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. PattanayakEmail author
  • Lakshmi Kant
Original Article


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.


Finger millet Association mapping Population structure SSR Blast 



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.


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)


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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

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