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Mining elite loci and candidate genes for root morphology-related traits at the seedling stage by genome-wide association studies in upland cotton(Gossypium hirsutum L.)

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Journal of Integrative Agriculture 2024年第10期23卷 3406-3418页

作者： Huaxiang Wu Xiaohui Song Muhammad Waqas-Amjid Chuan Chen Dayong Zhang Wangzhen Guo state key laboratory of crop genetics&germplasm enhancement and utilization/Engineering Research Center of Cotton germplasm enhancement and Application Ministry of Education/Nanjing Agricultural UniversityNanjing 210095China

Root system architecture plays an essential role in water and nutrient acquisition in plants,and it is significantly involved in plant adaptations to various environmental *** this study,a panel of 242 cotton accessions was collected to investigate six root morphological traits at the seedling stage,including main root length(MRL),root fresh weight(RFW),total root length(TRL),root surface area(RSA),root volume(RV),and root average diameter(AvgD).The correlation analysis of the six root morphological traits revealed strong positive correlations of TRL with RSA,as well as RV with RSA and AvgD,whereas a significant negative correlation was found between TRL and ***,a genome-wide association study(GWAS)was performed using the root phenotypic and genotypic data reported previously for the 242 accessions using 56,010 single nucleotide polymorphisms(SNPs)from the CottonSNP80K array.A total of 41 quantitative trait loci(QTLs)were identified,including nine for MRL,six for RFW,nine for TRL,12 for RSA,12 for RV and two for *** them,eight QTLs were repeatedly detected in two or more *** these results with a transcriptome analysis,we identified 17 candidate genes with high transcript values of transcripts per million(TPM)≥30 in the ***,we functionally verified the candidate gene GH_D05G2106,which encodes a WPP domain protein 2in root development.A virus-induced gene silencing(VIGS)assay showed that knocking down GH_D05G2106significantly inhibited root development in cotton,indicating its positive role in root system architecture ***,these results provide a theoretical basis and candidate genes for future studies on cotton root developmental biology and root-related cotton breeding.

关键词： cotton root-morphology traits quantitative trait loci candidate genes GWAS

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The CBL-interacting protein kinase OsCIPK1 phosphorylated by SAPK10 positively regulates responses to ABA and osmotic stress in rice

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The crop Journal 2024年第2期12卷 364-374页

作者： Caihua Qin Xing Fan Qianqian Fang Lan Ni Mingyi Jiang College of Life Sciences State Key Laboratory of Crop Genetics&Germplasm Enhancement and UtilizationKey Laboratory of Crop Physiology Ecology and Production ManagementMinistry of AgricultureNanjing Agricultural UniversityNanjing 210095JiangsuChina

SubclassⅢsucrose nonfermenting1-related protein kinase 2s(SnRK2s)function in ABA and abiotic stress responses by unknown *** found that osmotic stress/ABA-activated protein kinase 10(SAPK10),a member of rice SnRK2s,physically interacted with CBL-interacting protein kinase 1(OsCIPK1).OsCIPK1 expression was up-regulated by ABA and PEG treatment,and overexpression increased the ABA sensitivity of seed germination and root growth and plant osmotic stress *** stress or ABA-induced activation of OsCIPK1 is dependent on ***10 phosphorylates Thr-24 of OsCIPK1 in vitro,and this phosphorylation increases the activity of OsCIPK1 and positively regulates the function of OsCIPK1 in ABA responses and plant osmotic stress *** study suggests that OsCIPK1 is a direct phosphorylated substrate of SAPK10,and SAPK10-mediated phosphorylation of OsCIPK1 functions in ABA signaling and increases rice osmotic stress tolerance.

关键词： Rice ABA Osmotic stress OsCIPK1 SAPK10

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Suppressing a mitochondrial calcium uniporter activates the calcium signaling pathway and promotes cell elongation in cotton

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The crop Journal 2024年第2期12卷 411-421页

作者： Yujia Duan Xiaoguang Shang Ruiping Tian Weixi Li Xiaohui Song Dayong Zhang Wangzhen Guo state key laboratory of crop genetics&germplasm enhancement and utilization Nanjing Agricultural UniversityNanjing 210095JiangsuChina Engineering Research Center of Ministry of Education for Cotton germplasm enhancement and Application Nanjing Agricultural UniversityNanjing 210095JiangsuChina

