eprintid: 7049
rev_number: 22
eprint_status: archive
userid: 128
dir: disk0/00/00/70/49
datestamp: 2013-08-13 03:32:55
lastmod: 2014-01-30 11:10:20
status_changed: 2013-08-13 03:32:55
type: article
metadata_visibility: show
contact_email: Library-ICRISAT@cgiar.org
creators_name: Khera, P
creators_name: Upadhyaya, H D
creators_name: Pandey, M K
creators_name: Roorkiwal, M
creators_name: Sriswathi, M
creators_name: Janila, P
creators_name: Guo, Y
creators_name: McKain, M R
creators_name: Nagy, E D
creators_name: Knapp, S J
creators_name: Leebens-Mack, J
creators_name: Conner, J A
creators_name: Ozias-Akins, P
creators_name: Varshney, R K
icrisatcreators_name: Khera, P
icrisatcreators_name: Upadhyaya, H D
icrisatcreators_name: Pandey, M K
icrisatcreators_name: Roorkiwal, M
icrisatcreators_name: Sriswathi, M
icrisatcreators_name: Janila, P
icrisatcreators_name: Varshney, R K
affiliation: ICRISAT(Patancheru)
affiliation: The University of Georgia (Athens, GA)
country: India
country: USA
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
ispublished: pub
subjects: s1.3
subjects: s2.13
full_text_status: public
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.
date: 2013
date_type: published
publication: The Plant Genome
volume: 6
number: 3
publisher: Crop Science Society of America
pagerange: 1-11
refereed: TRUE
issn: 1940-3372
official_url: http://dx.doi.org/10.3835/plantgenome2013.06.0019
related_url_url: http://scholar.google.co.in/scholar?as_q=%22Single+Nucleotide+Polymorphism%E2%80%93based+Genetic+Diversity+in+the+Reference+Set+of+Peanut+%28Arachis+spp.%29+by+Developing+and+Applying+Cost-Effective+Kompetitive+Allele+Specific+Polymerase+Chain+Reaction+Ge
related_url_type: pub
funders: CGIAR Generation Challenge Programme (Theme Leader Discretionary Grant)
funders: The Bill & Melinda Gates Foundation (Tropical Legumes I & II)
projects: CGIAR Research Program on Grain Legumes
citation:   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     
document_url: http://oar.icrisat.org/7049/1/Plant-geno_2013_6_X_1-11.pdf
document_url: http://oar.icrisat.org/7049/5/plantgenome2013.06.0019-supplement1.xlsx
document_url: http://oar.icrisat.org/7049/3/plantgenome2013.06.0019-supplement2.xls
document_url: http://oar.icrisat.org/7049/4/plantgenome2013.06.0019-supplement3.xls