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Journal of Crop Science and Biotechnology

, Volume 21, Issue 5, pp 469–481 | Cite as

SPAR Markers-Assisted Assessment of Genetic Diversity and Population Structure in Finger Millet (Eleusine Coracana (L.) Gaertn) Mini-Core Collection

  • Subramani Pandian
  • Karuppasamy Marichelvam
  • Lakkakula Satish
  • Stanislaus Antony Ceasar
  • Shunmugiah Karutha Pandian
  • Manikandan RameshEmail author
Research Article
  • 22 Downloads

Abstract

Finger millet is an important staple food crop of semi-arid tropics also known as “super cereal” and has a higher calcium content than any other crops. Thousands of germplasm are being maintained and its genetic characterization is essential for further utilization in crop improvement. This research was performed to estimate the diversity and population genetic structure in the mini-core collection of finger millet by using SPAR markers, namely RAPD, ISSR, and DAMD markers. Altogether, 32 primers were used in this study, which produced 408 bands among which 344 were polymorphic. Analysis by combining all three marker systems revealed 84.31% of polymorphism among 90 genotypes of finger millet. Average polymorphism information content (PIC) produced by the ISSR, RAPD, and DAMD markers were 0.79, 0.81, 0.62, and average Rp values were 12.84, 8.17, and 8.53, respectively. The Jaccard's similarity value ranged from 0.233-0.861. IE 6059 and IE 5870 genotypes showed the highest Jaccard's similarity value of 0.861 in UPGMA analysis. Neighbor joining-based phylogenetic analysis produced two major clusters and the genotypes were grouped based on their geographical region of origin. Principal component analysis and principal coordinates analysis also confirmed the results. In population STRUCTURE analysis, the genotypes were divided into two subpopulations (P1and P2). These results confirmed that the genotypes we have assessed were genetically diverse and were clustered based on their geographic region of origin. The information obtained from this study will be useful in population management strategies and selection of genotypes for an effective breeding program in the future.

Key words

Finger millet genetic diversity molecular markers marker-assisted breeding population structure 

