Flowering time is one of the most important agronomic traits affecting the adaptation and yield of rice (Oryza sativa). Heading date 1 (Hd1) is a key factor in the photoperiodic control of flowering time. In this study, two basic helix-loop-helix (bHLH) transcription factors, Hd1 Binding Protein 1 (HBP1) and Partner of HBP1 (POH1) were identified as transcriptional regulators of Hd1. We generated knockout mutants of HBP1 and ectopically expressed transgenic lines of the two bHLH transcription factors and used these lines to investigate the roles of these two factors in regulating flowering time. HBP1 physically associated with POH1 forming homo- or heterodimers to perform their functions. Both HBP1 and POH1 bound directly to the cis-acting elements located in the promoter of Hd1 to activate its expression. CRISPR/Cas9-generated knockout mutations of HBP1, but not POH1 mutations, promoted earlier flowering time; conversely, HBP1 and POH1 overexpression delayed flowering time in rice under long-day and short-day conditions by activating the expression of Hd1 and suppressing the expression of Early heading date 1 (Ehd1), Heading date 3a (Hd3a), and Rice Flowering locus T 1 (RFT1), thus controlling flowering time in rice. Our findings revealed a mechanism for flowering time control through transcriptional regulation of Hd1 and laid theoretical and practical foundations for improving the growth period, adaptation, and yield of rice.

Given the notable ecological and breeding disparities between southern and northern rice regions, delving into the genetic diversity and divergence between southern and northern japonica rice contributes to enhancing the genetic pool for japonica rice breeding. In this study, we analyzed 90 southern and 51 northern japonica rice varieties, focusing on nucleotide diversity (Pi), agronomic trait variations, population structure, genetic divergence, and a neutral test. For genetic diversity, the results demonstrated higher Pi in northern japonica rice varieties (NJRVs) on Chr2, Chr5, Chr6, Chr8, and Chr10, whereas in southern japonica rice varieties (SJRVs) on Chr7 and Chr9. In addition, SJRVs exhibited higher grain width and thickness, whereas NJRVs featured a higher grain aspect ratio, filled grain number, and grain number per panicle. Regarding genetic divergence, geographic differentiation existed between NJRVs and SJRVs, with Chr5 exhibiting numerous higher genetic differentiation windows, including cloned grain shape-controlling genes RGA1 and SFD5, stemming from intensified selection pressure on SJRVs. In summary, SJRVs and NJRVs exhibited diversity differences and genetic differentiation. Hence, it was suggested to conduct genetic introgression between NJRVs and SJRVs to broaden the genetic basis of the local japonica rice germplasm. By exploiting their heterotic advantage, new japonica rice cultivars with superior comprehensive traits could be developed.

Floret opening (FO) in rice (Oryza sativa L.) is triggered by lodicule swelling. However, the regulatory mechanisms underlying lodicule-mediated FO remain largely unclear. In particular, it is unknown whether distinct floral cell types coordinately regulate lodicule osmotic potential and cell wall remodeling. To address this question, we performed single-cell transcriptome sequencing on spikelets sampled at pre-floret opening and FO stages. This study demonstrates strong communication between phloem and lodicule cells during FO, potentially involving transport of calcium ions, soluble sugars, and water. These osmolytes contribute to lowering lodicule osmotic potential, thereby facilitating swelling. Multiple FO genes involved in lodicule cell wall remodeling showed heterogeneous activation in lodicule cells, suggesting fine regulation of cell wall remodeling and cell deformation. Together, these findings provide single-cell insights into lodicule control of FO. In addition, we identified multiple FO regulators, providing genetic resources for improving FO.

