defined as distance less than 500 kb between a SNP and CpG site. These mQTLs include reported obesity, lipid and type 2 diabetes loci, e.g. ADCY3/POMC, APOA5, CETP, FADS2, GCKR, SORT1 and LEPR. Significant mQTLs were overrepresented in intergenic regions meanwhile underrepresented in promoter regions and CpG islands. We further identified 635 SNPs in significant cis-mQTLs associated with expression of 86 genes in adipose tissue including CHRNA5, G6PC2, GPX7, RPL27A, THNSL2 and ZFP57. SNPs in significant mQTLs were also associated with body mass index (BMI, lipid traits and glucose and insulin levels in our study cohort and public available consortia data. Importantly, the Causal Inference Test (CIT demonstrates how genetic variants mediate their effects on metabolic traits (e.g. BMI, cholesterol, high-density lipoprotein (HDL, hemoglobin A1c (HbA1c and homeostatic model assessment of insulin resistance (HOMA-IR via altered DNA methylation in human adipose tissue. This study identifies genome-wide interactions between genetic and epigenetic variation in both cis and trans positions influencing gene expression in adipose tissue and in vivo (dysmetabolic traits associated with the development of

The genetic basis of novel water utilisation and drinking behaviour traits and their relationship with biological performance in turkeys.

Science.gov (United States)

Rusakovica, Julija; Kremer, Valentin D; Plötz, Thomas; Rohlf, Paige; Kyriazakis, Ilias

2017-09-29

There is increasing interest in the definition, measurement and use of traits associated with water use and drinking behaviour, mainly because water is a finite resource and its intake is an important part of animal health and well-being. Analysis of such traits has received little attention, due in part to the lack of appropriate technology to measure drinking behaviour. We exploited novel equipment to collect water intake data in two lines of turkey (A: 27,415 and B: 12,956 birds). The equipment allowed continuous recording of individual visits to the water station in a group environment. Our aim was to identify drinking behaviour traits of biological relevance, to estimate their genetic parameters and their genetic relationships with performance traits, and to identify drinking behaviour strategies among individuals. Visits to the drinkers were clustered into bouts, i.e. time intervals spent in drinking-related activity. Based on this, biologically relevant traits were defined: (1) number of visits per bout, (2) water intake per bout, (3) drinking time per bout, (4) drinking rate, (5) daily bout frequency, (6) daily bout duration, (7) daily drinking time and (8) daily water intake. Heritability estimates for most drinking behaviour traits were moderate to high and the most highly heritable traits were drinking rate (0.49 and 0.50) and daily drinking time (0.35 and 0.46 in lines A and B, respectively). Genetic correlations between drinking behaviour and performance traits were low except for moderate correlations between daily water intake and weight gain (0.46 and 0.47 in lines A and B, respectively). High estimates of breeding values for weight gain were found across the whole range of estimated breeding values for daily water intake, daily drinking time and water intake per bout. We show for the first time that drinking behaviour traits are moderately to highly heritable. Low genetic and phenotypic correlations with performance traits suggest that current

Genetic evidence for causal relationships between maternal obesity-related traits and birth weight

NARCIS (Netherlands)

A.W.R. Tyrrell; R.C. Richmond (Rebecca C.); T.M. Palmer (Tom); B. Feenstra (Bjarke); J. Rangarajan (Janani); S. Metrustry (Sarah); A. Cavadino (Alana); L. Paternoster (Lavinia); L.L. Armstrong (Loren L.); N.M.G. De Silva (N. Maneka G.); A.R. Wood (Andrew); M. Horikoshi (Momoko); F. Geller (Frank); R. Myhre (Ronny); J.P. Bradfield (Jonathan); E. Kreiner-Møller (Eskil); I. Huikari (Ille); J.N. Painter (Jodie N.); J.J. Hottenga (Jouke Jan); C. Allard (Catherine); D. Berry (Diane); L. Bouchard (Luigi); S. Das (Shikta); D.M. Evans (David); H. Hakonarson (Hakon); M.G. Hayes (M. Geoffrey); J. Heikkinen (Jani); A. Hofman (Albert); B.A. Knight (Bridget); P.A. Lind (Penelope); M.I. McCarthy (Mark); G. Mcmahon (George); S.E. Medland (Sarah Elizabeth); M. Melbye (Mads); A.P. Morris (Andrew); M. Nodzenski (Michael); C. Reichetzeder (Christoph); S.M. Ring (Susan); S. Sebert (Sylvain); V. Sengpiel (Verena); T.I.A. Sørensen (Thorkild); G.A.H.M. Willemsen (Gonneke); E.J.C. de Geus (Eco); N.G. Martin (Nicholas); T.D. Spector (Timothy); C. Power (Christine); M.-R. Jarvelin (Marjo-Riitta); H. Bisgaard (Hans); S.F.A. Grant (Struan); C. Nohr (Christian); V.W.V. Jaddoe (Vincent); B. Jacobsson (Bo); J.C. Murray (Jeffrey C.); B. Hocher (Berthold); A.T. Hattersley (Andrew); D.M. Scholtens (Denise M.); G.D. Smith; M.-F. Hivert (Marie-France); J.F. Felix (Janine); E. Hypponen (Elina); W.L. Lowe Jr. (William); T.M. Frayling (Timothy); D.A. Lawlor (Debbie); R.M. Freathy (Rachel)

