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rice science 2024年第3期31卷 317-327,I0042-I0045页

作者： LI Dian DUAN Wenjing LIU Qun’en WU Weixun ZHAN Xiaodeng SUN Lianping ZHANG Yingxin CHENG Shihua State Key Laboratory of rice Biology and Breeding China National Rice Research InstituteHangzhou 310006China

Accurate genomic information is essential for advancing genetic breeding research in specific rice *** study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene ***,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)*** transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH *** analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall *** results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid *** association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH *** summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.

关键词： brown planthopper gapless genome genome assembly multi-omics Nilaparvata lugens rice

An orchestrated ethylene-gibberellin signaling cascade contributes to mesocotyl elongation and emergence of rice direct seeding

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Journal of Integrative Plant Biology 2024年第7期66卷 1427-1439页

作者： Yusong Lyu Xinli Dong Shipeng Niu Ruijie Cao Gaoneng Shao Zhonghua Sheng Guiai Jiao Lihong Xie Shikai Hu Shaoqing Tang Xiangjin Wei Peisong Hu State Key Laboratory of rice Biology and Breeding China National Center for Rice ImprovementChina National Rice Research InstituteHangzhou 310006China College of Agriculture and Biotechnology Zhejiang UniversityHangzhou 310058China

A mechanized direct seeding of rice with less labor and water usage,has been widely ***,this approach requires varieties that exhibit uniform seedling *** elongation(ME)offers the main drive of fast emergence of rice seedlings from soils;nevertheless,its genetic basis remains ***,we identify a major rice quantitative trait locus Mesocotyl Elongation1(qME1),an allele of the Green Revolution gene Semi-Dwarf1(SD1),encoding GA20-oxidase for gibberellin(GA)***1 expression is strongly induced by soil depth and *** rice grains are direct-seeded in soils,the ethylene core signaling factor OsEIL1 directly promotes ME1 transcription,accelerating bioactive GA *** GAs further degrade the DELLA protein SLENDER rice 1(SLR1),alleviating its inhibition of rice PHYTOCHROME-INTERACTING FACTOR-LIKE13(OsPIL13)to activate the downstream expansion gene OsEXPA4 and ultimately promote rice seedling ME and *** ancient traits of long mesocotyl and strong emergence ability in wild rice and landrace were gradually lost in company with the Green Revolution dwarf breeding process,and an elite ME1-R allele(D349H)is found in some modern Geng varieties(long mesocotyl lengths)in northern China,which can be used in the direct seeding and dwarf breeding of Geng ***,the ectopic and high expression of ME1 driven by mesocotyl-specific promoters resulted in rice plants that could be direct-seeded without obvious plant architecture or yield ***,we reveal the molecular mechanism of rice ME,and provide useful information for breeding new Green Revolution varieties with long mesocotyl suitable for direct-seeding practice.

关键词： rice(Oryza sativa L.) direct seeding Green Revolu-tion mesocotyl elongation ethylene gibberellin semi-dwarf1(SD1)

A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice

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National Science Review 2024年第6期11卷 105-118页

作者： Xiaoxia Li Xiaofan Dai Huiying He Yang Lv longbo Yang Wenchuang He Congcong Liu Hua Wei Xiangpei Liu Qiaoling Yuan Xianmeng Wang Tianyi Wang Bintao Zhang Hong Zhang Wu Chen Yue Leng Xiaoman Yu Hongge Qian Bin Zhang Mingliang Guo Zhipeng Zhang Chuanlin Shi Qianqian Zhang Yan Cui Qiang Xu Xinglan Cao Dandan Chen Yongfeng Zhou Qian Qian Lianguang Shang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences rice research institute Shenyang Agricultural University Yazhouwan National Laboratory State Key Laboratory of rice Biology China National Rice Research Institute National Key Laboratory of Tropical Crop Breeding Tropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural Sciences

Transposable elements(TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing *** the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms(SNPs), such as Os Rboh B, and validated Os Rboh B's relative expression activity using a dual-Luciferase(LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.

