Weedy rice (WR) (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among WR, landrace rice (LR), improved rice (IR) cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that WR populations have the highest level of genetic diversity (H_e = 0.8386) and can be divided into two groups (japonica‐type and indica‐type). The japonica‐type WR accessions from Heilongjiang province (HLJ), Jilin province (JL), Liaoning province (LN), and NX provinces clustered with the landraces grown in these same provinces. The indica‐types from Jiangsu province (JS) also clustered with the indica‐type landraces from JS province. Comparative transcriptome analysis of WR‚ IR and LR from HLJ, JL, and LN provinces showed that the WR still clustered with the LR, and that the IR lines comprise a single population. Thirty‐two differentially expressed genes were shared by the IR and LR groups as well as between the IR and WR groups. Using Gene ontology (GO) analysis, we identified 19 shared GO terms in the IR and LR groups as well as between the IR and WR groups. Our results suggest that WR populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN provinces suggests that IR populations have become a end point in the evolution of WR, which provides a new perspective for the study of WR origins and lays a solid foundation for rice breeding.

Direct-seeded rice (DSR) cultivation is an effective and important way to resolve agricultural labor scarcity, water scarcity and high production cost issues. Mesocotyl elongation (ME) is the main driver of the rapid emergence of rice seedlings from the soil and is an important indicator of the suitability of rice varieties for direct seeding. Hence, discovering ME-related genes is particularly important for breeding rice varieties suitable for direct seeding. In this study, a chromosome segment substitution line (CSSL) population generated from a cross between Dongxiang common wild rice and Nipponbare (Nip) was used to map quantitative trait loci (QTLs) for ME. Two QTLs for mesocotyl length were identified on chromosomes 3 and 6 with logarithm of odds (LOD) scores ranging from 5.47 to 6.04 and explaining 15.95–16.79% of the phenotypic variance. Among these QTLs, qML6 accounted for the highest phenotypic variance (16.79%). Then, to confirm the strongest QTL, we generated an F₂ segregating population via the CSL127 line harboring the qML6 locus and the recurrent parent Nip. The QTL qML6-1 associated with ME was mapped to a location between markers DX-C6-2 and DX-C6-4, which is consistent with the location of the previously mapped QTL qML6. qML6-1 had an LOD score of 8.45 and explained 30.56% of the phenotypic variance. The QTLs detected in this study provide promising targets for further genetic characterization and for use in marker-assisted selection to develop varieties with improved ME for the cultivation of DSR.

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 LOC_Os06g39270 and LOC_Os06g11860 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 LOC_Os06g11860 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 LOC_Os06g11860 (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.

Salt stress is one of the major abiotic factors limiting rice yield, with the tillering stage—an essential growth phase that strongly influences rice