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Establishment of a core collection of chilli germplasm using microsatellite analysis

Published online by Cambridge University Press:  30 June 2014

Orarat Mongkolporn ,
Suntree Hanyong ,
Julapark Chunwongse  and
Sirikul Wasee
Orarat Mongkolporn*
Affiliation:
Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
Suntree Hanyong
Affiliation:
Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
Julapark Chunwongse
Affiliation:
Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
Sirikul Wasee
Affiliation:
Tropical Vegetable Research and Development Center, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
*
*Corresponding author. E-mail: [email protected]
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Abstract

Chilli (Capsicum spp.) is an economically important vegetable and spice. The Tropical Vegetable Research and Development Center, Kasetsart University, Kamphaeng Saen Campus has collected more than 2500 chilli germplasm accessions since 1989. Investment to maintain and evaluate such a large germplasm collection is high. For efficient germplasm management and to reduce the cost of germplasm maintenance, a core collection needs to be established. Therefore, this study aimed to investigate the genetic diversity of chilli germplasm using microsatellites. A total of 230 chilli germplasm accessions were evaluated using ten anchored Capsicum microsatellite loci. These loci generated 42 alleles with a size ranging from 87 to 323 bp. The average polymorphic information content was 0.57, ranging from 0.414 to 0.681, and the probability of identity (PI) ranged from 0.17 to 0.49. The combined PI of the ten microsatellite loci was 2.30 × 10− 6. The similarity index ranged from 0.29 to 1.00. The 230 chilli accessions were divided into two major groups. Group I comprised mainly C. annuum, and group II comprised all four Capsicum species with the majority being C. frutescens, C. chinense and C. baccatum. The matrix comparison showed that a cophenetic correlation of 0.798 indicated the best fit of the obtained dendrogram. The PowerCore program selected 28 representative chilli accessions to form a core collection, which maintained a similar level of diversity to that of the overall 230 chilli accessions. The representative alleles in those 28 core accessions equalled all the alleles present in the entire collection.

Keywords

Capsicumchilli pepperdiversitysimple sequence repeat
Type
Research Article
Information
Plant Genetic Resources , Volume 13 , Issue 2 , August 2015 , pp. 104 - 110
Copyright
Copyright © NIAB 2014 

