Genetic dissection of foxtail millet bristles using combined QTL mapping and RNA-seq

QTL mapping of two RIL populations in multiple environments revealed a consistent QTL for bristle length, and combined with RNA-seq, a potential candidate gene influencing bristle length was identified. Foxtail millet bristles play a vital role in increasing yields and preventing bird damage. However, there is currently limited research on the molecular regulatory mechanisms underlying foxtail millet bristle formation, which constrains the genetic improvement and breeding of new foxtail millet varieties. This study leveraged genetic linkage maps from two populations: the published RYRIL population (Hongjiugu × Yugu 18) with 1420 bins and the newly established YYRIL population (Huangruangu × Yugu 18) with 542 bins. We identified 17 QTLs associated with bristle length, explaining 1.76-47.37% of the phenotypic variation. Among these, 6 were multi-environment QTLs, and 11 were environment-specific QTLs. Notably, qBL-1-1 and qBL-3-2 were detected in both populations, and exhibited epistasis interactions. By analyzing genotypic data from the RYRIL population and its parents, we identified two lines with significant variation in bristle length at the qBL-1-1 locus, designated CM3 (short) and CM4 (long). RNA-seq during the flowering phase identified 1812 differentially expressed genes (DEGs). Thirty-three DEGs were identified within 6 multi-environment QTL regions, and the RNA-seq results were validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Within the qBL-1-1 region, Seita.1G325800 is predicted to be a key candidate gene controlling foxtail millet bristle length. These findings provide preliminary insights into the genetic basis of bristle development and lay a foundation for the genetic improvement of foxtail millet bristle length.