Genome-Wide Association Study in Finger Millet for Resistance to Striga

Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive under extreme environmental conditions. The parasitic weed, Striga hermonthica, is one of the most destructive factors limiting finger millet production in Kenya. One hundred finger millet genotypes were evaluated for resistance against Striga under field conditions at Alupe and Kibos sites in Western Kenya. The genotypes were planted in control and experimental plots inoculated with Striga. Plant growth of plants was monitored from seedling stage to maturity. Data was taken for days to Striga germination and number of Striga plants per plot at 50% flowering and 50% maturity. All accessions were genotyped-by-sequencing (GBS) and data analyzed using the non-reference based Universal Network Enabled Analysis Kit (UNEAK) pipeline (Lu et al. 2013). Both genotypic and phenotypic data were imported into TASSEL and analysed using General Linear Model (GLM) and Mixed Linear Model (MLM). Sequences with SNP markers showing significant association with Striga were retrieved and used to search against public databases for functional characterization. Six genotypes showed high resistance to Striga with a mean Striga count of 0 while the most susceptible genotype had Striga count mean of 69.17 at maturity. We identified at least 12 SNPs showing significant association with Striga and the top 6 were further validated across the same germplasm panel using High-Resolution Melt analysis. Our results reveal the power of Next Generation Sequencing in developing functional markers for orphan crops such as finger millet.