Advertisement

Journal of Crop Science and Biotechnology

, Volume 21, Issue 1, pp 43–55 | Cite as

Comparative Germplasm Characterization of Maize (Zea mays L.) in Rajouri Region of Pir Panjal Himalaya J & K (India), based on Morphological and ISSR Markers

  • Tanvir H. Dar
  • Rubiada Shakeel
  • Shusheel Verma
Research Article
  • 60 Downloads

Abstract

The present study provides an assessment of genetic variability and relationship within and between different cultivars of maize grown across the Rajouri region of the Pir Panjal Himalaya, utilizing morphological and ISSR markers. Morphological descriptors showed significant diversity among cultivars; on morphological cluster analysis, the cultivars 9 and 7 were more related, while cultivars 10 and 3 were distinct. Fifty accessions (5 from each cultivar) were characterized using a DNA-based molecular marker, ISSR. In all, 108 amplification products were generated with 17 ISSR primers, 6.35 fragments with an average \per primer. Out of these, 83 were found to be polymorphic with an overall percentage polymorphism of 75.2%. Total genetic diversity (Ht) and the mean genetic diversity estimated within populations (HS) was 0.2613 and 0.0803, respectively. Gene flow (Nm) and Coefficient of gene differentiation (Gst) among the cultivars was 0.2220 and 0.6926, respectively. Nei’s genetic diversity index (H) and (I) were the lowest for cultivar 10 (H = 0.037; I = 0.056) and the highest for cultivar 8 (H = 0.121; I = 0.176). Analysis of molecular variance revealed 35% within group and 65% among group genetic diversity. Based on cluster analysis, cultivar 10 appeared distinct from rest of the cultivars. The high genetic diversity detected in the present study can be utilized in maize breeding programs, wherein the elite genotypes could be crossed with the existing cultivars to form novel gene and trait combinations.

