Multi-environment GWAS identifies genomic regions underlying grain nutrient traits in foxtail millet (Setaria italica)

Abstract

A total of 104 foxtail millet accessions were evaluated for 11 nutrients in three environments and 67 high-confidence marker-trait associations (MTAs) were identified. Six SNPs showed pleiotropic effect and associated with two or more nutrients, whereas 24 candidate genes were identified for 28 MTAs involving seven traits. Millets are known for their better nutritional profiles compared to major cereals. Foxtail millet (Setaria italica) is rich in nutrients essential to circumvent malnutrition and hidden hunger. However, the genetic determinants underlying this trait remain elusive. In this context, we evaluated 104 diverse foxtail millet accessions in three different environments (E1, E2, and E3) for 11 nutrients and genotyped with 30K SNPs. The genome-wide association study showed 67 high-confidence (Bonferroni-corrected) marker-trait associations (MTAs) for the nutrients except for phosphorus. Six pleiotropic SNPs were also identified, which were associated with two or more nutrients. Around 24 candidate genes (CGs) were identified for 28 MTAs involving seven nutrients. A total of 17 associated SNPs were present within the gene region, and five (5) were mapped in the exon of the CGs. Significant SNPs, desirable alleles and CGs identified in the present study will be useful in breeding programmes for trait improvement.