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

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. Peanut (Arachis hypogaea L.), an allotetraploid species, is a highly domesticated oilseed crop that originated through hybridization and chromosome doubling of two different genomes. Furthermore, domestication created a genetic bottleneck as no close relatives are available to share favorable alleles, resulting in an extremely narrow cultivated gene pool in the case of peanut. As a consequence, breeders have been obligated to harness available favorable alleles limited to elite breeding lines and some local landraces for developing improved cultivars. The above circumstances have greatly hampered peanut genetic improvement through conventional approaches as well as development of optimum genetic and genomic resources for molecular breeding in peanut (see Varshney et al., 2012). Nevertheless, rapid developments in availability of large scale genomic resources have now provided a well-set platform to conduct several genetic studies such as molecular diversity, genetic mapping, marker–trait association, and use of modern breeding strategies in peanut (see Pandey et al., 2012; see Varshney et al., 2013). Availability of Published in The Plant Genome 6 doi: 10.3835/plantgenome2013.06.0019 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. P. Khera, H.D. Upadhyaya, M.K. Pandey, M. Roorkiwal, M. Sriswathi, P. Janila, and R.K. Varshney, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; Y. Guo and E.D. Nagy, Center for Applied Genetic Technologies, The Univ. of Georgia, Athens, GA 30602; Y. Guo, J.A. Conner, and P. Ozias-Akins, Dep. of Horticulture, The Univ. of Georgia, Tifton, GA 31973; M.R. McKain and J. Leebens-Mack, Dep. of Plant Biology, The Univ. of Georgia, Athens, GA 30602; S.J. Knapp, The Institute of Plant Breeding, Genetics & Genomics, The Univ. of Georgia, Athens, GA 30602; R.K. Varshney, CGIAR Generation Challenge Programme, c/o CIMMYT, Mexico DF, Mexico. Received 5 June 2013. *Corresponding author ([email protected]). Abbreviations: Cl, cluster; DArT, Diversity Array Technology; EST, expressed sequence tag; GKAM, groundnut KASP assay marker; KASP, Kompetitive allele specific polymerase chain reaction; PCR, polymerase chain reaction; PIC, polymorphism information content; QTL, quantitative trait loci; SNP, single nucleotide polymorphism; SSR, simple sequence repeat; UPGMA, unweighted pair-group method with arithmetic mean.