2016-01-01

textabstractIMPORTANCE Neonates born to overweight or obese women are larger and at higher risk of birth complications. Many maternal obesity-related traits are observationally associated with birth weight, but the causal nature of these associations is uncertain. OBJECTIVE To test for genetic

Quantitative trait loci for behavioural traits in chicken

NARCIS (Netherlands)

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

2005-01-01

The detection of quantitative trait loci (QTL) of behavioural traits has mainly been focussed on mouse and rat. With the rapid development of molecular genetics and the statistical tools, QTL mapping for behavioural traits in farm animals is developing. In chicken, a total of 30 QTL involved in

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

Science.gov (United States)

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

2016-10-01

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

Genetic parameters for EUROP carcass traits within different groups of cattle in Ireland

OpenAIRE

Hickey, J.M.; Keane, M.G.; Kenny, D.A.; Cromie, A.R.; Veerkamp, R.F.

2007-01-01

The first objective of this study was to test the ability of systems of weighing and classifying bovine carcasses used in commercial abattoirs in Ireland to provide information that can be used for the purposes of genetic evaluation of carcass weight, carcass fatness class, and carcass conformation class. Secondly, the study aimed to test whether genetic and phenotypic variances differed by breed of sire. Variance components for carcass traits were estimated for crosses between dairy cows and...

Genetic parameters of linear conformation type traits and their relationship with milk yield throughout lactation in mixed-breed dairy goats.

Science.gov (United States)

McLaren, A; Mucha, S; Mrode, R; Coffey, M; Conington, J

2016-07-01

Conformation traits are of interest to many dairy goat breeders not only as descriptive traits in their own right, but also because of their influence on production, longevity, and profitability. If these traits are to be considered for inclusion in future dairy goat breeding programs, relationships between them and production traits such as milk yield must be considered. With the increased use of regression models to estimate genetic parameters, an opportunity now exists to investigate correlations between conformation traits and milk yield throughout lactation in more detail. The aims of this study were therefore to (1) estimate genetic parameters for conformation traits in a population of crossbred dairy goats, (2) estimate correlations between all conformation traits, and (3) assess the relationship between conformation traits and milk yield throughout lactation. No information on milk composition was available. Data were collected from goats based on 2 commercial goat farms during August and September in 2013 and 2014. Ten conformation traits, relating to udder, teat, leg, and feet characteristics, were scored on a linear scale (1-9). The overall data set comprised data available for 4,229 goats, all in their first lactation. The population of goats used in the study was created using random crossings between 3 breeds: British Alpine, Saanen, and Toggenburg. In each generation, the best performing animals were selected for breeding, leading to the formation of a synthetic breed. The pedigree file used in the analyses contained sire and dam information for a total of 30,139 individuals. The models fitted relevant fixed and random effects. Heritability estimates for the conformation traits were low to moderate, ranging from 0.02 to 0.38. A range of positive and negative phenotypic and genetic correlations between the traits were observed, with the highest correlations found between udder depth and udder attachment (0.78), teat angle and teat placement (0

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

Science.gov (United States)

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

2015-12-01

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

"Touching Triton": Building Student Understanding of Complex Disease Risk.

Science.gov (United States)

Loftin, Madelene; East, Kelly; Hott, Adam; Lamb, Neil

2016-01-01

Life science classrooms often emphasize the exception to the rule when it comes to teaching genetics, focusing heavily on rare single-gene and Mendelian traits. By contrast, the vast majority of human traits and diseases are caused by more complicated interactions between genetic and environmental factors. Research indicates that students have a deterministic view of genetics, generalize Mendelian inheritance patterns to all traits, and have unrealistic expectations of genetic technologies. The challenge lies in how to help students analyze complex disease risk with a lack of curriculum materials. Providing open access to both content resources and an engaging storyline can be achieved using a "serious game" model. "Touching Triton" was developed as a serious game in which students are asked to analyze data from a medical record, family history, and genomic report in order to develop an overall lifetime risk estimate of six common, complex diseases. Evaluation of student performance shows significant learning gains in key content areas along with a high level of engagement.

