Electronic Journal of Plant Breeding, 9 (2) : 564-576 (June 2018) ISSN 0975-928X 564 DOI: 10.5958/0975-928X.2018.00069.8 Research Article Assessment of molecular diversity in an elite set of finger millet ( Eleusine coracana (L.) Gaertn.) genotypes using SSR markers Manjappa 1 , Santosh Deshpande 2* , S. Rangaiah 3 and M.V.C. Gowda 4 * 1 Central Tasar Research and Training Institute, Ranchi, Jharkhand, India. 2 International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana State, India. 3 University of Agricultural Sciences, GKVK, Bengaluru, Karnataka, India. 4 Project Coordinating Unit (Small Millets), AICSMIP, Bengaluru, Karnataka, India. *E-Mail: mvcgowdapb@gmail.com; s.deshpande@cgiar.org (Received:28 Oct 2017; Revised: 28 May 2018; Accepted:28 May 2018) Abstract Genetic diversity was assessed among 47 elite finger millet genotypes (29 varieties and 18 African and Asian germplasm) using 16 SSR markers. Owing to polyploidy nature of crop seven SSR markers have amplified more than one dose of alleles per genotype. Thirteen markers were polymorphic with polymorphic information content from 0.02 (UGEP56) to 0.61 (UGEP64) with an average of 0.22. A total of 72 alleles were detected across genotypes and alleles per SSR marker loci ranged from 1 to 14 (UGEP107) with an average of 4.69. UPGMA based dendrogram generated by Jaccard’s similarity coefficient had grouped 47 genotypes in to three clusters and they were widely distributed on two dimension principle component analysis graph. Analysis of molecular variance revealed higher polymorphism in varieties (53.39 %) than in germplasm (39.71 %), implying higher genetic variability in cultivated varieties. The information gathered in the study will be useful in planning hybridization for further finger millet improvement. Key words Finger millet, molecular diversity, SSR marker, AMOVA, cluster Introduction Cultivated finger millet (Eleusine coracana subsp. coracana) is an allotetraploid (2n=4x=36) nutri- cereal crop species of the family Poaceae and sub- family Chloridoideae Srinivasachary et al. (2007). It has adapted to wide range of harsh eco-geographical conditions with minimal input and providing critical genetic resources for millions of poor farmers upon which they depend for staple food and livelihood income in infertile and marginal areas Hilu et al., (1979). It is the fourth most important millet covering 10 per cent of the global millet area in over 25 countries of Asia and Africa. India is the leading producer with an area of 1.13 million hectare and production of 1.82 million tonnes (MAFW, 2015-16) and major states growing finger millet are Karnataka, Tamil Nadu, Andhra Pradesh, Odisha, Maharashtra, Uttarakhand, Jharkhand and Gujarat. Nutritionally it is rich in dietary fibre, calcium, iron, manganese and methionine (Pragya and Rita, 2012), which are low or lacking in diets of millions who use rice as staple food. Because of its high nutritional value and excellent storage quality it is known as food security crop Dida et al.(2007). It has some medicinal properties also viz., hypoglycemic, hypocholestromic and is rich in antioxidants, hence highly valued for diabetics and for better gastrointestinal health Devi et al.( 2011). Assessment of genetic diversity of genotypes gives an idea to the breeder before attempting any hybridization program. Generally morphological traits are used in the assessment of genetic diversity, where phenotypic expression is invariably influenced by the environment. Use of Deoxyribonucleic Acid (DNA) markers which are environment insensitive would help in assessment of genetic variation at DNA level, which is more precise. In finger millet molecular diversity has been assessed using different marker systems viz., Random Amplified Polymorphic DNA (RAPD) Karad et al. (2013), Inter-Simple Sequence Repeat (ISSR) (Prabhu and Meenakshi 2013; Zuge et al. (2018), Simple Sequence Repeat (SSR) Prabhu and Meenakshi (2013); Nethra et al. (2014); Manyasa et al.(2015); Santie et al.(2015); Ramakrishnan et al.(2016); Gimode et al.(2016); Pandian et al.(2018) and Single Nucleotide Polymorphism (SNP) markers Kumar et al.(2016); Gimode,(2016). Among different marker systems SSR marker is more appropriate for assessing genetic diversity because it