Background/Objectives: Cold stress is the main environmental factor that affects the growth and development of rice, leading to a decrease in its yield and quality. However, the molecular mechanism of rice’s low-temperature resistance remains incompletely understood. Methods: In this study, we conducted a joint analysis of miRNA and mRNA expression profiles in the cold-resistant material Yongning red rice and the cold-sensitive material B3 using high-throughput sequencing. Results: 194 differentially expressed miRNAs (DEMIs) and 14,671 differentially expressed mRNAs (DEMs) were identified. Among them, 19 DEMIs, including miR1437, miR1156, miR166, miR1861, and miR396_2 family members, showed opposite expression during the early or late stages of low-temperature treatment in two varieties, while 13 DEMIs were specifically expressed in Yongning red rice, indicating that these miRNAs are involved in rice’s resistance to low temperature. In the transcriptome analysis, 218 DEMs exhibited opposite expressions during the early or late stages of low-temperature treatment in two varieties. GO enrichment analysis indicated that these DEMs were enriched in biological processes such as a defense response to fungi, a defense response to bacteria, a plant-type cell wall modification, single-organism cellular processes, a response to chitin, and the regulation of a plant-type hypersensitive response, as well as in cellular components such as the apoplast, nucleus, vacuole, plasma membrane, and plasmodesma. Twenty-one genes were further selected as potential candidates for low-temperature resistance. The joint analysis of miRNA and mRNA expression profiles showed that 38 miRNAs corresponding to 39 target genes were candidate miRNA–mRNA pairs for low-temperature resistance. Conclusions: This study provides valuable resources for determining the changes in miRNA and mRNA expression profiles induced by low temperatures and enables the provision of valuable information for further investigating the molecular mechanisms of plant resistance to low temperatures and for the genetic improvement of cold-resistant varieties.

Photoperiod sensitivity (PS) is the major determinant of flowering time in rice and has played a critical role in adaptation across diverse ecotypes. To dissect the genetic and molecular architecture of PS in MYR landraces, we combined GWAS with transcriptomic profiling on 236 diverse accessions. Thirteen major QTL underlying heading date were mapped on chromosomes 1, 2, 3, 6, 7, and 8, consisting of the previously reported flowering genes (OsHd1, OsFTIP9) and a number of novel loci specific to Myanmar germplasm. Comparative RNA-seq analysis, using a photoperiod-sensitive (V10) and a photoperiod-insensitive (V3) indica genotype to the japonica cultivar ‘H479B’ as reference, showed distinct transcriptional reprogramming in response to short-day conditions, with higher-expression plasticity occurring in V10. By integrating GWAS signals with differential expressions, we narrowed our candidate gene set of two high-confidence regulators: Os06g0275000, encoding a zinc finger transcription factor, and Os07g0606600 (NF-YB10). Both genes were highly expressed in a stage-specific manner and further confirmed by qRT-PCR. Our results suggest a complex genetic regulatory network attracting conserved photoperiod pathways with unique novel allelic variant populations in Myanmar landraces. These candidate genes will be potential targets for precision breeding to optimize flowering time and enhance adaptation both in response to climate change and photoperiodic changes.

Water deficit severely limits rice productivity. The elite Dian (D1)-type hybrid japonica rice ‘Dianheyou 615 (ZH1)’ exhibits exceptional drought adaptation in high-altitude rainfed uplands of the Yungui Plateau, yet the underlying molecular mechanisms remain unknown. We compared phenotypic and transcriptomic responses of ZH1 and six other japonica cultivars under well-watered and water-deficit conditions. Water-deficit stress significantly impaired agronomic traits across all cultivars; however, ZH1 uniquely maintained relatively stable flag leaf morphology and seed-setting rate, and displayed distinctive stomatal traits, in stark contrast to its parental lines and other cultivars. Transcriptomic profiling at the jointing-to-booting stage defined a core drought response module of 174 conserved genes across all cultivars. Critically, by intersecting 1097 ZH1-specific genes with drought-responsive elements, we pinpointed 15 core, cultivar-specific regulatory genes. These candidates are enriched in functions related to cuticle formation, carbohydrate metabolism, and stress signaling; among them, a DREB transcription factor (LOC4347618) is a prime candidate. qRT-PCR validated their expression. Using CRISPR/Cas9-mediated gene editing, we generated homozygous knockout mutants for LOC4333842, LOC4347618, and LOC4328441. Under 20% PEG-6000-simulated drought stress, all three mutant lines showed significantly increased drought susceptibility relative to wild-type controls, confirming the positive regulatory roles of these genes in drought stress tolerance in japonica rice. These results establish these three genes as promising targets for molecular breeding aimed at enhancing drought resistance in rice.