A 100-Year Review: Identification and genetic selection of economically important traits in dairy cattle.

Science.gov (United States)

Miglior, Filippo; Fleming, Allison; Malchiodi, Francesca; Brito, Luiz F; Martin, Pauline; Baes, Christine F

2017-12-01

Over the past 100 yr, the range of traits considered for genetic selection in dairy cattle populations has progressed to meet the demands of both industry and society. At the turn of the 20th century, dairy farmers were interested in increasing milk production; however, a systematic strategy for selection was not available. Organized milk performance recording took shape, followed quickly by conformation scoring. Methodological advances in both genetic theory and statistics around the middle of the century, together with technological innovations in computing, paved the way for powerful multitrait analyses. As more sophisticated analytical techniques for traits were developed and incorporated into selection programs, production began to increase rapidly, and the wheels of genetic progress began to turn. By the end of the century, the focus of selection had moved away from being purely production oriented toward a more balanced breeding goal. This shift occurred partly due to increasing health and fertility issues and partly due to societal pressure and welfare concerns. Traits encompassing longevity, fertility, calving, health, and workability have now been integrated into selection indices. Current research focuses on fitness, health, welfare, milk quality, and environmental sustainability, underlying the concentrated emphasis on a more comprehensive breeding goal. In the future, on-farm sensors, data loggers, precision measurement techniques, and other technological aids will provide even more data for use in selection, and the difficulty will lie not in measuring phenotypes but rather in choosing which traits to select for. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genetic Variability of 27 Traits in a Core Collection of Flax (Linum usitatissimum L.).

Science.gov (United States)

You, Frank M; Jia, Gaofeng; Xiao, Jin; Duguid, Scott D; Rashid, Khalid Y; Booker, Helen M; Cloutier, Sylvie

2017-01-01

Assessment of genetic variability of plant core germplasm is needed for efficient germplasm utilization in breeding improvement. A total of 391 accessions of a flax core collection, which preserves the variation present in the world collection of 3,378 accessions maintained by Plant Gene Resources of Canada (PGRC) and represents a broad range of geographical origins, different improvement statuses and two morphotypes, was evaluated in field trials in up to 8 year-location environments for 10 agronomic, eight seed quality, six fiber and three disease resistance traits. The large phenotypic variation in this subset was explained by morphotypes (22%), geographical origins (11%), and other variance components (67%). Both divergence and similarity between two basic morphotypes, namely oil or linseed and fiber types, were observed, whereby linseed accessions had greater thousand seed weight, seeds m -2 , oil content, branching capability and resistance to powdery mildew while fiber accessions had greater straw weight, plant height, protein content and resistance to pasmo and fusarium wilt diseases, but they had similar performance in many traits and some of them shared common characteristics of fiber and linseed types. Weak geographical patterns within either fiber or linseed accessions were confirmed, but specific trait performance was identified in East Asia for fiber type, and South Asia and North America for linseed type. Relatively high broad-sense heritability was obtained for seed quality traits, followed by agronomic traits and resistance to powdery mildew and fusarium wilt. Diverse phenotypic and genetic variability in the flax core collection constitutes a useful resource for breeding.

Genetic Analysis of Elevated Mastitis Risk Based on Mastitis Indicator Data

DEFF Research Database (Denmark)

Sørensen, Lars Peter; Løvendahl, Peter

Whole-genome sequences and multiple trait phenotypes from large numbers of individuals will soon be available. Well established statistical modeling approaches enable the genetic analyses of complex trait phenotypes while accounting for a variety of additive and non-additive genetic mechanisms....... These modeling approaches have proven to be highly useful to determine population genetic parameters as well as prediction of genetic risk or value. We present statistical modelling approaches that use prior biological information for evaluating the collective action of sets of genetic variants. We have applied...

Genome-wide association genetics of an adaptive trait in lodgepole pine.

Science.gov (United States)

Parchman, Thomas L; Gompert, Zachariah; Mudge, Joann; Schilkey, Faye D; Benkman, Craig W; Buerkle, C Alex

2012-06-01

Pine cones that remain closed and retain seeds until fire causes the cones to open (cone serotiny) represent a key adaptive trait in a variety of pine species. In lodgepole pine, there is substantial geographical variation in serotiny across the Rocky Mountain region. This variation in serotiny has evolved as a result of geographically divergent selection, with consequences that extend to forest communities and ecosystems. An understanding of the genetic architecture of this trait is of interest owing to the wide-reaching ecological consequences of serotiny and also because of the repeated evolution of the trait across the genus. Here, we present and utilize an inexpensive and time-effective method for generating population genomic data. The method uses restriction enzymes and PCR amplification to generate a library of fragments that can be sequenced with a high level of multiplexing. We obtained data for more than 95,000 single nucleotide polymorphisms across 98 serotinous and nonserotinous lodgepole pines from three populations. We used a Bayesian generalized linear model (GLM) to test for an association between genotypic variation at these loci and serotiny. The probability of serotiny varied by genotype at 11 loci, and the association between genotype and serotiny at these loci was consistent in each of the three populations of pines. Genetic variation across these 11 loci explained 50% of the phenotypic variation in serotiny. Our results provide a first genome-wide association map of serotiny in pines and demonstrate an inexpensive and efficient method for generating population genomic data. © 2012 Blackwell Publishing Ltd.

