QTL-seq analysis identifies two genomic regions determining the heading date of foxtail millet, <i>Setaria italica</i> (L.) P.Beauv.

Abstract

Heading date is an important event to ensure successful seed production. Although foxtail millet (<i>Setaria italica</i> (L.) P.Beauv.) is an important foodstuff in semiarid regions around the world, the genetic basis determining heading date is unclear. To identify genomic regions regulating days to heading (DTH), we conducted a QTL-seq analysis based on combining whole-genome re-sequencing and bulked-segregant analysis of an F₂ population derived from crosses between the middle-heading cultivar Shinanotsubuhime and the early-heading cultivar Yuikogane. Under field conditions, transgressive segregation of DTH toward late heading was observed in the F₂ population. We made three types of bulk samples: Y-bulk (early-heading), S-bulk (late-heading) and L-bulk (extremely late-heading). By genome-wide comparison of SNPs in the Y-bulk vs. the S-bulk and the Y-bulk vs. the L-bulk, we identified two QTLs associated with DTH. The first QTL, <i>qDTH2</i>, was detected on chromosome 2 from the Y-bulk and S-bulk comparison. The second QTL, <i>qDTH7</i>, was detected on chromosome 7 from the Y-bulk and L-bulk comparison. The Shinanotsubuhime allele for <i>qDTH2</i> caused late heading in the F₂ population, whereas the Yuikogane allele for <i>qDTH7</i> led to extremely late heading. These results suggest that allelic differences in both <i>qDTH2</i> and <i>qDTH7</i> determine regional adaptability in <i>S. italica</i>.