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Cross-genera transferability of rice and finger millet genomic SSRs to barnyard millet (Echinochloa spp.)

3 Biotech volume 8, Article number: 95 (2018) Cite this article

Abstract

Barnyard millet (Echinochloa spp.) is an important crop from nutritional point of view, nevertheless, the genetic information is very scarce. In the present investigation, rice and finger millet genomic SSRs were used for assessing cross transferability, identification of polymorphic markers, syntenic regions, genetic diversity and population structure analysis of barnyard millet genotypes. We observed 100% cross transferability for finger millet SSRs, of which 91% were polymorphic, while 71% of rice markers were cross transferable with 48% polymorphic out of them. Twenty-nine and sixteen highly polymorphic finger millet and rice SSRs yielded a mean of 4.3 and 3.38 alleles per locus in barnyard millet genotypes, respectively. The PIC values varied from 0.27 to 0.73 at an average of 0.54 for finger millet SSRs, whereas it was from 0.15 to 0.67 at an average of 0.44 for rice SSRs. High synteny was observed for markers related to panicle length, yield-related traits, spikelet fertility, plant height, root traits, leaf senescence, blast and brown plant hopper resistance. Although the rice SSRs located on chromosome 10 followed by chromosome 6 and 11 were found to be more transferable to barnyard millet, the finger millet SSRs were more polymorphic and transferable to barnyard millet genotypes. These SSR data of finger millet and rice individually as well as combined together grouped the 11 barnyard millet genotypes into 2 major clusters. The results of population structure analysis were similar to cluster analysis.

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References

  • Aoki D, Yamaguchi H (2009) Oryza sh4 gene homologue represents homoeologous genomic copies in polyploid Echinochloa. Weed Biol Manag 9:225–233

    CAS  Article  Google Scholar 

  • Babu BK, Senthil N, Michael Gomez S, Biji KR, Rajendraprasad NS, Satheesh Kumar S, Chandra Babu R (2007) Assessment of genetic diversity among finger millet (Eleusine coracana (L.) Gaertn.) accessions using molecular markers. Genet Res Crop Evol 54:399–404

    CAS  Article  Google Scholar 

  • Babu BK, Agrawal PK, Pandey D, Jaiswal JP, Kumar A (2014a) Association mapping of agro-morphological characters among the global collection of finger millet genotypes using genomic SSR markers. Mol Biol Rep 41(8):5287–5297

    Article  Google Scholar 

  • Babu BK, Pandey D, Agrawal PK, Sood S, Chandrashekara C, Bhatt JC, Kumar A (2014b) Comparative genomics and association mapping approaches for blast resistant genes in finger millet using SSRs. PLoS ONE 9(6):e99182. https://doi.org/10.1371/journal.pone.0099182

    Article  Google Scholar 

  • Babu BK, Pandey D, Agrawal PK, Sood S, Kumar A (2014c) In-silico mining, type and frequency analysis of genic microsatellites of finger millet (Eleusine coracana (L.) Gaertn.): a comparative genomic analysis of NBS–LRR regions of finger millet with rice. Mol Biol Rep 41(5):3081–3090

    Article  Google Scholar 

  • Babu BK, Joshi A, Sood S, Agrawal PK (2017) Identification of microsatellite markers for finger millet genomics application through cross transferability of rice genomic SSR markers. Indian J Genet 77(1):92–98

    Google Scholar 

  • Bharathi A (2011) Phenotypic and genotypic diversity of global finger millet (Eleusine coracana (L.) Gaertn.) composite collection. Dissertation, Tamil Nadu Agricultural University, Coimbatore

  • Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis. Models and estimation procedures. Am J Hum Genet 19(3):233–257

    CAS  Google Scholar 

  • Chandrashekhar A, Vaijayanthi PV, Rao AM, Ramesh S, Ravishankar P, Gowda MVC (2016) Transferability of cross cereal species SSR markers to finger millet (Eleusine coracana L. Gaertn.). Int J Agric Sci 8(49):2059–2062

    Google Scholar 

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

    CAS  Article  Google Scholar 

  • Dida MM, Wanyera N, Harrison Dunn MLN, Bennetzen JL, Devos KM (2008) Population structure and diversity in finger millet (Eleusine coracana) germplasm. Trop Plant Biol. https://doi.org/10.1007/s12042-008-9012-3

    Google Scholar 

  • Earl dent A, VonHoldt Bridgett M (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Cons Genet Res 4(2):359–361

    Article  Google Scholar 

  • Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Nat Acad Sci USA 95:1971–1974

    CAS  Article  Google Scholar 

  • Hamilton JP, Buell CR (2012) Advances in plant genome sequencing. Plant J 70(1):177–190

    CAS  Article  Google Scholar 

  • Kim CS, Koh HS, Fukami H (1994) Antifeedents of rice planthoppers in some millets. Appl Entomool Zool 29(1):71–79

    Article  Google Scholar 

  • Kumari K, Muthamilarasan M, Misra G, Gupta S, Subramanian A 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(6):e67742. https://doi.org/10.1371/journal.pone.0067742

    CAS  Article  Google Scholar 

  • Liu K, Muse M (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129

    CAS  Article  Google Scholar 

  • Moore G, Devos KM, Wang Z, Gale MD (1995) Grasses, line up and form a circle. Curr Biol 5:17–23

    Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8:4321–4326

    CAS  Article  Google Scholar 

  • Muthamilarasan M, Suresh Venkata, Pandey B, Kumari G, 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

    CAS  Article  Google Scholar 

  • Nirgude M, Kalyana Babu B, Yadav S, Singh UM, Upadhyaya HD, Kumar A (2014) Development and molecular characterization of genic molecular markers for grain protein and calcium content in finger millet (Eleusine coracana (L.) Gaertn.). Mol Biol Rep 41(3):1189–1200

    CAS  Article  Google Scholar 

  • Pandey G, Mishra G, Kumari K, Gupta S, Parida SK, Chattopadhyay D, Prasad M (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

    CAS  Article  Google Scholar 

  • Pritchard JK, Wen W (2003) Documentation for the structure software, version 2. Department of Human Genetics, University of Chicago, Chicago. http://pritch.bsd.uchicago.edu/software. Accessed 2 Feb 2017

  • Rajput SG, Tammy PH, Dipak KS (2014) Development and characterization of SSR markers in proso millet based on switchgrass genomics. Am J Plant Sci 5:175–186

    CAS  Article  Google Scholar 

  • Reddy BLIN, Lakshmi NM, Sivaramakrishnan S (2012) Identification and characterization of EST–SSRs in finger millet (Eleusine coracana (L.) Gaertn.). J Crop Sci Biotech 15(1):9–16

    Article  Google Scholar 

  • Roder MS, Plaschke J, Konig SU, Borner A, Sorrells ME, Tanksley SD, Ganal MW (1995) Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 246:327–333

    CAS  Article  Google Scholar 

  • Sambrook J, Fritschi EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

    Google Scholar 

  • Sood S, Khulbe RK, Gupta A, Agrawal PK, Upadhaya HD, Bhatt JC (2015) Barnyard millet-a potential food and feed crop of future. Plant Breed 134:135–147. https://doi.org/10.1111/pbr.12243

    Article  Google Scholar 

  • Udupa SM, Baum M (2001) High mutation rate and mutational bias at (TAA)n microsatellite loci of chickpea (Cicer arietinum L.). Mol Genet Genom 265:1097–1103

    CAS  Article  Google Scholar 

  • Ugare R, Chimmad B, Naik R, Bharati P, Itagi S (2014) Glycemic index and significance of barnyard millet (Echinochloa frumentacae) in type II diabetics. J Food Sci Technol 51:392–395

    CAS  Article  Google Scholar 

  • Varshney RK, Kumar A, Balyan HS, Roy JK, Prasad M, Gupta PK (2001) Characterization of microsatellites and development of chromosome specific STMS markers in bread wheat. Plant Mol Biol Rep 18:5–16

    Article  Google Scholar 

  • Veena S, Bharati VC, Rama KN, Shanthakumar G (2005) Physico-chemical and nutritional studies in barnyard millet. Karnataka J Agric Sci 18:101–105

    Google Scholar 

  • Yabuno T (1987) Japanese barnyard millet (Echinochloa utilis, Poaceae) in Japan. Econ Bot 41(4):484–493

    Article  Google Scholar 

  • Yadav OP, Mitchell SE, Fulton TM and Kresovich S (2008) Transferring molecular markers from sorghum, rice and other cereals to pearl millet and identifying polymorphic markers. J SAT Agric Res 6

  • Yadav S, Gaur VS, Jaiswal JP, Kumar A (2014) Simple sequence repeat (SSR) analysis in relation to calcium transport and signaling genes reveals transferability among grasses and a conserved behavior within finger millet genotypes. Plant Syst Evol 300:1561–1568

    CAS  Article  Google Scholar 

  • Zhao X, Kochert G (1993) Phylogenetic distribution and genetic mapping of a (GGC) n microsatellite from rice (Oryza sativa L.). Plant Mol Biol 21:607–6 14

    CAS  Article  Google Scholar 

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Acknowledgements

The authors thank Indian Council of Agricultural Research for financial support.

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Author notes

  1. B. Kalyana Babu

    Present address: ICAR-Indian Institute of Oil Palm Research, Pedavegi, West Godavari, AndhraPradesh, 534450, India

  2. Salej Sood

    Present address: ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India

  3. B. Kalyana Babu and Salej Sood have contributed equally to this work.

Affiliations

  1. ICAR-Vivekananda Parvatiya Krishi Anusanthan Sansthan, Almora, Uttarakhand, 263601, India

    B. Kalyana Babu, Salej Sood, Dinesh Kumar, Anjeli Joshi, A. Pattanayak & Lakshmi Kant

  2. International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502 324, India

    H. D. Upadhyaya

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  1. B. Kalyana Babu
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  2. Salej Sood
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Correspondence to B. Kalyana Babu or Salej Sood.

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Kalyana Babu, B., Sood, S., Kumar, D. et al. Cross-genera transferability of rice and finger millet genomic SSRs to barnyard millet (Echinochloa spp.). 3 Biotech 8, 95 (2018). https://doi.org/10.1007/s13205-018-1118-1

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  • DOI: https://doi.org/10.1007/s13205-018-1118-1

Keywords

  • Cross-genera transferability
  • Barnyard millet
  • SSR markers
  • Population structure
  • Orthologs