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Genome-wide association study (GWAS) delineates genomic loci for ten nutritional elements in foxtail millet (Setaria italica L.)

Jaiswal, Vandana, Bandyopadhyay, Tirthankar, Gahlaut, Vijay, Gupta, Sarika, Dhaka, Annvi, Ramchiary, Nirala, Prasad, Manoj
Journal of cereal science 2019 v.85 pp. 48-55
Setaria italica, alleles, boron, breeding, calcium, developing countries, food crops, genetic markers, genome-wide association study, genomics, grain crops, haplotypes, human health, iron, loci, magnesium, manganese, millets, nickel, nutrient content, nutrient deficiencies, nutritive value, phosphorus, potassium, single nucleotide polymorphism, sulfur, zinc
Nutritional deficiency is found to be a major threat to human health, especially in low-income countries. Thus it is essential to improve nutritional qualities of important food crops. Foxtail millet is second largest cultivated millet and 2–5 times nutritionally richer than major cereal crops. During the present study, we identified genetic determinants of ten nutritional elements including potassium, nickel, calcium, boron, magnesium, phosphorus, sulphur, zinc, manganese and iron for the first time in foxtail millet. For this purpose, genome-wide association studies (GWAS) were conducted using 93 diverse accessions and 10 K SNPs (distributed across all the nine foxtail millet chromosomes). Altogether, 74 marker-trait associations (MTAs) were identified to be associated with above mentioned ten elements, out of which ten (10) MTAs (associated with B, Mg, Zn and Fe) showed high confidence [-log(p) > 5.78]. Identified desirable SNP alleles and favourable haplotypes may prove useful in foxtail breeding. Also, significant pyramiding effect suggested that associated elements can be substantially enhanced through combining more than one MTA. Candidate genes residing within or near the association signal may be selected for functional characterization. Superior genotypes identified may prove as a potential donor in foxtail millet breeding assisted through the molecular marker.