Molecular Characterization of Mung Bean Germplasm from the USDA Core Collection Using Newly Developed KASP‐based SNP Markers

Abstract

Mung bean [Vigna radiata (L.) Wilczek] is an important, nutritious legume food crop for tropical and subtropical countries with high value in Asia and worldwide potential. However, the genetic improvement of mung bean is slowed by low polymorphism of previous molecular markers, even microsatellites. The goals of this study were to develop Kompetitive Allele Specific Polymerase Chain Reaction (KASP)‐based single‐nucleotide polymorphism (SNP) markers and use them for characterization of 94 cultivated mung bean genotypes from the USDA originating in 27 countries across 10 regions of the world, all being cultivars rather than wild accessions. We targeted 42 SNPs from previous sequencing and converted them into 20 robust KASP assays. Of these, 18 were polymorphic among the mung bean cultivars, with 38 alleles total and 1.9 alleles per locus average. The polymorphism information content of the newly developed markers ranged from zero for monomorphic markers to 0.375 for the most diverse biallelic polymorphic marker (MBkSNP_39) and averaged 0.250 across all loci. Population structure analysis grouped 90% of the accessions into two subpopulations, with 10% belonging to an admixture group, but did not follow geographic origins of the germplasm, suggesting no clear center of origin and blending of the subpopulations. An analysis of molecular variance revealed 22% of genetic variation among subpopulations and 78% within subpopulations. The first two axes of region‐wide principle coordinate analysis explained 81.26% variation of total variation, indicating the existence of genetic diversity among groups. The SNP markers of this study can be used in molecular breeding of mung bean and are the first to work with KASP detection.

Genome-Wide SNP Identification and Association Mapping for Seed Mineral Concentration in Mung Bean (Vigna radiata L.)

“…Since mung bean is one of the most important food legume crops in South, East and Southeast Asia, where 90% of global production currently occurs, historical germplasm exchange has been extensive for the crop. The unique genetic diversity of Iran mung bean accessions has been reported in other diversity studies (Islam and Blair, 2018;Noble et al, 2018), which could be due to the geographic isolation and breeding history of mung beans in West Asia, where a genetic bottleneck for dryland adaptation could have occurred.…”

“…We also found a gene similar to YLS7 on chromosome Vr07 but this one was associated with Zn accumulation. Joint association of Fe and Zn accumulation has been identified in other legumes and a functional SNP marker called "MBkSNP_38" from Islam and Blair (2018) was also discovered to be within a YSL gene. As this marker was validated as a KASP assay for mung bean it could be useful for mung bean nutritional breeding even if it was evaluated on a different genotype panel.…”

“…Single Nucleotide Polymorphism (SNP) markers have emerged as an interesting option for mung bean with over 300,000 discovered by Van et al (2013) . However, only 43 and 20 SNPs have been validated as competitive allele specific polymorphism (KASP) markers in the two studies conducted to date ( Van et al, 2013 ; Islam and Blair, 2018 ), respectively.…”

Genome-Wide Association Study of Growth Performance and Immune Response to Newcastle Disease Virus of Indigenous Chicken in Rwanda

“…Further examination is therefore required to prove these novel genes as putative genes for Ab response to ND in chicken. Kompetitive Allele Specific Polymerase Chain Reaction (KASP)-based markers (Semagn et al, 2014;Islam and Blair, 2018) could be developed using the SNPs significantly associated with Ab response to ND and validated before being used to screen targeted chicken breeds to establish the involvement of these genes in chicken immunity to ND. Another approach will be to develop an RNA-guided cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR-CAS9) protocol (Ran et al, 2013;Doudna and Charpentier, 2014) for chicken with the ultimate aim of silencing these genes to ascertain their role in the chicken immunity to ND.…”

New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses

“…SNPs converted to KASP markers can be genotyped in small labs using fluorescent resonance energy transfer (FRET)-capable plate readers and qPCR machines. SNP markers have been successfully converted to KASP markers and used for various applications in different crops, including the faba bean [ 33 ], mung bean [ 34 ], pea [ 35 ], peanut [ 36 ], rice [ 37 , 38 ], rye [ 39 ], sorghum [ 40 ], and wheat [ 41 , 42 , 43 ].…”