Journal of Crop Science and Biotechnology

, Volume 20, Issue 1, pp 37–44 | Cite as

Identification of SSR markers which could differentiate blast disease resistance accessions in finger millet (Eleusine coracana (L.) Gaertn.)

  • I. N. Bheema Lingeswara Reddy
  • S. Sivaramakrishnan
Research Article
First Online:
Received:
Revised:
Accepted:
  • 77 Downloads

Abstract

Microsatellites also known as SSR are the class of repetitive DNA sequences present throughout the genome of all eukaryotic organisms. The present study identified SSRs using biotinylated beads capture method. Ten sets of primers were designed based on sequences having at least (CT)10 repeats. A total of 27 accessions having a mix of both African (resistant) and Indian origin (resistant and susceptible) were assessed using 30 microsatellite markers. Amplification products were obtained for all 30 primers studied; 25 out of these primers were found to be polymorphic with 13 primers showing two alleles per locus. The current study identified markers which could differentiate between resistant and susceptible accessions and also segregate accessions based on geographical region. These informative SSR markers can be used in finger millet genetic improvement projects.

Key words

Finger millet microsatellite marker diversity 
This is a preview of subscription content, log in to check access.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Babu BK, Senthil N, Gomez SM. 2007. Assessment of genetic diversity among finger millet (Eleusine coracana (L.) Gaertn.) Accessions using molecular markers. Genet. Resour. Crop. Evol. 54: 399CrossRefGoogle Scholar
  2. Barbeau WE, Hilu KW. 1993. Protein, calcium, iron and amino acid content of selected wild and domesticated cultivars of finger millet. Plant Foods Hum. Nutr. 43: 97–104CrossRefPubMedGoogle Scholar
  3. Barnett T. 1999. The Emergence of Food Production in Ethiopia, BAR International Series 763. Oxford, ArchaeopressGoogle Scholar
  4. Bheema Lingeswara Reddy IN, Srinivas Reddy D, Prathap Reddy V, Lakshmi Narasu M, Sivaramakrishnan S. 2011. Efficient microsatellite enrichment in finger millet (Eleusine coracana (L.) Gaertn.)–An improved procedure to develop microsatellite markers. Asian Austal. J. Plant Sci. Biotechnol. 5(1): 47–51Google Scholar
  5. Botstein D, White RL, Skolnick MH, Davies RW. 1980. Construction of a genetic map in man using restriction fragment length polymorphism. Am. J. Hum. Genet. 32: 314–331PubMedPubMedCentralGoogle Scholar
  6. Brinkmann B, Klintschsar M, Neuhuber F, Huhne J, Rolf B. 1998. Mutation rate in human microsatellites: Influence of the structure and length of the tandem repeat. Am. J. Hum. Genet. 62: 1408–1415CrossRefPubMedPubMedCentralGoogle Scholar
  7. Chambers GK, MacAvoy ES. 2000. Microsatellites: consensus and controversy. Comp. Biochem. Physiol. 126: 455–476CrossRefGoogle Scholar
  8. Dida MM, Srinivasachary, Sujatha Ramakrishnan, Bennetzen JL, Gale MD, Devos KM. 2007. The genetic map of finger millet, Eleusine coracana. Theor. Appl. Genet. 114: 321–332CrossRefPubMedGoogle Scholar
  9. Ekwamu A. 1991. Influence of head blast infection on seed germination and yield components of finger millet (Eleusine coracana L. Gaertn.). Trop. Pest Manage. 37: 122–123CrossRefGoogle Scholar
  10. Fischer D, Bachmann K. 1998. Microsatellite enrichment in organisms with large genomes (Allium cepa L.). BioTechniques. 24: 796–802PubMedGoogle Scholar
  11. Gur-Arie R, Cohen CJ, Eitan Y, Shelef L, Hallerman EM, Kashi Y. 2000. Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism. Genome Res. 10: 62–71PubMedPubMedCentralGoogle Scholar
  12. Hilu KW, De Wet JMJ, Harlan JR. 1979. Archaeobotanical studies of E. coracana ssp. coracana (finger millet). Am. J. Bot 66(3): 330–343CrossRefGoogle Scholar
  13. IBPGR. 1985. Descriptors for Finger Millet (Eleusine coracana (L.) Gaertn.). Rome, Italy: International Board for Plant Genetic Resources. 20 ppGoogle Scholar
  14. La Rota M, Kantety R, Yu Y-K, Sorrells ME. 2005. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 6: 23–34CrossRefPubMedPubMedCentralGoogle Scholar
  15. Lagercrantz U, Ellegren H, Andersson L. 1993. The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res. 21: 1111–1115CrossRefPubMedPubMedCentralGoogle Scholar
