Rice Science最新文献

{"title":"OsGBP and NAL9 Modulate Source-Sink Coordination in Rice","authors":"Wang Wei, Wenqiang Chen, Huang Yutao, Mei Gaofu, Dongdong Cao","doi":"10.1016/j.rsci.2026.05.010","DOIUrl":"https://doi.org/10.1016/j.rsci.2026.05.010","url":null,"abstract":"","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148305613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic Variation and Population Structure of Asian Cultivated Rice","authors":"Wei LI ,&nbsp;Mengchen ZHANG ,&nbsp;Xiaoyang CHEN ,&nbsp;Yan LI ,&nbsp;Qun XU ,&nbsp;Shan WANG ,&nbsp;Yue FENG ,&nbsp;Xinghua WEI ,&nbsp;Yaolong YANG","doi":"10.1016/j.rsci.2026.02.010","DOIUrl":"10.1016/j.rsci.2026.02.010","url":null,"abstract":"<div><div>Rice germplasms serve as repositories of genetic variation. Population structure analysis is crucial for the effective utilization of rice germplasm and provides an evolutionary framework for future biological research. In this study, we constructed a genetic variation map using a large population of 20 056 rice accessions. A total of 34 426 306 variants were identified, including 29 251 099 biallelic and 5 175 207 multiallelic variants. Population structure analysis of a subset of 5 668 accessions classified Asian cultivated rice into eight distinct groups: <em>temperate japonica</em> 1 (TEJ1), <em>temperate japonica</em> 2 (TEJ2), <em>tropical japonica</em> (TRJ), <em>aromatic</em> (ARO), <em>aus</em> (AUS), <em>indica</em> 1 (IND1), <em>indica</em> 2 (IND2), <em>indica</em> 3 (IND3). Comparative analysis revealed that <em>japonica</em> accessions from China were predominantly composed of TEJ1 and TEJ2, while <em>indica</em> varieties were mainly from IND1. In contrast, introduced <em>japonica</em> accessions were primarily TEJ1 and TRJ, with IND2 representing the major <em>indica</em> group. Foreign accessions represented all eight groups, whereas Chinese accessions lacked the ARO, AUS, and IND3 groups. Genetic diversity analysis revealed that IND3 and TEJ1 exhibited the highest and lowest nucleotide diversity, respectively. Geographically, TRJ was largely distributed in the Americas, ARO was concentrated in the Middle East, and notably, TEJ2 was identified as a group specific to China. Furthermore, we identified 52 regions with significant genetic differentiation. Two of these regions, harboring the cold-tolerant genes <em>bZIP73</em> and <em>COLD1</em>, were selected for further analysis. Nucleotide diversity and haplotype network analyses indicated that both genes may have undergone positive selection and contribute to <em>indica</em>-<em>japonica</em> differentiation. Haplotype analysis also uncovered novel alleles, including a new mutation in <em>COLD1</em> that may represent a favorable variant for enhancing cold tolerance in <em>japonica</em> accessions. Our study demonstrates that large-scale population analysis of genetic variation is a powerful method for dissecting population structure, elucidating the mechanisms of genetic differentiation, and identifying novel functional alleles.</div></div>","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"33 3","pages":"Pages 367-380"},"PeriodicalIF":6.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148208458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of miRNA-mRNA Modules in Yuanjiang Common Wild Rice Conferring Resistance to Rice Blast","authors":"Jinlu LI ,&nbsp;Rong XIANG ,&nbsp;Suqin XIAO ,&nbsp;Yun ZHANG ,&nbsp;Ling CHEN ,&nbsp;Li LIU ,&nbsp;Qiaofang ZHONG ,&nbsp;Fuyou YIN ,&nbsp;Bo WANG ,&nbsp;Jiaxin XING ,&nbsp;Cong JIANG ,&nbsp;Dunyu ZHANG ,&nbsp;Yong ZHU ,&nbsp;Shengli ZHAO ,&nbsp;Zaiquan CHENG","doi":"10.1016/j.rsci.2026.02.001","DOIUrl":"10.1016/j.rsci.2026.02.001","url":null,"abstract":"","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"33 3","pages":"Pages 301-304"},"PeriodicalIF":6.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148208480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dual-Direction of DNA Methylome Reprogramming During Rice Domestication","authors":"Xiaoman YU ,&nbsp;Xiang CHENG ,&nbsp;Yilin LI ,&nbsp;Ruoqian YU ,&nbsp;Jiajia LIU ,&nbsp;Lingwei YANG ,&nbsp;Huiying HE ,&nbsp;Hua WEI ,&nbsp;Lianguang SHANG ,&nbsp;Yuexing WANG ,&nbsp;Xiangpei LIU","doi":"10.1016/j.rsci.2026.02.005","DOIUrl":"10.1016/j.rsci.2026.02.005","url":null,"abstract":"","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"33 3","pages":"Pages 287-291"},"PeriodicalIF":6.