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Neutral and functional marker based genetic diversity in kodo millet (Paspalum scrobiculatum L.)

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Abstract

Kodo millet (Paspalum scrobiculatum L.) is known for its high nutritive value, dietary fiber, antioxidant activity, as well as for drought tolerance. It is primarily grown as a grain in India and in Africa it is either cultivated or harvested in wild. Neutral—ISSR (inter simple sequence repeat) as well as functional—SCoT (start codon targeted) and SRAP (sequence-related amplified polymorphism) markers were employed for genetic diversity studies in 96 accessions of kodo millet collected from diverse regions of India. The genetic diversity parameters like average bands per primer, Polymorphic information content, Nei’s gene diversity and Shannon’s information index of 11.22, 9.69; 0.12, 0.11; 0.15 ± 0.14, 0.13 ± 0.13 and 0.26 ± 0.21, 0.22 ± 0.19 was observed with neutral and functional markers respectively. Neutral markers were showing higher values as compared to functional markers for the genetic diversity parameters as discussed. Structure based analysis placed all the accessions into four sub-groups not strictly according to their geographical locations. The accessions from Bihar followed by Karnataka were showing high diversity based on both the marker systems useful for designing exploration, conservation and germplasm enrichment strategies. Further, the set of diverse accessions selected based on these markers would serve as potential sources of unique alleles and may be exploited in future for enhancement and utilization of kodo millet germplasm. Usage of African gene pool and wild species for broadening the genetic base of Indian kodo millet was also suggested based on the present studies.

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References

  • Aneja B, Yadav NR, Yadav RC, Kumar R (2013) Sequence related amplified polymorphism (SRAP) analysis for genetic diversity and micronutrient content among gene pools in mungbean [Vigna radiata (L.) Wilczek]. Physiol Mol Biol Plants 19(3):399–407

  • Arya L, Narayanan RK, Verma M, Singh AK, Gupta V (2014) Genetic diversity and population structure analyses of Morinda tomentosa Heyne, with neutral and gene based markers. Genet Resour Crop Evol 61:1469–1479

    Article  CAS  Google Scholar 

  • Bhawna Abdin MZ, Arya L, Saha D, Sureja AK, Pandey C, Verma M (2014) Population structure and genetic diversity in bottle gourd [Lagenaria siceraria (Mol.) Standl.] germplasm from India assessed by ISSR markers. Plant Syst Evol 300:767–773

    Article  Google Scholar 

  • Blair MW, Panaud O, McCouch SR (1999) Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.). Theor Appl Genet 98:780–792

    Article  CAS  Google Scholar 

  • Burton GW (1940) A cytological study of some species in the genus Paspalum. J Agr Res 60:193–198

    Google Scholar 

  • Chandrasekara A, Shahidi F (2011) Determination of antioxidant activity in free and hydrolyzed fractions of millet grains and characterization of their phenolic profiles by HPLC-DAD-ESI-MS. J Funct Foods 3:144–158

    Article  CAS  Google Scholar 

  • Cidade FW, Dall Agnol M, Bered F, De Souza Chies TT (2008) Genetic diversity of the complex Paspalum notatum Flügge (Paniceae: Panicoideae). Genet Resour Crop Evol 55:235–246

    Article  CAS  Google Scholar 

  • Collard BCY, Mackill DJ (2009) Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Biol Rep 27(1):86–93

    Article  CAS  Google Scholar 

  • deWet JMJ, Rao KEP, Mengesha MH, Brink DE (1983) Diversity in kodo millet, Paspalum scrobiculatum. Econ Bot 37:159–163

    Article  Google Scholar 

  • Dwivedi S, Upadhyaya H, Senthilvel S, Hash C, Fukunaga K, Diao X. et al (2012) Millets: genetic and genomic resources, Plant Breeding Reviews. Janick J (ed), John Wiley and Sons, Inc, Hoboken, NJ pp 247–374

  • Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conser Genet Resour 4(2):359–361

    Article  Google Scholar 

  • FAOSTAT (2013) http://faostat3.fao.org/browse/Q/QC/E

  • Goron TL, Raizada MN (2015) Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution. Front Plant Sci 6:157. doi:10.3389/fpls.2015.00157

