scholarly journals Epistasis detection and modeling for genomic selection in cowpea (Vigna unguiculata. L. Walp.)

2019 ◽  
Author(s):  
Marcus O. Olatoye ◽  
Zhenbin Hu ◽  
Peter O. Aikpokpodion
Keyword(s):  
Genomic Selection ◽  
Flowering Time ◽  
Marker Assisted Selection ◽  
Fixed Effects ◽  
Genetic Architecture ◽  
Phytochrome A ◽  
Epistatic Interactions ◽  
Moderate Effect ◽  
Advanced Generation ◽  
Non Parametric

AbstractGenetic architecture reflects the pattern of effects and interaction of genes underling phenotypic variation. Most mapping and breeding approaches generally consider the additive part of variation but offer limited knowledge on the benefits of epistasis which explains in part the variation observed in traits. In this study, the cowpea multiparent advanced generation inter-cross (MAGIC) population was used to characterize the epistatic genetic architecture of flowering time, maturity, and seed size. In addition, considerations for epistatic genetic architecture in genomic-enabled breeding (GEB) was investigated using parametric, semi-parametric, and non-parametric genomic selection (GS) models. Our results showed that large and moderate effect sized two-way epistatic interactions underlie the traits examined. Flowering time QTL colocalized with cowpea putative orthologs of Arabidopsis thaliana and Glycine max genes like PHYTOCLOCK1 (PCL1 [Vigun11g157600]) and PHYTOCHROME A (PHY A [Vigun01g205500]). Flowering time adaptation to long and short photoperiod was found to be controlled by distinct and common main and epistatic loci. Parametric and semi-parametric GS models outperformed non-parametric GS model. Using known QTL as fixed effects in GS models improved prediction accuracy when traits were controlled by both large and moderate effect QTL. In general, our study demonstrated that prior understanding the genetic architecture of a trait can help make informed decisions in GEB. This is the first report to characterize epistasis and provide insights into the underpinnings of GS versus marker assisted selection in cowpea.

scholarly journals Comparative study of different non-parametric genomic selection methods under diverse genetic architecture

2020 ◽  
Vol 80 (04) ◽  
Author(s):  
Neeraj Budhlakoti ◽  
Anil Rai ◽  
D. C. Mishra ◽  
Seema Jaggi ◽  
Mukesh Kumar ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Statistical Models ◽  
Genetic Architecture ◽  
Animal Studies ◽  
Breeding Cycle ◽  
Parametric Methods ◽  
Selection Methods ◽  
Comparative Performance ◽  
Genetic Merit ◽  
Non Parametric

Genomic Selection (GS) is the most prevalent method in today’s scenario to access the genetic merit of individual under study. It selects the candidates for next breeding cycle on the basis of its genetic merit. GS has successfully been used in various plant and animal studies in last decade. Several parametric statistical models have been proposed and being used successfully in various GS studies. However, performance of parametric methods becomes very poor when we have non additive kind of genetic architecture. In such cases, generally performance of non-parametric methods are quite satisfactory as these methods do not require strict statistical assumptions. This article presents comparative performance of few most commonly used non-parametric methods for complex genetic architecture i.e. non-additive, using simulated dataset generated at different level of heritability and varying combination of population size. Among several non-parametric methods, SVM outperformed across a range of genetic architecture.

scholarly journals Genetic architecture and adaptation of flowering time among environments

2021 ◽  
Author(s):  
Wenjie Yan ◽  
Baosheng Wang ◽  
Emily Chan ◽  
Thomas Mitchell‐Olds
Keyword(s):  
Flowering Time ◽  
Genetic Architecture

scholarly journals The genetic architecture of leaf number and its genetic relationship to flowering time in maize

2015 ◽  
Vol 210 (1) ◽  
pp. 256-268 ◽  
Author(s):  
Dan Li ◽  
Xufeng Wang ◽  
Xiangbo Zhang ◽  
Qiuyue Chen ◽  
Guanghui Xu ◽  
...  
Keyword(s):  
Flowering Time ◽  
Genetic Relationship ◽  
Genetic Architecture ◽  
Leaf Number

scholarly journals Characterizing the oligogenic architecture of plant growth phenotypes informs genomic selection approaches in a common wheat population

