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

Abstract

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.

Keywords

SSRs Population structure Association mapping Capsaicin Fruit weight 

Supplementary material

438_2014_827_MOESM1_ESM.doc (170 kb)
Supplementary material 1 (DOC 170 kb)
438_2014_827_MOESM2_ESM.doc (90 kb)
Supplementary material 2 (DOC 90 kb)
438_2014_827_MOESM3_ESM.doc (174 kb)
Supplementary material 3 (DOC 173 kb)
438_2014_827_MOESM4_ESM.doc (150 kb)
Supplementary material 4 (DOC 150 kb)

References

  1. Aguilar-Melendez A, Morrell PL, Roose ML, Kim S-C (2009) Genetic diversity and structure in semiwild and domesticated chiles (Capsicum annuum; Solanaceae) from Mexico. Am J Bot 96(6):1190–1202PubMedCrossRefGoogle Scholar
  2. Arumugasundaram S, Ghosh M, Veerasamy S, Ramasamy Y (2011) Species discrimination, population structure and linkage disequilibrium in Eucalyptus camaldulensis and Eucalyptus tereticornis using SSR markers. PLoS One 6(12):e28252. doi:10.1371/journal.pone.0028252 PubMedCentralPubMedCrossRefGoogle Scholar
  3. Ben Chaim A, Paran I, Grube RC, Jahn M, van Wijk R, Peleman J (2001) QTL mapping of fruit-related traits in pepper (Capsicum annuum). Theor Appl Genet 102(6–7):1016–1028CrossRefGoogle Scholar
  4. Ben Chaim A, Borovsky Y, Rao GU, Tanyolac B, Paran I (2003) fs3.1: a major fruit shape QTL conserved in Capsicum. Genome 46(1):1–9PubMedCrossRefGoogle Scholar
  5. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57(1):289–300Google Scholar
  6. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23(19):2633–2635PubMedCrossRefGoogle Scholar
  7. Cong B, Barrero LS, Tanksley SD (2008) Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat Genet 40(6):800–804PubMedCrossRefGoogle Scholar
  8. Crossa J, Franco J (2004) Statistical methods for classifying genotypes. Euphytica 137(1):19–37CrossRefGoogle Scholar
  9. D’hoop B, Paulo MJ, Kowitwanich K, Sengers M, Visser RF, Eck H, Eeuwijk F (2010) Population structure and linkage disequilibrium unravelled in tetraploid potato. Theor Appl Genet 121(6):1151–1170PubMedCentralPubMedCrossRefGoogle Scholar
  10. Emanuelli F, Lorenzi S, Grzeskowiak L, Catalano V, Stefanini M, Troggio M, Myles S, Martinez-Zapater J, Zyprian E, Moreira F, Grando M (2013) Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape. BMC Plant Biol 13(1):1–17CrossRefGoogle Scholar
  11. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14(8):2611–2620PubMedCrossRefGoogle Scholar
  12. Grandillo S, Ku HM, Tanksley SD (1999) Identifying the loci responsible for natural variation in fruit size and shape in tomato. Theor Appl Genet 99(6):978–987CrossRefGoogle Scholar
  13. Hamblin MT, Warburton ML, Buckler ES (2007) Empirical comparison of simple sequence repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness. PLoS One 2(12):e1367. doi:10.1371/journal.pone.0001367 PubMedCentralPubMedCrossRefGoogle Scholar
  14. Han K, Jeong H-J, Sung J, Keum Y, Cho M-C, Kim J-H, Kwon J-K, Kim B-D, Kang B-C (2013) Biosynthesis of capsinoid is controlled by the Pun1 locus in pepper. Mol Breed 31(3):537–548. doi:10.1007/s11032-012-9811-y CrossRefGoogle Scholar
  15. Hao C, Wang L, Ge H, Dong Y, Zhang X (2011) Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers. PLoS One 6(2):e17279. doi:10.1371/journal.pone.0017279 PubMedCentralPubMedCrossRefGoogle Scholar