Genetic relationships between carcass cut weights predicted from video image analysis and other performance traits in cattle.

Science.gov (United States)

Pabiou, T; Fikse, W F; Amer, P R; Cromie, A R; Näsholm, A; Berry, D P

2012-09-01

The objective of this study was to quantify the genetic associations between a range of carcass-related traits including wholesale cut weights predicted from video image analysis (VIA) technology, and a range of pre-slaughter performance traits in commercial Irish cattle. Predicted carcass cut weights comprised of cut weights based on retail value: lower value cuts (LVC), medium value cuts (MVC), high value cuts (HVC) and very high value cuts (VHVC), as well as total meat, fat and bone weights. Four main sources of data were used in the genetic analyses: price data of live animals collected from livestock auctions, live-weight data and linear type collected from both commercial and pedigree farms as well as from livestock auctions and weanling quality recorded on-farm. Heritability of carcass cut weights ranged from 0.21 to 0.39. Genetic correlations between the cut traits and the other performance traits were estimated using a series of bivariate sire linear mixed models where carcass cut weights were phenotypically adjusted to a constant carcass weight. Strongest positive genetic correlations were obtained between predicted carcass cut weights and carcass value (min r g(MVC) = 0.35; max r(g(VHVC)) = 0.69), and animal price at both weaning (min r(g(MVC)) = 0.37; max r(g(VHVC)) = 0.66) and post weaning (min r(g(MVC)) = 0.50; max r(g(VHVC)) = 0.67). Moderate genetic correlations were obtained between carcass cut weights and calf price (min r g(HVC) = 0.34; max r g(LVC) = 0.45), weanling quality (min r(g(MVC)) = 0.12; max r (g(VHVC)) = 0.49), linear scores for muscularity at both weaning (hindquarter development: min r(g(MVC)) = -0.06; max r(g(VHVC)) = 0.46), post weaning (hindquarter development: min r(g(MVC)) = 0.23; max r(g(VHVC)) = 0.44). The genetic correlations between total meat weight were consistent with those observed with the predicted wholesale cut weights. Total fat and total bone weights were generally negatively correlated with carcass value, auction

Genetics of complex diseases

DEFF Research Database (Denmark)

Mellerup, Erling; Møller, Gert Lykke; Koefoed, Pernille

2012-01-01

A complex disease with an inheritable component is polygenic, meaning that several different changes in DNA are the genetic basis for the disease. Such a disease may also be genetically heterogeneous, meaning that independent changes in DNA, i.e. various genotypes, can be the genetic basis...... for the disease. Each of these genotypes may be characterized by specific combinations of key genetic changes. It is suggested that even if all key changes are found in genes related to the biology of a certain disease, the number of combinations may be so large that the number of different genotypes may be close...... to the number of patients suffering from the disease. This hypothesis is based on a study of bipolar disorder....

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

DEFF Research Database (Denmark)

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

2017-01-01

of an organism. Proteome analysis especially can provide new insights into the molecular mechanisms of complex traits like obesity. The role of genetic variation in determining protein level variation has not been assessed in obesity. To address this, we design a large-scale protein quantitative trait locus (p...

Variability in seed traits, oil content and genetic diversity in local and ...

African Journals Online (AJOL)

Variability in seed traits, oil content and genetic diversity of Jatropha curcas L. according to rainfall gradient in Senegal are hereby reported and discussed. Seed oil variability ranged from 58.61% in Sudanian zone to 46.94% in Sahelian zone. Seed oil content and seed thickness were correlated to rainfall with a correlation ...

Genetic analysis of growth traits in Polled Nellore cattle raised on pasture in tropical region using Bayesian approaches.

