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Gapless Genome Assembly of ZH8015 and Preliminary Multi-Omics Analysis to Investigate ZH8015's Responses Against Brown Planthopper Infestation

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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

A polygalacturonase gene OsPG1 modulates water homeostasis in rice

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The Crop Journal 2024年第1期12卷 79-91页

作者： Qinwen Zou Ranran Tu Jiajun Wu Tingting Huang Zhihao Sun Zheyan Ruan Hongyu Cao Shihui Yang Xihong Shen Guanghua He Hong Wang rice Research Institute Key Laboratory of Application and Safety Control of Genetically Modified CropsAcademy of Agricultural SciencesSouthwest UniversityChongqing 400715China State Key laboratory of rice Biology and Breeding Key Laboratory for Zhejiang Super Rice ResearchChina National Center for Rice ImprovementChina National Rice Research InstituteHangzhou 311401ZhejiangChina

A dynamic plant architecture is the basis of plant adaptation to changing *** many genes regulating leaf rolling have been identified,genes directly associated with water homeostasis are largely ***,we isolated a rice mutant,dynamic leaf rolling 1(dlr1),characterized by‘leaf unfolding in the morning-leaf rolling at noon-leaf unfolding in the evening’during a sunny *** content was decreased in rolled leaves and water sprayed on leaves caused reopening,indicating that in vivo water deficiency induced the leaf ***-based cloning and expression tests demonstrated that an A1400G single base mutation in Oryza sativa Polygalacturonase 1(OsPG1)/PHOTO-SENSITIVE LEAF ROLLING 1(PSL1)was responsible for the dynamic leaf rolling phenotype in the dlr1 ***1 encodes a polygalacturonase,one of the main enzymes that degrade demethylesterified homogalacturonans in plant cell ***1 was constitutively expressed in various tissues and was enriched in *** of the OsPG1 gene exhibited defects in stomatal closure and decreased stomatal density,leading to reduced transpiration and excessive water loss under specific conditions,but had normal root *** analysis revealed that mutation of OsPG1 led to reduced pectinase activity in the leaves and increased demethylesterified homogalacturonans in guard *** findings reveal a mechanism by which OsPG1 modulates water homeostasis to control dynamic leaf rolling,providing insights for plants to adapt to environmental variation.

关键词： Photosynthesis Stomata Transpiration Leaf rolling

Oriented Generation of Novel Thermo-Sensitive Genic Male Sterile Lines with Improved Grain Shape and Outcrossing Rate in Early-Season rice

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rice science 2024年第2期31卷 129-133,I0001-I0016页

作者： ZHANG Huali CHEN Junyu LI Ruiqing WANG Huimei DAI Dongqing LIANG Minmin WU Mingyue MA Liangyong State Key laboratory of rice Biology and Breeding/Chinese national Center for rice Improvement China National Rice Research InstituteHangzhou 310006China

Two-line hybrid rice with excellent quality is preferred in the Chinese ***,there is a trade-off between reducing costs for hybrid seed production and lowering the outcrossing rate of the sterile line,which is largely determined by the stigma exsertion rate(SER).In this study,we constructed mutants of male sterility lines with improved grain length(GL)and SER in three elite early-season indica rice varieties through targeted manipulation of the TMS5 and GS3 genes using CRISPR/Cas9-mediated multiplex *** obtained a series of marker-free gs3 single mutants and gs3tms5 double mutants with significantly higher SER,longer grains,and increased 1000-grain weight compared with the wild type(WT).Importantly,the typically thermo-sensitive genic male sterile(TGMS)trait with a higher SER was observed in gs3tms5 mutants,and their F1 hybrids exhibited remarkable improvements in grain shape and yield-related *** findings provided an efficient method to generate new valuable TGMS germplasm with improved SER through the mutagenesis of GS3 and TMS5 synergistically,and demonstrated that GS3 had pleiotropic effects on grain size,SER,and grain quality in early-season indica rice.

