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

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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.

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References

  • 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: 399

    Article  CAS  Google Scholar 

  • 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: 97–104

    Article  CAS  PubMed  Google Scholar 

  • Barnett T. 1999. The Emergence of Food Production in Ethiopia, BAR International Series 763. Oxford, Archaeopress

    Google Scholar 

  • 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): 47–51

    Google Scholar 

  • 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: 314–331

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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: 1408–1415

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chambers GK, MacAvoy ES. 2000. Microsatellites: consensus and controversy. Comp. Biochem. Physiol. 126: 455–476

    Article  CAS  Google Scholar 

  • Dida MM, Srinivasachary, Sujatha Ramakrishnan, Bennetzen JL, Gale MD, Devos KM. 2007. The genetic map of finger millet, Eleusine coracana. Theor. Appl. Genet. 114: 321–332

    Article  CAS  PubMed  Google Scholar 

  • 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: 122–123

    Article  Google Scholar 

  • Fischer D, Bachmann K. 1998. Microsatellite enrichment in organisms with large genomes (Allium cepa L.). BioTechniques. 24: 796–802

    CAS  PubMed  Google Scholar 

  • 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: 62–71

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hilu KW, De Wet JMJ, Harlan JR. 1979. Archaeobotanical studies of E. coracana ssp. coracana (finger millet). Am. J. Bot 66(3): 330–343

    Article  Google Scholar 

  • IBPGR. 1985. Descriptors for Finger Millet (Eleusine coracana (L.) Gaertn.). Rome, Italy: International Board for Plant Genetic Resources. 20 pp

    Google Scholar 

  • 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: 23–34

    Article  PubMed  PubMed Central  Google Scholar 

  • Lagercrantz U, Ellegren H, Andersson L. 1993. The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res. 21: 1111–1115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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): 97–100

    Article  CAS  Google Scholar 

  • Milbourne D. 1997. Comparison of PCR based marker systems for the analysis of genetic relationship in cultivated potato. Mol. Breed.3: 127–136

    Article  CAS  Google Scholar 

  • Morgante M, Hanafey M, Powell W. 2002. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat. Genet. 30: 194–200

    Article  CAS  PubMed  Google Scholar 

  • Morgante M, Olivieri AM. 1993. PCR-amplified microsatellites as markers in plant genetics. Plant J. 3: 175–182

    Article  CAS  PubMed  Google Scholar 

  • 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: 9

    Article  Google Scholar 

  • Panaud O, Chen X, McCouch SR. 1995. Frequency of microsatellite sequences in rice (Oryza sativa L.). Genome 38: 1170–1176

    Article  CAS  PubMed  Google Scholar 

  • Portères R. 1951. ‘Eleusine coracana Gaertn. Céréale des Humanités Pauvres des Pays Tropicaux’, Bulletin de l'Institut Français de l'Afrique Noire. 13: 1–78

    Google Scholar 

  • Portères R. 1958. ‘Les appellations des céréales en Afrique: V. Le Millet, Teff de l’Abyssinie’, J. Agric. Trop. Bot. Appl. 5: 454–463

    Google Scholar 

  • 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: 355–362

    CAS  PubMed  Google Scholar 

  • Rafalski JA, Tingey SV. 1993. Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. Trends. Genet. 9: 275–280

    Article  CAS  PubMed  Google Scholar 

  • 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: 120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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: 1–9

    Google Scholar 

  • Rohlf FJ. 1993. NTSYS-pc version 2.0, State University of New York, Exeter Software, Setauket, New York

    Google Scholar 

  • 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: 11

    Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

    Google Scholar 

  • Schlotterer C, Harr B. 2000. Drosophila virilis has long and highly polymorphic microsatellites. Mol. Biol. Evol. 17: 1641–1646

    Article  CAS  PubMed  Google Scholar 

  • 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: 1634

    Article  PubMed  PubMed Central  Google Scholar 

  • Stallings RL. 1992. CpG suppression in vertebrate genomes does not account for the rarity of (CpG)n microsatellite repeats. Genomics 17: 890–891

    Article  Google Scholar 

  • Summers R. 1958. Inyanga, Cambridge: Cambridge University Press p.1

    Google Scholar 

  • 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: 353–364

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Weber JL, Zhong G, Tanksley SD. 1994. Survey of plant short tandem repeats. Theor. Appl. Genet. 88: 1–6

    CAS  PubMed  Google Scholar 

  • 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: 187–194

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Dept. of Agricultural Biotechnology, Acharya N.G. Ranga Agricultural University (ANGRAU), Rajendranagar, Hyderabad, 500 030, Telangana, India

    I. N. Bheema Lingeswara Reddy

  2. Rajiv Gandhi Centre for Biotechnology, Poojappura, Thiruvananthapuram, 695 014, Kerala, India

    S. Sivaramakrishnan

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  1. I. N. Bheema Lingeswara Reddy
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  2. S. Sivaramakrishnan
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Correspondence to I. N. Bheema Lingeswara Reddy.

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Bheema Lingeswara Reddy, I.N., Sivaramakrishnan, S. Identification of SSR markers which could differentiate blast disease resistance accessions in finger millet (Eleusine coracana (L.) Gaertn.). J. Crop Sci. Biotechnol. 20, 37–44 (2017). https://doi.org/10.1007/s12892-016-0091-2

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  • DOI: https://doi.org/10.1007/s12892-016-0091-2

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