Mitochondrial calcium uniporter(MCU)is a conserved calcium ion(Ca^(2+))transporter in the mitochondrial inner membrane of eukaryotic *** MCU proteins regulate Ca^(2+)flow and modulate plant cell development remain largely ***,we identified the gene GhMCU4 encoding a MCU protein that negatively regulates plant development and fiber elongation in cotton(Gossypium hirsutum).GhMCU4expressed constitutively in various tissues with the higher transcripts in elongating fiber *** of GhMCU4 in cotton significantly elevated the plant height and root *** calcium signaling pathway was significantly activated and calcium sensor genes,including Ca^(2+)dependent modulator of interactor of constitutively active ROP(GhCMI1),calmodulin like protein(GhCML46),calciumdependent protein kinases(GhCPKs),calcineurin B-like protein(GhCBLs),and CBL-interacting protein kinases(GhCIPKs),were dramatically upregulated in GhMCU4-silenced *** processes were preferentially enriched,and genes related to regulation of transcription were upregulated in GhMCU4-silenced *** contents of Ca^(2+)and H_(2)O_(2)were significantly increased in roots and leaves of GhMCU4-silenced *** length and Ca^(2+)and H_(2)O_(2)contents in fibers were significantly increased in GhMCU4-silenced *** study indicated that GhMCU4 plays a negative role in regulating cell elongation in cotton,thus expanding understanding in the role of MCU proteins in plant growth and development.

关键词： Calcium signaling Hydrogen peroxide Metabolic processed Gossypium hirsutum

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The protein phosphatase qGL3/OsPPKL1 selfregulates its degradation to orchestrate brassinosteroid signaling in rice

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Plant Communications 2024年第6期5卷 89-99页

作者： Xiuying Gao Jianbo Li Jing Yin Yiheng Zhao Zhongsheng Wu Lijuan Ma Baoyi Zhang Hongsheng Zhang Ji Huang state key laboratory of crop genetics&germplasm enhancement and utilization College of AgricultureNanjing Agricultural UniversityNanjing 210095China Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology Nanjing 210095China

Brassinosteroids(BRs)are a class of phytohormones that regulate plant growth and *** previous studies,we cloned and identified PROTEIN PHOSPHATASE WITH KELCH-LIKE1(OsPPKL1)as the causal gene for the quantitative trait locus GRAIN LENGTH3(qGL3)in rice(Oryza sativa).We also showed that qGL3/OsPPKL1 is mainly located in the cytoplasm and nucleus and negatively regulates BR signaling and grain *** qGL3 is a negative regulator of BR signaling,its turnover is critical for rapid response to changes in ***,we demonstrate that qGL3 interacts with the WD40-domain-containing protein WD40-REPEAT PROTEIN48(OsWDR48),which contains a nuclear export signal(NES).The NES signal is crucial for the cytosolic localization of OsWDR48 and also functions in the self-turnover of *** show that OsWDR48 physically interacts with and genetically acts through qGL3 to modulate BR ***,qGL3 may indirectly promote the phosphorylation of OsWDR48 at the Ser-379 and Ser-386 *** of both phosphorylation sites in OsWDR48 to non-phosphorylatable alanine enhanced the strength of the OsWDR48-qGL3 ***,we found that brassinolide can promote the accumulation of non-phosphorylated OsWDR48,leading to strong interaction intensity between qGL3 and *** together,our results show that OsWDR48 facilitates qGL3 retention and induces degradation of qGL3 in the *** findings suggest that qGL3 self-modulates its turnover by binding to OsWDR48 to regulate its cytoplasmic localization and stability,leading to efficient orchestration of BR signal transduction in rice.

关键词： Oryza sativa brassinosteroid grain length qGL3/OsPPKL1 self-regulation

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BBX9 forms feedback loops with PIFs and BBX21 to promote photomorphogenic development

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Journal of Integrative Plant Biology 2024年第9期66卷 1934-1952页

作者： Zhaoqing Song Wanying Ye Qing Jiang Huan Lin Qing Hu Yuntao Xiao Yeting Bian Fengyue Zhao Jie Dong Dongqing Xu state key laboratory of crop genetics&germplasm enhancement and utilization National Center for Soybean ImprovementCollege of AgricultureNanjing Agricultural UniversityNanjing 210095China Institute of crop Science College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China

Light is one of the most essential environmental factors that tightly and precisely control various physiological and developmental processes in plants.B-box CONTAINING PROTEINs(BBXs)play central roles in the regulation of light-dependent *** this study,we report that BBX9 is a positive regulator of light ***9 interacts with the red light photoreceptor PHYTOCHROME B(phyB)and transcription factors PHYTOCHROME-INTERACTING FACTORs(PIFs).phyB promotes the stabilization of BBX9 in light,while BBX9 inhibits the transcriptional activation activity of *** turn,PIFs directly bind to the promoter of BBX9 to repress its *** the other hand,BBX9 associates with the positive regulator of light signaling,BBX21,and enhances its biochemical ***21 associates with the promoter regions of BBX9 and transcriptionally up-regulates its ***,this study unveiled that BBX9 forms a negative feedback loop with PIFs and a positive one with BBX21 to ensure that plants adapt to fluctuating light conditions.

