Advertisement

Molecular Breeding

, Volume 34, Issue 3, pp 1185–1200 | Cite as

Development and characterization of microsatellite markers in Indian sesame (Sesamum indicum L.)

  • Malathi Surapaneni
  • Vijay Yepuri
  • Lakshminarayana R. Vemireddy
  • Anuradha Ghanta
  • E. A. Siddiq
Article

Abstract

The genetic characterization of Indian sesame cultivars and related wild species was analysed using 102 simple sequence repeat (SSR; microsatellite) markers. Of these, 62 were novel sesame-specific microsatellites isolated in the course of the present investigation by constructing genomic libraries. Characterization of the 68 sesame accessions and three related wild species using 72 polymorphic SSR primers resulted in the detection of 170 alleles. The number of alleles ranged from two to four with an average of 2.5 alleles per locus. Polymorphic information content of the markers ranged from 0.43 to 0.88 with an average of 0.66. UPGMA cluster analysis grouped all the accessions into two major clusters with a genetic similarity ranging from 0.40 to 0.91. A moderate to high level of genetic variability was observed. The three wild accessions used in the study formed separate clades and distant genetic relationships were observed between the cultivar lines and wild species. Differentiation of genotypes according to geographical region was not observed. Analysis of molecular variance (AMOVA) analysis revealed that a high percentage of variation was within populations (87.1 %). An overall F st of 0.11 among the populations indicated low population differentiation. The SSR markers developed will be useful for further genetic analysis, linkage mapping and selection of parents in future breeding programmes.

Keywords

SSR Microsatellite Sesamum Population 

Notes

Acknowledgments

We are grateful to National Agriculture Innovative Project (NAIP) for financial support. Thanks are due to Dr. K.V. Bhat (NRC for DNA Fingerprinting) and to National Bureau of Plant Genetic Resources (NBPGR, New Delhi), Directorate of Oilseed Research (DOR) for providing the sesame accessions for molecular characterization.

Supplementary material

11032_2014_109_MOESM1_ESM.jpg (61 kb)
EMS_1: Amplification profile of 71 sesame accessions using SSR101. The samples run on gel were according to table 1 (JPEG 61 kb)
11032_2014_109_MOESM2_ESM.doc (32 kb)
EMS_2: Genetic diversity indices of sesame accessions in four populations (DOC 32 kb)