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References

  1. Aruna C, Priya AR, Neeraja CN, Patil JV, Visarada KB. 2012. Diversity analysis using ISSR markers for resistance to shoot pests in sorghum. Crop Prot. 35: 110–7CrossRefGoogle Scholar
  2. Arya L, Verma M, Gupta VK, Seetharam A. 2013. Use of genomic and genic SSR markers for assessing genetic diversity and population structure in Indian and African finger millet (Eleusine coracana (L.) Gaertn.) germplasm. Plant Syst. Evol. 299: 1395–1401CrossRefGoogle Scholar
  3. Ayres DR, Ryan FJ. 1999. Genetic diversity and structure of the narrow endemic Wyethia reticulata and its congener W. bolanderi (Asteraceae) using RAPD and allozyme techniques. Am. J. Bot. 86: 344–353CrossRefGoogle Scholar
  4. Babu BK, Dinesh P, Agrawal PK, Sood S, Chandrashekara C, Bhatt JC, Kumar A. 2014. Comparative genomics and association mapping approaches for blast resistant genes in finger millet using SSRs. PLoS One. 10: 9(6): e99182CrossRefGoogle Scholar
  5. Babu B, Senthil N, Gomez S, Biji K, Rajendraprasad N, Kumar S, Babu R. 2007. Assessment of genetic diversity among finger millet (Eleusine coracana (L) Gaertn) accessions using molecular markers. Genet. Resour. Crop Evol. 54: 399–404CrossRefGoogle Scholar
  6. Bhatt D, Negi M, Sharma P, Saxena SC, Dobriyal AK, Arora S. 2011. Responses to drought induced oxidative stress in five finger millet varieties differing in their geographical distribution. Physiol. Mol. Biol. Plants 17: 347–353.CrossRefGoogle Scholar
  7. Botstein D, White RL, Skolnick M, Davis RW. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Amer. J. Hum. Genet. 32: 314–331Google Scholar
  8. Comino C, Pignata G, Portis E, Dolzhenko Y, Casale M, Nicola S. 2015. Selection in Artemisia umbelliformis Lam. Piedmont ecotypes to improve cultivation in alpine environment. Genet. Resour. Crop Evol. 62: 567–577CrossRefGoogle Scholar
  9. Das S, Mishra RC, Rout GR, Aparajita S. 2007. Genetic variability and relationships among thirty genotypes of finger millet (Eleusine coracana L. Gaertn.) using RAPD markers. Zeitschrift fur Naturforschung. C. 62: 116–122CrossRefGoogle Scholar
  10. Dida MM, Srinivasachary, Ramakrishnan S, Bennetzen JL, Gale MD, Devos KM. 2007. The genetic map of finger millet, Eleusine coracana. Theor. Appl. Genet. 114: 321–332CrossRefGoogle Scholar
  11. Dida MM, Wanyera N, Dunn MLH, Bennetzen JL, Devos KM. 2008. Population structure and diversity in finger millet Eleusine coracana germplasm. Trop. Plant. Biol. 1: 131–141CrossRefGoogle Scholar
  12. Doyle JJ, Doyle JL. 1990. Isolation of plant DNA from fresh tissue. Focus 12: 13–15Google Scholar
  13. Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611–2620CrossRefGoogle Scholar
  14. Fakrudin B, Shashidhar HE, Kulkarni RS, Hittalmani S. 2004. Genetic diversity assessment of finger millet, (Eleusine coracana (Gaertn.), germplasm through RAPD analysis. PGR Newslett. 138: 50–54Google Scholar
  15. Frankham, R. 2003. Genetics and conservation biology. C. R. Biol. 326: 22–29CrossRefGoogle Scholar
  16. Gupta R, Verma K, Joshi DC, Yadav D, Singh M. 2010. Assessment of Genetic Relatedness among Three Varieties of Finger Millet with Variable Seed Coat Color Using RAPD and ISSR Markers. Genet. Eng. Biotechnol. J. 2: 19Google Scholar
  17. Gupta S, Kumari K, Muthamilarasan M, Parida SK, Prasad M. 2014. Population structure and association mapping of yield contributing agronomic traits in foxtail millet. Plant Cell Rep. 33: 881–893CrossRefGoogle Scholar
  18. Hammer Ø, Harper DAT, Ryan PD. 2001. PAST: paleontological statistics software package for education and data analysis. Palaeontol. Electron. 4: 9Google Scholar
  19. Hema R, Vemanna RS, Sreeramulu S, Reddy CP, Senthil–Kumar M, Udayakumar M. 2014. Stable expression of mtlD gene imparts multiple stress tolerance in finger millet. PLoS One 9: e99110CrossRefGoogle Scholar
