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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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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 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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Dosage effect genes modulate grain development in synthesized Triticum durum-Haynaldia villosa allohexaploid

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Journal of genetics and Genomics 2024年第10期51卷 1089-1100页

作者： Yu Z. Cui B. Xiao J. Jiao W. Wang H. Wang Z. Sun L. Song Q. Yuan J. Wang X. state key lab of crop genetics & germplasm enhancement and utilization Cytogenetics Institute Nanjing Agricultural University/JCIC-MCP/Zhongshan Biological Breeding Laboratory Jiangsu Nanjing 210095 China

Polyploidization in plants often leads to increased cell size and grain size, which may be affected by the increased genome dosage and transcription abundance. The synthesized Triticum durum (AABB)-Haynaldia villosa (VV) amphiploid (AABBVV) has significantly increased grain size, especially grain length, than the tetraploid and diploid parents. To investigate how polyploidization affects grain development at the transcriptional level, we perform transcriptome analysis using the immature seeds of T. durum, H. villosa, and the amphiploid. The dosage effect genes are contributed more by differentially expressed genes from genome V of H. villosa. The dosage effect genes overrepresent grain development-related genes. Interestingly, the vernalization gene TaVRN1 is among the positive dosage effect genes in the T. durum‒H. villosa and T. turgidum‒Ae. tauschii amphiploids. The expression levels of TaVRN1 homologs are positively correlated with the grain size and weight. The TaVRN1-B1 or TaVRN1-D1 mutation shows delayed florescence, decreased cell size, grain size, and grain yield. These data indicate that dosage effect genes could be one of the important explanations for increased grain size by regulating grain development. The identification and functional validation of dosage effect genes may facilitate the finding of valuable genes for improving wheat yield. © 2024 Institute of genetics and Developmental Biology, Chinese Academy of Sciences, and genetics Society of China

关键词： Allopolyploid Dosage effect Grain size Polyploidization TaVRN1 Wheat

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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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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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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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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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Fast,simple,efficient Agrobacterium rhizogenes-mediated transformation system to non-heading Chinese cabbage with transgenic roots

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Horticultural Plant Journal 2024年第2期10卷 450-460页

作者： Huiyu Wang Yushan Zheng Qian Zhou Ying Li Tongkun Liu Xilin Hou state key laboratory of crop genetics&germplasm enhancement Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(East China)Ministry of Agriculture and Rural Affairs of ChinaEngineering Research Center of Germplasm Enhancement and Utilization of Horticultural CropsMinistry of Education of ChinaNanjing Agricultural UniversityNanjingJiangsu 210095China Nanjing Suman Plasma Engineering Research Institute Nanjing Agricultural UniversityNanjingJiangsu 210095China

Non-heading Chinese cabbage, a variety of Brassica campestris, is an important vegetable crop in the Yangtze River Basin of China. However,the immaturity of its stable transformation system and its low transformation efficiency limit gene function research on non-heading Chinese cabbage. Agrobacterium rhizogenes-mediated(ARM) transgenic technology is a rapid and effective transformation method that has not yet been established for non-heading Chinese cabbage plants. Here, we optimized conventional ARM approaches(one-step and two-step transformation methods) suitable for living non-heading Chinese cabbage plants in nonsterile environments. Transgenic roots in composite non-heading Chinese cabbage plants were identified using phenotypic detection, fluorescence observation, and PCR analysis. The transformation efficiency of a two-step method on four five-day-old non-heading Chinese cabbage seedlings(Suzhouqing, Huangmeigui, Wuyueman, and Sijiu Caixin) was 43.33%-51.09%, whereas using the stout hypocotyl resulted in a transformation efficiency of 54.88% for the 30-day-old Sijiu *** one-step method outperformed the two-step method;the transformation efficiency of different varieties was above 60%, and both methods can be used to obtain transgenic roots for functional studies within one month. Finally, optimized ARM transformation methods can easily,quickly, and effectively produce composite non-heading Chinese cabbage plants with transgenic roots, providing a reliable foundation for gene function research and non-heading Chinese cabbage genetic improvement breeding.

关键词： Agrobacterium rhizogenes Non-heading Chinese cabbage Transgenic roots Composite plant Transformation efficiency

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DcGA20ox2 and DcGA2ox1 alter endogenous gibberellin contents and adjust lignin accumulation in carrot

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Horticultural Plant Journal 2024年第6期10卷 1398-1413页

作者： Jia M. Wang Y. Chen C. Zhang R. Wang G. Xiong A. state key laboratory of crop genetics & germplasm enhancement and utilization Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China College of Horticulture Nanjing Agricultural University Jiangsu Nanjing 210095 China School of Life Science and Food Engineering Huaiyin Institute of Technology Jiangsu Huaian 223003 China

Gibberellins (GAs) are a class of plant hormones that can affect plant growth and development. GA-oxidases are rate-limiting enzymes, which play a direct role in GA accumulation in plants. However, the roles of GA-oxidase on carrot (Daucus carota L.) taproot development are still unclear. In this study, two GA-oxidase genes, DcGA20ox2 and DcGA2ox1, were identified in carrot. Transgenic carrot plants were obtained by using Agrobacterium-mediated genetic transformation method. The results showed that overexpression of DcGA20ox2 significantly promoted the accumulation of active GAs in carrot, increased plant height, generated more branches, and enhanced xylem development. Overexpression of DcGA2ox1 significantly reduced the total contents of active GAs compared with the control group, resulting in a dwarf phenotype and markedly increased lignin content of the transgenic carrot. The expression profiling showed that the genes of GA metabolic pathway responded to the negative feedback regulation mechanism. At the same time, the expression of most genes in lignin biosynthesis and polymerization process was up-regulated, corresponding to the massive accumulation of lignin. These findings indicated that DcGA20ox2 and DcGA2ox1 affected carrot growth and development by regulating the levels of endogenous GAs. The results from current work might shed light on further studies aimed to regulate lignification in carrot and other crops. © 2023 Chinese Society for Horticultural Science (CSHS) and Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS).

关键词： Daucus carota GA accumulation GA-oxidase Gibberellin Lignin

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