Key words

Genetic diversity morphological descriptors ISSR markers maize germplasm 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Agarwal M, Shrivastava N, Padh, H. 2008. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 27: 617–631CrossRefPubMedGoogle Scholar
  2. Babic M, Babic V, Prodanovic S, Filipovic M, Andelkovic V. 2012. Comparison of morphological and molecular genetic distances of maize inbreds. Genetica 44: 119–128Google Scholar
  3. Beyene T, Botha AM, Myburg, AA. 2005a. Phenotypic diversity for morphological and agronomic traits in traditional Ethiopian highland maize accessions. South Afr. J. Plant Soil 22: 100–105CrossRefGoogle Scholar
  4. Beyene Y, Botha AM, Myburg AA. 2005b. A comparative study of molecular and morphological methods of describing genetic relationships in traditional Ethiopian highland maize. Afr. J. Biotech. 4: 586–595Google Scholar
  5. Bracco M, Lia VV, Gottlieb AM, Hernández JC, Poggio L. 2009. Genetic diversity in maize landraces from indigenous settlements of Northeastern Argentina. Genetica 135: 39–49CrossRefPubMedGoogle Scholar
  6. Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C. 2006. Uneven chromosome contraction and expansion in the maize genome. Genome Res. 16: 1241–1251CrossRefPubMedPubMedCentralGoogle Scholar
  7. Camus-Kulandaivelu L, Veyrieras JB, Madur D, Combes V, Fourmann M, Barraud S, Dubreuil P, Gouesnard B, Manicacci D, Charcosset A. 2006. Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf gene. Genetics 172: 2449–2463CrossRefPubMedPubMedCentralGoogle Scholar
  8. Carvalho VP, Ruas PM, Ruas CF, Ferreira JM, Moreira RM. 2002. Assessment of genetic diversity in maize (Zea mays L.) landraces using inter simple sequence repeat (ISSR) markers. Crop Breed. Appl. Biotechnol. 2: 557–568CrossRefGoogle Scholar
  9. CIMMYT 2005. Laboratory protocols: CIMMYT Applied Molecular Genetics Laboratory. Third Ed. Mexico, D.F. CIMMYTGoogle Scholar
  10. Dar TH, Raina SN, Goel S. 2013. Molecular analysis of genomic changes in synthetic autotetraploid Phlox drummondii Hook. Biol. J. Linn. Soc. 110: 591–605CrossRefGoogle Scholar
  11. Dar TH, Raina SN, Goel S. 2017. Cytogenetic and molecular evidences revealing genomic changes after autopolyploidization: A case study of synthetic autotetraploid Phlox drummondii Hook. Physiol. Mol. Biol. Plants 23: 641–650CrossRefPubMedGoogle Scholar
  12. Dubreuil P, Dufour P, Krejci E, Causse M, De VD, Gallais A, Charcosset A. 1996. Organization of RFLP diversity among inbred lines of maize representing the most significant heterotic groups. Crop Sci. 36: 790–799CrossRefGoogle Scholar
  13. Endler JA. 1977. Geographic variation, speciation, and clines (No. 10). Princeton University Press. Princeton, NJGoogle Scholar
  14. FAOSTAT 2010. Statistical databases and data-sets of the Food and Agriculture Organization of the United Nations (http://faostat.fao.org/default.aspx)Google Scholar
  15. Gauthier P, Gouesnard B, Dallard J, Redaelli R, Rebourg C, Charcosset A, Boyat, A. 2002. RFLP diversity and relationships among traditional European maize populations. Theor. Appl. Genet. 105: 91–99CrossRefPubMedGoogle Scholar
  16. Godwin ID, Aitken EA, Smith LW. 1997. Application of inter simple sequence repeat (ISSR) markers to plant genetics. Electrophoresis 18: 1524–1528CrossRefPubMedGoogle Scholar
  17. Hoxha S, Shariflou MR, Sharp P. 2004. Evaluation of genetic diversity in Albanian maize using SSR markers. Maydica 49: 97–104Google Scholar
  18. Idris AE, Hamza NB, Yagoub SO, Ibrahim AI, El-Amin HK. 2012. Maize (Zea mays L.) Genotypes diversity study by utilization of inter-simple sequence repeat (ISSR) markers. Aust. J. Bas. Appl. Sci. 6: 42–47Google Scholar
  19. Joshi PK, Singh NP, Singh NN, Gerpacio RV, Pingali PL. 2005. Maize in India: Production systems, constraints, and research priorities. Mexico, D.E.CIMMYTGoogle Scholar
  20. Kantety RV, Zeng X, Bennetzen J, Zehr BE. 1995. Assessment of genetic diversity in dent and popcorn (Zea mays L.) inbred lines using inter-simple sequence repeat (ISSR) amplification. Mol. Breed. 1: 365–373CrossRefGoogle Scholar
  21. Kashiani P, Saleh G, Panandam JM, Abdullah NAP, Selamat A. 2012. Molecular characterization of tropical sweet corn inbred lines using microsatellite markers. Maydica 57: 154–163Google Scholar