  16. Hernández-Verdugo S, Luna-Reyes R, Oyama K (2001) Genetic structure and differentiation of wild and domesticated populations of Capsicum annuum (Solanaceae) from Mexico. Plant Syst Evol 226(3–4):129–142. doi:10.1007/s006060170061 CrossRefGoogle Scholar
  17. Hill TA, Ashrafi H, Reyes-Chin-Wo S, Yao J, Stoffel K, Truco M-J, Kozik A, Michelmore RW, Van Deynze A (2013) Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30 K unigene pepper genechip. PLoS One 8(2):e56200. doi:10.1371/journal.pone.0056200 PubMedCentralPubMedCrossRefGoogle Scholar
  18. Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14):1801–1806PubMedCrossRefGoogle Scholar
  19. Jin L, Lu Y, Xiao P, Sun M, Corke H, Bao J (2010) Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theor Appl Genet 121(3):475–487PubMedCrossRefGoogle Scholar
  20. Liu S-R, Li W-Y, Long D, Hu C-G, Zhang J-Z (2013) Development and characterization of genomic and expressed SSRs in citrus by genome-wide analysis. PLoS One 8(10):e75149. doi:10.1371/journal.pone.0075149 PubMedCentralPubMedCrossRefGoogle Scholar
  21. Matsuoka Y, Mitchell SE, Kresovich S, Goodman M, Doebley J (2002) Microsatellites in Zea—variability, patterns of mutations, and use for evolutionary studies. Theor Appl Genet 104(2–3):436–450PubMedCrossRefGoogle Scholar
  22. Mazourek M, Pujar A, Borovsky Y, Paran I, Mueller L, Jahn MM (2009) A dynamic interface for capsaicinoid systems biology. Plant Physiol 150(4):1806–1821PubMedCentralPubMedCrossRefGoogle Scholar
  23. Minamiyama Y, Tsuro M, Hirai M (2006) An SSR-based linkage map of Capsicum annuum. Mol Breed 18(2):157–169CrossRefGoogle Scholar
  24. Munos S, Ranc N, Botton E, Berard A, Rolland S, Duffe P, Carretero Y, Le Paslier MC, Delalande C, Bouzayen M, Brunel D, Causse M (2011) Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL. Plant Physiol 156(4):2244–2254PubMedCentralPubMedCrossRefGoogle Scholar
  25. Ohashi J, Tokunaga K (2003) Power of genome-wide linkage disequilibrium testing by using microsatellite markers. J Hum Genet 48(9):487–491PubMedCrossRefGoogle Scholar
  26. Paran I (2003) Marker-assisted utilization of exotic germplam. In: Nguyen HT, Blum A (eds) Physiology and biotechnology integration for plant breeding. Marcel Dekker, New YorkGoogle Scholar
  27. Paran I, Aftergoot E, Shifriss C (1998) Variation in Capsicum annuum revealed by RAPD and AFLP markers. Euphytica 99(3):167–173CrossRefGoogle Scholar
  28. Pickersgill (1997) Genetic resources and breeding of Capsicum spp. Euphytica 96:129–133CrossRefGoogle Scholar
  29. Portis E, Barchi L, Acquadro A, Macua JI, Lanteri S (2005) Genetic diversity assessment in cultivated cardoon by AFLP (amplified fragment length polymorphism) and microsatellite markers. Plant Breed 124(3):299–304CrossRefGoogle Scholar
  30. Powis TG, Gallaga Murrieta E, Lesure R, Lopez Bravo R, Grivetti L, Kucera H, Gaikwad NW (2013) Prehispanic use of chili peppers in Chiapas, Mexico. PLoS One 8(11):e79013. doi:10.1371/journal.pone.0079013 PubMedCentralPubMedCrossRefGoogle Scholar
  31. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959PubMedCentralPubMedGoogle Scholar
  32. Reddy UK, Almeida A, Abburi VL, Alaparthi SB, Unselt D, Hankins G, Park M, Choi D, Nimmakayala P (2014) Identification of gene-specific polymorphisms and association with capsaicin pathway metabolites in Capsicum annuum L. collections. PLoS One 9(1):e86393. doi:10.1371/journal.pone.0086393 PubMedCentralPubMedCrossRefGoogle Scholar
