Open AccessSingle 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
Author(s) -
Khera Pawan,
Upadhyaya Hari D.,
Pandey Manish K.,
Roorkiwal Manish,
Sriswathi Manda,
Janila Pasupuleti,
Guo Yufang,
McKain Michael R.,
Nagy Ervin D.,
Knapp Steven J.,
LeebensMack James,
Conner Joann A.,
OziasAkins Peggy,
Varshney Rajeev K.
Publication year - 2013
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2013.06.0019
Subject(s) - biology , genetic diversity , arachis hypogaea , arachis , genetics , genotyping , genotype , subspecies , genome , polymerase chain reaction , single nucleotide polymorphism , molecular marker , genetic marker , botany , gene , population , paleontology , demography , sociology
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.