Advertisement

Journal of Plant Biochemistry and Biotechnology

, Volume 27, Issue 4, pp 401–414 | Cite as

Mapping quantitative trait loci for important agronomic traits in finger millet (Eleusine coracana) mini core collection with genomic and genic SSR markers

  • B. Kalyana Babu
  • Salej Sood
  • C. Chandrashekara
  • A. Pattanayak
  • Lakshmi Kant
Original Article
  • 71 Downloads

Abstract

Allele identification for agro-morphological traits and stress resistance is a major concern across the globe for improving productivity of finger millet. Here, we used 46 genomic and 58 genic simple sequence repeats (SSRs) markers in a set of 66 accessions used to constitute a global mini-core collection for analysing their genetic structure as a population and establishing association among markers and twenty morphological traits including resistance to finger blast. Phenotypic data revealed a wide range of variation for all traits except flag leaf width and flag leaf sheath width. We got amplification of 81 alleles by the 31 genomic SSRs at an average of 2.61 alleles per locus. Polymorphism information content (PIC) values varied from 0.21 to 0.75 and average gene diversity was 0.49. Structure analysis of the population using the genomic SSR data divided the accessions into two clusters where Indian and exotic accessions were grouped in separate clusters. Genic SSRs which were associated with blast resistance genes, amplified 36 alleles at an average of 2 alleles per locus. PIC values ranged from 0.32 to 0.37 and average gene diversity was 0.45. Population structure analysis using data from these SSRs grouped the accessions into three clusters, which broadly correspond to their reaction to blast disease. Twenty-two significant associations were found using the GLM approach for 20 agro-morphological traits both in 2012 and 2014, while, 7 and 5 significant marker-trait associations were identified using MLM in 2012 and 2014 respectively. The SSR markers FMBLEST35 and FMBLEST36 designed from the Pi21 gene sequence of rice were found to be associated with blast disease resistance in finger millet indicating that the gene homologues play a significant role in an important role for neck blast resistance.

Keywords

Finger millet Association mapping Population structure SSR Blast 

Notes

Acknowledgements

The work was supported by the Institute grant received from Indian Council of Agricultural Research, New Delhi, India. Authors are thankful to Mr. G.S. Bisht, technical officer, ICAR-VPKAS, Almora for assistance in phenotypic data generation.

Funding

The Study was funded by Indian Council of Agricultural Research.

Compliance with ethical standards

Conflict of interest

Authors declare that they have no conflict of interest.

Supplementary material

13562_2018_449_MOESM1_ESM.docx (603 kb)
Supplementary material 1 (DOCX 602 kb)
13562_2018_449_MOESM2_ESM.doc (262 kb)
Supplementary material 2 (DOC 262 kb)