  33. Reyes-Valdés MH, Santacruz-Varela A, Martínez O, Simpson J, Hayano-Kanashiro C, Cortés-Romero C (2013) Analysis and optimization of bulk DNA sampling with binary scoring for germplasm characterization. PLoS One 8(11):e79936. doi:10.1371/journal.pone.0079936 PubMedCentralPubMedCrossRefGoogle Scholar
  34. Robbins MD, Sim S-C, Yang W, Van Deynze A, van der Knaap E, Joobeur T, Francis DM (2011) Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato. J Exp Bot 62(6):1831–1845PubMedCentralPubMedCrossRefGoogle Scholar
  35. Rosenberg NA (2004) Distruct: a program for the graphical display of population structure. Mol Ecol Notes 4(1):137–138CrossRefGoogle Scholar
  36. Rousset F (2008) Genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8(1):103–106PubMedCrossRefGoogle Scholar
  37. Schneider, Roessli D, Excoffier L (2000) Arlequin: a software for population genetics data analysis User manualGoogle Scholar
  38. Sidak Z (1967) Rectangular confidence regions for the means of multivariate normal distributions. J Am Stat Assoc 62(318):626–633Google Scholar
  39. Slatkin M (1985) Gene flow in natural populations. Annu Rev Ecol Syst 16:393–430CrossRefGoogle Scholar
  40. Sonah H, Deshmukh RK, Sharma A, Singh VP, Gupta DK, Gacche RN, Rana JC, Singh NK, Sharma TR (2011) Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium. PLoS One 6(6):e21298. doi:10.1371/journal.pone.0021298 PubMedCentralPubMedCrossRefGoogle Scholar
  41. Sugita T, Semi Y, Sawada H, Utoyama Y, Hosomi Y, Yoshimoto E, Maehata Y, Fukuoka H, Nagata R, Ohyama A (2013) Development of simple sequence repeat markers and construction of a high-density linkage map of Capsicum annuum. Mol Breed 31(4):909–920CrossRefGoogle Scholar
  42. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739PubMedCentralPubMedCrossRefGoogle Scholar
  43. Tenaillon MI, U’Ren J, Tenaillon O, Gaut BS (2004) Selection versus demography: a multilocus investigation of the domestication process in maize. Mol Biol Evol 21(7):1214–1225PubMedCrossRefGoogle Scholar
  44. Tomason Y, Nimmakayala P, Levi A, Reddy U (2013) Map-based molecular diversity, linkage disequilibrium and association mapping of fruit traits in melon. Mol Breed 31(4):829–841CrossRefGoogle Scholar
  45. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38(6):1358–1370CrossRefGoogle Scholar
  46. Yarnes SC, Ashrafi H, Reyes-Chin-Wo S, Hill TA, Stoffel KM, Van Deynze A, Gulick P (2012) Identification of QTLs for capsaicinoids, fruit quality, and plant architecture-related traits in an interspecific Capsicum RIL population. Genome 56(1):61–74CrossRefGoogle Scholar
  47. Yeh YR, Boyle T (1999) POPGENE Version 1.31. Microsoft Window-based Freeware for Population Genetic Analysis Quick User GuideGoogle Scholar
  48. Yi G, Lee JM, Lee S, Choi D, Kim BD (2006) Exploitation of pepper EST-SSRs and an SSR-based linkage map. Theor Appl Genet 114(1):113–130PubMedCrossRefGoogle Scholar
  49. Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17(2):155–160PubMedCrossRefGoogle Scholar
  50. Zhang J, Hao C, Ren Q, Chang X, Liu G, Jing R (2011) Association mapping of dynamic developmental plant height in common wheat. Planta 234(5):891–902PubMedCrossRefGoogle Scholar
  51. Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P, Nordborg M (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3(1):e4PubMedCentralPubMedCrossRefGoogle Scholar
  52. Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. Plant Gen 1(1):5–20CrossRefGoogle Scholar

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

Personalised recommendations