  22. Kumar A, Bennetzen JL. 2000. Retrotransposons: central players in the structure, evolution and function of plant genomes. Trends Plant. Sci. 5: 509–510CrossRefPubMedGoogle Scholar
  23. Leal AA, Mangolin CA, Amaral Júnior AT, Gonçalves LSA, Scapim CA, Mott AS, Eloi IBO, Cordoves V, Da Silva MFP. 2010. Efficiency of RAPD versus SSR markers for determining genetic diversity among popcorn lines. Genet. Mol. Res. 9: 9–18CrossRefPubMedGoogle Scholar
  24. Lenka D, Tripathy SK, Kumar R, Behera M, Ranjan R. 2015. Assessment of genetic diversity in quality protein maize (QPM) inbreds using ISSR markers. J. Environ. Biol. 36: 985–992Google Scholar
  25. Liu K, Goodman M, Muse S, Smith JS, Buckler E, Doebley J. 2003. Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165: 2117–2128PubMedPubMedCentralGoogle Scholar
  26. Louette D, Smale M. 1996. Genetic diversity and maize seed management in a traditional Mexican community: Implications for in situ conservation of maizeGoogle Scholar
  27. McDermott JM, McDonald BA. 1993. Gene flow in plant pathosystems. Ann. Rev. Phytopath. 31: 353–373CrossRefGoogle Scholar
  28. Mohammadi SA, Prasanna BM. 2003. Analysis of genetic diversity in crop plants—salient statistical tools and considerations. Crop Sci. 43: 1235–1248CrossRefGoogle Scholar
  29. Morgante M, Olivieri AM. 1993. PCR amplified microsatellites as markers in plant genetics. Plant J. 3: 175–182CrossRefPubMedGoogle Scholar
  30. Munhoz REF, Prioli AJ, Amaral Júnior AT, Scapim CA, Simon GA. 2009. Genetic distances between popcorn populations based on molecular markers and correlations with heterosis estimates made by diallel analysis of hybrids. Genet. Mol. Res. 8: 951–96CrossRefPubMedGoogle Scholar
  31. Nagy E, Gyulai G, Szabo Z, Hegyi Z, Marton LC. 2003. Application of morphological descriptions and genetic markers to analyse polymorphism and genetic relationships in maize (Zea mays L.). Acta Agro. Hung. 51: 257–265CrossRefGoogle Scholar
  32. Nass LL, Pellicano IJ, Valois ACC. 1993. Utilization of genetic resources for maize and soybean breeding in Brazil. Braz. J. Genet. 16: 983–988Google Scholar
  33. Nei M. 1973. Analysis of gene diversity in subdivided populations. Proc. Nat. Acad. Sci. USA. 70: 3321–3323CrossRefPubMedPubMedCentralGoogle Scholar
  34. Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583–590PubMedPubMedCentralGoogle Scholar
  35. Oliveira EC, Amaral Júnior AT, Gonçalves LSA, Pena GF, Freitas Júnior SP, Ribeiro RM, Pereira MG. 2010 Optimizing the efficiency of the touchdown technique for detecting inter-simple sequence repeat markers in corn (Zea mays). Genet. Mol. Res. 9: 835–842CrossRefGoogle Scholar
  36. Ortiz R, Crossa J, Franco J, Sevilla R, Burgueno J. 2008. Classification of Peruvian highland maize races using plant traits. Genet. Res. Crop Evol. 55: 151–162CrossRefGoogle Scholar
  37. Peakall PE, Smouse R. 2012. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research —an update. Bioinformatics 28: 2537–2539PubMedGoogle Scholar
  38. Perrier X, Jacquemond-Collet JP. 2006. DARwin softwareGoogle Scholar
  39. Prasanna BM, Sharma L. 2005. The landraces of maize (Zea mays L.): diversity and utility. Ind. J. Plant Genet. Res. 18: 155–168Google Scholar
  40. Prasanna BM. 2010. Phenotypic and molecular diversity of maize landraces: characterization and utilization. Ind. J. Genet. Plant Breed. 70: 315–327Google Scholar
  41. Prasanna BM, Pixley K, Warburton ML, Xie CX. 2010. Molecular marker-assisted breeding options for maize improvement in Asia. Mol. Breed. 26: 339–356CrossRefGoogle Scholar
  42. Prasanna BM. 2012. Diversity in global maize germplasm: Characterization and utilization. J. Biosci. 37: 843–855CrossRefGoogle Scholar
  43. Raina SN, Jain S, Sehgal D, Kumar A, Dar TH, Bhat V, Pandey V, Vaishnavi S, Bhargav A, Singh V, Rani V. 2012. Diversity and relationships of multipurpose seabuckthorn (Hippophae L.) germplasm from the Indian Himalayas as assessed by AFLP and SAMPL markers. Genet. Res. Crop. Evol. 59: 1033–1053CrossRefGoogle Scholar
  44. Rebaa F, Abid G, Aouida M, Abdelkarim S, Aroua I, Muhovski Y, Baudoin JP, M’hamdi M, Sassi K, Moez J. 2017. Genetic variability in Tunisian populations of faba bean (Vicia faba L. var. major) assessed by morphological and SSR markers. Physiol. Mol. Biol. Plants DOI 10.1007/s12298-017-0419-xGoogle Scholar
