DEVELOPMENT, VALIDATION AND TRANSFERABILITY OF NOVEL MICROSATELLITE MARKERS AND THEIR UTILIZATION TO TAG IMPORTANT SEED YIELD CONTRIBUTING TRAITS IN FINGER MILLET [Eleusine coracana (L.) Gaertn]
Loading...
Files
Date
2019-12-27
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
UNIVERSITY OF AGRICULTURAL SCIENCES GKVK, BENGALURU
Abstract
The 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.