Phenotypic evaluation and mapping QTLs for drought tolerance in an interspecific RIL population from a Setaria italica × Setaria viridis cross

BACKGROUND: Drought tolerance is an important breeding objective for improving the yield of cereal crops. Identifying key drought-tolerant loci/genes from Setaria viridis and Setaria italica is essential for enhancing the yield and stress resistance of foxtail millet via molecular breeding technologies. RESULTS: Here, an interspecific recombinant inbred line (RIL) population was constructed by crossing the S. italica cultivar Yugu1 with the wild S. viridis H1. Phenotypic evaluation and QTL mapping for drought tolerance were conducted from the grain filling to the maturity stage. Five strong drought-tolerant lines were screened using the drought resistance index (DRI). Phenotypic variance analysis indicated that the period of duration was the key factor affecting drought tolerance in the population. Furthermore, the RIL population was subjected to whole-genome sequencing, and a high-density linkage map was constructed, comprising 3,029 bin markers spanning 709.34 cM with an average interval of 0.24 cM. A total of 10 QTLs were detected for panicle number per plot (PNP), grain weight per plant (GWP), and 1000-grain weight (TGW). Eight QTLs were associated with PNP, and the favorable alleles at all loci except qPNP4.1 were derived from Setaria viridis H1. The favorable alleles of the other two QTLs for GWP and TGW were all from Yugu1. Based on functional homology alignment, five genes located within three PNP-related QTL intervals (Seita.5G420900, Seita.7G306400, Seita.5G312700, Seita.5G319000, Seita.5G319500) were predicted to modulate the tillering, grain yield under drought stress conditions. CONCLUSION: These findings provide an important basis for drought-tolerant breeding and the dissection of the drought tolerance mechanisms in foxtail millet and its close species.