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

• Published in: Tropical plant biology 2020-03, Vol.13 (1), p.1-12
• Main Authors: Breria, Caleb Manamik, Hsieh, Ching Hsiang, Yen, Jo-Yi, Nair, Ramakrishnan, Lin, Chen-Yu, Huang, Shu-Mei, Noble, Thomas J., Schafleitner, Roland
• Format: Article
• Language: English
• Subjects: Agronomy; Beans; Biomedical and Life Sciences; Chromosome 5; Chromosomes; Collection; Gene mapping; Genome-wide association studies; Genomes; Genotyping; Legumes; Life Sciences; Linkage disequilibrium; Loci; Luster; Mapping; Markers; Nucleotides; Plant Breeding/Biotechnology; Plant Ecology; Plant Genetics and Genomics; Plant Sciences; Polymorphism; Population; Population structure; Population studies; Seed coats; Single-nucleotide polymorphism; Small farms; Soil stabilization; Structural analysis; Transgenics; Vegetables; Vigna radiata
• ISSN: 1935-9756; 1935-9764
• DOI: 10.1007/s12042-019-09236-0

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 r 2 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.