Accessing and Dissecting Genomic Regions for High Grain Iron and Zinc Content Using GWAS in Pearl Millet

On a global scale, over three billion people suffer from chronic micronutrient malnutrition with Fe and Zn deficiencies being the most prevalent. This is a persistent challenge for global development, the consequences of which predominantly apply to nutritionally vulnerable populations within developing countries. Pearl millet is accessible to most of these populations and has many nutritional properties, as compared with other staple crops. Fe and Zn levels were quantified in a pearl millet germplasm population consisting of 230 diverse lines by ICP-AES and ranged between 29.18–135.27mg/kg and 22.07–93.28mg/kg, respectively. Anti-nutritional factors affecting Fe/Zn bioavailability were also considered, including the effects of phytate and two metal chelating flavonoids ~ Apigenin and Luteolin. STRUCTURE analysis revealed insignificant population structure, further supported by PCA. The extent of LD was also assessed among all pairs of loci and found to be especially prominent on chromosomes 3 and 5. A GWAS using 3 million pearl millet SNPs, generated by GBS resulted in hundreds of significant marker trait associations for grain Fe and Zn content with P-values ranging from 3.99 E-06–7.54 E-07. Using the 4kb region surrounding the 35 most significant SNPs, a BLASTn search of the NCBI database revealed 6 candidate genes associated with Fe/Zn uptake, the most significant of which being the YUCCA-11 gene, which is known to drive Zn efficiency via auxin biosynthesis. This study can aid the breeding of elite lines with enhanced micronutrient levels in pearl millet, leading to improved health and well-being especially for women and children.