关键词： transposable element super pan-genome pan-TE rice

A 9.5-kb deletion in the 1st intron of OsMADS51 enhances temperature sensitivity in rice

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The Crop Journal 2024年第4期12卷 1031-1040页

作者： Lei Zhao Haifei Hu Junyu Chen Chongrong Wang Yibo Chen Hong Li Daoqiang Huang Zhidong Wang Degui Zhou Rong Gong Yangyang Pan Junliang Zhao Liangyong Ma Shaochuan Zhou rice research institute Guangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina State Key Laboratory of rice Biology and Chinese National Center for rice Improvement China National Rice Research InstituteHangzhou 310006ZhejiangChina Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510640GuangdongChina Key Laboratory of Genetics and Breeding of High Quality rice in Southern China(Co-construction by Ministry and Province) Ministry of Agriculture and Rural AffairsGuangzhou 510640GuangdongChina Guangdong rice Engineering Laboratory Guangzhou 510640GuangdongChina Guangdong Key Laboratory of New Technology in rice Breeding Guangzhou 510640GuangdongChina

Temperature is an important environmental factor affecting heading date of *** its importance,genes responsible for temperature-sensitive heading in rice have remained *** previous study identified a quantitative trait locus qHd1 which advances heading date under high temperatures.A 9.5-kb insertion was found in the first intron of OsMADS51 in indica variety Zhenshan 97(ZS97).However,the function of this natural variant in controlling temperature sensitivity has not been *** this study,we used CRISPR/Cas9 to knock out the 9.5-kb insertion in *** conducted under cotrolled conditions in phytotrons confirmed that deletion increased temperature sensitivity and advanced heading by downregulating the expression level of ***-hybrid assays in yeast,ChIP-quantitative polymerase chain reaction,electrophoretic mobility shift,and luciferase-based transient transactivation assays collectively confirmed that OsMADS51 affects heading date by regulation of heading date gene *** further determined that the long non-coding RNA HEATINR is generated from the first intron of OsMADS51,offering an explanation for how the 9.5-kb insertion affects temperature *** also found that OsMADS51 was strongly selected in early/late-season rice varieties in South China,possibly accounting for their strong temperature *** insights not only advance our understanding of the molecular mechanisms underlying the temperature-responsive regulation of heading date in rice but also provide a valuable genetic target for molecular breeding.

关键词： OsMADS51 Insertion long non-coding RNA Oryza sativa

Appropriate Supply of Ammonium Nitrogen and Ammonium Nitrate Reduces Cadmium Content in rice Seedlings by Inhibiting Cadmium Uptake and Transport

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rice science 2024年第5期31卷 587-602,I0062-I0064页

作者： HU Yunchao YAN Tiancai GAO Zhenyu WANG Tiankang LU Xueli YANG long SHEN Lan ZHANG Qiang HU Jiang REN Deyong ZHANG Guangheng ZHU Li LI Li ZENG Dali QIAN Qian LI Qing State Key Laboratory for rice Biology and Breeding China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou 311401China State Key Laboratory of Hybrid rice Hunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangsha 410125China The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province College of Advanced Agricultural SciencesZhejiang A&F UniversityHangzhou 311300China

Reasonable nitrogen(N) application is a promising strategy for reducing crop cadmium(Cd) toxicity. However, the specific form of N and the required amount that affect Cd tolerance and accumulation in rice remain unclear. This study explored the influence of different N-fertilizer forms(NH_(4)NO_(3), NH_4Cl, and KNO_(3)) and dosages on Cd tolerance and uptake in Cd-stressed N-sensitive and N-insensitive indica rice accessions. The results indicated that the Cd tolerance of N-sensitive indica accessions is more robust than that of N-insensitive ones. Furthermore, the shoot Cd content and Cd translocation rate in both N-sensitive and N-insensitive indica accessions decreased with an appropriate supply of NH_(4)NO_(3) and NH_4Cl, whereas they were comparable or slightly increased with increased KNO_(3). Unfortunately, we did not find significant and regular differences in Cd accumulation or translocation between N-sensitive and N-insensitive rice accessions. Consistent with the reduction of shoot Cd content, the addition of NH_(4)NO_(3) and NH_4Cl also inhibited the instantaneous root Cd^(2+) uptake. The expression changes of Cd transport-related genes under different N forms and dosages suggested that the decreased shoot Cd content, caused by the increased supply of NH_(4)NO_(3) and NH_4Cl, is likely achieved by reducing the transcription of OsNRAMP1 and OsIRT1. In summary, our findings reveal that an appropriate supply of NH_(4)NO_(3) and NH_4Cl could reduce Cd uptake and transport in rice seedlings, suggesting that rational N management could reduce the Cd risk in rice production.