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Lopes, Fernando Brito; Magnabosco, Cláudio Ulhôa; Paulini, Fernanda; da Silva, Marcelo Corrêa; Miyagi, Eliane Sayuri; Lôbo, Raysildo Barbosa

2013-01-01

Components of (co)variance and genetic parameters were estimated for adjusted weights at ages 120 (W120), 240 (W240), 365 (W365) and 450 (W450) days of Polled Nellore cattle raised on pasture and born between 1987 and 2010. Analyses were performed using an animal model, considering fixed effects: herd-year-season of birth and calf sex as contemporary groups and the age of cow as a covariate. Gibbs Samplers were used to estimate (co)variance components, genetic parameters and additive genetic effects, which accounted for great proportion of total variation in these traits. High direct heritability estimates for the growth traits were revealed and presented mean 0.43, 0.61, 0.72 and 0.67 for W120, W240, W365 and W450, respectively. Maternal heritabilities were 0.07 and 0.08 for W120 and W240, respectively. Direct additive genetic correlations between the weight at 120, 240, 365 and 450 days old were strong and positive. These estimates ranged from 0.68 to 0.98. Direct-maternal genetic correlations were negative for W120 and W240. The estimates ranged from -0.31 to -0.54. Estimates of maternal heritability ranged from 0.056 to 0.092 for W120 and from 0.064 to 0.096 for W240. This study showed that genetic progress is possible for the growth traits we studied, which is a novel and favorable indicator for an upcoming and promising Polled Zebu breed in Tropical regions. Maternal effects influenced the performance of weight at 120 and 240 days old. These effects should be taken into account in genetic analyses of growth traits by fitting them as a genetic or a permanent environmental effect, or even both. In general, due to a medium-high estimate of environmental (co)variance components, management and feeding conditions for Polled Nellore raised at pasture in tropical regions of Brazil needs improvement and growth performance can be enhanced.

Diallel crossing in Pinus cembra: IV. age trends in genetic parameters and genetic gain for growth and branching traits

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Ioan Blada

2013-12-01

Full Text Available This paper reports results from a complete 10 x 10 diallel carried out in a natural population of Swiss stone pine (Pinus cembra L. from the southern Carpathian Mountains. At age six, after nursery testing, the material was field planted on one site, using a completely randomized block design with 100 families, four replicates and 15 tree row-plots per replication, spaced 2.5 x 2.5m. Total and annual height growth, root collar diameter, number of branches per whorl and survival were assessed at successive ages between ages eight and 14 after seed. In addition, several traits that were assessed during the nursery test were used in correlation and some other analyses. Plot means of the measured traits were analyzed using the general least-squares method by means of the computer DIALL programme prepared by Schaffer and Usanis (1969. Across the field testing periods, significant (p<0.05 and highly significant (p<0.01; p<0.001 differences occurred in total height growth and root collar diameter for general and specific combining ability as well for maternalinteraction effects. These results suggest that the traits are controlled by nuclear (additive and non-additive and by nuclear x extra-nuclear gene interactions. In an ascendant trend, the additive variance, as a percent of the total genetic variance, ranged from 35% at age eight to 66% at age 14 for total height growth, while that for root collar diameter trend varied less between 16% and 34%. In a descendant trend, the dominance ratios s2SCA/ s2GCA for total height growth ranged from 0.9 at age eight to 0.3 at age 14, suggesting that the additive variance should be used in the breeding programme. Parents with significant general combining effects for all but one trait were found. For total height growth, the narrow-sense family mean heritability estimates varied in an ascendant trend between 0.45 and 0.65 while the narrow- sense individual tree heritability varied irregularly from year to year

Genetic associations of ketosis and displaced abomasum with milk production traits in early first lactation of Canadian Holsteins.

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Koeck, A; Miglior, F; Jamrozik, J; Kelton, D F; Schenkel, F S

2013-07-01

The aim of this study was to investigate the genetic associations of ketosis and displaced abomasum with milk production traits in early first lactation of Canadian Holsteins. Health data recorded by producers were available from the national dairy cattle health system in Canada. Test-day records of milk, fat, and protein yields were obtained from the routine milk recoding scheme. Ketosis and displaced abomasum were defined as binary traits (0 = healthy; 1 = sick) based on whether or not the cow had at least 1 case of the respective disease in the period from calving to 100 d after calving. Mean frequencies of ketosis and displaced abomasum were 4.1 and 2.7%, respectively. The following milk production traits were considered: milk yield, fat percentage (Fat%), protein percentage (Prot%), fat-to-protein (F:P) ratio, and F:P ratio >1.5. The trait F:P ratio >1.5 was scored as 1 or 0, based on whether or not the cow had an F:P ratio >1.5. For milk production traits, the first (5-30 d in milk) and the second (31-60 d in milk) test days were considered. Data were analyzed using bivariate linear animal models. Average heritabilities of 0.02 and 0.04 were obtained for ketosis and displaced abomasum, respectively. For milk production traits, the lowest heritabilities were obtained for F:P >1.5 (0.04 to 0.08), whereas the highest estimates were found for Prot% (0.27 to 0.38). Ketosis and displaced abomasum were genetically uncorrelated with milk yield in early lactation. Moderate favorable correlations were found between metabolic diseases and milk composition traits. Ketosis was significantly correlated with Fat% (0.33), F:P ratio (0.30), and F:P ratio >1.5 (0.35) at the first test day, whereas all genetic correlations with milk composition traits at the second test day were not significant and close to zero. Significant favorable genetic correlations were also found between displaced abomasum and F:P ratio (0.26), F:P ratio >1.5 (0.25) and Prot% (-0.19) at the first test

