The head milled rice rate (HMRR) is the most important trait of milling quality, which affects the final yield and quality of rice. However, few genes related to HMRR have been identified and the regulatory mechanism of HMRR remains elusive. In this study, we performed a comparative analysis integrating the transcriptome sequencing of developing seeds at the grain-filling stage and a metabolome analysis of brown rice between two groups of accessions with contrasting performances in HMRR. A total of 768 differentially expressed genes (DEGs) were identified between the transcriptome profiles of low-HMRR and high-HMRR accessions. In comparison to the high-HMRR accessions, 655 DEGs were up-regulated in the low-HMRR accessions, which was 4.79 folds higher than the number of down-regulated genes. These up-regulated DEGs were enriched in various metabolic and biosynthetic processes, oxidation reduction, phosphorylation, ion transport and ATP-related processes. However, the 113 down-regulated DEGs in the low-HMRR accessions were concentrated in carbohydrate metabolic processes, cell-death-related processes and defense response. Among the 30 differential metabolites, 20 and 10 metabolites were down-/up-regulated, respectively, in the accessions with low HMRR. In addition, 10 differential metabolites, including five metabolites of the shikimate pathway and five metabolites of the pyruvate pathway, were integrated into two separate pathways, starting from sucrose. Our global analysis of HMRR provides an invaluable resource for a better understanding of the molecular mechanism underlying the genetic regulation of HMRR.

Grain transparency (GT) is a key determinant of rice appearance quality and consumer preference, yet its genetic basis remains poorly understood. In this study, we evaluated GT in a panel of 450 rice accessions grown in two environments (Guangzhou and Yangjiang). Nineteen quantitative trait loci (QTL) for GT were identified by a genome-wide association study (GWAS), distributed across all rice chromosomes except chromosomes 2 and 12. Among these, four QTL (qGT-1b, qGT-3b, qGT-4b, and qGT-5b) were consistently detected in both environments. Notably, qGT-3b and qGT-5b co-localized with the grain shape genes GRAIN SIZE 3 (GS3) and GRAIN WIDTH 5 (GW5), respectively. For the novel and stable QTL qGT-4b, linkage disequilibrium decay analysis delimited an approximately 300 kb candidate region. Integrative transcriptomic and genomic analyses pointed to two candidate genes: LOC_Os04g40370 (OsFbx142), encoding an F-box domain protein, and LOC_Os04g40720 (OsSUBSrP1), encoding a subtilisin-like serine protease. Haplotype analysis further revealed that specific haplotypes of these genes were significantly associated with GT variation across environments. Our findings provide genetic insights into the regulation of rice grain transparency and offer candidate genes for further functional validation and potential application in improving rice appearance quality.

Seed vigor critically determines sowing performance, while grain quality fundamentally influences commercial value. Elucidating the genetic mechanisms governing these traits is critical for enhancing both seed vigor and grain quality in rice cultivation. Here, we demonstrate that the endosperm-specific gene OsEnS-42 is highly expressed in germinating seeds and developing seeds at the early filling stage. OsEnS-42 is localized in the nucleus and cytoplasm. The seed vigor of OsEnS-42 knockout plants decreased, manifested as decreases in germination rate, seedling length, and root length. In addition, OsEnS-42 knockout plants showed increased chalkiness and amylose content. The transcriptome and physiological indicators showed that OsEnS-42 regulates seed vigor through soluble sugars and redox metabolism, and regulates grain quality via soluble sugars and seed development-related enzymes. Haplotype analysis of OsEnS-42 across global rice germplasm revealed four distinct haplotypes (Hap 1–4) with subspecies-specific distributions. Crucially, accessions with Hap 4 exhibit a lower percentage of grain with chalkiness than accessions with Hap 1 (predominantly indica), enabling marker-assisted introgression to reduce chalkiness without subspecies barriers. Meanwhile, accessions with Hap 2 show lower amylose content, providing targets for specialty rice breeding. Our findings elucidate the pathways through which OsEnS-42 regulates seed vigor and grain quality, and provide new molecular breeding targets for improving seed vigor and grain quality in rice.

Rice is a short-day thermophilic crop that originated from the low latitudes of the tropics and subtropics; it requires high temperatures for growth but is sensitive to low temperatures. Therefore, it is highly important to explore and analyze the molecular mechanism of cold tolerance in rice to expand rice planting areas. Here, we report a phenotypic evaluation based on low-temperature stress in indica rice (R998) and wild rice (GZW) and a comparative transcriptomic study conducted at six time points. After 7 days of low-temperature treatment at 10 °C, R998 exhibited obvious yellowing and greening of the leaves, while GZW exhibited high low-temperature resistance, and the leaves maintained their normal morphology and exhibited no yellowing; GZW has a higher survival rate. Principal component analysis (PCA) and cluster analysis of the RNA-seq data revealed that the difference in low-temperature resistance between the two cultivars was caused mainly by the difference in low-temperature treatment after 6 h. Differential expression analysis revealed 2615 unique differentially expressed genes (DEGs) in the R998 material, 1578 unique DEGs in the GZW material, 1874 unique DEGs between R998 and GZW, and 2699 DEGs that were differentially expressed not only between cultivars but also at different time points in the same material under low-temperature treatment. A total of 15,712 DEGs were detected and were significantly enriched in the phenylalanine metabolism, photosynthesis, plant hormone signal transduction, and starch and sucrose metabolism pathways. These 15,712 DEGs included 1937 genes encoding transcription factors (TFs), of which 10 have been identified with functional validation in previous studies. In addition, a gene regulatory network was constructed via weighted gene correlation network analysis (WGCNA), and 12 key genes related to low-temperature tolerance in rice were identified, including five genes encoding TFs, one of which was identified and verified in previous studies. These results provide a theoretical basis for an in-depth understanding of the molecular mechanism of low-temperature tolerance in rice and provide new genetic resources for the study of low-temperature tolerance in rice.

Salt stress is an injurious concern of global climate change that negatively impacts the growth and yield of rice plants. Identifying salt tolerance genes is essential to understanding the molecular mechanism regulating salt tolerance in rice. In this study, we treated two rice varieties, Xiangxiuzhan (XXZ) and Changxiang (CXG), with 100 mM NaCl to examine the effect on the germination and growth stages. Transcriptome analysis was investigated for changes in gene expression between the two varieties. During the germination stage, the CXG variety had higher germination potential than the XXZ variety, whereas in the growth stage, the XXZ variety showed higher survival efficiency than the CXG variety. Transcriptome analysis showed that the XXZ variety had more DEGs in grains, while CXG displayed greater DEGs in leaves and roots. Gene Ontology (GO) and KEGG pathway showed that beta-alanine metabolism, cutin biosynthesis, and plant hormone signal transduction were over-represented, whereas heatmap analysis showed cellular and environmental signal transduction. This study focuses on the molecular pathways of the salt stress tolerance mechanism of Xiangxiuzhan and Changxiang varieties.