ORIGINAL ARTICLE 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 1,2 • Salej Sood 1,3 • C. Chandrashekara 1 • A. Pattanayak 1 • Lakshmi Kant 1 Received: 18 June 2017 / Accepted: 8 February 2018 Ó Society for Plant Biochemistry and Biotechnology 2018 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 Á Association mapping Á Population structure Á SSR Á Blast Introduction Finger millet is a potential nutraceutical food grain crop, widely grown in East Africa and India. It is highly self- fertilized allotetraploid (2n = 4x = 36) annual plant, belongs to Poaceae family. It has a wide range of seasonal adaptation, and is grown at sea level i.e. Andhra Pradesh and Tamil Nadu to high hills (Uttarakhand, Sikkim and Arunachal Pradesh) in India. Its seeds are consumed in variety of forms, such as unleavened bread (roti), thin or thick porridge, fermented porridge, and also used in brewing. Karnataka state is the major producer of finger millet in India, where it is mostly consumed in the form of finger millet balls (locally known as ragi mudde). The crop has high nutritional value, storage quality and also provides food security because of its climate resilience (Dida et al. 2007). Grains are rich source of calcium, dietary fibre and B. Kalyana Babu and Salej Sood have contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13562-018-0449-7) contains supplementary material, which is available to authorized users. & A. Pattanayak apat.icarneh@gmail.com 1 ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand 263601, India 2 Present Address: ICAR-Indian Institute of Oil Palm Research, Pedavegi, Andhra Pradesh 534450, India 3 Present Address: ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001, India 123 Journal of Plant Biochemistry and Biotechnology https://doi.org/10.1007/s13562-018-0449-7