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Standard Framework Construction of technology and Equipment for Big Data in Crop Phenomics

engineering 2024年第11期42卷 175-184页

作者： Weiliang Wen Shenghao Gu Ying Zhang Wanneng Yang Xinyu Guo Information Technology Research Center Beijing Academy of Agriculture and Forestry SciencesBeijing 100097China Beijing Key Lab of Digital Plant National Engineering Research Center for Information Technology in AgricultureBeijing 100097China National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research Huazhong Agricultural UniversityWuhan 430070China

Crop phenomics has rapidly progressed in recent years due to the growing need for crop functional geno-mics,digital breeding,and smart *** this advancement,the lack of standards for the cre-ation and usage of crop phenomics technology and equipment has become a bottleneck,limiting the industry’s high-quality *** paper begins with an overview of the crop phenotyping indus-try and presents an industrial mapping of technology and equipment for big data in crop *** analyzes the necessity and current state of constructing a standard framework for crop ***,this paper proposes the intended organizational structure and goals of the standard *** details the essentials of the standard framework in the research and development of hardware and equipment,data acquisition,and the storage and management of crop phenotyping ***,it discusses promoting the construction and evaluation of the standard framework,aiming to provide ideas for developing a high-quality standard framework for crop phenotyping.

关键词： Crop phenomics Big data Phenotyping technology and equipment Standard framework Industrial mapping

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Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice

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Journal of Integrative Plant Biology 2024年第1期66卷 66-85页

作者： Ding Ren Hui Liu Xuejun Sun Fan Zhang Ling Jiang Ying Wang Ning Jiang Peiwen Yan Jinhao Cui Jinshui Yang Zhikang Li Pingli Lu Xiaojin Luo State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology School of Life SciencesFudan UniversityShanghai 200438China State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China MOE Key Laboratory of Crop Physiology Ecology and Genetic Breeding College of AgronomyJiangxi Agricultural UniversityNanchang 330045China State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100081China College of Agronomy Anhui Agricultural UniversityHefei 230036China

RNA-binding proteins(RBPs)are components of the post-transcriptional regulatory system,but their regulatory effects on complex traits remain *** an integrated strategy involving map-based cloning,functional characterizations,and transcriptomic and population genomic analyses,we revealed that RBP-K(LOC_Os08g23120),RBP-A(LOC_Os11g41890),and RBP-J(LOC_Os10g33230)encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related *** of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function ***,RBP-J most likely affects GA pathways,resulting in considerable increases in grain and panicle lengths,but decreases in grain width and *** contrast,RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport,with substantial effects on the rice grain filling process as well as grain length and ***,RBP-K is relatively ancient and highly conserved,whereas RBP-J and RBP-A are more ***,the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency,efficiency,and versatility,as well as increased evolutionary *** results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex ***,rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted select

关键词： GL11 grain weight and shape post-transcriptional regulation RNA-binding proteins

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Transfer of disulfide bond formation modules via yeast artificial chromosomes promotes the expression of heterologous proteins in Kluyveromyces marxianus

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mLife 2024年第1期3卷 129-142页

作者： Pingping Wu Wenjuan Mo Tian Tian Kunfeng Song Yilin Lyu Haiyan Ren Jungang Zhou Yao Yu Hong Lu State Key Laboratory of Genetic Engineering School of Life SciencesFudan UniversityShanghaiChina Shanghai Engineering Research Center of Industrial Microorganisms ShanghaiChina

Kluyveromyces marxianus is a food-safe yeast with great potential for producing heterologous *** the yield in *** remains a challenge and incorporating large-scale functional modules poses a technical obstacle in *** address these issues,linear and circular yeast artificial chromosomes of ***(KmYACs)were constructed and loaded with disulfide bond formation modules from Pichia pastoris or *** modules contained up to seven genes with a maximum size of 15 *** carried telomeres either from *** or *** were transferred successfully into *** and stably propagated without affecting the normal growth of the host,regardless of the type of telomeres and configurations of *** increased the overall expression levels of disulfide bond formation genes and significantly enhanced the yield of various heterologous *** high-density fermentation,the use of KmYACs resulted in a glucoamylase yield of 16.8 g/l,the highest reported level to date in *** and metabolomic analysis of cells containing KmYACs suggested increased flavin adenine dinucleotide biosynthesis,enhanced flux entering the tricarboxylic acid cycle,and a preferred demand for lysine and arginine as features of cells overexpressing heterologous ***,supplementing lysine or arginine further improved the ***,KmYAC provides a powerful platform for manipulating large modules with enormous potential for industrial applications and fundamental *** the disulfide bond formation module via YACs proves to be an efficient strategy for improving the yield of heterologous proteins,and this strategy may be applied to optimize other microbial cell factories.

