Hostname: page-component-586b7cd67f-r5fsc Total loading time: 0 Render date: 2024-11-23T22:05:47.707Z Has data issue: false hasContentIssue false
  • English
  • Français

Assessment of molecular genetic diversity and population structure of sesame (Sesamum indicum L.) core collection accessions using simple sequence repeat markers

Published online by Cambridge University Press:  19 September 2013

Jong-Hyun Park ,
Sundan Suresh ,
Gyu-Taek Cho ,
Nag-Gor Choi ,
Hyung-Jin Baek ,
Chul-Won Lee  and
Jong-Wook Chung
Jong-Hyun Park
Affiliation:
National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Suwon441-853, Republic of Korea
Sundan Suresh
Affiliation:
National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Suwon441-853, Republic of Korea
Gyu-Taek Cho
Affiliation:
National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Suwon441-853, Republic of Korea
Nag-Gor Choi
Affiliation:
Sejong Agricultural Technology Center, Sejong-Si339-814, Republic of Korea
Hyung-Jin Baek
Affiliation:
National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Suwon441-853, Republic of Korea
Chul-Won Lee
Affiliation:
Department of Agronomy, Chungbuk National University, Cheongju361-763, Republic of Korea
Jong-Wook Chung*
Affiliation:
National Agrobiodiversity Center, National Academy of Agricultural Science, Rural Development Administration, Suwon441-853, Republic of Korea
*
*Corresponding author. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Sesame (Sesamum indicum L.) is one of the oldest oil crops and is widely cultivated in Asia and Africa. The aim of this study was to assess the genetic diversity, phylogenetic relationships and population structure of 277 sesame core collection accessions collected from 15 countries in four different continents. A total of 158 alleles were detected among the sesame accessions, with the number varying from 3 to 25 alleles per locus and an average of 11.3. Polymorphism information content values ranged from 0.34 to 0.84, with an average of 0.568. These values indicated a high genetic diversity at 14 loci both among and within the populations. Of these, 44 genotype-specific alleles were identified in 12 of the 14 polymorphic simple sequence repeat markers. The core collection preserved a much higher level of genetic variation. Therefore, 10.1% was selected as the best sampling percentage from the whole collection when constructing the core collection. The 277 core collection accessions formed four robust clusters in the unweighted pair group method and the arithmetic averages (UPGMA) dendrogram, although the clustering did not indicate any clear division among the sesame accessions based on their geographical locations. Similar patterns were obtained using model-based structure analysis and country-based dendrograms, as some accessions situated geographically far apart were grouped together in the same cluster. The results of these analyses will increase our understanding of the genotype-specific alleles, genetic diversity and population structure of core collections, and the information can be used for the development of a future breeding strategy to improve sesame yield.