关键词： Arabidopsis BBX21 BBX9 light signaling photo-morphogenesis phyB PIF

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Knockout of a rice K5.2 gene increases Ca accumulation in the grain

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Journal of Integrative Plant Biology 2024年第2期66卷 252-264页

作者： Peitong Wang Naoki Yamaji Namiki Mitani-Ueno Jun Ge Jian Feng Ma National key laboratory of crop genetics&germplasm enhancement and utilization College of Resources and Environmental SciencesNanjing Agricultural UniversityNanjing 210095China Institute of Plant Science and Resources Okayama UniversityKurashiki 710-0046Japan

Rice is a staple food for half of the world’s population,but it is a poor dietary source of calcium(Ca)due to the low *** is an important issue to boost Ca concentration in this grain to improve Ca deficiency risk,but the mechanisms underlying Ca accumulation are poorly ***,we obtained a rice(Oryza sativa)mutant with high shoot Ca *** mutant exhibited 26%-53% higher Ca in shoots than did wild-type rice(WT)at different Ca *** concentration in the xylem sap was 36% higher in the mutant than in the *** was no difference in agronomic traits between the WT and mutant,but the mutant showed 25% higher Ca in the polished grain compared with the ***-based cloning combined with a complementation test revealed that the mutant phenotype was caused by an 18-bp deletion of a gene,OsK5.2,belonging to the Shaker-like K+channel ***5.2 was highly expressed in the mature region of the roots and its expression in the roots was not affected by Ca levels,but upregulated by low *** showed that OsK5.2 was mainly expressed in the pericycle of the *** together,our results revealed a novel role for OsK5.2 in Ca translocation in rice,and will be a good target for Ca biofortification in rice.

关键词： accumulation biofortification calcium OsK5.2 pericycle rice translocation

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Genetic and molecular mechanisms of reproductive isolation in the utilization of heterosis for breeding hybrid rice

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Journal of genetics and Genomics 2024年第6期51卷 583-593页

作者： Chaolong Wang Xiaowen Yu Jian Wang Zhigang Zhao Jianmin Wan state key laboratory for crop genetics&germplasm enhancement and Utlization Nanjing Agricultural UniversityZhongshan Biological Breeding LaboratoryNanjingJiangsu210095China state key laboratory of crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Heterosis,also known as hybrid vigor,is commonly observed in rice *** hybridization of rice species or subspecies exhibits robust hybrid vigor,however,the direct harnessing of this vigor is hindered by reproductive ***,we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific *** review encompasses the genetic model of reproductive isolation within and among Oryza sativa species,emphasizing the essential role of mitochondria in this ***,we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes,elucidating their significant contribution to reproductive ***,our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in *** on these advances,we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.

关键词： Hybrid vigor Reproductive isolation Hybrid ricebreeding

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Identification of key genes regulating the synthesis of quercetin derivatives in Rosa roxburghii through integrated transcriptomics and metabolomics

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Journal of Integrative Agriculture 2024年第3期23卷 876-887页

作者： Liyao Su Min Wu Tian Zhang Yan Zhong Zongming(Max) Cheng state key laboratory of crop genetics and germplasm enhancement College of HorticultureNanjing Agricultural UniversityNanjing210095China

Rosa roxburghii fruit is rich in flavonoids, but little is known about their biosynthetic pathways. In this study, we employed transcriptomics and metabolomics to study changes related to the flavonoids at five different stages of R. roxburghii fruit development. Flavonoids and the genes related to their biosynthesis were found to undergo significant changes in abundance across different developmental stages, and numerous quercetin derivatives were identified. We found three gene expression modules that were significantly associated with the abundances of the different flavonoids in R. roxburghii and identified three structural UDP-glycosyltransferase genes directly involved in the synthesis of quercetin derivatives within these modules. In addition, we found that RrBEH4, RrLBD1 and RrPIF8could significantly increase the expression of downstream quercetin derivative biosynthesis genes. Taken together,these results provide new insights into the metabolism of flavonoids and the accumulation of quercetin derivatives in R. roxburghii.