    PubMed  PubMed Central  Google Scholar 

  • Islam S, Munshi AD, Verma M, Arya L, Mandal B, Behera TK, Kumar R, Lal SK (2011) Screening of Luffa cylindrica Roem against Tomato Leaf Curl New Delhi Virus, Inheritance of Resistance and Identification of SRAP Markers Linked to Resistance Gene. J Hort Sci Biotechnol 86(6):661–667

    CAS  Google Scholar 

  • Jarret RL, Ozias-Akins P, Phatak S, Nadimpalli R, Duncan R, Hiliard S (1995) DNA contents in Paspalum spp. determined by flow cytometry. Genet Resour Crop Evol 42:237–242

    Article  Google Scholar 

  • Kole C, Muthamilarasan M, Henry R et al (2015) Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. Front Plant Sci 6:563. doi:10.3389/fpls.2015.00563

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar A, Arya L, Kumar V, Sharma S (2006) Inter simple sequence repeat (ISSR) analysis of cytoplasmic male sterile, male fertile lines and hybrids of pearl millet [Pennisetum glaucum (L.) R. Br.]. Indian J Crop Sci 1:117–119

    Google Scholar 

  • Kumari R, Dikshit N, Sharma D, Bhat KV (2011) Analysis of molecular genetic diversity in a representative collection of foxtail millet [Setaria italica (L.) P. Beauv.] from different agro-ecological regions of India. Physiol Mol Biol Plants 17(4):363–374

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumari K, Muthamilarasan M, Misra G, Gupta S, Subramanian A, Parida SK et al (2013) Development of eSSR-markers in Setaria italica and their applicability in studying genetic diversity, cross-transferability and comparative mapping in millet and non-millet species. PLoS One 8:e67742. doi:10.1371/journal.pone.0067742

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kushwaha H, Jilo KW, Singh VK, Kumar A, Yadav D (2015) Assessment of genetic diversity among cereals and millets based on PCR amplification using Dof (DNA binding with One Finger) transcription factor gene-specific primers. Plant Syst Evol 301:833–840

    Article  Google Scholar 

  • Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461

    Article  CAS  Google Scholar 

  • Lin XC, Lou YF, Liu J, Peng JS et al (2010) Crossbreeding of Phyllostachys species (Poaceae) and identification of their hybrids using ISSR markers. Genet Mol Res 9:1398–1404

    Article  CAS  PubMed  Google Scholar 

  • Luo C, He XH, Chen H, Ou SJ, Gao MP (2010) Analysis of diversity and relationships among mango cultivars using Start Codon Targeted (SCoT) markers. Biochem Syst Ecol 38:1176–1184

    Article  CAS  Google Scholar 

  • M’Ribu HK, Hilu KW (1996) Application of random amplified polymorphic DNA to study genetic diversity in Paspalum scrobiculatum L. (Kodo millet, Poaceae). Genet Resour Crop Evol 43:203–210

    Article  Google Scholar 

  • Muthamilarasan M, Prasad M (2015) Advances in Setaria genomics for genetic improvement of cereals and bioenergy grasses. Theor Appl Genet 128:1–14. doi:10.1007/s00122-014-2399-3

    Article  CAS  PubMed  Google Scholar 

  • Muthamilarasan M, Venkata Suresh B, Pandey G, Kumari K, Parida SK, Prasad M (2014) Development of 5123 intron-length polymorphic markers for large-scale genotyping applications in foxtail millet. DNA Res 21:41–52. doi:10.1093/dnares/dst039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muthamilarasan M et al (2015) Exploration of millet models for developing nutrient rich graminaceous crops. Plant Sci. doi:10.1016/j.plantsci.2015.08.023

    PubMed  Google Scholar 

  • Pandey G, Misra G, Kumari K, Gupta S, Parida SK, Chattopadhyay D et al (2013) Genome-wide development and use of microsatellite markers for large- scale genotyping applications in foxtail millet [Setaria italica (L.)]. DNA Res 20:197–207. doi:10.1093/dnares/dst002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. 28:2537–2539

  • Porteres R (1976) African cereals: Eleusine, fonio, black fonio, teff, brachiaria, paspalum, pennisetum, and African rice, Origin of African Plant Domestication. Harlan JR, DeWet JMJ, Stemler A (eds), Mouton Press, The Hague, pp 409–452

