Genome Sequence and Association Analysis Reveal Allelic Variants for Agronomically Important Traits in Foxtail Millet (Setaria italica L.) Germplasm

Foxtail millet ( Setaria italica L.), a small-grained, diploid C4 panicoid millet with a genome size of 515 Mb, is the second most widely cultivated crop globally. It serves as a model species for agronomic and nutritional research. This study employed double-digest restriction-site-associated DNA sequencing (ddRAD-seq) to characterize genomic variation within 30 foxtail millet genetic resources. The analysis identified 206,483 high-quality polymorphic SNPs through NGS-ddRAD path. Number of SNPs on individual genotypes ranged from 1184(Si-7) to 131873 (Si-3) at Read Depth 10. Results revealed three distinct clusters, effectively separating most landraces and released cultivars, thereby indicating population differentiation based on their classification and geographic origin. Among the landraces, genotypes Si-17, Si-15, Si-5, and Si-16 exhibited high yields, early flowering, and early maturation compared to release cultivars Further examination of SNPs in landraces uncovered variations in minor allele frequency (MAF), highlighting high-frequency alleles within the Setaria genotype. A total 83 significant MTAs (Marker-trait associations) were identified by GWAS for Eight traits across the genome. High confidence MTAs for three important traits including total tiller number per panicle (TNPP), Plant base color (PBC), and Grain weight per panicle (GWPa) were identified. These MTAs facilitated the identification of 57 candidate genes with potential applications in molecular breeding. Additionally, a mini-core selection of 30 genotypes, representing the majority of genetic diversity indicated notable genetic traces of landraces, particularly for those three traits. These landraces show promise for use in breeding programs aimed at developing climate-resilient foxtail millet varieties.