关键词： sterile elite season

OsbZIP01 Affects Plant Growth and Development by Regulating OsSD1 in rice

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rice science 2024年第1期31卷 77-86,I0018,I0019页

作者： DONG Xinli ZHOU Yang ZHANG Yaqi RONG Fuxi DU Jiahong HONG Zheyuan HU Peisong LÜYusong College of Agriculture and Biotechnology Zhejiang UniversityHangzhou 310058China State Key laboratory of rice Biology and Breeding/China national Center for rice Improvement China National Rice Research InstituteHangzhou 310006China

As the‘Green Revolution’gene,SD1(encoding GA20ox2),has been widely applied to improve yield in rice ***,research on its transcriptional regulation is ***,we identified a transcription factor OsbZIP01,which can suppress the expression of SD1 and regulate gibberellin(GA)biosynthesis in *** mutants of OsbZIP01 exhibited increased plant height,while the overexpression lines showed a semi-dwarf phenotype and diminished germination ***,the semi-dwarf phenotype of OE-bZIP01,was caused by the reduced internode length,which was accompanied by a thin stem *** predominant expression of OsbZIP01 was observed in leaves and ***01 protein was localized in the nucleus and showed transcriptional repression *** addition,OsbZIP01 could directly bind to the promoter of the OsSD1 gene,and inhibit its *** semi-dwarf phenotype of OE-bZIP01 could be rescued by exogenous GA_(3).Meanwhile,the bzip01 sd1 double mutant showed a shorter shoot length compared with the wild type,indicating that OsbZIP01 regulated plant growth mainly through the GA biosynthesis ***,OsbZIP01 negatively regulates GA biosynthesis by restraining SD1 transcription,thereby affecting plant growth and development.

关键词： OsbZIP01 SD1 gibberellin biosynthesis dwarf and germination

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 48-bp deletion upstream of LIGULELESS 1 alters rice panicle architecture

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The Crop Journal 2024年第2期12卷 354-363页

作者： Linhua Wu Min Hu Shuwei Lyu Wenfeng Chen Hang Yu Qing Liu Wei He Chen Li Zuofeng Zhu rice Research Institute Guangdong Academy of Agricultural SciencesGuangzhou 510640GuangdongChina national Center for Evaluation of Agricultural Wild Plants(rice) Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China State Key laboratory for rice Biology and Breeding China National Rice Research InstituteHangzhou 310006ZhejiangChina 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 Key laboratory of New Technology in rice Breeding Guangzhou 510640GuangdongChina Guangdong rice engineering laboratory Guangzhou 510640GuangdongChina

Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop *** investigate its molecular mechanisms in rice,we performed map-based cloning and characterization of OPEN PANICLE 1(OP1),a gain-of-function allele of LIGULELESS 1(LG1),controlling the spread-panicle *** allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary *** OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1(sp1).Knocking out BRASSINOSTEROID UPREGULATED1(BU1)gene in the background of OP1 complementary plants resulted in compact panicles,suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling *** regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture.

关键词： Upstream region Panicle architecture Gene expression BR rice

Molecular Mechanism of rice Necrotic Lesion for Optimized Yield and Disease Resistance

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rice science 2024年第3期31卷 285-299页

作者： HOU Xinyue WANG Yuping QIAN Qian REN Deyong State Key laboratory of rice Biology and Breeding China National Rice Research InstituteHangzhou 310006China State Key laboratory of Crop Gene Exploration and Utilization in Southwest China Rice Research InstituteSichuan Agricultural UniversityChengdu 611130China

How to balance rice resistance and yield is an important issue in rice *** with mutated necrotic lesion genes often have persistent broad-spectrum resistance,but this broad-spectrum resistance usually comes at the expense of ***,many necrotic lesion mutants in rice have been identified,and these genes are involved in disease resistance *** review provides a detailed introduction to the characteristics,classification,and molecular mechanisms of necrotic lesion ***,we review the molecular regulatory pathways of genes involved in rice disease ***,we summarize the relationship between resistance and yield in rice using newly developed gene editing *** discuss a rational and precise breeding strategy to better utilize molecular design technology for breeding disease-resistant and high-yield rice varieties.

