Single Nucleotide Polymorphism–based Genetic Diversity in the Reference Set of Peanut (Arachis spp.) by Developing and Applying Cost‐Effective Kompetitive Allele Specific Polymerase Chain Reaction Genotyping Assays

Abstract

Kompetitive allele-specific polymerase chain reaction (KASP) assays have emerged as cost-effective marker assays especially for molecular breeding applications. Therefore, a set of 96 informative single nucleotide polymorphisms (SNPs) was used to develop KASP assays in groundnut or peanut (Arachis spp.). Developed assays were designated as groundnut KASP assay markers (GKAMs) and screened on 94 genotypes (validation set) that included parental lines of 27 mapping populations, seven synthetic autotetraploid and amphidiploid lines, and 19 wild species accessions. As a result, 90 GKAMs could be validated and 73 GKAMs showed polymorphism in the validation set. Validated GKAMs were screened on 280 diverse genotypes of the reference set for estimating diversity features and elucidating genetic relationships. Cluster analysis of marker allelic data grouped accessions according to their genome type, subspecies, and botanical variety. The subspecies Arachis hypogaea L. subsp. fastigiata Waldron and A. hypogaea subsp. hypogaea formed distinct cluster; however, some overlaps were found indicating their frequent intercrossing during the course of evolution. The wild species, having diploid genomes, were grouped into a single cluster. The average polymorphism information content value for polymorphic GKAMs was 0.32 in the validation set and 0.31 in the reference set. These validated and highly informative GKAMs may be useful for genetics and breeding applications in Arachis species.

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

“…Two species, C. cajanifolius and C. scarabaeoides (L.) Thouars, showed a close relationship with each other; however, C. cajanifolius was closest to C. cajan. Other marker systems used to estimate the polymorphism in Cajanus were RAPD (Ratnaparkhe et al, 1995), AFLP (Punguluri et al, 2006), DArT (Yang et al, 2006), SSR (Saxena et al, 2010a, b;Bohra et al, 2011a), and, recently, single-nucleotide polymorphism (Saxena et al, 2012;Roorkiwal et al, 2013). All marker-based studies have revealed that a very low level of diversity is present in cultivated pigeonpea, whereas the wild relatives of pigeonpea showed enormous diversity (Ratnaparkhe et al, 1995;Punguluri et al, 2006;Saxena et al, 2010a, b;Bohra et al, 2011a).…”

“…Earlier, genetic diversity studies using a range of molecular markers reported a very low level of diversity in the primary gene pool Subramaninan et al, 2000;Herselman, 2003). Nevertheless, in the few other studies in which large germplasm sets were used reported low levels of diversity in primary gene pools, while better genetic diversity still exists within the wild relatives (Varshney et al, 2009a;Koppolu et al, 2010;Khera et al, 2013). Similarly, diversity array technology (DArT) and kompetitive allele specific PCR (KASP) markers showed very low polymorphism in cultivated genotypes and moderate polymorphism in diploid wild relatives (see Varshney et al, 2013b).…”

Legume Genomics: From Genomic Resources to Molecular Breeding

“…Functional genomics plays a significant role in the identification of genes and determining the mechanisms (Sato et al 2008) Functional Genomics (Fukai et al 2013) Peanut (Arachis hypogaea) 2n = 4x = 40 2890 Underway (http://www.peanutbioscience.com) Diversity and Domestication (Gowda et al 2013) Applied Genomics (Khera et al 2013;Wang et al 2013) Pongamia (Pongamia pinnata) 2n = 2x = 22 -Not available Genomic Resources (Biswas et al 2013) Soybean (Glycine max) 2n = 2x = 20 1115 Draft assembly (Schmutz et al 2010) Applied Genomics (Liu et al 2013) conferring resistance and/or tolerance to biotic and abiotic stresses of legumes. Functional genomics uses genomic data to describe gene functions and interactions by utilizing large-scale assays to measure and track many genes or proteins in parallel under different environmental conditions.…”

“…This section includes five research articles that describe the diversity, QTL analysis, and also the practical use of molecular breeding by introgression of QTL using MABC. The first article by Khera et al (2013) reports the development of Kompetitive allele-specific polymerase chain reaction (KASP) assays in groundnut and their utility to understand diversity features and elucidating genetic relationships in the groundnut reference set. In the case of GAB where only a few SNPs are required for genotyping a varying number of samples, the KASP assay seems to be the most cost effective in comparison to GoldenGate assays.…”

Utility of AhTE Markers for Genetic and Genomic Studies in Groundnut (Arachis hypogaea L.)

“…Of them, the development and use of DNA markers is the frontrunner with significant applications in developing new crop varieties with considerable genetic gain (Yuan et al, 2017). Though several types of marker systems are available in groundnut, most of them suffer from low polymorphism especially in cultivated groundnut (Song et al, 2010;Khera et al, 2013) over the wild types (Moretzsohn et al, 2009), which limits their application in crop improvement (for review, Holbrook et al, 2011).…”