Epistasis detection and modeling for genomic selection in cowpea (<i>Vigna unguiculata</i>. L. Walp.)

Olatoye, Marcus O.; Hu, Zhenbin; Aikpokpodion, Peter O.

doi:10.1101/576819

Cited by 4 publications

(15 citation statements)

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“…Result further showed that students did not differ significantly in test anxiety with respect to their sex. Result of present study contradicted to the findings of many previous studies (Rana and Mahmood, 2010;Erdem, 2007;Hashmat et al, 2008) though other studies (Ndirangu, et al, 2009;Olatoye, 2009;Faleye 2010) outlined the findings similar to the results of present study. In present study, despite the fact that students did not differ statistically in terms of test anxiety, female students were having higher test anxiety as compared to their male counterpart.…”

Section: Resultscontrasting

confidence: 92%

Test Anxiety: Prevalence and Correlates

Subba¹,

Bhandary²

2018

Int.J.Curr.Res.Aca.Rev.

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Article InfoAcademic success can be measured in various terms and academic grades or Grade Point Scott (2010) and Adjustment Inventory for School Students (Sinha and Singh, 2013) were used to measure test anxiety and related constructs. Tests were at first translated in Nepali by following rigorous translation process. Result of the study showed that 76.3% of the students were suffering from some level of test anxiety. Result further showed that private school students had significantly high test anxiety as compared to government school students. Also, test anxiety did not differ significantly with respect to sex, type of family, academic achievement motivation, self-efficacy, emotional intelligence and adjustment.

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Section: Resultscontrasting

confidence: 92%

Test Anxiety: Prevalence and Correlates

Subba¹,

Bhandary²

2018

Int.J.Curr.Res.Aca.Rev.

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“…The two FEM models used in BLINK were the following In this study, we focused on the SNPs associated with the tolerance index trait. However, we rerun the traits investigated by Huynh et al 20 and Olatoye et al 22 using BLINK and the SNPs identified for these traits were analyzed in the network analysis section. LD heatmaps were established in R® v.3.6.1 using the package 'LDheatmap' 39 .…”

Section: Genome-wide Association Studymentioning

confidence: 99%

“…The nodes in the network corresponded to the traits and the significant SNPs associated with each trait. The traits investigated by Huynh et al 20 and Olatoye et al 22 were represented by solid circles, whereas the tolerance index traits were visualized by solid diamonds. The SNPs associated with each trait were denoted using solid dark grey circles.…”

Section: Association Networkmentioning

confidence: 99%

“…Genetic maps, recombination frequency analysis, and significant QTLs related to the aforementioned traits were established for the MAGIC cowpea population 20 . This study was complemented using a genome-wide association study (GWAS) approach 22 . GWAS provides a greater mapping resolution over QTL mapping and efficiently permits the discovery of new genes 23,24 .…”

Section: Introductionmentioning

confidence: 99%

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Loci discovery, network-guided approach, and genomic prediction for drought tolerance index in a multi-parent advanced generation intercross (MAGIC) cowpea population

2021

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Cowpea is a nutrient-dense legume that significantly contributes to the population’s diet in sub-Saharan Africa and other regions of the world. Improving cowpea cultivars to be more resilient to abiotic stress such as drought would be of great importance. The use of a multi-parent advanced generation intercross (MAGIC) population has been shown to be efficient in increasing the frequency of rare alleles that could be associated with important agricultural traits. In addition, drought tolerance index has been reported to be a reliable parameter for assessing crop tolerance to water-deficit conditions. Therefore, the objectives of this study were to evaluate the drought tolerance index for plant growth habit, plant maturity, flowering time, 100-seed weight, and grain yield in a MAGIC cowpea population, to conduct genome-wide association study (GWAS) and identify single nucleotide polymorphism (SNP) markers associated with the drought tolerance indices, to investigate the potential relationship existing between the significant loci associated with the drought tolerance indices, and to conduct genomic selection (GS). These analyses were performed using the existing phenotypic and genotypic data published for the MAGIC population which consisted of 305 F8 recombinant inbred lines (RILs) developed at University of California, Riverside. The results indicated that: (1) large variation in drought tolerance indices existed among the cowpea genotypes, (2) a total of 14, 18, 5, 5, and 35 SNPs were associated with plant growth habit change due to drought stress, and drought tolerance indices for maturity, flowering time, 100-seed weight, and grain yield, respectively, (3) the network-guided approach revealed clear interactions between the loci associated with the drought tolerance traits, and (4) the GS accuracy varied from low to moderate. These results could be applied to improve drought tolerance in cowpea through marker-assisted selection (MAS) and genomic selection (GS). To the best of our knowledge, this is the first report on marker loci associated with drought tolerance indices in cowpea.

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“…Olatoye et al (2019) ‘Epistasis detection and modeling for genomic selection in cowpea (Vigna unguiculata. L.…”

Section: Acknowledgmentsmentioning

confidence: 99%

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

Olatoye

Aikpokpodion

2019

Front. Genet.

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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.

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

Cited by 4 publications

References 99 publications

Test Anxiety: Prevalence and Correlates

Test Anxiety: Prevalence and Correlates

Loci discovery, network-guided approach, and genomic prediction for drought tolerance index in a multi-parent advanced generation intercross (MAGIC) cowpea population

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

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