Diabetes-specific genetic effects on obesity traits in American Indian populations: the Strong Heart Family Study

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Howard Barbara V

2008-10-01

Full Text Available Abstract Background Body fat mass distribution and deposition are determined by multiple environmental and genetic factors. Obesity is associated with insulin resistance, hyperinsulinemia, and type 2 diabetes. We previously identified evidence for genotype-by-diabetes interaction on obesity traits in Strong Heart Family Study (SHFS participants. To localize these genetic effects, we conducted genome-wide linkage scans of obesity traits in individuals with and without type 2 diabetes, and in the combined sample while modeling interaction with diabetes using maximum likelihood methods (SOLAR 2.1.4. Methods SHFS recruited American Indians from Arizona, North and South Dakota, and Oklahoma. Anthropometric measures and diabetes status were obtained during a clinic visit. Marker allele frequencies were derived using maximum likelihood methods estimated from all individuals and multipoint identity by descent sharing was estimated using Loki. We used variance component linkage analysis to localize quantitative trait loci (QTLs influencing obesity traits. We tested for evidence of additive and QTL-specific genotype-by-diabetes interactions using the regions identified in the diabetes-stratified analyses. Results Among 245 diabetic and 704 non-diabetic American Indian individuals, we detected significant additive gene-by-diabetes interaction for weight and BMI (P P Conclusion These results suggest distinct genetic effects on body mass in individuals with diabetes compared to those without diabetes, and a possible role for one or more genes on chromosome 1 in the pathogenesis of obesity.

Genetic architecture of a hormonal response to gene knockdown in honey bees.

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Ihle, Kate E; Rueppell, Olav; Huang, Zachary Y; Wang, Ying; Fondrk, M Kim; Page, Robert E; Amdam, Gro V

2015-01-01

Variation in endocrine signaling is proposed to underlie the evolution and regulation of social life histories, but the genetic architecture of endocrine signaling is still poorly understood. An excellent example of a hormonally influenced set of social traits is found in the honey bee (Apis mellifera): a dynamic and mutually suppressive relationship between juvenile hormone (JH) and the yolk precursor protein vitellogenin (Vg) regulates behavioral maturation and foraging of workers. Several other traits cosegregate with these behavioral phenotypes, comprising the pollen hoarding syndrome (PHS) one of the best-described animal behavioral syndromes. Genotype differences in responsiveness of JH to Vg are a potential mechanistic basis for the PHS. Here, we reduced Vg expression via RNA interference in progeny from a backcross between 2 selected lines of honey bees that differ in JH responsiveness to Vg reduction and measured JH response and ovary size, which represents another key aspect of the PHS. Genetic mapping based on restriction site-associated DNA tag sequencing identified suggestive quantitative trait loci (QTL) for ovary size and JH responsiveness. We confirmed genetic effects on both traits near many QTL that had been identified previously for their effect on various PHS traits. Thus, our results support a role for endocrine control of complex traits at a genetic level. Furthermore, this first example of a genetic map of a hormonal response to gene knockdown in a social insect helps to refine the genetic understanding of complex behaviors and the physiology that may underlie behavioral control in general. © The American Genetic Association. 2015.

Genetic parameter estimates among scale activity score and farrowing disposition with reproductive traits in swine.

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Schneider, J F; Rempel, L A; Rohrer, G A; Brown-Brandl, T M

2011-11-01

The primary objective of this study was to determine if certain behavior traits were genetically correlated with reproduction. If 1 or both of the behavior traits were found to be correlated, a secondary objective was to determine if the behavior traits could be useful in selecting for more productive females. A scale activity score taken at 5 mo of age and a farrowing disposition score taken at farrowing were selected as the behavioral traits. Scale activity score ranged from 1 to 5 and farrowing disposition ranged from 1 to 3. Reproductive traits included age at puberty, number born alive, number born dead, litter birth weight, average piglet birth weight, number weaned, litter weaning weight, average weaning weight, wean-to-estrus interval, ovulation rate including gilts, and postweaning ovulation rate. Genetic correlations between scale activity score and reproduction ranged from -0.79 to 0.61. Three of the correlations, number born alive (P < 0.01), average piglet birth weight (P < 0.001), and wean-to-estrus interval (P = 0.014), were statistically significant but included both favorable and antagonistic correlations. In contrast, all but 1 of the farrowing disposition correlations was favorable and ranged from -0.66 to 0.67. Although only the correlation with litter birth weight was significant (P = 0.018), the consistent favorable direction of all farrowing disposition correlations, except average weaning weight, shows a potential for inclusion of farrowing disposition into a selection program.

