Genetic variability and genome‐wide marker association studies for starch traits contributing to low glycaemic index in pearl millet

Pearl millet grains are naturally rich in high quality starch, dietary fibre, polyphenols and important micronutrients. Grains from a random subset of the global diversity panel (PMiGAP) comprising 166 pearl millet accessions were assessed for total starch (TS), rapidly digestible Starch (RDS), slowly digestible starch (SDS) and resistant starch (RS) content based on available glucose percentage after digestion at various time points. Highly significant genetic variations for SDS, RS and other starch traits were evident amongst the PMiGAP accessions leading to the identification of best accessions for use in the future pearl millet-breeding programmes. To identify potential candidate genes associated with these starch traits, genome-wide association studies (GWAS) were performed using 78K single-nucleotide polymorphisms (SNPs) well distributed across the seven chromosomes of pearl millet. A total of 902 SNPs showed a strong association with various starch traits at -log p-value range from 4.0–9.08. A total of 364 probable candidate genes were identified in the flanking regions of the significantly associated SNPs and high LD (linkage disequilibrium) region, which explains a correlation between nearby variants. Out of these, 19 probable candidate genes exhibited functional relationships with the starch biosynthesis pathway. Three starch synthase genes (Pgl_GLEAN_10026059 and Pgl_GLEAN_10027180) were found to be key probable candidate genes for SDS owing to their prior demonstrated involvement in amylose biosynthesis. Pgl_GLEAN_10018323, encoding β-amylase and Pgl_GLEAN_10009197, encoding α-amylase enzyme were identified as probable candidate genes for RDS content. The genetic variability being reported for SDS and RS in the germplasm panel, and the SNP markers associated with such variability, raises the possibility of developing pearl millet varieties with low glycaemic index using conventional and molecular breeding approaches.