  16. Lalit Arya, Manjusha Verma, VK Gupta and JL Karihaloo. 2009. Development of EST-SSRs in finger millet (Eleusine coracana ssp coracana) and their transferability to pearl millet (Pennisetum glaucum). J. Plant Biochem. Biotechnol. 18(1): 97–100CrossRefGoogle Scholar
  17. Milbourne D. 1997. Comparison of PCR based marker systems for the analysis of genetic relationship in cultivated potato. Mol. Breed.3: 127–136CrossRefGoogle Scholar
  18. Morgante M, Hanafey M, Powell W. 2002. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat. Genet. 30: 194–200CrossRefPubMedGoogle Scholar
  19. Morgante M, Olivieri AM. 1993. PCR-amplified microsatellites as markers in plant genetics. Plant J. 3: 175–182CrossRefPubMedGoogle Scholar
  20. Naga BLRI, Mangamoori LN, Subramanyam S. 2012. Identification and characterization of EST-SSRs in finger millet (Eleusine coracana (L.) Gaertn.). J. Crop Sci. Biotechnol. 15: 9CrossRefGoogle Scholar
  21. Panaud O, Chen X, McCouch SR. 1995. Frequency of microsatellite sequences in rice (Oryza sativa L.). Genome 38: 1170–1176CrossRefPubMedGoogle Scholar
  22. Portères R. 1951. ‘Eleusine coracana Gaertn. Céréale des Humanités Pauvres des Pays Tropicaux’, Bulletin de l'Institut Français de l'Afrique Noire. 13: 1–78Google Scholar
  23. Portères R. 1958. ‘Les appellations des céréales en Afrique: V. Le Millet, Teff de l’Abyssinie’, J. Agric. Trop. Bot. Appl. 5: 454–463Google Scholar
  24. Qi X, Lindup S, Pittaway TS, Allouis S, Gale MD, Devos KM. 2001. Development of simple sequence repeatmarkers from bacterial artificial chromosomes without subcloning. Biotechniques 31: 355–362PubMedGoogle Scholar
  25. Rafalski JA, Tingey SV. 1993. Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. Trends. Genet. 9: 275–280CrossRefPubMedGoogle Scholar
  26. Ramakrishnan M, Antony Ceasar S, Duraipandiyan V, Al-Dhabi NA, Ignacimuthu S. 2016. Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn.) using genomic SSR markers. SpringerPlus 5: 120CrossRefPubMedPubMedCentralGoogle Scholar
  27. Reddy VG, Upadhyaya HD, Gowda CLL, Singh S. 2009. Characterization of eastern African finger millet germplasm for qualitative and quantitative characters at ICRISAT. J. SAT Agric. Res. 7: 1–9Google Scholar
  28. Rohlf FJ. 1993. NTSYS-pc version 2.0, State University of New York, Exeter Software, Setauket, New YorkGoogle Scholar
  29. Saha D, Rana RS, Arya L, Verma M, Gowda MVC, Upadhyaya, HD. 2016. Genetic polymorphisms among and between blast disease resistant and susceptible finger millet, Eleusine coracana (L.) Gaertn. Plant Gen. Res. 1: 11Google Scholar
  30. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring HarborGoogle Scholar
  31. Schlotterer C, Harr B. 2000. Drosophila virilis has long and highly polymorphic microsatellites. Mol. Biol. Evol. 17: 1641–1646CrossRefPubMedGoogle Scholar
  32. Sood S, Kumar A, Kalyana Babu B, Gaur VS, Pandey D, Kant L, Pattnayak A. 2016. Gene Discovery and Advances in Finger Millet [Eleusine coracana (L.) Gaertn.] Genomics-An Important Nutri-Cereal of Future. Front. Plant Sci. 7: 1634CrossRefPubMedPubMedCentralGoogle Scholar
  33. Stallings RL. 1992. CpG suppression in vertebrate genomes does not account for the rarity of (CpG)n microsatellite repeats. Genomics 17: 890–891CrossRefGoogle Scholar
  34. Summers R. 1958. Inyanga, Cambridge: Cambridge University Press p.1Google Scholar
  35. Vadivoo AS, Joseph R, Ganesan NM. 1998. Genetic variability and diversity for protein and calcium contents in finger millet (Eleusine coracana (L.) Gaertn.) in relation to grain colour. Plant Foods Hum. Nutr. 52: 353–364CrossRefPubMedGoogle Scholar
  36. Wang Z, Weber JL, Zhong G, Tanksley SD. 1994. Survey of plant short tandem repeats. Theor. Appl. Genet. 88: 1–6PubMedGoogle Scholar
  37. Yang GP, Saghai Maroof MA, Xu CG, Zhang Q, Biyashev RM. 1994. Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars. Mol. Gen. Genet.245: 187–194CrossRefPubMedGoogle Scholar

Copyright information

© Korean Society of Crop Science and Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  • I. N. Bheema Lingeswara Reddy
    • 1
  • S. Sivaramakrishnan
    • 2
  1. 1.Dept. of Agricultural BiotechnologyAcharya N.G. Ranga Agricultural University (ANGRAU)Rajendranagar, HyderabadIndia
  2. 2.Rajiv Gandhi Centre for BiotechnologyPoojappura, ThiruvananthapuramIndia

Personalised recommendations