Background: Genetic diversity of finger millet (
Eleusine coracana
), a nutritious neglected staple cereal in Africa
and South Asia is largely uncharacterized. This study analysed 82 published SSR markers for finger millet
across 10 diverse accessions to compile an informative set for genetic characterisation. Extensive optimization
compared single samples with bulked leaf or bulked DNA samples for capturing within accession genetic
diversity. The markers were evaluated to determine (1) how efficiently they amplified target loci during
high-throughput genotyping with a generic PCR protocol, (2) ease of scoring PCR products and (3)
polymorphism and ability to discern genetic diversity within the tested finger millet germplasm.
Results: Across 88 samples, the 52 markers that worked well amplified 274 alleles, ranging from 2 to 14 per locus
with a mean of 4.89. Major allele frequency ranged from 0.18 to 0.93 with a mean of 0.57. Polymorphic
Information Content (PIC) ranged from 0.13 to 0.88 with a mean of 0.5 and availability varied between 64 and
100% with a mean of 92.8%. Heterozygosity ranged from 0 to 1.0, with a mean of 0.26.
Discussion: Five individual samples from an accession captured the largest number of alleles per locus compared
to the four different bulked sampling strategies but this difference was not significant. The identified set
comprised 20 markers: UGEP24, UGEP53, UGEP84, UGEP27, UGEP98, UGEP95, UGEP64, UGEP33, UGEP67,
UGEP106, UGEP110, UGEP57, UGEP96, UGEP66, UGEP46, UGEP79, UGEP20, UGEP12, UGEP73 and UGEP5 and
was since used to assess East African finger millet genetic diversity in two separate studies.