关键词： rice necrotic lesion regulation mechanism high yield high resistance

Single-cell transcriptome sequencing reveals the mechanism regulating rice plumule development

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The Crop Journal 2024年第3期12卷 688-697页

作者： Mingdong Zhu Meng Zhang Kunyong Huang Feifei Lu Hong Wang Shaolu Zhao Yinghong Yu Shaoqing Tang Haining Wu Peisong Hu Xiangjin Wei State Key laboratory of rice Biology and Breeding China National Center for Rice ImprovementChina National Rice Research InstituteHangzhou 310006ZhejiangChina b State Key laboratory of Hybrid rice Hunan Rice Research InstituteHunan Academy of Agricultural SciencesChangsha 410125HunanChina Hunan Provincial Key laboratory of Plant Functional Genomics and Developmental Regulation College of BiologyHunan UniversityChangsha 410082HunanChina Hubei University Wuhan 430062HubeiChina

Seed plumules comprise multiple developing tissues and are key sites for above-ground plant organ ***,the spatial expression of genes in developing rice seed plumules was characterized by single-cell transcriptome sequencing in Zhongjiazao 17,a popular Chinese indica rice *** 15 cell clusters,13 were assigned to cell types using marker genes and cluster-specific *** genes of multiple cell types were expressed in several clusters,suggesting a complex developmental *** genes for signaling by phytohormones such as abscisic acid were highly expressed in specific *** cis-elements in the promoters of genes specifically expressed in cell clusters were calculated,and some key hormone-related motifs were frequent in certain *** expression patterns of genes involved in rapid seed germination,seedling growth,and development were *** findings enhanced our understanding of cellular diversity and specialization within plumules of rice,a monocotyledonous model crop.

关键词： rice Plumule Single-cell sequencing Regulatory network

Ruthenium-lead oxide for acidic oxygen evolution reaction in proton exchange membrane water electrolysis

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Nano Research 2024年第10期17卷 8671-8677页

作者： Feng-Yang Chen Chang Qiu Zhen-Yu Wu Tae-Ung Wi YZou Finfrock Haotian Wang Department of Chemical and Biomolecular engineering Rice UniversityHoustonTX 77005USA Structural Biology Center X-ray Science DivisionArgonne National LaboratoryLemontIL 60439USA Department of Materials Science and Nanoengineering Rice UniversityHoustonTX 77005USA Department of Chemistry Rice UniversityHoustonTX 77005USA

Developing an active and stable anode catalyst for the proton exchange membrane water electrolyzer(PEM-WE)is a critical objective to enhance the economic viability of green hydrogen ***,the expensive iridium-based electrocatalyst remains the sole practical material with industrial-level stability for the acidic oxygen evolution reaction(OER)at the ***-based catalysts have been proposed as more cost-effective alternatives with improved activity,though their stability requires *** current urgent goal is to reduce costs and noble metal loading of the OER catalyst while maintaining robust activity and *** this study,we design a Ru-based OER catalyst incorporating Pb as a supporting *** electrocatalyst exhibits an OER overpotential of 201 mV at 10 mA·cm^(-2),simultaneously reducing Ru noble metal loading by~40%.Normalization of the electrochemically active surface area unveils improved intrinsic activity compared to the pristine RuO_(2) *** a practical stability test in a PEM-WE setup,our developed catalyst sustains stable performance over 300 h without notable degradation,underscoring its potential for future applications as a reliable anodic catalyst.

关键词： electrocatalysis oxygen evolution reaction water splitting proton exchange membrane water electrolyzer