Cadmium (Cd) accumulation in rice grain poses a serious threat to human health. While several transport systems have been reported, the complexity of rice Cd transport and accumulation indicates the necessity of identifying additional genes, especially those that are responsible for Cd accumulation divergence between indica and japonica rice subspecies. Here, we show that a gene, OsCd1, belonging to the major facilitator superfamily is involved in root Cd uptake and contributes to grain accumulation in rice. Natural variation in OsCd1 with a missense mutation Val449Asp is responsible for the divergence of rice grain Cd accumulation between indica and japonica. Near-isogenic line tests confirm that the indica variety carrying the japonica allele OsCd1^V449 can reduce the grain Cd accumulation. Thus, the japonica allele OsCd1^V449 may be useful for reducing grain Cd accumulation of indica rice cultivars through breeding.

Improving the performance of rice (Oryza sativa) under drought stress has the potential to significantly affect rice productivity. Here, we report that the ERF family transcription factor OsLG3 positively regulates drought tolerance in rice. In our previous work, we found that OsLG3 has a positive effect on rice grain length without affecting grain quality. In this study, we found that OsLG3 was more strongly expressed in upland rice than in lowland rice under drought stress conditions. By performing candidate gene association analysis, we found that natural variation in the promoter of OsLG3 is associated with tolerance to osmotic stress in germinating rice seeds. Overexpression of OsLG3 significantly improved the tolerance of rice plants to simulated drought, whereas suppression of OsLG3 resulted in greater susceptibility. Phylogenetic analysis indicated that the tolerant allele of OsLG3 may improve drought tolerance in cultivated japonica rice. Introgression lines and complementation transgenic lines containing the elite allele of OsLG3^IRAT109 showed increased drought tolerance, demonstrating that natural variation in OsLG3 contributes to drought tolerance in rice. Further investigation suggested that OsLG3 plays a positive role in drought stress tolerance in rice by inducing reactive oxygen species scavenging. Collectively, our findings reveal that natural variation in OsLG3 contributes to rice drought tolerance and that the elite allele of OsLG3 is a promising genetic resource for the development of drought-tolerant rice varieties.

Summary: Grain size, one of the important components determining grain yield in rice, is controlled by the multiple quantitative trait loci (QTLs). Intensive artificial selection for grain size during domestication is evidenced in modern cultivars compared to their wild relatives. Here, we report the molecular cloning and characterization of OsLG3b, a QTL for grain length in tropical japonica rice that encodes MADS‐box transcription factor 1 (OsMADS1). Six SNPs in the OsLG3b region led to alternative splicing, which were associated with grain length in an association analysis of candidate region. Quantitative PCR analysis indicated that OsLG3b expression was higher during the panicle and seed development stages. Analysis of haplotypes and introgression regions revealed that the long‐grain allele of OsLG3b might have arisen after domestication of tropical japonica and spread to subspecies indica or temperate japonica by natural crossing and artificial selection. OsLG3b is therefore a target of human selection for adaptation to tropical regions during domestication and/or improvement of rice. Phylogenetic analysis and pedigree records showed that OsLG3b had been employed by breeders, but the gene still has much breeding potential for increasing grain length in indica. These findings will not only aid efforts to elucidate the molecular basis of grain development and domestication, but also facilitate the genetic improvement of rice yield.