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Population Structure of the World Vegetable Center Mungbean Mini Core Collection and Genome-Wide Association Mapping of Loci Associated with Variation of Seed Coat Luster

Population Structure of the World Vegetable Center Mungbean Mini Core Collection and Genome-Wide... Mungbean [Vigna radiata (L.) R. Wilczek var. radiata] is an important legume crop for South East Asia. Smallholder farmers rely on this crop to diversify income streams and enrich soils through N-fixation. To produce new varieties that stabilize mungbean productivity under biotic and abiotic stresses, breeders need to take advantage of genomic tools. Genome-Wide Association Studies (GWAS) are an effective strategy to associate agronomic traits with underlying genes. A key factor to avoid false associations in GWAS is a thorough understanding of the population structure. In this study, we analyzed the population structure of the World Vegetable Center’s (WorldVeg) mungbean mini core collection and performed a GWAS to identify loci associated with seed coat luster (SCL) utilizing SNP markers. The mini core collection consisted of 297 most genetically diverse accessions selected from 6700 global accessions held by the WorldVeg genebank. Genotyping by Sequencing (GBS) produced a total of 24,870 Single Nucleotide Polymorphism (SNP) markers. After filtering, 5288 highly polymorphic SNPs were used for analysis. Population structure analysis predicted four sub-populations based on the non-parametric Wilcoxon test. Linkage disequilibrium (LD) was found to decline to half of the maximal r2 value at approximately 350 kb; and a pilot GWAS study investigating seed coat luster (SCL) revealed two loci in chromosome 5 significantly associated with SCL. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Tropical Plant Biology Springer Journals

Population Structure of the World Vegetable Center Mungbean Mini Core Collection and Genome-Wide Association Mapping of Loci Associated with Variation of Seed Coat Luster

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References (30)

Publisher
Springer Journals
Copyright
Copyright © Springer Science+Business Media, LLC, part of Springer Nature 2019
Subject
Life Sciences; Plant Sciences; Plant Genetics and Genomics; Plant Breeding/Biotechnology; Plant Ecology; Transgenics
ISSN
1935-9756
eISSN
1935-9764
DOI
10.1007/s12042-019-09236-0
Publisher site
See Article on Publisher Site

Abstract

Mungbean [Vigna radiata (L.) R. Wilczek var. radiata] is an important legume crop for South East Asia. Smallholder farmers rely on this crop to diversify income streams and enrich soils through N-fixation. To produce new varieties that stabilize mungbean productivity under biotic and abiotic stresses, breeders need to take advantage of genomic tools. Genome-Wide Association Studies (GWAS) are an effective strategy to associate agronomic traits with underlying genes. A key factor to avoid false associations in GWAS is a thorough understanding of the population structure. In this study, we analyzed the population structure of the World Vegetable Center’s (WorldVeg) mungbean mini core collection and performed a GWAS to identify loci associated with seed coat luster (SCL) utilizing SNP markers. The mini core collection consisted of 297 most genetically diverse accessions selected from 6700 global accessions held by the WorldVeg genebank. Genotyping by Sequencing (GBS) produced a total of 24,870 Single Nucleotide Polymorphism (SNP) markers. After filtering, 5288 highly polymorphic SNPs were used for analysis. Population structure analysis predicted four sub-populations based on the non-parametric Wilcoxon test. Linkage disequilibrium (LD) was found to decline to half of the maximal r2 value at approximately 350 kb; and a pilot GWAS study investigating seed coat luster (SCL) revealed two loci in chromosome 5 significantly associated with SCL.

Journal

Tropical Plant BiologySpringer Journals

Published: Mar 20, 2020

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