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148208459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advancing Rice Resilience to Heat Stress: Insights from CRISPR/Cas9 Genome Editing","authors":"Zakirullah KHAN ,&nbsp;Rahmatullah JAN ,&nbsp;Saleem ASIF ,&nbsp;Hayati Aulia MAHARANI ,&nbsp;Muhammad FAROOQ ,&nbsp;Kyung-Min KIM","doi":"10.1016/j.rsci.2026.02.003","DOIUrl":"10.1016/j.rsci.2026.02.003","url":null,"abstract":"<div><div>Heat stress during reproductive stages remains one of the most critical constraints on rice yield and grain quality, yet progress in developing heat-resilient cultivars is slowed by the complex, polygenic nature of thermotolerance and lengthy breeding cycles. Despite incremental gains through conventional breeding, high temperatures above 35 °C continue to cause severe spikelet sterility, yield losses, and quality deterioration. The emergence of CRISPR/Cas genome-editing offers a precise and efficient platform to dissect heat-stress mechanisms, and accelerate the development of heat-tolerant rice. CRISPR/Cas9 studies have validated and edited key genes involved in calcium signaling, hormone pathways, reproductive processes, photosynthesis, reactive oxygen species homeostasis, and transcriptional regulation, such as <em>OsCNGC14/16</em>, <em>OsNCED1</em>, <em>OsSPL7</em>, and <em>OsHSP60-3b</em>. Beyond stress resilience, genome editing has improved major yield components, including grain size, panicle architecture, and spikelet number, through targets such as <em>GS3</em>, <em>GW3</em>, <em>Gn1a</em>, and <em>OsSPL16</em>, achieving 28%–40% increases in grain weight and 15%–25% improvements in panicle traits, alongside enhanced grain quality attributes. Remaining challenges, including off-target effects, genotype dependence, limited field validation, and regulatory constraints, are being addressed through high-fidelity Cas variants, optimized sgRNA design, DNA-free editing, and integration with genomic selection and speed breeding. This review synthesizes advances in heat-stress biology and CRISPR/Cas applications in rice, and highlights future opportunities in base and prime editing, transcriptional reprogramming, multiplex genome engineering, and field deployment.</div></div>","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"33 3","pages":"Pages 340-350"},"PeriodicalIF":6.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148208456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enigma of Prolonged Submergence Tolerance in Rice: Rediscovering Critical Factors Beyond SUB1A","authors":"Koushik CHAKRABORTY ,&nbsp;Subhankar MONDAL ,&nbsp;Biswaranjan DAS ,&nbsp;Priyanka JENA ,&nbsp;Sagar BANERJEE ,&nbsp;Mridul CHAKRABORTI ,&nbsp;Krishnendu CHATTOPADHYAY ,&nbsp;Ramani Kumar SARKAR","doi":"10.1016/j.rsci.2026.02.009","DOIUrl":"10.1016/j.rsci.2026.02.009","url":null,"abstract":"<div><div>The discovery and subsequent introgression of <em>SUB1A-1</em> gene into rice produces remarkable success in tolerating complete submergence for about two weeks. However, the tolerance of <em>Sub1</em>-introgressed cultivar Swarna Sub1 is still inferior to that of FR13A, the donor of the gene. To investigate this discrepancy, we examined the submergence tolerance potential of FR13A and several superior landraces that show significantly better tolerance than Swarna Sub1 under prolonged submergence. We found that several landraces (AC42088, AC42087, and AC1303) and FR13A carried functional alleles of both SUB1 and SNORKEL genes, along with a dominant allele of <em>SD1</em>. Genotypes carrying the <em>SD1</em> allele exhibited greater initial plant height, and the combined presence of both SUB1 and SNORKEL genes might confer better survivability by allowing moderate shoot elongation under prolonged submergence, particularly beyond two weeks. Interestingly, <em>OsSUB1A-1</em> expression was not suppressed despite high expression of SNORKEL genes in several superior landraces and FR13A. These genotypes also had relatively thicker leaf gas films and delayed depletion of those films under water. Higher epicuticular wax concentration in these genotypes contributed to prolonged persistence of the gas film and improved maintenance of chlorophyll in inundated leaf tissues. Scanning electron microscopy revealed a thick layer of deposition on the leaf surfaces of these landraces and FR13A. Higher transcript abundance of wax biosynthesis genes and a strong, positive, significant correlation between these transcripts and leaf wax concentration suggested the presence of very long-chain fatty acids that may delay loss of leaf hydrophobicity in these landraces. Overall, this study suggests that <em>SUB1A</em>-mediated quiescence, supplemented by moderate elongation via SNORKEL genes, could be beneficial for survival under prolonged submergence beyond two weeks.