Addictive behaviors and addiction-prone personality traits: associations with a dopamine multilocus genetic profile.

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Davis, Caroline; Loxton, Natalie J

2013-07-01

The purpose of this study was to examine reward-related genetic risk for addictive behaviors in a healthy community sample (n=217) of men and women. We tested a mediation model predicting that a quantitative multilocus genetic profile score - reflecting the additive effects of alleles known to confer relatively increased dopamine signaling in the ventral striatum - would relate positively to a composite measure of addictive behaviors, and that this association would be mediated by personality traits consistently associated with addiction disorders. Our model was strongly supported by the data, and accounted for 24% of the variance in addictive behaviors. These data suggest that brain reward processes tend to exert their influence on addiction risk by their role in the development of relatively stable personality traits associated with addictive behaviors. Copyright © 2013 Elsevier Ltd. All rights reserved.

Examining the Genetic and Environmental Associations between Autistic Social and Communication Deficits and Psychopathic Callous-Unemotional Traits.

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Elizabeth O'Nions

Full Text Available Difficulties in appropriate social interaction are characteristic of both children with autism spectrum disorders and children with callous-unemotional traits (who are at risk of developing psychopathy. Extant experimental studies suggest that the nature of atypical social cognition that characterises these two profiles is not identical. However, 'empathizing' difficulties have been hypothesised for both groups, raising questions about the degree of aetiological separation between social impairments that characterize each disorder. This study explored the relative contribution of independent vs. shared aetiological influences to social and communication impairments associated with autistic traits and callous-unemotional traits, indexed by parent-report in a population-based cohort of twins.Participants were over 5,000 twin pairs from a UK cohort (the Twins Early Development Study; TEDS, assessed for callous-unemotional traits at 7 years and autistic social and communication impairments at 8 years. Multivariate model-fitting was used to explore the relative contribution of independent vs. overlapping genetic/environmental influences on these traits.Both social and communication impairments and callous-unemotional traits were highly heritable, although the genetic and environmental influences accounting for individual differences on each domain were predominantly independent.Extant evidence from experimental and neuro-imaging studies has suggested that, despite some superficially overlapping behaviours, the social difficulties seen in children with autism spectrum disorders and callous-unemotional traits are largely distinct. The current study is the first to demonstrate considerable aetiological independence of the social interaction difficulties seen in children with autism spectrum disorders and those with callous-unemotional traits.

Root phenotyping: from component trait in the lab to breeding.

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Kuijken, René C P; van Eeuwijk, Fred A; Marcelis, Leo F M; Bouwmeester, Harro J

2015-09-01

In the last decade cheaper and faster sequencing methods have resulted in an enormous increase in genomic data. High throughput genotyping, genotyping by sequencing and genomic breeding are becoming a standard in plant breeding. As a result, the collection of phenotypic data is increasingly becoming a limiting factor in plant breeding. Genetic studies on root traits are being hampered by the complexity of these traits and the inaccessibility of the rhizosphere. With an increasing interest in phenotyping, breeders and scientists try to overcome these limitations, resulting in impressive developments in automated phenotyping platforms. Recently, many such platforms have been thoroughly described, yet their efficiency to increase genetic gain often remains undiscussed. This efficiency depends on the heritability of the phenotyped traits as well as the correlation of these traits with agronomically relevant breeding targets. This review provides an overview of the latest developments in root phenotyping and describes the environmental and genetic factors influencing root phenotype and heritability. It also intends to give direction to future phenotyping and breeding strategies for optimizing root system functioning. A quantitative framework to determine the efficiency of phenotyping platforms for genetic gain is described. By increasing heritability, managing effects caused by interactions between genotype and environment and by quantifying the genetic relation between traits phenotyped in platforms and ultimate breeding targets, phenotyping platforms can be utilized to their maximum potential. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Transmission traits of malaria parasites within the mosquito: Genetic variation, phenotypic plasticity, and consequences for control.

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Lefevre, Thierry; Ohm, Johanna; Dabiré, Kounbobr R; Cohuet, Anna; Choisy, Marc; Thomas, Matthew B; Cator, Lauren

2018-04-01

Evaluating the risk of emergence and transmission of vector-borne diseases requires knowledge of the genetic and environmental contributions to pathogen transmission traits. Compared to the significant effort devoted to understanding the biology of malaria transmission from vertebrate hosts to mosquito vectors, the strategies that malaria parasites have evolved to maximize transmission from vectors to vertebrate hosts have been largely overlooked. While determinants of infection success within the mosquito host have recently received attention, the causes of variability for other key transmission traits of malaria, namely the duration of parasite development and its virulence within the vector, as well as its ability to alter mosquito behavior, remain largely unknown. This important gap in our knowledge needs to be bridged in order to obtain an integrative view of the ecology and evolution of malaria transmission strategies. Associations between transmission traits also need to be characterized, as they trade-offs and constraints could have important implications for understanding the evolution of parasite transmission. Finally, theoretical studies are required to evaluate how genetic and environmental influences on parasite transmission traits can shape malaria dynamics and evolution in response to disease control.