关键词： Rosa roxburghii quercetin derivatives weighted gene co-expression network analysis transcription factor transcriptome metabolome

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E3 ubiquitin ligase PbrATL18 is a positive factor in pear resistance to drought and Colletotrichum fructicola infection

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Horticultural Plant Journal 2024年第3期10卷 698-712页

作者： Likun Lin Qiming Chen Kaili Yuan Caihua Xing Qinghai Qiao Xiaosan Huang Shaoling Zhang state key laboratory of crop genetics and germplasm enhancement/College of Horticulture Nanjing Agricultural UniversityNanjingJiangsu210095China

The Arabidopsis Toxicos en Levadura(ATL)protein is a subfamily of the E3 ubiquitin ligases,which exists widely in plants and is extensively involved in plant growth and *** the ATL family has been identified in other species,such as Arabidopsis,Oryza sativa,and grapevine,few reports on pear ATL gene families have been *** this study,92 PbrATL genes were identified and analyzed from the Pyrus breschneideri *** analysis and phylogenetic tree generation divided them into nine subgroups,and chromosome localization analysis showed that the 92 PbrATL genes were distributed in 16 of 17 pear *** data and quantitative real-time polymerase chain reaction(qRT-PCR)experiments demonstrated that PbrATL18,PbrATL41,and PbrATL88 were involved in both pear drought resistance and Colletotrichum fructicola *** addition,Arabidopsis thaliana overexpressing PbrATL18 showed greater resistance to drought stress than the wild type(WT),and PbrATL18-silenced pear seedlings showed greater sensitivity to drought and *** infection than the ***18 regulated plant resistance by regulating chitinase(CHI),phenylalanine ammonia-lyase(PAL),polyphenol oxidase(PPO),catalase(CAT),peroxidase(POD),and superoxide dismutase(SOD)*** study provided a reference for further exploring the functions of the PbrATL gene in drought resistance and *** infection.

关键词： Pear Colletotrichum fructicola Arabidopsis Toxicos en Levadura(ATL) Drought stress

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Autophagy receptor ZmNBR1 promotes the autophagic degradation of ZmBRI1a and enhances drought tolerance in maize

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Journal of Integrative Plant Biology 2024年第6期66卷 1068-1086页

作者： Yang Xiang Guangdong Li Qian Li Yingxue Niu Yitian Pan Yuan Cheng Xiangli Bian Chongyang Zhao Yuanhong Wang Aying Zhang College of Life Sciences Nanjing Agricultural UniversityNanjing210095 China state key laboratory of crop genetics&germplasm enhancement and utilization Nanjing Agricultural UniversityNanjing210095 China Sanya Institute of Nanjing Agricultural University Nanjing Agricultural UniversitySanya572025 China

Drought stress is a crucial environmental factor that limits plant growth,development,and *** of misfolded proteins can help alleviate the damage caused in plants experiencing ***,the mechanism of autophagy-mediated drought tolerance in plants remains largely ***,we cloned the gene for a maize(Zea mays)selective autophagy receptor,NEXT TO BRCA1GENE 1(ZmNBR1),and identified its role in the response to drought *** observed that drought stress increased the accumulation of *** sequencing and reverse transcriptionquantitative polymerase chain reaction showed that ZmNBR1 is markedly induced by drought ***1 overexpression enhanced drought tolerance,while its knockdown reduced drought tolerance in *** results established that ZmNBR1 mediates the increase in autophagosomes and autophagic activity under drought ***1 also affects the expression of genes related to autophagy under drought ***,we determined that BRASSINOSTEROID INSENSITIVE1A(ZmBRI1a),a brassinosteroid receptor of the BRI1-like family,interacts with *** analysis showed that ZmBRI1a negatively regulates drought tolerance in maize,and genetic analysis indicated that ZmNBR1 acts upstream of ZmBRI1a in regulating drought ***,ZmNBR1facilitates the autophagic degradation of ZmBRI1a under drought *** together,our results reveal that ZmNBR1 regulates the expression of autophagy-related genes,thereby increasing autophagic activity and promoting the autophagic degradation of ZmBRI1a under drought stress,thus enhancing drought tolerance in *** findings provide new insights into the autophagy degradation of brassinosteroid signaling components by the autophagy receptor NBR1 under drought stress.

关键词： autophagy receptor drought tolerance Zea mays ZmBRI1a ZmNBR1

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