关键词： Oryza sativa cadmium nitrogen ammonium nitrate ammonium chloride

A hybrid CNN-LSTM model for diagnosing rice nutrient levels at the rice panicle initiation stage

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Journal of Integrative Agriculture 2024年第2期23卷 711-723页

作者： Fubing Liao Xiangqian Feng Ziqiu Li Danying Wang Chunmei Xu Guang Chu Hengyu Ma Qing Yao Song Chen School of Computer Science and Technology Zhejiang Sci-Tech UniversityHangzhou 310018China China National rice research institute Chinese Academy of Agricultural SciencesHangzhou 310006China School of Agriculture Yangtze UniversityJingzhou 434025China

Nitrogen(N)and potassium(K)are two key mineral nutrient elements involved in rice *** diagnosis of N and K status is very important for the rational application of fertilizers at a specific rice growth ***,we propose a hybrid model for diagnosing rice nutrient levels at the early panicle initiation stage(EPIS),which combines a convolutional neural network(CNN)with an attention mechanism and a long short-term memory network(LSTM).The model was validated on a large set of sequential images collected by an unmanned aerial vehicle(UAV)from rice canopies at different growth stages during a two-year *** with VGG16,AlexNet,GoogleNet,DenseNet,and inceptionV3,ResNet101 combined with LSTM obtained the highest average accuracy of 83.81%on the dataset of Huanghuazhan(HHZ,an indica cultivar).When tested on the datasets of HHZ and Xiushui 134(XS134,a japonica rice variety)in 2021,the ResNet101-LSTM model enhanced with the squeeze-and-excitation(SE)block achieved the highest accuracies of 85.38 and 88.38%,*** the cross-dataset method,the average accuracies on the HHZ and XS134 datasets tested in 2022 were 81.25 and 82.50%,respectively,showing a good *** proposed model works with the dynamic information of different rice growth stages and can efficiently diagnose different rice nutrient status levels at EPIS,which are helpful for making practical decisions regarding rational fertilization treatments at the panicle initiation stage.

关键词： dynamic model of deep learning UAV rice panicle initiation nutrient level diagnosis image classification

Morpho-Physiological Changes in Roots of rice Seedling upon Submergence

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rice science 2019年第3期26卷 167-177页

作者： Liem T.BUI Evangelina S.ELLA Maribel L.DIONISIO-SESE Abdelbagi M.ISMAIL Department of Plant Biotechnology Cuu Long Delta Rice Research Institute Crop and Environmental Sciences Division International Rice Research Institute institute of Biological Sciences University of the Philippines Los Ba?os College

Submergence is a serious environmental condition that causes large loss in rice production in rain fed lowland and flood affected area. This study evaluated morphological and physiological responses of rice roots to submergence using two tolerant rice genotypes FR13A and Swarna-Sub 1 and two sensitive ones Swarna and IR42. The tolerant genotypes had higher survival rate and less shoot elongation but greater root elongation during submergence than the sensitive ones. After submergence,the tolerant genotypes also had higher root dry weight and more active roots than the sensitive *** genotypes exhibited less root injury, with less malondialdehyde production and slower electrolyte leakage after submergence. Tolerant genotypes also maintained higher concentrations of soluble sugar and starch in roots and shoots and higher chlorophyll retention after submergence than the sensitive *** data showed that root traits such as root activity and root growth are associated with survival rate after submergence. This is probably accomplished through higher energy supply, and membrane integrity is necessary to preserve root function and reduce injury during submergence. These root traits are important for submergence tolerance in rice.

关键词： peroxidase root activity submergence rice seedling Sub1a gene

rice Heat Tolerance Breeding: A Comprehensive Review and Forward Gaze

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rice science 2024年第4期31卷 375-400,I0022页

作者： Ravindran Lalithambika VISAKH Sreekumar ANAND Sukumaran Nair ARYA Behera SASMITA Uday Chand JHA Rameswar Prasad SAH Radha BEENA Department of Genetics and Plant Breeding College of AgricultureVellayaniKerala Agricultural UniversityThiruvananthapuramKerala 695522India Crop Improvement Division Indian Council of Agricultural Research-National Rice Research InstituteCuttackOdisha 7530006India Department of Plant Breeding and Genetics Indian Institute of Pulse ResearchKanpur 208024India Department of Plant Physiology College of AgricultureVellayaniKerala Agricultural UniversityThiruvananthapuramKerala 695522India

The yield potential of rice is seriously affected by heat stress due to climate change. Since rice is a staple food globally, it is imperative to develop heat-resistant rice varieties. Thus, a thorough understanding of the complex molecular mechanisms underlying heat tolerance and the impact of high temperatures on various critical stages of the crop is needed. Adoption of both conventional and innovative breeding strategies offers a long-term advantage over other methods, such as agronomic practices, to counter heat stress. In this review, we summarize the effects of heat stress, regulatory pathways for heat tolerance, phenotyping strategies, and various breeding methods available for developing heat-tolerant rice. We offer perspectives and knowledge to guide future research endeavors aimed at enhancing the ability of rice to withstand heat stress and ultimately benefit humanity.

