Chloroplasts play a vital role in plant growth and development, which are the main sites of photosynthesis and the production of hormones and metabolites. Despite their significance, the regulatory mechanisms governing chloroplast development remain unclear. In our investigation, we identified a rice mutant with defective chloroplasts in rice (Oryza sativa L.), named albino lethal 13 (osal13), which displayed a distinct albino phenotype in leaves, ultimately resulting in seedling lethality. Molecular cloning revealed that OsAL13 encodes a novel rice protein with no homologous gene or known conserved domain. This gene was located in the chloroplast and exhibited constitutive expression in various tissues, particularly in green tissues and regions of active cell growth. Our study's findings reveal that RNAi‐mediated knockdown of OsAL13 led to a pronounced albino phenotype, reduced chlorophyll and carotenoid contents, a vesicle chloroplast structure, and a decrease in the expression of chloroplast‐associated genes. Consequently, the pollen fertility and seed setting rate were lower compared with the wild type. In contrast, the overexpression of OsAL13 resulted in an increased photosynthetic rate, a higher total grain number per panicle, and enhanced levels of indole‐3‐acetic acid (IAA) in the roots and gibberellin A3 (GA3) in the shoot. These outcomes provide new insights on the role of OsAL13 in regulating chloroplast development in rice.

‘Dianheyou615’ (DHY615) is an elite Dian (D1)-type hybrid japonica rice variety, renowned for its high yield, exceptional grain quality, and unique adaptability to both irrigated and rainfed conditions in the Yungui Plateau of southwestern China. However, the genetic mechanisms underlying the agronomic performance of the D1-type hybrid japonica rice remain unclear. In this study, a comprehensive analysis of ‘DHY615’’s agronomic performance, genetic genealogy, and molecular genetic foundation was conducted to dissect its desirable traits for upland rainfed cultivation across diverse ecological environments. The main findings indicate that ‘DHY615’ possesses 6432 heterozygous SNPs, with 57.48% and 14.43% located in the promoter and coding regions, respectively, potentially affecting key phenotypic traits. High-impact SNPs variants and numerous well-known functional genes were identified, such as OsAAP6, GS3, Sd1, Rf1, BADH2, BPh14, Rymv1, OsFRO1, NRT1.1B, SKC1, OsNCED2, and qUVR-10, which are likely linked to traits including plant architecture, grain yield, grain quality, and resistance to various biotic and abiotic stresses (e.g., disease, cold, drought, salt, high iron, and high UV radiation). Notably, ‘Nan615’ harbors a greater number of functional allele variants compared to ‘H479A’, which potentially explaining its superior grain yield and remarkable adaptability. This study offers novel and valuable insights into the molecular genetic foundation of the plateau D1-type hybrid japonica rice, underscoring its potential for sustainable rice production across diverse ecological zones, especially with its unparalleled high-altitude adaptability to rainfed upland planting.

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.

The chloroplast is important organelle responsible for photosynthesis and various bio- synthetic functions essential to green plants. However, the regulatory mechanism of chloroplast development remains elusive. Here, we characterized a mutant with defective chloroplasts in rice (Oryza sativa L.) named it albino and lethal 13(osal13), which exhibited a distinct albino phenotype in leaves, eventually leading to seedling lethality. Molecular cloning revealed that OsAL13 encodes a novel protein in rice for which no homologous gene or known conserved domain was found. Analysis of the biological characteristics showed that the RNAi2 leaf was completely albino phenotype, the root and shoot lengths were significantly inhibited compared with wild type. Transmission electron microscopy indicated that RNAi2 were defective in chloroplast development. Overexpression of OsAL13 resulted the photosynthetic rate increase, So the total grain number per panicle also would be significantly increase. Besides, OsAL13 was located in chloroplast and constitutively expressed in various tissues, including green and non-green tissues. In addition, disruption of OsAL13 resulted in altered expression of plastid-encoded polymerases and nuclear-encoded chloroplast genes, OsAL13 also affected hormone levels in plant tissues. Therefore, our results provide new insights into the role of OsAL13 in regulating chloroplast development in rice.

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.

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.