  20. Hilu KW, De Wet JM. 1976. Domestication of Eleusine coracana. Econ. Bot. 30: 199–208CrossRefGoogle Scholar
  21. Hilu KW. 1995. Evolution of finger millet: evidence from random amplified polymorphic DNA. Genome. 38: 232–8CrossRefGoogle Scholar
  22. Kumar A, Babu BK, Yadav S, Agrawal PK. 2016a. Allele mining for resistance gene analogs (RGAs) in crop plants: A special emphasis on blast resistance in finger millet (Eleusine coracana L.). Indian J. Genet. Plant Breed. 76: 1–9CrossRefGoogle Scholar
  23. Kumar H, Priya P, Singh N, Kumar M, Choudhary BK, Kumar L, Singh IS, Kumar N. 2016b. RAPD and ISSR marker–based comparative evaluation of genetic diversity among indian germplasms of euryale ferox: an aquatic food plant. App. Biochem. Biotechnol. 180: 1345–1360CrossRefGoogle Scholar
  24. Lande R. 1988. Genetics and demography in biological conservation. Science 241: 1455–1460.CrossRefGoogle Scholar
  25. Latha MA, Venkateswara Rao K, Dashavantha Reddy V. 2005. Production of transgenic plants resistant to leaf blast disease in finger millet (Eleusine coracana (L.) Gaertn.) Plant Sci. 169: 657–667Google Scholar
  26. Laurentin H. 2009. Data analysis for molecular characterization of plant genetic resources. Genet. Resour. Crop Evol. 56: 277–292CrossRefGoogle Scholar
  27. Liu Q, Jiang B, Wen J, Peterson PM. 2014. Low–copy nuclear gene and McGISH resolves polyploidy history of Eleusine coracana and morphological character evolution in Eleusine. Turk. J. Bot. 38: 1–12CrossRefGoogle Scholar
  28. Liu WL, Shih HC, Weng IS, Ko YZ, Tsai CC, Chou CH, Chiang YC. 2016. Characterization of genomic inheritance of intergeneric hybrids between Ascocenda and Phalaenopsis cultivars by GISH, PCR–RFLP and RFLP. PloS One 11: e0153512CrossRefGoogle Scholar
  29. Pandian S, Sivasankar C, Muthuramalingam P, Ramesh M. 2017. An amazing nutritional value in wonderful finger millet makes this “The Most Lovable Food Crop” to the world. Sci. J. Food Sc. Nutr. 3: 034–036Google Scholar
  30. Pandian S, Satish L, Rameshkumar R, Muthuramalingam P, Rency AS, Rathinapriya P, Ramesh M. 2018. Analysis of population structure and genetic diversity in an exotic germplasm collection of Eleusine coracana (L.) Gaertn. using genic–SSR markers. Gene 653: 80–90CrossRefGoogle Scholar
  31. Panwar P, Saini RK, Sharma N, Yadav D, Kumar A. 2010. Efficiency of RAPD, SSR and cytochrome P450 gene based markers in accessing genetic variability amongst finger millet (Eleusine coracana) accessions. Mol. Biol. Rep. 37: 4075–82CrossRefGoogle Scholar
  32. Peakall R, Smouse PE. 2012. GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research–an update. Bioinformatics 28: 2537–2539Google Scholar
  33. Prevost A, Wilkinson MJ. 1999. A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Appl. Genet. 98: 107–112.CrossRefGoogle Scholar
  34. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959Google Scholar
  35. Rahman SN, Islam MS, Alam MS, Nasiruddin KM. 2007. Genetic polymorphism in rice (Oryza sativa L.) through RAPD analysis. Indian J. Biotechnol. 6: 224–229Google Scholar
  36. Rajendran HAD, Muthusamy R, Stanislaus AC, Krishnaraj T, Kuppusamy S, Ignacimuthu S & AlDhabi NA. 2016. Analysis of molecular variance and population structure in southern Indian finger millet genotypes using three different molecular markers. J. Crop Sci. Biotechnol. 19: 275–283CrossRefGoogle Scholar
  37. Ramakrishnan M, Ceasar SA, Duraipandiyan V, Vinod KK, Kalpana K, Al–Dhabi NA, Ignacimuthu S. 2016a. Tracing QTLs for leaf blast resistance and agronomic performance of finger millet (Eleusine coracana (L.) Gaertn.) genotypes through association mapping and in silico comparative genomics analyses. PLoS One 11: e0159264CrossRefGoogle Scholar
  38. Ramakrishnan M, Ceasar SA, Duraipandiyan V, Al–Dhabi NA, Ignacimuthu S. 2016b. Using molecular markers to assess the genetic diversity and population structure of finger millet (Eleusine coracana (L.) Gaertn.) from various geographical regions. Genet. Resour. Crop Evol. 63: 361–376CrossRefGoogle Scholar
