Dataset Information

Epistasis Detection and Modeling for Genomic Selection in Cowpea (Vigna unguiculata L. Walp.).

ABSTRACT: Genetic architecture reflects the pattern of effects and interaction of genes underlying 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, consideration 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, while using known quantitative trait nucleotide(s) (QTNs) as fixed effects improved prediction accuracy when traits were controlled by large effect loci. In general, our study demonstrated that prior understanding of the genetic architecture of a trait can help make informed decisions in GEB.

SUBMITTER: Olatoye MO

PROVIDER: S-EPMC6682672 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

Epistasis Detection and Modeling for Genomic Selection in Cowpea (<i>Vigna unguiculata</i> L. Walp.).

Olatoye Marcus O MO Hu Zhenbin Z Aikpokpodion Peter O PO

Frontiers in genetics 20190730

Genetic architecture reflects the pattern of effects and interaction of genes underlying 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 s ...[more]

PMID: 31417604

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Project description:BackgroundCowpea is the most important food grain legume in Sub-Saharan Africa. However, no study has so far assessed rhizobial biodiversity and/or nodule functioning in relation to strain IGS types at the continent level. In this study, 9 cowpea genotypes were planted in field experiments in Botswana, South Africa and Ghana with the aim of i) trapping indigenous cowpea root-nodule bacteria (cowpea "rhizobia") in the 3 countries for isolation, molecular characterisation using PCR-RFLP analysis, and sequencing of the 16S - 23S rDNA IGS gene, ii) quantifying N-fixed in the cowpea genotypes using the 15N natural abundance technique, and iii) relating the levels of nodule functioning (i.e. N-fixed) to the IGS types found inside nodules.ResultsField measurements of N2 fixation revealed significant differences in plant growth, delta15N values, %Ndfa and amounts of N-fixed between and among the 9 cowpea genotypes in Ghana and South Africa. Following DNA analysis of 270 nodules from the 9 genotypes, 18 strain IGS types were found. Relating nodule function to the 18 IGS types revealed significant differences in IGS type N2-fixing efficiencies. Sequencing the 16S - 23S rDNA gene also revealed 4 clusters, with cluster 2 forming a distinct group that may be a new Bradyrhizobium species. Taken together, our data indicated greater biodiversity of cowpea bradyrhizobia in South Africa relative to Botswana and Ghana.ConclusionsWe have shown that cowpea is strongly dependant on N2 fixation for its N nutrition in both South Africa and Ghana. Strain IGS type symbiotic efficiency was assessed for the first time in this study, and a positive correlation was discernible where there was sole nodule occupancy. The differences in IGS type diversity and symbiotic efficiency probably accounts for the genotype x environment interaction that makes it difficult to select superior genotypes for use across Africa. The root-nodule bacteria nodulating cowpea in this study all belonged to the genus Bradyrhizobium. Some strains from Southern Africa were phylogenetically very distinct, suggesting a new Bradyrhizobium species.

Dataset Information

Epistasis Detection and Modeling for Genomic Selection in Cowpea (Vigna unguiculata L. Walp.).

Publications

Epistasis Detection and Modeling for Genomic Selection in Cowpea (<i>Vigna unguiculata</i> L. Walp.).

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