References

  1. Aldrich PR, Doebley J (1992) Restriction fragment variation in the nuclear and chloroplast genomes of cultivated and wild Sorghum bicolor. Theor Appl Genet 85:293–302PubMedCrossRefGoogle Scholar
  2. Ali GM, Yasumoto S, Katsuta MS (2007) Assessment of genetic diversity in sesame (Sesamum indicum L.) detected by amplified fragment length polymorphism markers. Electron J Biotechnol 10:12–23CrossRefGoogle Scholar
  3. Bayda H, Turgut I, Turgut K (1997) Variation of certain characters and line selection for yield, oil, oleic and linoleic acids in the Turkish sesame (Sesamum indicum L.) populations. Turk J Agric For 23:431–441Google Scholar
  4. Bhat KV, Babrekar PP, Lakhanpaul S (1999) Study of genetic diversity in Indian and exotic sesame (Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers. Euphytica 110:21–33CrossRefGoogle Scholar
  5. Bisht IS, Mahajan RK, Loknathan TR, Agrawal RC (1998) Diversity in Indian sesame collection and stratification of germplasm accessions in different diversity groups. Genet Resour Crop Evol 45:325–335CrossRefGoogle Scholar
  6. Cho Y-Il, Park JH, Lee CW, Ra WH, Chung JW, Lee JR, Ma KH, Lee SY, Lee KS, Lee MC, Park YJ (2011) Evaluation of the genetic diversity and population structure of sesame (Sesamum indicum L.) using microsatellite markers. Genes Genomics 33(2):187–195CrossRefGoogle Scholar
  7. Dixit A, Jin MH, Chung JW, Yu JW, Chung HK, Ma KH, Park YJ, Cho EG (2005) Development of polymorphic microsatellite markers in sesame (Sesamum indicum L.). Mol Ecol Notes 5:736–738CrossRefGoogle Scholar
  8. Ercan AG, Taskin M, Turgut K (2004) Analysis of genetic diversity in Turkish sesame (Sesamum indicum L.) populations using RAPD markers. Genet Resour Crop Evol 51:599–607CrossRefGoogle Scholar
  9. Excoffier L, Guillaume L, Stefan S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform 1:47–50Google Scholar
  10. Gebremichael DE, Heiko KP (2010) Genetic variability among landraces of sesame in Ethiopia. Afr Crop Sci J 19:1–13Google Scholar
  11. Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis in bread wheat. Euphytica 113:163–185CrossRefGoogle Scholar
  12. Hartl DL, Clark AG (1997) Principles of population genetics, 3rd edn. Sinauer Associates, SunderlandGoogle Scholar
  13. Kim DH, Zur G, Danin-Poleg Y (2002) Genetic relationships of sesame germplasm collection as revealed by inter-simple sequence repeats. Plant Breed 121:259–262CrossRefGoogle Scholar
  14. Kobayashi T (1981) The wild and cultivated species in the genus Sesamum. Sesame: status and improvement. Proceeding of Expert Consultation, Rome, pp 8–12Google Scholar
  15. Kumar V, Sharma SN (2011) Comparative potential of phenotypic, ISSR and SSR markers for characterization of sesame (Sesamum indicum L.) varieties from India. J Crop Sci Biotechnol 14:163–171CrossRefGoogle Scholar
  16. Laurentin H, Karlovsky P (2006) Genetic relationship and diversity in a sesame (Sesamum indicum L.) germplasmcollection using amplified fragment length polymorphism. BMC Genet 7:10PubMedCrossRefPubMedCentralGoogle Scholar
  17. Nyongesa BO, Were BA, Gudu S, Dangasuk OG, Onkware AO (2013) Genetic diversity in cultivated sesame (Sesamum indicum L.) and related wild species in East Africa. J Crop Sci Biotechnol 16(1):9–15CrossRefGoogle Scholar
  18. Parsaeian M, Mirlohi A, Saeidi G (2011) Study of genetic variation in sesame (Sesamum indicum L.) using agro-morphological traits and ISSR markers. Genetica 47:359–367Google Scholar
  19. Paterson AH, Brubaker CL, Wendel JF (1993) A rapid method for extraction of Cotton (Gossypium spp) genomic DNA suitable for RFLP or PCR analysis. Plant Mol Biol Rep 11:122–127CrossRefGoogle Scholar
  20. Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Science Publishers, Montpellier, pp 43–76Google Scholar
  21. Pham TD, Geleta M, Bui TM, Bui TC, Merker A, Carlsson AS (2011) Comparative analysis of genetic diversity of sesame (Sesamum indicum L.) from Vietnam and Cambodia using agro-morphological and molecular markers. Hereditas 148:28–35PubMedCrossRefGoogle Scholar
  22. Rohlf FJ (2000) NTSYS-pc: numerical taxonomy and multivariable analysis system. State university of New York, stony brooks, NYGoogle Scholar
  23. Sharma SN, Kumar V, Mathur S (2009) Comparativeanalysis of RAPD and ISSR markers for characterization of sesame (Sesamum indicum L.) genotypes. J Plant Biochem Biotechnol 18:37–43CrossRefGoogle Scholar
  24. Spandana B, Prathap Reddy V, John Prasanna G, Anuradha G, Sivaramakrishnan S (2012) Development and characterization of microsatellite markers (SSR) in sesamum (Sesamum indicum L.) species. Appl Biochem Biotechnol 168:1594–1607PubMedCrossRefGoogle Scholar
  25. Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138PubMedCrossRefPubMedCentralGoogle Scholar
  26. Wei LB, Zhang HY, Zheng YZ, Guzo WZ, Zhang TZ (2008) Development and utilization of EST-derived microsatellites in sesame (Sesamum indicum L.). Acta Agronomica Sinica 34:2077–2084CrossRefGoogle Scholar
  27. Yeh FC, Yan R, Boyle T (1999) A Microsoft Windows based freeware for population genetic analysis. Version 1.31, University of Alberta, CanadaGoogle Scholar
  28. Yue WD, Wei LB, Zhang TD (2012) Genetic diversity and population structure of germplasm resources in sesame (Sesamum indicum L.) by SSR markers. Acta Agronomica Sinica 38(12):2286–2296CrossRefGoogle Scholar
  29. Zhang XR, Chen KR, Peng J, Xu ZY (2004) The RAPD analysis and genetic diversity of selected sesame germplasm. Chin J Oil Crop Sci 26:34–37Google Scholar
  30. Zhang Y, Zhang X, Hua W (2010) Analysis of genetic diversity among indigenous landraces from sesame (Sesamum indicum L.) core collection in China as revealed by SRAP and SSR markers. Genes Genomics 32(3):207–215CrossRefGoogle Scholar
  31. Zhang YX, Sun J, Zhang XR, Wang L, Che Z (2011) Analysis on genetic diversity and genetic basis of the main sesame cultivars released in china. Agricultural Sciences in China 10(4):509–518CrossRefGoogle Scholar
  32. Zhang H, Wei L, Miao H, Zhang T, Wang C (2012a) Development and validation of genic-SSR markers in sesame by RNA-seq. BMC Genom 13:316CrossRefGoogle Scholar
  33. Zhang Y, Zhang X, Che Z (2012b) Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection. BMC Genet 13(1):102PubMedCrossRefPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Malathi Surapaneni
    • 1
  • Vijay Yepuri
    • 1
  • Lakshminarayana R. Vemireddy
    • 1
  • Anuradha Ghanta
    • 1
  • E. A. Siddiq
    • 1
  1. 1.Institute of BiotechnologyANGRAURajendranagar, HyderabadIndia

Personalised recommendations