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…
By P. Khera, H. D. Upadhyaya, M. Pandey, Manish Roorkiwal, Manda Sriswathi, P. Janila, Yufang Guo, M. McKain, E. Nagy, S. Knapp and 4 more. 2013
116 citations recorded by the source corpus.
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.
Subfields: Inorganic Chemistry, Plant Science
View Paper: https://www.semanticscholar.org/paper/319046a46e74a75055e36e730e68d29e80025fe5
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In Plant Science
Citations in the corpus
- Legume Crops Phylogeny and Genetic Diversity for Science and Breeding (2015, background): “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).”
- High-Throughput SNP Genotyping to Accelerate Crop Improvement (2014, methodology): “…described for Sequence-Based Genotyping (SBG; Truong et al. 2012; Poecke et al. 2013), Diversity Array Technology sequencing (DArTseq; Cruz et al. 2013); RESTriction Fragment SEQuencing (RESTseq; Stolle and Moritz 2013), and Restriction Enzyme Site Comparative Analysis (RESCAN; Kim and Tai 2013).”