RAVIKUMAR, R. L.SUNIL SUBRAMANYA, A. E.2020-10-072020-10-072019-12-27Th-12569https://krishikosh.egranth.ac.in/handle/1/5810152702The whole genome sequence of finger millet (1.23 GB) was in silico mined for microsatellite identification and primer development using Krait software. Totally 2, 92,621 perfect microsatellites were identified with a relative abundancy of 263.62 SSR loci/Mb. The primer pairs were designed for 2,28,577 microsatellites, using Primer3 embedded in the Krait, of which 400 primer pairs were randomly chosen and synthesized for wet lab validation. The annealing temperature of 362 primers out of 400 have been determined by using the DNA samples of 4 different genotypes. One hundred primer pairs were used for validation across 45 diverse finger millet genotypes, comprising of 37 cultivated E. coracana subsp coracana genotypes from India and Africa and 8 wild Eleusine species. The gene diversity (0.09) and PIC (0.07) among the cultivated finger millet genotypes from India and Africa were lower compared to other Eleusine species (0.24 and 0.19 respectively). The molecular diversity analysis among 45 diverse finger millet accessions clearly grouped all the cultivated tetraploid accession of India in a single cluster and cultivated tetraploid accessions from Africa and Uganda into another cluster. The transferability of 100 ragi SSR to other millets revealed the highest transferability in sorghum (63 %) and least in pearl millet (43 %). The comparative genomics of microsatellite abundance revealed higher abundance of GC rich motifs in monocots genomic and coding sequence. The coding sequence of both monocots and dicots were biased towards (AG/CT)n motif and (CCG/CGG)n motifs over other motifs. The SSR genotyping of parental lines of a bi-parental mapping population (GE208 X GE156) revealed very low polymorphism with only 5 polymorphic marker. Single marker analysis showed marker trait association for plant height, finger width, peduncle length, earhead weight, days to 50 per cent flowering, number of earheads and grain yield per plant.EnglishThesis