The accumulation of arsenic (As) in rice poses a significant threat to food safety and human health. Breeding rice varieties with low As accumulation is an effective strategy for mitigating the health risks associated with arsenic-contaminated rice. However, the genetic mechanisms underlying As accumulation in rice grains remain incompletely understood. We evaluated the As accumulation capacity of 313 diverse rice accessions grown in As-contaminated soils with varying As concentrations. Six rice lines with low As accumulation were identified. Additionally, a genome-wide association studies (GWAS) analysis identified 5 QTLs significantly associated with As accumulation, with qAs4 being detected in both of the experimental years. Expression analysis demonstrated that the expression of LOC_Os04g50680, which encodes an MYB transcription factor, was up-regulated in the low-As-accumulation accessions compared to the high-As-accumulation accessions after As treatment. Therefore, LOC_Os04g50680 was selected as a candidate gene for qAs4. These findings provide insights for exploiting new functional genes associated with As accumulation and facilitating the development of low-As-accumulation rice varieties through marker-assisted breeding.

Cold stress significantly limits rice productivity, particularly at the early seedling stage. Identifying key genes responsible for cold tolerance is crucial for breeding resilient rice varieties. In the study, we identified a quantitative trait locus (QTL), qESCT2, associated with cold tolerance at the early seedling stage. The QTL was mapped into an interval of RM1347–RM5356 on chromosome 2 using an F_2:3 population derived from a cross between XZX45, a cold-sensitive early rice variety from China, and IL43, an introgression line developed by marker-assisted backcrossing. IL43 was created using XN1, a highly cold-resistant cultivar, as the donor parent and XZX45 as the recurrent parent. By integrating transcriptomic data from the target region, we identified Os02g0181300 as the candidate gene for qESCT2. This gene encodes a transcription factor, OsWRKY71. Edited lines of OsWRKY71 exhibited a significantly lower survival rate under cold tolerance compared to the wild type Nipponbare. Further analysis revealed that OsWRKY71 likely regulated cold tolerance at the early seedling stage by a glutathione metabolism related pathway. Additionally, OsWRKY71 exhibits differentiation between indica and japonica subspecies with distinct haplotypes. These findings will facilitate to further research into the genetic basis of cold tolerance at the early seedling stage and enhance the development of cold-resistant rice varieties by marker-assisted selection.

Drought is a major abiotic stress limiting rice production worldwide. Identifying genes that enhance drought tolerance is essential for breeding resilient varieties. In this study, we report the map-based cloning and functional characterization of DT1, a novel cytochrome P450 gene conferring drought tolerance in rice. Using near isogenic lines (NILs) derived from a cross between Xiang743 and Katy, we delimited DT1 into a 115 kb interval on chromosome 3, where contains 18 open read frames (ORFs). Quantitative real-time polymerase chain reaction (qRT-PCR) analysis identified Os03g55250 as the candidate gene. Clustered regularly interspaced short palindromic repeats-associated nuclease 9 (CRISPR/Cas9) knockout mutants of Os03g55250 exhibited increased drought sensitivity, while overexpression lines showed enhanced drought tolerance, confirming that Os03g55250 was the target gene and positively regulates drought resistance. DT1 was mainly expressed in stems, leaves, and leaf sheaths, and the DT1 protein localized in the endoplasmic reticulum. Haplotype analysis identified Hap1 as a favorable allele in japonica rice. Our findings provide a promising genetic resource for breeding drought-resistant rice varieties and offers new insights into the role of P450 genes in abiotic stress adaptation.

Arsenic (As) contamination in rice poses a serious risk to food safety and human health. Genetic dissection of As-related quantitative trait loci (QTLs) provides a sustainable strategy for breeding low-As cultivars. In this study, we aimed to improve the detection of minor-effect QTLs for total As accumulation by optimizing both environmental and genetic factors. A recombinant inbred line (RIL) population derived from the cross between Yuzhenxiang (YZX, indica) and YBK (Javanica) was used for initial QTL mapping, and a single locus, qAs1, was identified on chromosome1. To enhance As uptake and phenotypic differentiation, we conducted QTL validation and fine mapping under high-As and continuously flooded conditions using near-isogenic lines (NILs) to minimize background genetic interference. The effect of qAs1 was consistently validated across generations, and the locus was refined to a 159.5 kb genomic interval. Transcriptome analysis revealed three differentially expressed genes (LOC_Os01g52110, LOC_Os01g52214, and LOC_Os01g52260) involved in redox regulation and detoxification. These findings demonstrate the effectiveness of NIL-based fine mapping under optimized environmental conditions and provide promising targets for the genetic improvement of low-As rice cultivars.