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Noah DeWitt ◽  
Mohammed Guedira ◽  
Edwin Lauer ◽  
J. Paul Murphy ◽  
David Marshall ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Plant Growth ◽  
Genomic Selection ◽  
Plant Height ◽  
Prediction Models ◽  
Growth Traits ◽  
Heading Date ◽  
Additive Genetic Variation ◽  
Moderate Effect ◽  
Over Time

Abstract Background Genetic variation in growth over the course of the season is a major source of grain yield variation in wheat, and for this reason variants controlling heading date and plant height are among the best-characterized in wheat genetics. While the major variants for these traits have been cloned, the importance of these variants in contributing to genetic variation for plant growth over time is not fully understood. Here we develop a biparental population segregating for major variants for both plant height and flowering time to characterize the genetic architecture of the traits and identify additional novel QTL. Results We find that additive genetic variation for both traits is almost entirely associated with major and moderate-effect QTL, including four novel heading date QTL and four novel plant height QTL. FT2 and Vrn-A3 are proposed as candidate genes underlying QTL on chromosomes 3A and 7A, while Rht8 is mapped to chromosome 2D. These mapped QTL also underlie genetic variation in a longitudinal analysis of plant growth over time. The oligogenic architecture of these traits is further demonstrated by the superior trait prediction accuracy of QTL-based prediction models compared to polygenic genomic selection models. Conclusions In a population constructed from two modern wheat cultivars adapted to the southeast U.S., almost all additive genetic variation in plant growth traits is associated with known major variants or novel moderate-effect QTL. Major transgressive segregation was observed in this population despite the similar plant height and heading date characters of the parental lines. This segregation is being driven primarily by a small number of mapped QTL, instead of by many small-effect, undetected QTL. As most breeding populations in the southeast U.S. segregate for known QTL for these traits, genetic variation in plant height and heading date in these populations likely emerges from similar combinations of major and moderate effect QTL. We can make more accurate and cost-effective prediction models by targeted genotyping of key SNPs.

scholarly journals Large-scale meta-analysis across East Asian and European populations updated genetic architecture and variant-driven biology of rheumatoid arthritis, identifying 11 novel susceptibility loci

2020 ◽  
pp. annrheumdis-2020-219065
Author(s):  
Eunji Ha ◽  
Sang-Cheol Bae ◽  
Kwangwoo Kim
Keyword(s):  
Rheumatoid Arthritis ◽  
Transcription Factors ◽  
T Cell Activation ◽  
Fixed Effects ◽  
Genetic Architecture ◽  
Association Studies ◽  
Meta Analysis ◽  
Chromatin Interaction ◽  
Susceptibility Loci ◽  
European Populations

ObjectivesNearly 110 susceptibility loci for rheumatoid arthritis (RA) with modest effect sizes have been identified by population-based genetic association studies, suggesting a large number of undiscovered variants behind a highly polygenic genetic architecture of RA. Here, we performed the largest-ever trans-ancestral meta-analysis with the aim to identify new RA loci and to better understand RA biology underlying genetic associations.MethodsGenome-wide RA association summary statistics in three large case–control collections consisting of 311 292 individuals of Korean, Japanese and European populations were used in an inverse-variance-weighted fixed-effects meta-analysis. Several computational analyses using public omics resources were conducted to prioritise causal variants and genes, RA variant-implicating features (tissues, pathways and transcription factors) and potentially repurposable drugs for RA treatment.ResultsWe identified 11 new RA susceptibility loci that explained 6.9% and 1.8% of the single-nucleotide polymorphism-based heritability in East Asians and Europeans, respectively, and confirmed 71 known non-human leukocyte antigens (HLA) susceptibility loci, identifying 90 independent association signals. The RA variants were preferentially located in binding sites of various transcription factors and in cell type-specific transcription–activation histone marks that simultaneously highlighted the importance of CD4+ T-cell activation and the potential role of non-immune organs in RA pathogenesis. A total of 615 plausible effector genes, based on gene-based associations, expression-associated variants and chromatin interaction, included targets of drugs approved for RA treatments and potentially repurposable drugs approved for other indications.ConclusionOur findings provide useful insights regarding RA genetic aetiology and variant-driven RA pathogenesis.

