Genome-wide association mapping and comparative genomics identifies genomic regions governing grain nutritional traits in finger millet (Eleusine coracana L. Gaertn.)

Abstract

Micronutrient deficiency is a serious and underestimated global health concern. Identifying existing micronutritional richness in traditional crops, and breeding this potential into staple crops that are more frequently consumed, could offer a potential low-cost, sustainable solution to micronutrient deficiency. Here, we provide the first insight into genetic control of grain micronutrient content in the staple food crop finger millet (Eleusine coracana). Quantifying the existing natural variation in nutritional traits, and identifying the regions of the genome associated with these traits, will underpin future breeding efforts to improve not only global food and nutrition security, but also human health. Summary: Finger millet is an excellent cereal crop to alleviate micronutrient malnutrition in marginal communities because of its nutrient-dense grains. Identification of the alleles governing these characteristics will help to develop improved germplasm. An assembly of 190 genotypes was evaluated for six minerals (iron, zinc, calcium, magnesium, potassium, and sodium) and protein content. A combination of genotyping-by-sequencing (GBS) and genome-wide association study (GWAS) was applied to identify marker-trait associations (MTAs). Candidate genes underlying significant associations were predicted through comparative mapping with other cereals. A wide range of variation was observed for all traits. GBS generated 169,365 single-nucleotide polymorphisms and three subpopulations were identified. GWAS, using general linear and mixed model approaches to correct for population structure and genetic relatedness, identified 418 common markers (p-value ≤ 10–3, FDR < 0.1) linked with mineral content. Of these, 34 markers crossed the Bonferroni threshold, out of which 18 showed homology with candidate genes having putative functions in binding, remobilization or transport of metal ions. This is the first report to utilize the phenotypic variability of grain minerals in finger millet genotypes to identify MTAs and predict associated putative candidate genes. Postvalidation, these markers may be employed to improve grain nutrient quality through marker-assisted breeding.