Weedy rice, a wild relative of cultivated rice, is highly stress-resistant and proliferates in paddy fields. In this study, 353 weedy rice accessions were analyzed to identify salt-tolerance genes using population evolution analysis, phenotypic screening, genome-wide association studies (GWAS), transcriptome analysis, haplotype characterization, gene knockout experiments, and Na+ and K+ ion flux assays. Population structure analysis classified the accessions into six distinct groups. Three salt-tolerant accessions-HW131, HW136, and HW119-were identified based on leaf rolling degree (LRD), leaf withering degree (LWD), chlorophyll content (ChlC), and nitrogen content (NC) traits. GWAS and transcriptome data pinpointed LOCOs06g39270 and LOCOs06g11860 as candidate salt-tolerance genes. Haplotype analysis and qPCR confirmed two major haplotypes: AHap2 and BHap1. A 2-bp deletion (TC) at position 818 bp in LOCOs06g11860 was associated with severe salt sensitivity (phenotypic grade 7), whereas the wild-type exhibited strong tolerance (grade1). Knockout mutants exhibited significantly increased Na+ and K+ flux across mesophyll cell membranes compared to wild-type plants, validating LOCOs06g11860 (OsERFH1) as a crucial salt-tolerance gene. This study provides novel genetic insights into salt-stress adaptation in weedy rice, paving the way for breeding enhanced salt-tolerant varieties.
Zou et al. (Mon,) studied this question.