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Mol Genet Genomics (2014) 289:513521 DOI 10.1007/s00438-014-0827-3
ORIGINAL PAPER
Linkage disequilibrium and populationstructure analysis among Capsicum annuum L. cultivars for use in association mapping
Padma Nimmakayala Venkata L. Abburi Lavanya Abburi Suresh Babu Alaparthi Robert Cantrell Minkyu Park Doil Choi Gerald Hankins Sridhar Malkaram Umesh K. Reddy
Abstract Knowledge of population structure and linkage disequilibrium among the worldwide collections of peppers currently classied as hot, mild, sweet and ornamental types is indispensable for applying association mapping and genomic selection to improve pepper. The current study aimed to resolve the genetic diversity and relatedness of Capsicum annuum germplasm by use of simple sequence repeat (SSR) loci across all chromosomes in samples collected in 2011 and 2012. The physical distance covered by the entire set of SSRs used was 2,265.9 Mb from the 3.48-Gb hot-pepper genome size. The model-based program STRUCTURE was used to infer ve clusters, which was further conrmed by classical molecular-genetic diversity analysis. Mean heterozygosity of various loci was estimated to be 0.15. Linkage disequilibrium (LD) was used to identify 17 LD blocks across various chromosomes with sizes from 0.154 Kb to 126.28 Mb. CAMS-142 of chromo-some 1 was signicantly associated with both capsaicin
P. Nimmakayala, V. L. Abburi and U. K. Reddy contributed equally to this work.
Communicated by S. Hohmann.
Electronic supplementary material The online version of this article (doi:http://dx.doi.org/10.1007/s00438-014-0827-3
Web End =10.1007/s00438-014-0827-3 ) contains supplementary material, which is available to authorized users.
P. Nimmakayala V. L. Abburi L. Abburi S. B. Alaparthi
R. Cantrell G. Hankins S. Malkaram U. K. Reddy (*) Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000, USAe-mail: [email protected]
M. Park D. Choi
Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-321, Republic of Korea
Received: 13 November 2013 / Accepted: 11 February 2014 / Published online: 2 March 2014 Springer-Verlag Berlin Heidelberg 2014
(CA) and dihydrocapsaicin (DCA) levels. Further, CAMS-142 was located in an LD block of 98.18 Mb. CAMS-142 amplied bands of 244, 268, 283 and 326 bp. Alleles 268 and 283 bp had positive effects on both CA and DCA levels, with an average R2 of 12.15 % (CA) and 12.3 % (DCA). Eight markers from seven different...