Molecular Genetics and Genomics

, Volume 289, Issue 4, pp 513–521 | Cite as

Linkage disequilibrium and population-structure 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
Original Paper


Knowledge of population structure and linkage disequilibrium among the worldwide collections of peppers currently classified 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 five clusters, which was further confirmed 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 chromosome 1 was significantly associated with both capsaicin (CA) and dihydrocapsaicin (DCA) levels. Further, CAMS-142 was located in an LD block of 98.18 Mb. CAMS-142 amplified 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 chromosomes were significantly associated with fruit weight, contributing an average effect of 15 %. CAMS-199, HpmsE082 and CAMS-190 are the three major quantitative trait loci located on chromosomes 8, 9, and 10, respectively, and were associated with fruit weight in samples from both years of the study. This research demonstrates the effectiveness of using genome-wide SSR-based markers to assess features of LD and genetic diversity within C. annuum.


SSRs Population structure Association mapping Capsaicin Fruit weight 

Supplementary material

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Supplementary material 1 (DOC 170 kb)
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Supplementary material 2 (DOC 90 kb)
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Supplementary material 3 (DOC 173 kb)
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Supplementary material 4 (DOC 150 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Padma Nimmakayala
    • 1
  • Venkata L. Abburi
    • 1
  • Lavanya Abburi
    • 1
  • Suresh Babu Alaparthi
    • 1
  • Robert Cantrell
    • 1
  • Minkyu Park
    • 2
  • Doil Choi
    • 2
  • Gerald Hankins
    • 1
  • Sridhar Malkaram
    • 1
  • Umesh K. Reddy
    • 1
  1. 1.Department of Biology, Gus R. Douglass InstituteWest Virginia State UniversityInstituteUSA
  2. 2.Department of Plant Science, Plant Genomics and Breeding InstituteCollege of Agriculture and Life Sciences, Seoul National UniversitySeoulRepublic of Korea

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