Skip to main content

Microsatellite marker-based diversity and population genetic analysis of selected lowland and mid-altitude maize landrace accessions of India

Abstract

Maize (Zea mays L.) harbours significant genetic diversity not only in its centre of origin (Mexico) but also in several countries worldwide, including India, in the form of landraces. In this study, DNA fingerprinting of 48 landrace accessions from diverse regions of India was undertaken using 42 fluorescent dye-labeled Simple Sequence Repeat (SSR) markers, followed by allele resolution using DNA sequencer and analysis of molecular diversity within and among these landraces. The study revealed a large number of alleles (550), with high mean number of alleles per locus (13.1), and Polymorphism Information Content (PIC) of 0.60, reflecting the level of diversity in the landrace accessions. Besides identification of 174 unique alleles in 44 accessions, six highly frequent SSR alleles were detected at six loci (phi014, phi090, phi112, umc1367, phi062 and umc1266) with individual frequencies greater than 0.75, indicating that chromosomal regions harboring these SSR alleles are not selectively neutral. F statistics revealed very high genetic differentiation, population subdivision and varying levels of inbreeding in the landraces. Analysis of Molecular Variance showed that 63 % of the total variation in the accessions could be attributed to within-population diversity, and 37 % represented between population diversity. Cluster analysis of SSR data using Nei’s genetic distance and UPGMA revealed considerable genetic diversity in these populations, although no clear separation of accessions was observed based on their geographic origin.

This is a preview of subscription content, access via your institution.

Fig. 1

Abbreviations

PIC:

Polymorphism Information Content

AMOVA:

Analysis of Molecular Variance

UPGMA:

Unweighted Pair Group Method using Arithmetic means

H o :

Observed heterozygosity

H e :

Expected heterozygosity

F :

Inbreeding coefficient

A :

Number of alleles per locus

A e :

Effective number of alleles

GD:

Genetic distances

SSR:

Simple sequence repeat

SNP:

Single nucleotide polymorphism

References

  1. Berg EE, Hamrick JL (1997) Quantification of genetic diversity at allozyme loci. Can J Forest Res 27:415–424

    Article  CAS  Google Scholar 

  2. Daniels J, Holmans P, Williams N, Turic D, McGuffin P, Plomin R, Owen MJ (1998) A simple method for analyzing microsatellite allele image patterns generated from DNA pools and its application to allelic association studies. Am J Hum Genet 62:1189–1197

    PubMed  Article  CAS  Google Scholar 

  3. R Development Core Team (2005) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (http://www.R-project.org)

  4. Dubreuil P, Warburton M, Chastanet M, Hoisington D, Charcosset A (2006) More on the introduction of temperate maize into Europe: large-scale bulk SSR genotyping and new historical elements. Maydica 51:281–291

    Google Scholar 

  5. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379

    PubMed  Article  CAS  Google Scholar 

  6. Eschholz TW, Peter R, Stamp P, Hund A (2008) Genetic diversity of Swiss maize assessed with individuals and bulks on agarose gels. Genet Resour Crop Evol 55:971–983

    Article  Google Scholar 

  7. Excoffier L, Laval G, Schneider S (2005) Arlequin version 3.1: an integrated software package for population genetics data analysis. Evol Bioinformatics Online 1:47–50

    CAS  Google Scholar 

  8. Gomez OJ, Matthew W, Blair P, Bodil E, Frankow-Lindberg C, Urban G (2004) Molecular and phenotypic diversity of common bean landraces from Nicaragua. Crop Sci 44:1412–1418

    Article  CAS  Google Scholar 

  9. Henderson ST, Petes TD (1992) Instability of simple sequence DNA in Saccharomyces cerevisiae. Mol Cell Biol 12:2749–2757

    PubMed  CAS  Google Scholar 

  10. Joshi PK, Singh NP, Singh NN, Gerpacio RV, Pingali PL (2005) Maize in India: production system. Constraints and Research Priorities, CIMMYT, Mexico DF

    Google Scholar 

  11. Kimura M, Crow JR (1964) The number of alleles that can be maintained in a finite population. Genetics 49:725–738

    PubMed  CAS  Google Scholar 

  12. LeDuc C, Miller P, Lichell J, Parry P (1995) Batched analysis of genotypes. PCR Methods Appl 4:331–336

    PubMed  Article  CAS  Google Scholar 

  13. Liu K, Muse SV (2005) PowerMarker: an integrated analysis of environment for genetic marker analysis. Bioinformatics 21:2128–2129

    PubMed  Article  CAS  Google Scholar 

  14. Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez GJ, Buckler E, Doebley JA (2002) Single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci USA 99:6080–6084

    PubMed  Article  CAS  Google Scholar 

  15. Nass LL, Pellicano IT, Valois ACC (1993) Utilization of genetic resources for maize and soybean breeding in Brazil. Brazilian J Genet 16:983–988