scholarly journals Identification of Quantitative Trait Loci Relating to Flowering Time, Flag Leaf and Awn Characteristics in a Novel Triticum dicoccum Mapping Population

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 829
Author(s):  
Tally I.C. Wright ◽  
Angela C. Burnett ◽  
Howard Griffiths ◽  
Maxime Kadner ◽  
James S. Powell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quantitative Trait Loci ◽  
Flowering Time ◽  
Quantitative Trait ◽  
Marker Assisted Selection ◽  
Mapping Population ◽  
Flag Leaf ◽  
Snp Array ◽  
Leaf Length ◽  
Trait Loci

Tetraploid landraces of wheat harbour genetic diversity that could be introgressed into modern bread wheat with the aid of marker-assisted selection to address the genetic diversity bottleneck in the breeding genepool. A novel bi-parental Triticum turgidum ssp. dicoccum Schrank mapping population was created from a cross between two landrace accessions differing for multiple physiological traits. The population was phenotyped for traits hypothesised to be proxies for characteristics associated with improved photosynthesis or drought tolerance, including flowering time, awn length, flag leaf length and width, and stomatal and trichome density. The mapping individuals and parents were genotyped with the 35K Wheat Breeders’ single nucleotide polymorphism (SNP) array. A genetic linkage map was constructed from 104 F4 individuals, consisting of 2066 SNPs with a total length of 3295 cM and an average spacing of 1.6 cM. Using the population, 10 quantitative trait loci (QTLs) for five traits were identified in two years of trials. Three consistent QTLs were identified over both trials for awn length, flowering time and flag leaf width, on chromosomes 4A, 7B and 5B, respectively. The awn length and flowering time QTLs correspond with the major loci Hd and Vrn-B3, respectively. The identified marker-trait associations could be developed for marker-assisted selection, to aid the introgression of diversity from a tetraploid source into modern wheat for potential physiological trait improvement.

Non‐parametric models in binary choice fixed effects panel data

2011 ◽  
Vol 14 (3) ◽  
pp. 351-367 ◽  
Author(s):  
Stefan Hoderlein ◽  
Enno Mammen ◽  
Kyusang Yu
Keyword(s):  
Panel Data ◽  
Fixed Effects ◽  
Parametric Models ◽  
Binary Choice ◽  
Non Parametric

Prior genetic architecture impacting genomic regions under selection: An example using genomic selection in two poultry breeds

2015 ◽  
Vol 171 ◽  
pp. 1-11 ◽  
Author(s):  
Xinyue Zhang ◽  
Ignacy Misztal ◽  
Marzieh Heidaritabar ◽  
John W.M. Bastiaansen ◽  
Randy Borg ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Genetic Architecture ◽  
Genomic Regions

scholarly journals Genetic Architecture of Growth Traits Revealed by Global Epistatic Interactions

2011 ◽  
Vol 3 ◽  
pp. 909-914 ◽  
Author(s):  
Lin Xu ◽  
Huifeng Jiang ◽  
Hong Chen ◽  
Zhenglong Gu
Keyword(s):  
Genetic Architecture ◽  
Growth Traits ◽  
Epistatic Interactions

The Genetic Architecture of Flowering Time and Photoperiod Sensitivity in Maize as Revealed by QTL Review and Meta Analysis

2012 ◽  
Vol 54 (6) ◽  
pp. 358-373 ◽  
Author(s):  
Jie Xu ◽  
Yaxi Liu ◽  
Jian Liu ◽  
Moju Cao ◽  
Jing Wang ◽  
...  
Keyword(s):  
Flowering Time ◽  
Genetic Architecture ◽  
Meta Analysis ◽  
Photoperiod Sensitivity
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