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rohlf FJ (2000) NTSYS-PC, numerical taxonomy system for the PC Exeter Software, Version 2.1. Applied Biostatistics Inc Setauket, USA

  • Roldan-Ruiz IJ, Dendauw EVB, Depicker A, De Loose M (2000) AFLP markers reveal high polymorphic rates in the rye-grasses (Lolium spp.). Mol Breed 6:125–134

    Article  CAS  Google Scholar 

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81:8014–8018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saini N, Jain N, Jain S, Jain RK (2004) Assessment of genetic diversity within and among basmati and non-basmati rice varieties using AFLP. ISSR and SSR markers. Euphytica 140(3):133–146

    Article  CAS  Google Scholar 

  • Singh SK, Suresh BG, Lavanya GR, Arya L, Bhat KV, Hussain Z, Verma M (2014) Assessment of genetic variability in mutant lines of greengram (Vigna radiata) using ISSR markers. Indian J Agr Sci 84(4):534–539

    Google Scholar 

  • Suresh VB, Muthamilarasan M, Misra G, Prasad M (2013) FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research. PLoS One 8(8):e71418. doi:10.1371/journal.pone.0071418

    Article  Google Scholar 

  • Trivedi AK, Arya L, Verma M, Verma SK, Tyagi RK, Hemantaranjan A (2015) Genetic variability in proso millet [Panicum miliaceum] germplasm of Central Himalayan Region based on morpho-physiological traits and molecular markers. Acta Physiol Plant 37(2):1–16

    Article  CAS  Google Scholar 

  • Upadhyaya HD, Dwivedi SL, Singh SK, Singh S, Vetriventhan M, Sharma S (2014) Forming core collections in barnyard, kodo, and little millets using morpho agronomic descriptors. Crop Sci 54:1–10

    Article  Google Scholar 

  • Yadav CB, Bonthala VS, Muthamilarasan M, Pandey G, Khan Y, Prasad M (2015) Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database. DNA Res 22:79–90. doi:10.1093/dnares/dsu039

    Article  PubMed  PubMed Central  Google Scholar 

  • Yeh FC, Boyle T, Rongcai Y, Ye Z, Xian JM (1999) Popgene, A Microsoft Windows based freeware for population genetic analysis, Ver 1.31. Edmonton: University of Alberta and Center for International Forestry Research

  • Yildiz M, Ekbic E, Keles D, Sensoy S, Abak K (2011) Use of ISSR, SRAP, and RAPD markers to assess genetic diversity in Turkish melons. Sci Hortic 130:349–353

    Article  Google Scholar 

  • Zilli AL, Hojsgaard DH, Brugnoli EA, Acuna CA, Honfi AI, Urbani MH, Quarin CL, Martinez EJ (2014) Genetic relationship among Paspalum species of the subgenus Anachyris: taxonomic and evolutionary implications. Flora 209:604–612

    Article  Google Scholar 

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Acknowledgments

The Authors are grateful to Dr. K. C. Bansal, Director, ICAR-NBPGR, New Delhi for financial support and thankful to DST (Department of Science and Technology, New Delhi) and Dr. Shailesh Marker Director Research, SHIATS Allahabad to facilitate and accept the research proposal.

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Authors and Affiliations

  1. Department of Genetics and Plant Breeding, Sam Higginbottom Institute of Agriculture, Technology and Sciences, Allahabad, 211007, India

    Yuvraj Yadav & G. R. Lavanya

  2. Division of Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India

    Sushil Pandey

  3. Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India

    Manjusha Verma, Chet Ram & Lalit Arya

Authors
  1. Yuvraj Yadav
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  2. G. R. Lavanya
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  3. Sushil Pandey
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  4. Manjusha Verma
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  5. Chet Ram
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  6. Lalit Arya
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Correspondence to Lalit Arya.

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Communicated by M Prasad.

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Yadav, Y., Lavanya, G.R., Pandey, S. et al. Neutral and functional marker based genetic diversity in kodo millet (Paspalum scrobiculatum L.). Acta Physiol Plant 38, 75 (2016). https://doi.org/10.1007/s11738-016-2090-1

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  • DOI: https://doi.org/10.1007/s11738-016-2090-1

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