Genome-wide association mapping of agronomic and quality traits in foxtail millet

Abstract Foxtail millet [Setaria italica L.] is a particularly momentous cereal and forage crop in arid and semi-arid regions, and was recognised worldwide for its potential as a health-promoting functional food. An understanding of the genomic variation and alleles underpinning its agronomic and quality traits is important for improving foxtail millet breeding. Therefore, high-quality single nucleotide polymorphisms (SNPs) to perform a genome-wide association study (GWAS) was employed to better understand the diversity of foxtail millet and facilitate the genetic dissection of its key traits. Using genotyping-by-sequencing, 107 foxtail millet accessions were sequenced; further analysis revealed 72,181 high-quality SNPs, 46 of which were significantly associated with 13 agronomic and quality traits. These SNPs were distributed across the 8 chromosomes; 36 were located in intergenic regions, whereas 1 and 5 SNPs were located in exon and intron regions, respectively. The GWAS revealed that 28 SNPs were associated with a single trait (Peak time). For some of the significant SNPs, favourable genotypes showed pyramiding effects for several traits. The 46 loci identified in present study will therefore be helpful for breeding plans aimed at foxtail millet improvement. Overall, the results provide sufficient fundamental for excellent cultivar breeding in the sustainable development of foxtail millet.