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References

Bombarely, A, Menda, N, Tecle, IY, Buels, RM, Strickler, S, Fischer-York, T, Pujar, A, Leto, J, Gosselin, J and Mueller, LA (2011) The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Research 39: D1149–D1155.Google Scholar
Bosland, PW and Baral, JB (2007) ‘Bhut Jolokia’ – the world's hottest known chile pepper is a putative naturally occurring interspecific hybrid. HortScience 42: 222–224.Google Scholar
Botstein, D, White, RL, Skolnick, M and Davis, RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314–331.Google ScholarPubMed
FAOSTAT (2012) Agricultural production, FAO. Available at http://faostat.fao.org/.Google Scholar
Frankel, OH and Brown, AHD (1984) Plant genetic resources today: a critical appraisal. In: Holden, JHW and Williams, JT (eds) Crop Genetic Resources: Conservation and Evaluation. London: George Allen and Unwin, pp. 249–257.Google Scholar
Gupta, PK, Balyan, HS, Sharma, PC and Ramesh, B (1996) Microsatellites in plants: a new class of molecular markers. Current Science 70: 45–54.Google Scholar
Huang, SW, Zhang, BX, Milbourne, D, Cardle, L, Yang, GM and Guo, JZ (2000) Development of pepper SSR markers from sequence databases. Euphytica 117: 163–168.Google Scholar
Huang, HH, Zhang, ZH, Zhang, ZH, Mao, SL, Wang, LH and Zhang, BX (2011) Analysis of SSRs information in Capsicum spp. from EST database. Agricultural Sciences in China 10: 1532–1536.Google Scholar
Idury, RM and Cardon, LR (1997) A simple method for automated allele binning in microsatellite markers. Genome Research 7: 1104–1109.Google Scholar
IPGRI, AVRDC and CATIE(1995) Descriptors for Capsicum (Capsicum spp.): International Plant Genetic Resources Institute, Rome, Italy; the Asian Vegetable Research and Development Center, Taipei, Taiwan, and the Centro Agronómico Tropical de Investigación y Enseñanza, Turrialba, Costa Rica.Google Scholar
Kaul, R, Singh, A, Vijh, RK, Tantia, MS and Behl, R (2001) Evaluation of the genetic variability of 13 microsatellite markers in native Indian pigs. Journal of Genetics 80: 149–153.Google Scholar
Kim, KW, Chung, HK, Cho, GT, Ma, KH, Chandrabalan, D, Gwag, JG, Kim, TS, Cho, EG and Park, YJ (2007) PowerCore: a program applying the advanced M strategy with a heuristic search for establishing allele mining sets. Bioinformatics 23: 2155–2162.Google Scholar
Lagercrantz, U, Ellegren, H and Andersson, L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Research 21: 1111–1115.Google Scholar
Lee, JM, Nahm, SH, Kim, YM and Kim, BD (2004) Characterization and molecular genetic mapping of microsatellite loci in pepper. Theoretical and Applied Genetics 108: 619–627.Google Scholar
Mongkolporn, O, Dokmaihom, Y, Kanchana-Udomkan, C and Pakdeevaraporn, P (2004) Genetic purity test of F1 hybrid Capsicum using molecular analysis. Journal of Horticultural Science and Biotechnology 79: 449–451.CrossRefGoogle Scholar
Mongkolporn, O and Taylor, PWJ (2011) Capsicum . In: Kole, C (ed.) Wild Crop Relatives: Genomic and Breeding Resources. vol. V: Vegetables 1st edn. New York: Springer, pp. 43–57.CrossRefGoogle Scholar
Nagy, I, Stagel, A, Sasvari, Z, Roder, M and Ganal, M (2007) Development, characterization, and transferability to other Solanaceae of microsatellite markers in pepper (Capsicum annuum L.). Genome 50: 668–688.Google Scholar
Nei, M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Science U S A 70: 3321–3323.CrossRefGoogle ScholarPubMed
Nei, M and Li, WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences U S A 76: 5269–5273.Google Scholar
Portis, E, Nagy, I, Sasvári, Z, Stágel, A, Barchi, L and Lanteri, S (2007) The design of Capsicum spp. SSR assays via analysis of in silico DNA sequence, and their utility for genetic mapping. Plant Science 172: 640–648.Google Scholar
Purkayastha, J, Alam, SI, Gogoi, HK, Singh, L and Veer, V (2012) Molecular characterization of ‘Bhut Jolokia’ the hottest chili. Journal of Biosciences 37: 757–768.Google Scholar
Reed, BM, Engelmann, F, Dulloo, ME and Engels, JMM (2004) Technical Guidelines for the Management of Field and in vitro Germplasm Collections. IPGRI Handbooks for Genebanks No. 7. Rome, Italy: International Plant Genetic Resources Institute.Google Scholar
Rohlf, FJ (1997) NTSYS-pc 2.1: Numerical Taxonomy and Multivariate Analysis System. Setauket, New York: Exeter Software.Google Scholar
Schoen, DJ and Brown, AHD (1993) Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers. Proceedings of the National Academy of Sciences U S A 90: 10623–10627.Google Scholar
Wasee, S, Kaewson, P, Srisawat, N, Chunwongse, C, Damrongkittikul, S and Chunwongse, J (2005) Morphological cluster analysis of chili germplasm. Proceedings of the Fifth National Horticulture Congress. Chon Buri, Thailand (in Thai language), pp. 109.Google Scholar
Yap, IV and Nelson, RJ (1996) WinBoot: A Program for Performing Bootstrap Analysis of Binary Data to Determine the Confidence Limits of UPGMA-based Dendrograms (Computer Program). Manila, Philippines: International Rice Research Institute.Google Scholar