Genome-wide association study for dissecting lipid and fatty acid variation in a global collection of pearl millet germplasm

Pearl millet ( Pennisetum glaucum ) is a highly nutritious and climate resilient cereal cultivated on marginal lands in Asia and Africa underscoring its importance in global food security. Despite its nutritional value, the lipid and fatty acid variation and their genetic factors in pearl millet remain poorly understood. The Pearl Millet Inbred Germplasm Association Panel (PMiGAP), encompassing global diversity, provides a unique opportunity to explore these traits. This study investigated the variation in lipid and fatty acid composition within the PMiGAP population and applied GWAS to identify candidate genes. The total lipid content ranged from 3.93 % to 9.49 % with fourteen different fatty acids detected in this study. The linoleic acid and oleic acid were the most abundant fatty acids found in the PMiGAP. Palmitic acid varied from 4.35 % to 11.13 %, stearic acid from 0.12 % to 4.63 %, oleic acid from 7.33 % to 64.47 %, linoleic acid from 28.31 % to 85.51 %, and linolenic acid from 0.34 % to 1.69 %. Further, GWAS identified 64 significant marker-trait associations and 52 candidate genes within a 50 kb distance near these associations. The study provided novel insights on the genetic architecture of lipids and fatty acids, and a set of SNPs and candidate genes, which could be exploited in deriving pearl millet varieties through marker assisted breeding. • Wide genetic variation identified for lipid content and fatty acid in PMiGAP. • The linoleic and oleic acid were most abundant fatty acids in the PMiGAP. • GWAS identified 64 SMTAs and 52 candidate genes within a 50 kb distance. • Fifteen genes within 1 kb exhibited strong marker trait associations (-log10P≥6). • The IP10085, IP11584, IP7967 and IP11765 have high essential (omega2&3) fatty acids.