Background: The differing floret opening times between subsp. indica and subsp. japonica in rice limit the potential for increased hybrid seed production. Objectives: To elucidate the physiological basis underlying the differences in floret opening time between indica and japonica rice. Materials: A comparative analysis involved nine indica and ten japonica rice varieties. Methods: Using paraffin sectioning, transcriptome sequencing, RT-PCR, and endogenous substance quantification, we investigated the structural variations in floral organs, the differences in the initiation timing of floret opening regulatory pathways, and endogenous regulators. Results: The results indicated insignificant differences in lemma thickness, lodicule thickness, lodicule area, and the coupling-lodicule length between indica and japonica rice. However, japonica rice exhibited larger lodicule-lemma gaps and more vascular bundles compared to indica rice. Within the 9:00 a.m. to 10:00 a.m. interval, the expression of OsAOS1 in α-linolenic acid metabolism and OsISA3 in starch and sucrose metabolism notably increased in indica rice, with no significant change in japonica rice. Additionally, the endogenous JA and α-amylase surged more significantly in indica rice than in japonica rice. The increase in soluble carbohydrate in indica rice is greater than in japonica rice, but the difference is not significant. Conclusions: These findings suggest that in the process of the floret opening, the α-linolenic acid metabolism and starch and sucrose metabolism are initiated earlier in indica rice, accompanied by a more pronounced elevation in endogenous JA and α-amylase. Furthermore, the smaller lodicule-lemma gap in indica rice contributes to earlier floret opening compared to japonica rice.

Background Japonica rice (Oryza sativa L.) is a subspecies of the Asian cultivated rice and is popular because of its better quality. The genetic diversity of japonica rice germplasm resources is the basis for japonica variety breeding and improvement. Genetic diversity is evaluated by means of phenotypic identification and molecular markers. Molecular markers are more stable and less susceptible to interference by environmental factors, whereas phenotypes are susceptible to environmental factors. In this study, 150 japonica rice varieties from different ecological zones were used to analyze their kinship and population structure by next-generation sequencing technology. The phenotypic diversity was then evaluated using ten agronomic traits under two different environmental conditions, Guiyang and Hainan, respectively, and the effect of different environmental conditions on the phenotypic diversity evaluation was analyzed. The present study will provide a comprehensive assessment of the genetic diversity of japonica rice varieties from different ecological zones and provide a theoretical foundation for parental selection in conventional japonica rice breeding. Result The results of sequencing and population structure analysis showed that the 150 japonica varieties were abundant in genetic variation, without homogeneity and subgroup differentiation. The identification of phenotypic diversity also showed that the phenotypes of these japonica rice varieties from different ecological zones are rich in diversity under different environmental conditions. In addition, different environments had a significant impact on the results of phenotypic diversity evaluation such as diversity index, enrichment intervals, agronomic trait correlations, and composite scores based on regression analysis for japonica rice varieties from different ecological zones. In Guiyang, the top 10 overall agronomic traits were Yungingnuo (JR_LN38), Chugeng37 (JR_LN32), Chugeng28 (JR_LN34), Fuhedao255 (JR_LN50), Guangminggeng2Hao (JR_LN96), Chugeng7 (JR_LN39), Chugeng40 (JR_LN33), Liaogeng401 (JR_LN102), Bigeng44 (JR_LN107), Sugeng45 (JR_LN76), however, in Hainan, the top 10 in terms of overall performance were, respectively, Chugeng7 (JR_LN39), Lemont (JR_LN149), Chugeng32 (JR_LN43), Chugeng28 (JR_LN34), Bidao126 (JR_LN105), Tenggeng2 (JR_LN45), Chugeng26 (JR_LN41), Tengxi138 (JR_LN153), Hexi27-2 (JR_LN145), Chugeng39 (JR_LN44). Conclusion 150 Japonica rice varieties from different ecological zones are abundantly genetically diverse, with no homogeneity and no subpopulation differentiation that can be utilized as parental resources for Japonica rice variety breeding. In conventional breeding, breeders often rely on phenotypes as an important basis for parental selection. Given that different environments have a strong influence on the evaluation of phenotypic diversity of japonica rice germplasm resources, it is necessary to conduct a comprehensive evaluation of germplasm resources based on a large amount of agronomic trait data obtained in the local environment to screen for desirable parents after the breeding target has been determined.