References

  1. Arya L, Verma M, Gupta VK, Karihaloo JL (2009) Development of EST SSRs in finger millet (Eleusine coracana ssp coracana) and their transferability to pearl millet (Pennisetum glaucum). J Plant Biochem Biotech 18(1):97–100CrossRefGoogle Scholar
  2. 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 41:5287–5297CrossRefGoogle Scholar
  3. Babu BK, Agrawal PK, Pandey D, Kumar A (2014b) Comparative genomics and association mapping approaches for opaque2 modifier genes in finger millet accessions using genic, genomic and candidate gene-based simple sequence repeat markers. Mol Breed 34:1261–1279CrossRefGoogle Scholar
  4. Babu BK, Pandey D, Agrawal PK, Sood S, Chandrashekara C et al (2014c) 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 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bharathi A (2011) Phenotypic and genotypic diversity of global finger millet (Eleusine coracana (L.) Gaertn.) composite collection. Dissertation, Tamil Nadu Agriculture University, IndiaGoogle Scholar
  6. Bodmer WF (2011) Human genetics: the molecular challenge. Cold Spring Harb Symp Quant Biol 51:1–13CrossRefGoogle Scholar
  7. Bradbury P, Zhang Z, Kroon D, Casstevens T, Ramdoss Y, Buckler E (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23(19):2633–2635CrossRefGoogle Scholar
  8. 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
  9. 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 1:131–141CrossRefGoogle Scholar
  10. 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
  11. Fukuoka S, Okuno K (2001) QTL analysis and mapping of pi21, a recessive gene for field resistance to rice blast in Japanese upland rice. Theor Appl Genet 103:185–190CrossRefGoogle Scholar
  12. IBPGR (1985) Descriptors for finger millet. International Board for Plant Genetic Resources Secretariat, Rome, Italy. http://www.bioversityinternational.org. http://www.bioversityinternational.org/fileadmin/user_upload/online_library/publications/pdfs/417.pdf. Accessed 2 Feb 2017
  13. Jeung JU, Kim BR, Cho YC, Han SS, Moon HP, Lee YT, Jena KK (2007) A novel gene, Pi40(t), linked to the DNA markers derived from NBS-LRR motifs confers broad spectrum of blast resistance in rice. Theor Appl Genet 115:1163–1177CrossRefGoogle Scholar
  14. Kumar A, Sharma N, Panwar P, Gupta AK (2012) Use of SSR, RAPD markers and protein profiles based analysis to differentiate Eleusine coracana genotypes differing in their protein content. Mol Biol Rep 39(4):4949–4960CrossRefGoogle Scholar
  15. Kumar A, Yadav S, Panwar P, Gaur VS, Sood S (2015) Identification of anchored simple sequence repeat markers associated with calcium content in finger millet (Eleusine coracana). Proc Natl Acad Sci India Sect B Biol Sci 85(1):311–317CrossRefGoogle Scholar
  16. Liu K, Muse M (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129CrossRefGoogle Scholar
  17. Mott R, Talbot CJ, Turri MG, Collins AC, Flint J (2000) From the cover: a method for fine mapping quantitative trait loci in outbred animal stocks. Proc Natl Acad Sci USA 97:12649–12654CrossRefGoogle Scholar
  18. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4326CrossRefGoogle Scholar
  19. Nagaraja A, Jagadish PS, Ashok EG, Krishne Gowda KT (2007) Avoidance of finger millet blast by ideal sowing time and assessment of varietal performance under rainfed production situations in Karnataka. J Mycopathol Res 45(2):237–240Google Scholar
  20. Nirgude M, KalyanaBabu B, Shambhavi Y, 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):1189–1200CrossRefGoogle Scholar
  21. Pritchard JK, Wen W (2003) Documentation for the structure software, version 2. Department of Human Genetics, University of Chicago, Chicago. http://pritchardlab.stanford.edu/software/readme_2_1/. Accessed 2 Feb 2017
  22. Ramakrishnan M, Antony Ceasar S, Duraipandiyan V, AlDhabi NA, Ignacimuthu S (2016a) 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 5:120CrossRefGoogle Scholar
  23. Ramakrishnan M, Antony Ceasar S, Duraipandiyan V, AlDhabi 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(2):361–376CrossRefGoogle Scholar
  24. Rao ANS (1990) Estimates of losses in finger millet (Eleusine coracana) due to blast disease (Pyricularia grisea). J Agric Sci 24:57–60Google Scholar
  25. Reddy INBL, Narasu ML, Sivaramakrishnan S (2012) Identification and characterization of EST-SSRs in finger millet (Eleusine coracana (L.) Gaertn.). J Crop Sci Biotechnol 15(1):9–16CrossRefGoogle Scholar
  26. Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138CrossRefGoogle Scholar
  27. Roy S, Banerjee A, Mawkhlieng B, Misra AK, Pattanayak A, Harish GD, Singh SK, Ngachan SV, Bansal KC (2015) Genetic diversity and population structure in aromatic and quality rice (Oryza sativa L.) landraces from north-eastern India. PLoS ONE 10(6):e0129607.  https://doi.org/10.1371/journal.pone.0129607 CrossRefPubMedPubMedCentralGoogle Scholar
  28. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422CrossRefGoogle Scholar
  29. Udupa SM, Baum M (2001) High mutation rate and mutational bias at (TAA)n microsatellite loci of chickpea (Cicer arietinum L.). Mol Genet Genomics 265:1097–1103CrossRefGoogle Scholar
  30. Upadhyaya HD, Gowda CLL, Pundir RPS, Reddy VG, Singh S (2006) Development of core subset of finger millet germplasm using geographical origin and data on 14 quantitative traits. Genet Resour Crop Evol 53:679–685CrossRefGoogle Scholar

Copyright information

© Society for Plant Biochemistry and Biotechnology 2018

Authors and Affiliations

  1. 1.ICAR-Vivekananda Institute of Hill AgricultureAlmoraIndia
  2. 2.ICAR-Indian Institute of Oil Palm ResearchPedavegiIndia
  3. 3.ICAR-Central Potato Research InstituteShimlaIndia

Personalised recommendations