  45. 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: 895–903CrossRefPubMedGoogle Scholar
  46. Reddy MP, Sarla N, Siddiq EA. 2002. Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128: 9–17CrossRefGoogle Scholar
  47. Rogers SO, Bendich AJ. 1994. Extraction of total cellular DNA from plants, algae and fungi. In Plant Molecular Biology Manual, Springer Netherlands, pp 183–190CrossRefGoogle Scholar
  48. Sanchez JJ, Goodman MM, Stuber CW. 2000. Isozymatic and morphological diversity in the races of maize in Mexico. Eco. Bot. 54: 43–59CrossRefGoogle Scholar
  49. Schulman AH. 2007. Molecular markers to assess genetic diversity. Euphytica 158: 313–321CrossRefGoogle Scholar
  50. Sehgal D, Rajpal, VR, Raina SN, Sasanuma T, Sasakuma T. 2009. Assaying polymorphism at DNA level for genetic diversity diagnostics of the safflower (Carthamus tinctorius L.) world germplasm resources. Genetica 135: 457–470CrossRefPubMedGoogle Scholar
  51. Senior ML, Murphy JP, Goodman MM, Stuber CW. 1998. Utility of SSRs for determining genetic similarities an relationships in maize using an agarose gel system. Crop Sci. 38: 1088–1098CrossRefGoogle Scholar
  52. Sharma L, Prasanna BM, Ramesh B. 2010. Analysis of phenotypic and microsatellite-based diversity of maize landraces in India, especially from the North East Himalayan region. Genetica 138: 619–631CrossRefPubMedGoogle Scholar
  53. Singh B. 1977. Races of maize in India. Indian Council of Agricultural Research, New DelhiGoogle Scholar
  54. Song R, Messing J. 2003. Gene expression of a gene family in maize based on noncollinear haplotypes. Proc. Nat. Acad. Sci. USA. 100: 9055–9060CrossRefPubMedPubMedCentralGoogle Scholar
  55. Van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, Gonzalez JDJS, Ross-Ibarra J. 2011. Genetic signals of origin, spread, and introgression in a large sample of maize landraces. Proc. Nat. Acad. Sci. USA. 108: 1088–1092CrossRefPubMedGoogle Scholar
  56. Vigouroux Y, Glaubitz JC, Matsuoka Y, Goodman MM, Sánchez J, Doebley J. 2008. Population structure and genetic diversity of New World maize races assessed by DNA microsatellites. Amer. J. Bot. 95: 1240–1253CrossRefGoogle Scholar
  57. Vivodik M, Balazova Z, Galova Z, Hlozakova TK. 2015. Genetic diversity of maize (Zea mays) accessions revealed by random amplified polymorphic DNA markers. Hort. Biotech. Res. 1: 30–34Google Scholar
  58. Warburton ML, Wilkes G, Taba S, Charcosset A, Mir C, Dumas F, Madur D, Dreisigacker S, Bedoya C, Prasanna BM, Xie CX. 2011. Gene flow among different teosinte taxa and into the domesticated maize gene pool. Genet. Res. Crop. Evol. 58: 1243–1261CrossRefGoogle Scholar
  59. Wasala SK, Prasanna BM. 2013. Microsatellite marker-based diversity and population genetic analysis of selected lowland and mid-altitude maize landrace accessions of India. J. Plant. Biochem. Biotech. 22: 392–400CrossRefGoogle Scholar
  60. Weir BS. 1996. Genetic data analysis. Methods for discrete population genetic data. Sinauer Associates, Inc. PublishersGoogle Scholar
  61. Xiang K, Zhang ZM, Reid LM, Zhu XY, Yuan GS, Pan, GT. l2010. A meta-analysis of QTL associated with ear rot resistance in maize. Maydica 55, p 281Google Scholar
  62. Yadav OP. 2015. Annual Maize workshop PAU Ludhiana, 4-6 April, 2015Google Scholar
  63. Yadav VK, Singh IS. 2010. Comparative evaluation of maize inbred lines (Zea mays L.) according to dus testing using morphological, physiological and molecular markers. Agri. Sci. 1: 131–142Google Scholar
  64. Yeh FC, Yang RC, Boyle TBJ, Ye ZH, Mao JX. 1997. POPGENE, version 1.2, Molecular Biology and Biotechnology Centre, University of Alberta, EdmontonGoogle Scholar
  65. Yuan Q, Hill J, Hsiao J, Moffat K, Ouyang S, Cheng Z, Jiang J, Buell C. 2002. Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion. Mol. Genet. Genom. 267: 713–720CrossRefGoogle Scholar

Copyright information

© Korean Society of Crop Science and Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Tanvir H. Dar
    • 1
  • Rubiada Shakeel
    • 1
  • Shusheel Verma
    • 1
  1. 1.School of Biosciences & BiotechnologyBaba Ghulam Shah Badshah UniversityRajouriIndia

Personalised recommendations