| Summary: | Drought tolerance is one of the most important targets for wheat breeding. Previous population genetics studies have uncovered 20 large-effect quantitative trait loci (QTLs) that contribute to stress-responsive agronomic traits. Here, we identified 19,035,814 single nucleotide polymorphisms and 719,049 insertion/deletion variations in the genomes of two popular winter wheat cultivars, Lu-Mai 14 and Han-Xuan 10, using a whole-genome re-sequencing assay. There were 4972 loss-of-function mutations carried by protein-coding genes, such as <i>CCA1/LHY</i>, <i>AGO1</i>, <i>ABI3/VP1</i>, <i>EIN3</i>, <i>T</i><i>PP</i>, and <i>ARFs</i>. We carried out a time-course abscisic acid (ABA)-treatment experiment and profiled 61,251 expressed genes in the roots using a strand-specific RNA sequencing approach. A large number of genes showed time-point specific and/or cultivar-preferential responsive expression patterns. Gene ontology enrichment analysis revealed that ABA-responsive genes were associated with stress-related functions. Among the 20 QTLs, we uncovered 306 expressed genes with high- and/or moderate-effect variations and 472 differentially expressed genes. Detailed analysis and verification of the homozygous genomic variations in the candidate genes encoding sulfotransferase, proteinase, kinase, nitrate transporter, and transcription factors suggested previously unexpected pathways associated with abiotic stress responses in wheat.
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