Keywords

core collectiongenetic diversitypopulation structureSesamum indicum
Type
Research Article
Information
Plant Genetic Resources , Volume 12 , Issue 1 , April 2014 , pp. 112 - 119
Copyright
Copyright © NIAB 2013 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Aranzana, MJ, Carbo, J and Arus, S (2003) Using amplified fragment-length polymorphisms (AFLPs) to identify peach cultivars. Journal of the American Society for Horticultural Science 128: 672–677.CrossRefGoogle Scholar
Ashri, A (1998) Sesame breeding. In: Janick, J (ed.) Plant Breeding Reviews. New York: John Wiley & Sons Inc.Google Scholar
Bhat, KV, Babrekar, PP and Lakhanpaul, S (1999) Study of genetic diversity in Indian and exotic sesame (Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers. Euphytica 110: 21–33.CrossRefGoogle Scholar
Bhattacharjee, R, Khairwal, IS, Bramel, PJ and Reddy, KN (2007) Establishment of a pearl millet [Pennisetum glaucum (L.) Br.] core collection based on geographical distribution and quantitative traits. Euphytica 155: 35–45.CrossRefGoogle Scholar
Cho, YG, Mccouch, SR, Kuiper, M, Kang, MR, Pot, J, Groenen, JTM and Eun, MY (1998) Integrated map of AFLP, SSLP and RFLP markers using a recombinant inbred population of rice (Oryza sativa L.). Theoretical and Applied Genetics 97: 370–380.CrossRefGoogle Scholar
Cho, YL, Park, JH, Lee, CW, Ra, WH, Chung, JW, Lee, JR, Ma, KH, Lee, SJ, Lee, KS, Lee, MC and Park, YJ (2011) Evaluation of the genetic diversity and population structure of sesame (Sesamum indicum L.) using microsatellite markers. Genes and Genomics 33: 187–195.CrossRefGoogle Scholar
Dangi, RS, Lagu, MD, Choudhary, LB, Ranjekar, PK and Gupta, VS (2004) Assessment of genetic diversity in Trigonella foenum-graecum and Trigonella caerulea using ISSR and RAPD markers. BMC Plant Biology 4: 13.CrossRefGoogle ScholarPubMed
Day, SJ (2000) Development and maturation of sesame seeds and capsules. Field Crops Research 67: 1–9.CrossRefGoogle Scholar
Dellaporta, S, Wood, J and Hicks, JB (1983) A plant DNA minipreparation: version II. Plant Molecular Biology Reporter 1: 19–21.CrossRefGoogle Scholar
Dixit, A, Jin, MH, Chung, JW, Yu, JW, Chung, HK, Ma, KH, Park, YJ and Cho, EG (2005) Development of polymorphic microsatellite markers in sesame (Sesamum indicum L.). Molecular Ecology Notes 5: 736–738.CrossRefGoogle Scholar
Donini, P, Stephenson, P, Bryan, GJ and Koebner, RMD (1998) The potential of microsatellites for high throughput genetic diversity assessment in wheat and barley. Genetic Resources and Crop Evolution 45: 415–421.CrossRefGoogle Scholar
Ercan, AG, Taskin, M and Turgut, K (2004) Analysis of genetic diversity in Turkish sesame (Sesamum indicum L.) populations using RAPD markers. Genetic Resources and Crop Evolution 51: 599–607.CrossRefGoogle Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.CrossRefGoogle ScholarPubMed
Falush, D, Stephens, M and Pritchard, JK (2003) Inference of population structure using multilocus genotypes data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587.CrossRefGoogle ScholarPubMed
Frankel, OH (1984) Genetic perspectives of germplasm conservation. In: Arber, WK, Llimensee, K, Peacock, WJ and Starlinger, P (eds) Genetic Manipulation: Impact on Man and Society. Cambridge: Cambridge University Press, pp. 161–170.Google Scholar
Fukuda, Y, Nagata, M, Osawa, T and Namiki, M (2007) Contribution of lignan analogues to antioxidative activity of refined unroasted sesame seed oil. Journal of the American Oil Chemists' Society 63: 1027–1031.CrossRefGoogle Scholar
Gao, LZ, Zhang, CH, Chang, LP, Jia, JZ, Qiu, ZE and Dong, YS (2005) Microsatellite diversity within Oryza sativa with emphasis on indica–japonica divergence. Genetics Research 85: 1–14.CrossRefGoogle ScholarPubMed
Gwag, JG, Dixit, A, Park, YJ, Ma, KH, Kwon, SJ, Cho, GT, Lee, GA, Lee, SY, Kang, HK and Lee, SH (2010) Assessment of genetic diversity and population structure in mungbean. Genes and Genomics 32: 299–308.CrossRefGoogle Scholar
Hamrick, JL and Godt, MJW (1989) Allozyme diversity in plants. In: Brown, AHD, Clegg, MT, Kahler, AL and Weir, BS (eds) Plant Population Genetics, Breeding and Germplasm Resources. Sunderland, MA: Sinauer, pp. 43–63.Google Scholar
Hansen, LB, Siegismund, HR and Jorgensen, RB (2003) Progressive introgression between Brassica napus (oilseed rape) and Brassica rapa . Heredity 91: 276–283.CrossRefGoogle Scholar
Hodgkin, T, Brown, AHD, Hintum, TJLV and Morales, EAV (1995) Core Collections of Plant Genetic Resources. A Co-publication with the International Plant Genetic Resources Institute (IPGRI). Chichester: A Wily Sayce Publication, pp. 213–228.Google Scholar
