Soil salinity is a serious menace in rice production threatening global food security. Rice responses to salt stress involve a series of biological processes, including antioxidation, osmoregulation or osmoprotection, and ion homeostasis, which are regulated by different genes. Understanding these adaptive mechanisms and the key genes involved are crucial in developing highly salt-tolerant cultivars. In this review, we discuss the molecular mechanisms of salt tolerance in rice—from sensing to transcriptional regulation of key genes—based on the current knowledge. Furthermore, we highlight the functionally validated salt-responsive genes in rice.

Salt stress is one of the major constraints to rice cultivation worldwide. Thus, the development of salt-tolerant rice cultivars becomes a hotspot of current rice breeding. Achieving this goal depends in part on understanding how rice responds to salt stress and uncovering the molecular mechanism underlying this trait. Over the past decade, great efforts have been made to understand the mechanism of salt tolerance in rice through genomics, transcriptomics, proteomics, metabolomics, and epigenetics. However, there are few reviews on this aspect. Therefore, we review the research progress of omics related to salt tolerance in rice and discuss how these advances will promote the innovations of salt-tolerant rice breeding. In the future, we expect that the integration of multi-omics salt tolerance data can accelerate the solution of the response mechanism of rice to salt stress, and lay a molecular foundation for precise breeding of salt tolerance.

R2R3-MYB transcription factors belong to one of the largest gene subfamilies in plants, and they are involved in diverse biological processes. However, the role of R2R3-MYB transcription factor subfamily genes in the response of rice (Oryza sativa L.) to salt stress has been rarely reported. In this study, we performed a genome-wide characterization and expression identification of rice R2R3-MYB transcription factor subfamily genes. We identified a total of 117 R2R3-MYB genes in rice and characterized their gene structure, chromosomal location, and cis-regulatory elements. According to the phylogenetic relationships and amino acid sequence homologies, the R2R3-MYB genes were divided into four groups. qRT-PCR of the R2R3-MYB genes showed that the expression levels of 10 genes significantly increased after 3 days of 0.8% NaCl treatment. We selected a high expression gene OsMYB2-115 for further analysis. OsMYB2-115 was highly expressed in the roots, stem, leaf, and leaf sheath. OsMYB2-115 was found to be localized in the nucleus, and the yeast hybrid assay showed that OsMYB2-115 has transcriptional activation activity. This result provides important information for the functional analyses of rice R2R3-MYB transcription factor subfamily genes related to the salt stress response and reveals that OsMYB2-115 may be an important gene associated with salt tolerance in rice.

Brown rice traits are critical to both grain yield and quality. In the present study, the chromosome segment substitution lines (CSSLs) population derived from a cross between japonica Koshihikari and indica Nona Bokra was used to analyze the brown rice length (BRL), brown rice width (BRW), length–width ratio of brown rice (BLWR), brown rice thickness (BRT), brown rice perimeter (BRP), brown rice area (BRA), thousand-grain weight of brown rice (BRGW), brown rice ratio (BRR), taste value of brown rice (BTV), and water content of brown rice (BWC). Correlations analysis showed that most of the brown rice traits had significant correlations with each other, except for BRR, BTV, and BWC. A total of sixty-one QTLs for these traits were identified under three environments, which mapped to chromosomes 1, 2, 3, 5, 6, 7, 8, 10, 11, and 12, with the LOD ranging from 2.52 to 16.68 and accounting for 2.60 to 25.38% of the total phenotypic variations. Moreover, thirty pairs of epistatic interactions for BRL, BRW, BLWR, BRP, and BRA were estimated and distributed on all chromosomes except 10. These findings will provide a further understanding of the genetic basis of brown rice traits and facilitate the genetic improvement of rice yield and quality through breeding.

The whiteness of rice grains (WRG) is a key indicator of appearance quality, directly impacting its commercial value. The trait is quantitative, influenced by multiple factors, and no specific genes have been cloned to date. In this study, we first examined the correlation between the whiteness of polished rice, cooked rice, and rice flour, finding that the whiteness of rice flour significantly correlated with both polished and cooked rice. Thus, the whiteness of rice flour was chosen as the indicator of WRG in our QTL analysis. Using a set of chromosome segment substitution lines (CSSL) with japonica rice Koshihikari as the recipient and indica rice Nona Bokra as the donor, we analyzed QTLs for WRG across two growth environments and identified six WRG QTLs. Notably, qWRG9 on chromosome 9 displayed stable genetic effects in both environments. Through chromosomal segment overlapping mapping, qWRG9 was narrowed to a 1.2 Mb region. Additionally, a BC₄F₂ segregating population confirmed that low WRG was a dominant trait governed by the major QTL qWRG9, with a segregation ratio of low to high WRG approximating 3:1, consistent with Mendelian inheritance. Further grain quality analysis on the BC₄F₂ population revealed that rice grains carrying the Indica-type qWRG9 allele not only exhibited lower WRG but also had significantly higher protein content. These findings support the fine mapping of the candidate gene and provide an important QTL for improving rice grain quality through genetic improvement.

Leaves represent an important organ in plant photosynthesis, and moderately rolled leaves would be beneficial in establishing an ideal plant architecture and thereby increasing rice yields. In this study, a stable inherited rolled leaf mutant was obtained via ethyl methanesulfonate (EMS) mutagenesis from japonica variety WYJ27, which was named rll2 (rolling leaf 2). rll2 showed a leaf-rolling phenotype at the seedling stage, which increased with growth. Compared with the wild type, the leaves at all levels of rll2 were significantly shorter and narrower, and the leaf-rolling index gradually decreased from the highest leaf to the third-highest leaf. Semi-thin sections showed that the bulliform cells of rll2 were significantly larger than those of the wild type, and the number of cells was significantly higher than that of the wild type. Genetic analysis showed that rll2 is controlled by a pair of recessive nuclear genes. Map-based cloning revealed that RLL2 encodes a conserved and plant-specific calpain-like cysteine proteinase. RLL2 was mainly expressed in young roots, shoots, spikelets, and panicles. Transcriptome sequencing showed that a total of 104 genes were differentially expressed in the wild type and rll2. Moreover, several transcription factor genes were significantly altered in the rll2 mutant. Taken together, our findings indicate that RLL2 plays an important role in leaf rolling by regulating bulliform cells, which may be useful in breeding rice with an ideal plant architecture.