    Google Scholar 

  16. Nei M (1972) Genetic distance between populations. Am Natur 106:283–292

    Article  Google Scholar 

  17. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358

    PubMed  CAS  Google Scholar 

  18. Perlin MW, Lancia G, Ng SK (1995) Towards fully automated genotyping: genotyping microstatellite markers by deconvolution. Am J Hum Genet 57:1199–1210

    PubMed  CAS  Google Scholar 

  19. Prasanna BM (2010) Phenotypic and molecular diversity of maize landraces: characterization and utilization. Indian J Genet 70:315–327

    Google Scholar 

  20. Prasanna BM (2012) Diversity in global maize germplasm and novel initiatives for characterization and utilization. J Biosci 34 (In Press)

  21. Prasanna BM, Sharma L (2005) The landraces of maize (Zea mays L.): diversity and utility. Indian J Plant Genet Resour 18:155–168

    Google Scholar 

  22. Prasanna BM, Vasal SK, Kassahun B, Singh NN (2001) Quality protein maize. Curr Sci 81:1308–1319

    CAS  Google Scholar 

  23. Prasanna BM, Pixley K, Warburton ML, Xie CX (2010) Molecular marker-assisted breeding options for maize improvement in Asia. Mol Breed 26:339–356

    Article  CAS  Google Scholar 

  24. Pressoir G, Berthaud J (2004) Patterns of population structure in maize landraces from the Central Valleys of Oaxaca in Mexico. Heredity 92:88–94

    PubMed  Article  CAS  Google Scholar 

  25. Qi-Lun Y, Ping F, Ke-Cheng K, Guang-Tang P (2008) Genetic diversity based on SSR markers in maize (Zea mays L.) landraces from Wuling mountain region in China. J Genet 87:287–291

    PubMed  Article  Google Scholar 

  26. Rebourg C, Gousnard B, Charcosset A (2001) Large scale molecular analysis of traditional European maize populations: relationships with morphological variation. Heredity 86:574–587

    PubMed  Article  CAS  Google Scholar 

  27. Rebourg C, Chastanet M, Gouesnard B, Welcker C, Dubreuil P, Charcosset A (2003) Maize introduction into Europe: the history reviewed in the light of molecular data. Theor Appl Genet 106:895–903

    PubMed  CAS  Google Scholar 

  28. Reif JC, Xia XM, Melchinger AE, Warburton ML, Hoisington D, Beck D, Frisch M (2004) Genetic diversity determined within and among CIMMYT maize populations of tropical sub tropical and temperate germplasm by SSR markers. Crop Sci 44:326–334

    Article  CAS  Google Scholar 

  29. Ribaut J-M, Hoisington DA, Deutsch JA, Jiang C, Gonzalez-de-Leon D (1996) Identification of quantitative trait loci under drought conditions in tropical maize: 1. Flowering parameters and the anthesis-silking interval. Theor Appl Genet 92:905–914

    Article  CAS  Google Scholar 

  30. Sharma L, Prasanna BM, Ramesh B (2010) Phenotypic and microsatellite-based diversity and population genetic structure of maize landraces in India, especially from the North East Himalayan region. Genetica 138:619–631

    PubMed  Article  CAS  Google Scholar 

  31. Singh B (1977) Races of maize in India. Indian Council of Agricultural Research (ICAR), New Delhi

    Google Scholar 

  32. Warburton ML, Xianchun X, Franco J, Melchinger AE, Frisch M, Bohn M, Hoisington D (2002) Genetic characterization of CIMMYT inbred maize lines and open pollinated populations using large scale fingerprinting methods. Crop Sci 42:1832–1840

    Article  Google Scholar 

  33. Warburton ML, Wilkes G, Taba S, Charcosset A, Mir C, Bedoya C, Prasanna BM, Xie CX, Hearne SH, Franco J (2011) Gene flow between different teosinte species and into the domesticated maize gene pool. Genetic Resour Crop Evol 58:1243–1261

    Article  Google Scholar 

  34. Yeh FC, Yang RC, Boyle TBJ, Ye ZH, Mao JX (1997) POPGENE, version 1.2, Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton

Download references

Acknowledgements

The study was undertaken as a part of the ICAR National Fellow Project (2005–2010) awarded to BMP. The authors thank the Division of Germplasm Conservation, NBPGR, New Delhi (especially Dr Kalyani Srinivasan) for providing seed material of some landrace accessions used in this study.

Author information

Affiliations

Authors

Corresponding author

Correspondence to B. M. Prasanna.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Wasala, S.K., Prasanna, B.M. Microsatellite marker-based diversity and population genetic analysis of selected lowland and mid-altitude maize landrace accessions of India. J. Plant Biochem. Biotechnol. 22, 392–400 (2013). https://doi.org/10.1007/s13562-012-0167-5

Download citation

Keywords

  • Genetic diversity
  • India
  • Landraces
  • Population structure
  • Zea mays L