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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

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Relation http://oar.icrisat.org/7049/
http://dx.doi.org/10.3835/plantgenome2013.06.0019
 
Title 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
 
Creator Khera, P
Upadhyaya, H D
Pandey, M K
Roorkiwal, M
Sriswathi, M
Janila, P
Guo, Y
McKain, M R
Nagy, E D
Knapp, S J
Leebens-Mack, J
Conner, J A
Ozias-Akins, P
Varshney, R K
 
Subject Groundnut
Genetics and Genomics
 
Description 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.
 
Publisher Crop Science Society of America
 
Date 2013
 
Type Article
PeerReviewed
 
Format application/pdf
application/vnd.ms-excel
application/vnd.ms-excel
application/vnd.ms-excel
 
Language en
en
en
en
 
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Identifier http://oar.icrisat.org/7049/1/Plant-geno_2013_6_X_1-11.pdf
http://oar.icrisat.org/7049/5/plantgenome2013.06.0019-supplement1.xlsx
http://oar.icrisat.org/7049/3/plantgenome2013.06.0019-supplement2.xls
http://oar.icrisat.org/7049/4/plantgenome2013.06.0019-supplement3.xls
Khera, P and Upadhyaya, H D and Pandey, M K and Roorkiwal, M and Sriswathi, M and Janila, P and Guo, Y and McKain, M R and Nagy, E D and Knapp, S J and Leebens-Mack, J and Conner, J A and Ozias-Akins, P and Varshney, R K (2013) 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. The Plant Genome, 6 (3). pp. 1-11. ISSN 1940-3372