Identification of a stable major locus and candidate genes for drought tolerance during wheat germination

We identified QRSH.scwl-4B as a pleiotropic QTL for basal shoot growth and drought-stress response at the wheat germination stage, predicted its putative candidate genes, and confirmed it as a promising locus for drought-tolerance and limited yield loss. Drought stress during germination severely reduces the wheat germination rate and seedling establishment, leading to significant yield losses. Understanding the genetic control of this trait is important for breeding drought-tolerant and high-yielding wheat varieties. Here, we detected 21 quantitative trait loci (QTLs) for maximum root length (MRL), root number (RN) and shoot height (SH) under control (CK) and drought treatment (DT) at the germination stage using a recombinant inbred line (RIL) population. Among them, QSH.scwl-CK-4B, QSH.scwl-DT-4B and QRSH.scwl-4B were co-localized to a common region on chromosome arm 4BS, which exhibited pleiotropic effects on both basal shoot growth and the drought-stress response. QRSH.scwl-4B was also identified by bulked segregant analysis sequencing (BSA-Seq), mapped to a 2.09 Mb interval on 4BS, and explained 24.32%-30.89% of the phenotypic variation (PVE). Through RNA-seq, BSA-Seq and parental genome sequencing, TraesCS4B03G0104700 and TraesCS4B03G0102800 were identified as the putative candidate genes. KEGG enrichment analysis suggested that TraesCS4B03G0104700 may regulate drought tolerance during germination via jasmonic acid (JA) biosynthesis. Moreover, the positive allele of QRSH.scwl-4B increased productive tiller number (PTN) by 13.37%, while showing only limited adverse effects on other yield-related traits. This suggests that QRSH.scwl-4B is a promising locus for improving wheat drought tolerance, with potentially minimal negative impact on yield. Collectively, these findings provide a foundation for cloning QRSH.scwl-4B and for improving drought tolerance in wheat through molecular breeding.