QTL-Seq for Rapid Identification of Regulating Heading Date and Plant Height in Foxtail Millet (Setaria italica)

Foxtail millet (Setaria italica) has long history cultivation in ancient China. This crop is a member of the Poaceae grasses that is small genome (~515 Mb) with a small number of chromosomes (2n = 18). Heading date is an important agronomic trait controlled by quantitative trait loci (QTLs). The underlying molecular and genetic mechanisms that regulate heading date remain unclear in foxtail millet. QTL-seq is rapid identification of plant QTLs by whole-genome resequencing of DNAs from two populations each composed of 20-50 individuals showing different phenotype. In the present study, we applied QTL-seq to foxtail millet F₂ populations and identified QTL for heading date in the field. Foxtail millet inbred lines Yuikogane (Yui) and Shinanotsubuhime (Shi) were crossed segregating populations for QTL-seq of heading date. Field examinations shows that, Yui (50.7± 1.7) headed about 2 weeks earlier than Shi (63 ± 1.3). The segregation of heading date in F₂ population showed transgressive segregation. Most individuals headed intermediate between those of parents, Yui and Shi. However, some individuals showed extreme late heading phenotype than those parents. Genome-wide SNP profiling of extreme late heading phenotypic bulks from the F₂ population identified a significant genomic region, SiHd07 on chromosome 7 for heading date. We designed SNP/indel markers near of the QTL candidate region to confirm each individual genotyping in bulk-sample. SiHd07 was mapped to a 0.9 Mb region between 29.8 Mb-30.7 Mb on chromosome 7. Our results suggest that SiHd07 regulate extreme late heading phenotype but another QTLs affect this phenotype.