Genome-wide association study reveals the genetic architecture of grain calcium accumulation in finger millet

Calcium (Ca) is an essential macromineral and required in relatively large dietary quantities for maintaining a sound overall health. Therefore, significant progress is needed for biofortification of staple crops to enhance grain Ca content. Among all cultivated cereals, finger millet [Eleusine coracana (L.) Gaertn.], has the highest concentration of Ca (350mg/100g) in its grains and can serve as
an excellent sustainable candidate for Ca biofortification. With the aim to identify genomic loci underlying grain Ca content, we performed genome-wide association (GWA) analysis utilizing a world collection of finger millet germplasm. Grain Ca contents showed very high variability among the collection with distinct differences observed among African, Asian, European and American
genotypes. Large-scale genotyping-by sequencing was employed and 154238 bialleleic, polymorphic SNPs with a MAF ≥ 1 % across the genotypes were employed for GWA mapping. Associations were done by fitting three statistical models. After correction for population structure and family relatedness, loci showing strong associations with grain Ca content have been identified. This is the first GWA study based on large-scale SNP genotyping in finger millet for grain Ca content. The novel genomic loci identified can facilitate positional cloning of underlying causal genes. These results will facilitate further improvement of finger millet and also other staple crops. Such crops will be a tremendous boost for smallholder farmers, agriculture sectors, and food industries which will help to reduce the burden of Ca deficiency.