Construction of SNP-based KASP fingerprints and population genetic analysis of 40 core mung bean germplasm resources

Abstract

The objective of this work was to construct a DNA fingerprinting database of 40 core mung bean (Vigna radiata) germplasm using the single nucleotide polymorphism (SNP)-based kompetitive allele specific PCR (KASP) markers identified by genotyping-by-sequencing. After a rigorous filtering, 2,987,425 high-quality SNPs with a high ratio of transitions to transversions (1.97) were obtained, which were mainly synonymous or nonsynonymous single-nucleotide variants, located in intergenic regions and 1.0-kb regions upstream of the transcriptional start sites. The principal component analysis, population structural analysis, and genetic evolutionary tree analysis indicated that the 40 evaluated germplasms were best classified into three groups, which, however, were inconsistent with their geographical origins, indicating that the genetic backgrounds of these germplasms are complex and diverse. Through stringent selection criteria, 25,611 of these high-quality SNPs were successfully converted into KASP markers. The mean values of polymorphism information content, minor allele frequency, and heterozygosity of these KASP markers were 0.366, 0.421, and 0.04, respectively. Finally, 50 core KASP markers were filtered out, and eight of these were verified as able to effectively construct the genetic fingerprints of the 40 core mung bean germplasms.