关键词： genetic mechanism high-temperature stress molecular breeding genomics selection

A centromere map based on super pan-genome highlights the structure and function of rice centromeres

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Journal of Integrative Plant Biology 2024年第2期66卷 196-207页

作者： Yang Lv Congcong Liu Xiaoxia Li Yueying Wang Huiying He Wenchuang He Wu Chen longbo Yang Xiaofan Dai Xinglan Cao Xiaoman Yu Jiajia Liu Bin Zhang Hua Wei Hong Zhang Hongge Qian Chuanlin Shi Yue Leng Xiangpei Liu Mingliang Guo Xianmeng Wang Zhipeng Zhang Tianyi Wang Bintao Zhang Qiang Xu Yan Cui Qianqian Zhang Qiaoling Yuan Noushin Jahan Jie Ma Xiaoming Zheng Yongfeng Zhou Qian Qian longbiao Guo Lianguang Shang State Key Laboratory of rice Biology China National Rice Research InstituteHangzhou 310006China Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya City 572024China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

rice(Oryza sativa)is a significant crop worldwide with a genome shaped by various evolutionary *** centromeres are crucial for chromosome segregation,and contain some unreported *** to the diverse and complex centromere region,a comprehensive understanding of rice centromere structure and function at the population level is *** constructed a high-quality centromere map based on the rice super pangenome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African *** showed that rice centromeres have diverse satellite repeat CentO,which vary across chromosomes and subpopulations,reflecting their distinct evolutionary *** also revealed that long terminal repeats(LTRs),especially young Gypsy-type LTRs,are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and ***,high-quality genome assembly and complete telomere-to-telomere(T2T)reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being *** investigated the association between structural variations and gene expression in the rice centromere.A centromere gene,OsMAB,which positively regulates rice tiller number,was further confirmed by expression quantitative trait loci,haplotype analysis and clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein9 *** revealing the new insights into the evolutionary patterns and biological roles of rice centromeres,our finding will facilitate future research on centromere biology and crop improvement.

关键词： centromere super pan-genome CentoO satellite repeat rice

Underground communication:long non-coding RNA signaling in the plant rhizosphere

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Plant Communications 2024年第7期5卷 28-51页

作者： Muhammad Fahad Leeza Tariq Sajid Muhammad Liang Wu Hainan institute Zhejiang UniversitySanyaHainan 572000China Zhejiang Provincial Key Laboratory of Crop Genetic Resources College of Agriculture and BiotechnologyZhejiang UniversityHangzhouZhejiang 310058China National Key Laboratory for rice Biology Institute of BiotechnologyZhejiang UniversityHangzhou 310058China

long non-coding RNAs(lncRNAs)have emerged as integral gene-expression regulators underlying plant growth,development,and *** adapt to the heterogeneous and dynamic rhizosphere,plants use interconnected regulatory mechanisms to optimally fine-tune gene-expression-governing interactions with soil biota,as well as nutrient acquisition and heavy metal ***,high-throughput sequencing has enabled the identification of plant lncRNAs responsive to rhizosphere biotic and abiotic ***,we examine lncRNA biogenesis,classification,and mode of action,highlighting the functions of lncRNAs in mediating plant adaptation to diverse rhizosphere *** then discuss studies that reveal the significance and target genes of lncRNAs during developmental plasticity and stress responses at the rhizobium interface.A comprehensive understanding of specific lncRNAs,their regulatory targets,and the intricacies of their functional interaction networks will provide crucial insights into how these transcriptomic switches fine-tune responses to shifting rhizosphere *** ahead,we foresee that single-cell dissection of cell-type-specific lncRNA regulatory dynamics will enhance our understanding of the precise developmental modulation mechanisms that enable plant rhizosphere *** future challenges through multi-omics and genetic approaches will more fully reveal the integral roles of lncRNAs in governing plant adaptation to the belowground environment.

关键词： biotic and abiotic cues heavy metals long non-coding RNAs nutrients phytoremediation rhizosphere microbiome