Phenotypic characterization and genetic factor identification of starch content-related traits in foxtail millet (Setaria italica L.).

Key message: Twenty-two QTL controlling starch synthesis were identified in foxtail millet, and 14 potential candidate genes were predicted. The content of starch, including amylose and amylopectin, is an essential trait for foxtail millet quality, but its complexity and genetic basis are still poorly understood. Here, a recombinant inbred line (RIL) population, comprising 215 foxtail millet lines, was employed to analyze the variation in three starch content-related traits and to identify the associated quantitative trait loci (QTL) in six environments. We found abundant phenotypic variation and very high heritability (86.52-97.77%) for three starch content-related traits among the RIL population. The QTL mapping identified 22 QTL, 36 combined QTL, and 55 epistatic QTL pairs for starch content-related traits. Of these, 17 QTL were identified in two to six environments, and three co-located QTL clusters were revealed, including the triple QTL cluster qC4.1, which was detected 16 times in six environments. The pathway-driven analysis revealed 14 candidate genes, one of which is Seita.4G022400, which encodes a granule-bound starch synthase in the starch and sucrose metabolism pathway, as the causal gene for the QTL cluster qC4.1. Using phenotypic and genotype data of 224 foxtail millet accessions, we conducted haplotype analysis for Seita.4G022400, which showed high correlations with amylose content, suggesting potential applications for Seita.4G022400 in foxtail millet starch and yield improvement. Additionally, the haplotype analysis identified five other genes (Seita.2G114900, Seita.3G209500, Seita.5G419900, Seita.2G137100, and Seita.3G011400) that exhibit high correlations with three starch content-related traits. Our results provide a foundation for further fine mapping and molecular cloning of starch content-related traits in foxtail millet.