  39. Reed DH, Frankham R. 2003. Correlation between fitness and genetic diversity. Conserv. Biol. 17: 230–237CrossRefGoogle Scholar
  40. Saker MM, Youssef SS, Abdallah NA, Bashandy HS, El Sharkawy AM. 2005. Genetic analysis of some Egyptian rice genotypes using RAPD, SSR and AFLP. Afr. J. Biotechnol. 1: 4Google Scholar
  41. Satish L, Ceasar SA, Shilpha J, Rency AS, Rathinapriya P, Ramesh M. 2015. Direct plant regeneration from in vitro–derived shoot apical meristems of finger millet (Eleusine coracana (L.) Gaertn.). In Vitro Cell Dev. Biol. Plant. 51: 192–200CrossRefGoogle Scholar
  42. Satish L, Shilpha J, Pandian S, Rency AS, Rathinapriya P, Ceasar SA, Largia MJ, Kumar AA, Ramesh M. 2016. Analysis of genetic variation in sorghum (Sorghum bicolor (L.) Moench) genotypes with various agronomical traits using SPAR methods. Gene. 576: 581–585CrossRefGoogle Scholar
  43. Sehr EM, Okello–Anyanga W, Hasel–Hohl K, Burg A, Gaubitzer S, Rubaihayo PR, Okori P, Vollmann J, Gibson P, Fluch S. 2016. Assessment of genetic diversity amongst Ugandan sesame (Sesamum indicum L.) landraces based on agromorphological traits and genetic markers. J. Crop Sci. Biotechnol. 19: 117–24CrossRefGoogle Scholar
  44. Shilpha J, Silambarasan T, Pandian SK, Ramesh M. 2013. Assessment of genetic diversity in Solanum trilobatum L., an important medicinal plant from South India using RAPD and ISSR markers. Genet Resour. Crop Evol. 60: 807–18CrossRefGoogle Scholar
  45. Souza E, Sorrells ME. 1991. Relationships among 70 North American oat germplasms: II. Cluster analysis using qualitative characters. Crop Sci. 31: 605–612Google Scholar
  46. Tehrim S, Pervaiz ZH, Rabbani MA. 2012. Molecular characterization of traditional and improved rice cultivars based on random amplified polymorphic DNAs (RAPDs) markers. Afr. J. Biotechnol. 11: 10297–10304Google Scholar
  47. Uma S, Prasad TG, Kumar MU. 1995. Genetic variability in recovery growth and synthesis of stress proteins in response to polyethylene glycol and salt stress in finger millet. Ann. Bot. 76: 43–9CrossRefGoogle Scholar
  48. Verma S, Rana TS. 2013. Genetic relationships among wild and cultivated accessions of curry leaf plant (Murraya koenigii (L.) Spreng.), as revealed by DNA fingerprinting methods. Mol. Biotechnol. 53: 139–49CrossRefGoogle Scholar
  49. Verma S, Singh S, Sharma S, Tewari SK, Roy RK, Goel AK, Rana TS. 2015. Assessment of genetic diversity in indigenous turmeric (Curcuma longa) germplasm from India using molecular markers. Physiol. Mol. Biol. Plants. 21: 233–242CrossRefGoogle Scholar
  50. Weir BS. 1990. Genetic Data Analysis: Methods for Discrete Population Genetic Data. Sinauer Assoc., Inc. Pub. Sunderland, Massachusetts, 377 ppGoogle Scholar
  51. Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18: 6531–6535CrossRefGoogle Scholar
  52. Yaman H, Tarıkahya–Hacıoglu B, Arslan Y, Subas I. 2014. Molecular characterization of the wild relatives of safflower (Carthamustinctorius L.) in Turkey as revealed by ISSRs. Genet. Resour. Crop. Evol. 61: 595–602CrossRefGoogle Scholar

Copyright information

© Korean Society of Crop Science (KSCS) and Springer Nature B.V. 2018

Authors and Affiliations

  • Subramani Pandian
    • 1
  • Karuppasamy Marichelvam
    • 1
  • Lakkakula Satish
    • 1
    • 2
  • Stanislaus Antony Ceasar
    • 3
    • 4
  • Shunmugiah Karutha Pandian
    • 1
  • Manikandan Ramesh
    • 1
    Email author
  1. 1.Department of Biotechnology, Science CampusAlagappa UniversityKaraikudiIndia
  2. 2.Department of Biotechnology EngineeringBen-Gurion University of NagevBeer ShevaIsrael
  3. 3.Division of Plant Biotechnology, Entomology Research InstituteLoyola CollegeChennaiIndia
  4. 4.InBioS - PhytoSystems and Center for Protein Engineering, Department of Life SciencesUniversity of LiègeLiègeBelgium

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