Genome-Wide Association Study for Flowering Time in Korean Cowpea Germplasm

Seo, Eunju; Kim, Kipoong; Kang, Ryulyi; Kim, Gyu-Tae; Park, Aron; Kim, Woon Ji; Sun, Hokeun; Ha, Bo‐Keun

doi:10.9787/pbb.2020.8.4.413

Cited by 7 publications

(6 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The cowpea dataset includes 49,683 SNPs with 384 samples, while the peanut dataset has 32,145 SNPs with 301 samples. The cowpea dataset has 6 phenotypes, including 2 quantitative and 4 binary traits [ 44 ]. 2 quantitative traits are pod length (PL) and seed numbers per pod (SNPP), while 4 binary traits are mature pod color (MPCOL), mature pod curve (MPCUV), seed density (SD) and shattering (ST).…”

Section: Resultsmentioning

confidence: 99%

New statistical selection method for pleiotropic variants associated with both quantitative and qualitative traits

Kim,

Jun,

et al. 2023

BMC Bioinformatics

Self Cite

View full text Add to dashboard Cite

Background Identification of pleiotropic variants associated with multiple phenotypic traits has received increasing attention in genetic association studies. Overlapping genetic associations from multiple traits help to detect weak genetic associations missed by single-trait analyses. Many statistical methods were developed to identify pleiotropic variants with most of them being limited to quantitative traits when pleiotropic effects on both quantitative and qualitative traits have been observed. This is a statistically challenging problem because there does not exist an appropriate multivariate distribution to model both quantitative and qualitative data together. Alternatively, meta-analysis methods can be applied, which basically integrate summary statistics of individual variants associated with either a quantitative or a qualitative trait without accounting for correlations among genetic variants. Results We propose a new statistical selection method based on a unified selection score quantifying how a genetic variant, i.e., a pleiotropic variant associates with both quantitative and qualitative traits. In our extensive simulation studies where various types of pleiotropic effects on both quantitative and qualitative traits were considered, we demonstrated that the proposed method outperforms the existing meta-analysis methods in terms of true positive selection. We also applied the proposed method to a peanut dataset with 6 quantitative and 2 qualitative traits, and a cowpea dataset with 2 quantitative and 6 qualitative traits. We were able to detect some potentially pleiotropic variants missed by the existing methods in both analyses. Conclusions The proposed method is able to locate pleiotropic variants associated with both quantitative and qualitative traits. It has been implemented into an R package ‘UNISS’, which can be downloaded from http://github.com/statpng/uniss.

show abstract

Section: Resultsmentioning

confidence: 99%

New statistical selection method for pleiotropic variants associated with both quantitative and qualitative traits

Kim,

Jun,

et al. 2023

BMC Bioinformatics

Self Cite

View full text Add to dashboard Cite

show abstract

“…Genome-wide association studies (GWAS) were therefore helped in this direction, through SNPs and candidate genes identification and their correspondence to desirable plant traits such as flowering time and pod indehiscence, and tolerance to biotic and abiotic stresses [ 46 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 , 122 ]. Cowpea genetic similarities with other widely studied legumes such as soybean ( Glycine max (L.) Merr.…”

Section: Breeding Methodsmentioning

confidence: 99%

Cowpea Constraints and Breeding in Europe

Lazaridi

Bebeli

2023

Plants

View full text Add to dashboard Cite

Cowpea (Vigna unguiculata (L.) Walp.) is a legume with a constant rate of cultivation in Southern European countries. Consumer demand for cowpea worldwide is rising due to its nutritional content, while Europe is constantly attempting to reduce the deficit in the production of pulses and invest in new, healthy food market products. Although the climatic conditions that prevail in Europe are not so harsh in terms of heat and drought as in the tropical climates where cowpea is mainly cultivated, cowpea confronts with a plethora of abiotic and biotic stresses and yield-limiting factors in Southern European countries. In this paper, we summarize the main constraints for cowpea cultivation in Europe and the breeding methods that have been or can be used. A special mention is made of the availability plant genetic resources (PGRs) and their potential for breeding purposes, aiming to promote more sustainable cropping systems as climatic shifts become more frequent and fiercer, and environmental degradation expands worldwide.

show abstract

“…Paudel et al [ 72 ] used 368 cowpea accessions (including landraces) and conducted GWAS managing to identify seven candidate genes associated with flowering time. Additionally, Seo et al [ 73 ] performing GWAS on a collection of 384 Korean cowpea genotypes including landraces, identified four major candidate genes significantly associated with flowering time. Many other GWAS studies in collections that included landraces’ material, revealed candidate genes for phenological and morphological traits in cowpeas and other Vigna species [ 72 , 73 , 74 , 75 , 76 , 77 , 78 ].…”

Section: Application Of New Genomic Technologies In Landraces and Ind...mentioning

confidence: 99%

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

Lazaridi,

Kapazoglou,

Gerakari

et al. 2024

Plants

View full text Add to dashboard Cite

Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.

show abstract

Genome-Wide Association Study for Flowering Time in Korean Cowpea Germplasm

Cited by 7 publications

References 63 publications

New statistical selection method for pleiotropic variants associated with both quantitative and qualitative traits

New statistical selection method for pleiotropic variants associated with both quantitative and qualitative traits

Cowpea Constraints and Breeding in Europe

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

Contact Info

Product

Resources

About