Huang, XQ, Borner, A, Roder, MS and Ganal, MW (2002) Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers. Theoretical and Applied Genetics 105: 699–707.CrossRefGoogle ScholarPubMed
Jarvis, DI and Hodgkin, T (1998) Wild relatives and crop cultivars: conserving the connection. In: Zencirci, N, Kaya, Z, Anikster, Y and Adams, WT (eds) The Proceedings of an International Symposium on in situ Conservation of Plant Genetic Diversity. London: George Allen & Unwin, pp. 163–179.Google Scholar
Jarvis, DI and Hodgkin, T (1999) Wild relatives and crop cultivars: detecting natural introgression and farmer selection of new genetic combinations in agroecosystems. Molecular Ecology 8: S159–S173.CrossRefGoogle Scholar
Jin, MH, Lee, JR, Yu, JW, Chung, JW, Ma, KH, Dixit, A, Kim, DH, Paek, NC, Cho, EG and Park, YJ (2009) Development and characterization of microsatellite markers for utilization in diversity analysis of sesame (Sesamum indicum L.) germplasm collection. Konkuk Journal of Life Science and Environment 31: 1–10.Google Scholar
Khlestkina, EK, Huang, XQ, Quenum, FJB, Chebotar, S, Roder, MS and Borner, A (2004) Genetic diversity in cultivated plants-loss or stability? Theoretical and Applied Genetics 108: 1466–1472.CrossRefGoogle ScholarPubMed
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 core sets. Bioinformatics 23: 2155–2162.CrossRefGoogle ScholarPubMed
Li, Z, Zhang, H, Zeng, Y, Yang, Z, Shen, S, Sun, C and Wang, X (2002) Studies on sampling schemes for the establishment of core collection of rice landraces in Yunnan China. Genetic Resources and Crop Evolution 49: 67–74.CrossRefGoogle Scholar
Liu, KJ and Muse, SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128–2129.CrossRefGoogle ScholarPubMed
Nyongesa, BO, Were, BA, Gudu, S, Dangasuk, OG and Onkware, AO (2013) Genetic diversity in cultivated sesame (Sesamum indicum L.) and related wild species in East Africa. Journal of Crop Science and Biotechnology 16: 9–15.CrossRefGoogle Scholar
Pathirana, R (1994) Natural cross-pollination in sesame (Sesamum indicum L.). Plant Breeding 112: 167–170.CrossRefGoogle Scholar
Peakall, R and Smouse, PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics 28: 2537–2539.CrossRefGoogle ScholarPubMed
Powell, W, Machray, GC and Provan, J (1996) Polymorphism revealed by simple sequence repeats. Trends in Plant Science 1: 215–222.CrossRefGoogle Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population genetic structure using multilocus genotype data. Genetics 155: 945–959.CrossRefGoogle ScholarPubMed
Roussel, V, Koenig, J, Beckert, M and Balfourier, F (2004) Molecular diversity in French bread wheat accessions related to temporal trends and breeding programs. Theoretical and Applied Genetics 108: 920–930.CrossRefGoogle Scholar
Salazar, B, Laurentin, H, Davila, M and Castillo, MA (2006) Reliability of the RAPD technique for germplasm analysis of sesame (Sesamum indicum L.) from Venezuela. Interciencia 31: 456–460.Google Scholar
Schuelke, M (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18: 233–234.CrossRefGoogle ScholarPubMed
Tamura, K, Dudley, J, Nei, M and Kumar, S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596–1599.CrossRefGoogle ScholarPubMed
Vinod, K and Sharma, SN (2011) Comparative potential of phenotypic, ISSR and SSR markers for characterization of sesame (Sesamum indicum L.) varieties from India. Journal of Crop Science and Biotechnology 14: 163–171.Google Scholar
Wang, Linhai, Zhang, Yanxin, Qi, Xiaoqiong, Gao, Yuan and Zhang, Xiurong (2012) Development and characterization of 59 polymorphic cDNA-SSR markers for the edible oil crop Sesamum indicum (Pedaliaceae). American Journal of Botany 99: e394–e398.CrossRefGoogle ScholarPubMed
Yermanos, DM (1980) Sesame. In: Fehr, WR and Hadley, HH (eds) Hybridization of Crop Plants. Madison, WI: American Society of Agronomy and Crop Science Society of America, pp. 549–563.Google Scholar
Yifru, T, Hammer, K, Huang, XQ and Roder, MS (2006) Regional patterns of microsatellite diversity in Ethiopian tetraploid wheat accessions. Plant Breeding 125: 125–130.CrossRefGoogle Scholar
Zhang, H, Wei, L, Miao, H, Zhang, T and Wang, C (2012a) Development and validation of genic-SSR markers in sesame by RNA-seq. BMC Genomics 13: 316.CrossRefGoogle ScholarPubMed
Zhang, Y, Zhang, X, Che, Z, Wang, L, Wei, W and Li, D (2012b) Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection. BMC Genetics 13: 102–126.CrossRefGoogle Scholar
Supplementary material: File

Park Supplementary Material

Table

Download Park Supplementary Material(File)
File 826.9 KB