</div></div>","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"33 3","pages":"Pages 351-366"},"PeriodicalIF":6.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148208457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering Prime Editing System for Concurrent Gene Knockout and Point Mutation Induction (KAPSi) in Rice","authors":"Xiaoshuang LIU ,&nbsp;Chong MA ,&nbsp;Dongmei WANG ,&nbsp;Youshen XU ,&nbsp;Ruiying QIN ,&nbsp;Juan LI ,&nbsp;Rongfang XU ,&nbsp;Pengcheng WEI","doi":"10.1016/j.rsci.2026.02.008","DOIUrl":"10.1016/j.rsci.2026.02.008","url":null,"abstract":"","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"33 3","pages":"Pages 277-281"},"PeriodicalIF":6.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148208463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conversion of Double-Cropping Rice into Rice-Vegetable Rotation System Increases Net Economic Benefit with Lower Environmental Cost","authors":"Fengbo LI ,&nbsp;Xiaoyu WANG ,&nbsp;Ting BAO ,&nbsp;Xiaorong MO ,&nbsp;Mingzhuo ZHOU ,&nbsp;Chunchun XU ,&nbsp;Yaobin LIU ,&nbsp;Jinfei FENG ,&nbsp;Fuping FANG","doi":"10.1016/j.rsci.2026.03.001","DOIUrl":"10.1016/j.rsci.2026.03.001","url":null,"abstract":"","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"33 3","pages":"Pages 305-308"},"PeriodicalIF":6.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148208481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global Patterns of Stage-Specific Alternative Polyadenylation in Rice Tillering Revealed by Nanopore Long Read Sequencing and Proteomics","authors":"Xinyi LI ,&nbsp;Junying HUANG ,&nbsp;Dahu ZHOU ,&nbsp;Yicong CAI ,&nbsp;Xiaorong CHEN ,&nbsp;Lifang HU ,&nbsp;Linjuan OUYANG ,&nbsp;Junru FU ,&nbsp;Qingshun LI ,&nbsp;Haohua HE ,&nbsp;Haihui FU","doi":"10.1016/j.rsci.2026.03.002","DOIUrl":"10.1016/j.rsci.2026.03.002","url":null,"abstract":"<div><div>Tiller number is a crucial agronomic trait that directly influences the grain yield per unit area of rice. Alternative polyadenylation (APA), an essential post-transcriptional regulatory mechanism, plays a significant role in rice growth and development by generating transcripts with varying 3ʹ untranslated region (3ʹUTR) lengths. However, the specific role of APA in rice tillering remains poorly understood. We employed nanopore cDNA sequencing and tandem mass tag proteomics to analyze tiller axillary buds at different developmental stages in rice. Our findings revealed that genes at the early stages of tillering (effective tillering) tend to utilize longer transcripts, whereas those at the later stages (ineffective tillering) favor shorter transcripts. APA-related genes at both the effective and ineffective tillering stages are enriched in known rice tillering-associated pathways, such as the terpenoid backbone biosynthesis pathway and the carotenoid biosynthesis pathway. Additionally, APA-related genes at the ineffective tillering stage are further enriched in pathways such as leaf and organ senescence. The results demonstrate that APA-mediated gene length variation regulates rice tillering in a spatiotemporally specific pattern, and APA further impacts the protein abundance of genes involved in tillering. Genes that utilize the distal AAUAAA signal and produce longer transcripts exhibit stronger expression than those using the proximal signal, while genes using the proximal AAUAAA signal and generating shorter transcripts show stronger expression than those using the distal signal. This study clarifies the regulatory patterns of APA in rice tillering, laying a molecular foundation for the potential breeding of rice with ideal plant architecture.</div></div>","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"33 3","pages":"Pages 392-410"},"PeriodicalIF":6.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148208426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of Leaf Spectra (150–1100 nm) in Tetraploid Rice and Their Spontaneously Reverted Diploid Counterparts","authors":"Árpád SZÉKELY ,&nbsp;Tímea SZALÓKI ,&nbsp;Ildikó KOLOZSVÁRI ,&nbsp;Aftab JAMAL ,&nbsp;Mihály JANCSÓ","doi":"10.1016/j.rsci.2026.04.002","DOIUrl":"10.1016/j.rsci.2026.04.002","url":null,"abstract":"","PeriodicalId":56069,"journal":{"name":"Rice Science","volume":"33 3","pages":"Pages 292-296"},"PeriodicalIF":6.1,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148208460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}