Functional mapping imprinted quantitative trait loci underlying developmental characteristics

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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.

Genetic analyses of partial egg production in Japanese quail using multi-trait random regression models.

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Karami, K; Zerehdaran, S; Barzanooni, B; Lotfi, E

2017-12-01

1. The aim of the present study was to estimate genetic parameters for average egg weight (EW) and egg number (EN) at different ages in Japanese quail using multi-trait random regression (MTRR) models. 2. A total of 8534 records from 900 quail, hatched between 2014 and 2015, were used in the study. Average weekly egg weights and egg numbers were measured from second until sixth week of egg production. 3. Nine random regression models were compared to identify the best order of the Legendre polynomials (LP). The most optimal model was identified by the Bayesian Information Criterion. A model with second order of LP for fixed effects, second order of LP for additive genetic effects and third order of LP for permanent environmental effects (MTRR23) was found to be the best. 4. According to the MTRR23 model, direct heritability for EW increased from 0.26 in the second week to 0.53 in the sixth week of egg production, whereas the ratio of permanent environment to phenotypic variance decreased from 0.48 to 0.1. Direct heritability for EN was low, whereas the ratio of permanent environment to phenotypic variance decreased from 0.57 to 0.15 during the production period. 5. For each trait, estimated genetic correlations among weeks of egg production were high (from 0.85 to 0.98). Genetic correlations between EW and EN were low and negative for the first two weeks, but they were low and positive for the rest of the egg production period. 6. In conclusion, random regression models can be used effectively for analysing egg production traits in Japanese quail. Response to selection for increased egg weight would be higher at older ages because of its higher heritability and such a breeding program would have no negative genetic impact on egg production.

Genetic mapping and QTL analysis of agronomic traits in Indian Mucuna pruriens using an intraspecific F₂population.

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Mahesh, S; Leelambika, M; Jaheer, Md; Anithakumari, A M; Sathyanarayana, N

2016-03-01

Mucuna pruriens is a well-recognized agricultural and horticultural crop with important medicinal use. However, antinutritional factors in seed and adverse morphological characters have negatively affected its cultivation. To elucidate the genetic control of agronomic traits, an intraspecific genetic linkage map of Indian M. pruriens has been developed based on amplified fragment length polymorphism (AFLP) markers using 200 F₂ progenies derived from a cross between wild and cultivated genotypes. The resulting linkage map comprised 129 AFLP markers dispersed over 13 linkage groups spanning a total distance of 618.88 cM with an average marker interval of 4.79 cM. For the first time, three QTLs explaining about 6.05-14.77% of the corresponding total phenotypic variation for three quantitative (seed) traits and, eight QTLs explaining about 25.96% of the corresponding total phenotypic variation for three qualitative traits have been detected on four linkage groups. The map presented here will pave a way for mapping of genes/QTLs for the important agronomic and horticultural traits contrasting between the parents used in this study.

Structural and Temporal Variation in Genetic Diversity of European Spring Two-Row Barley Cultivars and Association Mapping of Quantitative Traits

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Alessandro Tondelli

2013-07-01

Full Text Available Two hundred sixteen barley ( L. cultivars were selected to represent the diversity and history of European spring two-row barley breeding and to search for alleles controlling agronomic traits by association genetics. The germplasm was genotyped with 7864 gene-based single nucleotide polymorphism markers and corresponding field trial trait data relating to growth and straw strength were obtained at multiple European sites. Analysis of the marker data by statistical population genetics approaches revealed two important trends in the genetic diversity of European two-row spring barley, namely, i directional selection for approximately 14% of total genetic variation of the population in the last approximately 50 yr and ii highly uneven genomic distribution of genetic diversity. Association analysis of the phenotypic and genotypic data identified multiple loci affecting the traits investigated, some of which co-map with selected regions. Collectively, these data show that the genetic makeup of European two-row spring barley is evolving under breeder selection, with signs of extinction of diversity in some genomic regions, suggesting that “breeding the best with the best” is leading towards fixation of some breeder targets. Nevertheless, modern germplasm also retains many regions of high diversity, suggesting that site-specific genetic approaches for allele identification and crop improvement such as association genetics are likely to be successful.