关键词： disulfide bond formation expression of heterologous proteins Kluyveromyces marxianus telomere yeast artificial chromosome

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Big data and artificial intelligence-aided crop breeding:Progress and prospects

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Journal of Integrative Plant Biology 2025年第3期67卷 722-739页

作者： Wanchao Zhu Weifu Li Hongwei Zhang Lin Li Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region College of AgronomyNorthwest A&F UniversityYangling 712100China National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China College of Informatics Huazhong Agricultural UniversityWuhan 430070China Engineering Research Center of Intelligent Technology for Agriculture Ministry of EducationWuhan 430070China State Key Laboratory of Crop Gene Resources and Breeding National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

The past decade has witnessed rapid developments in gene discovery, biological big data(BBD),artificial intelligence(AI)-aided technologies, and molecular breeding. These advancements are expected to accelerate crop breeding under the pressure of increasing demands for food. Here, we first summarize current breeding methods and discuss the need for new ways to support breeding efforts. Then, we review how to combine BBD and AI technologies for genetic dissection, exploring functional genes, predicting regulatory elements and functional domains, and phenotypic ***, we propose the concept of intelligent precision design breeding(IPDB) driven by AI technology and offer ideas about how to implement IPDB. We hope that IPDB will enhance the predictability, efficiency, and cost of crop breeding compared with current technologies. As an example of IPDB, we explore the possibilities offered by Crop GPT, which combines biological techniques, bioinformatics, and breeding art from breeders, and presents an open, shareable, and cooperative breeding system. IPDB provides integrated services and communication platforms for biologists, bioinformatics experts, germplasm resource specialists, breeders, dealers, and farmers,and should be well suited for future breeding.

关键词： artificial intelligence biological big data breeding precision design breeding systems biology

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genetic analysis and fine mapping of a grain size QTL in the smallgrain sterile rice line Zhuo201S

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Journal of Integrative Agriculture 2024年第7期23卷 2155-2163页

作者： Bin Lei Jiale Shao Feng Zhang Jian Wang Yunhua Xiao Zhijun Cheng Wenbang Tang Jianmin Wan College of Agronomy Hunan Agricultural UniversityChangsha 410128China National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China State Key Laboratory for Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center Nanjing Agricultural UniversityNanjing 210095China State Key Laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterChangsha 410125China

The development and application of the small-grain rice sterile line Zhuo201S(Z201S)has demonstrated its potential for mechanized hybrid rice seed production,leading to significant cost ***,the molecular mechanism responsible for the small-grain size characteristic of Z201S remains *** this study,we conducted a genetic analysis using near-isogenic lines constructed from Z210S,a small-grain rice sterile line,and R2115,a normal-grain *** results revealed that the small-grain trait in Z201S is governed by a single partially dominant gene which also enhances grain *** mapping,we localized the causal gene to the short arm of chromosome 2,within a 113 kb physical region delimited by the molecular markers S2-4-1 and *** analysis and gene expression assays indicated LOC_Os02g14760 as the most likely candidate gene,suggesting that the small-grain size trait of Z201S is controlled by a novel locus that has not been previously identified.

关键词： rice grain size map-based cloning

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Calcineurin inactivation inhibits pyruvate dehydrogenase complex activity and induces the Warburg effect (vol 40, pg 6692, 2021)

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ONCOgene 2025年第8期44卷 559-560页

作者： Zhang, Jianong Zhang, Liang Nie, Ji Lin, Yan Li, Yao Xu, Wei Zhao, Jian-Yuan Zhao, Shi-Min Wang, Chenji Obstetrics & Gynecology Hospital of Fudan University State Key Laboratory of Genetic Engineering MOE Engineering Research Center of Gene Technology Key Laboratory of Reproduction Regulation of NPFPC (SIPPR IRD) School of Life Sciences Fudan University Shanghai 200438 China Shanghai Fifth People’s Hospital and Institutes of Biomedical Sciences Fudan University Shanghai 200032 China State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai 200438 China

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Multi-genome evolutionary study of the ABC1 gene family and identification of the pleiotropic effects of OsABC1-13 in rice development

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The Crop Journal 2024年第4期12卷 1022-1030页

作者： Fuying Ma Mingyu Liu Peiwen Yan Shicong He Jian Hu Xinwei Zhang Fuan Niu Jinhao Cui Xinyu Yuan Xiaoyun Xin Liming Cao Jinshui Yang Ying Wang Xiaojin Luo State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology(Ministry of Education) School of Life SciencesFudan UniversityShanghai 200433China Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering Department of Ecology and Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200433China Institute of Crop Breeding and Cultivation Shanghai Academy of Agricultural SciencesShanghai 200241China Ministry of Education Key Laboratory of Crop PhysiologyEcology and Genetic Breeding College of AgronomyJiangxi Agricultural UniversityNanchang 330045JiangxiChina

In four rice genomes,85 ABC1-family genes were identified by comparative genomics,evolution,genetics,and ***,OsABC1-13,was shown by knockdown and knockout experiments to affect plant height,grain size,and photosynthet... 详细信息

关键词： Multi-genome analysis Activity of bc1 complex gene Photosynthesis Biomass Osabc1-13 Haplotype

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The kinase OsSK41/OsGSK5 negatively regulates amylose content in rice endosperm by affecting the interaction between OsEBP89 and OsBP5

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Journal of Integrative Plant Biology 2023年第7期65卷 1782-1793页

作者： Zejun Hu Fuan Niu Peiwen Yan Kai Wang Lixia Zhang Ying Yan Yu Zhu Shiqing Dong Fuying Ma Dengyong Lan Siwen Liu Xiaoyun Xin Ying Wang Jinshui Yang Liming Cao Shujun Wu Xiaojin Luo Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops(Co‐construction by Ministry and Province) Ministry of Agriculture and Rural AffairsCrop Breeding and Cultivation Research InstituteShanghai Academy of Agricultural SciencesShanghai 201403China State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology School of Life SciencesFudan UniversityShanghai 200438China MOE Key Laboratory of Crop Physiology Ecology and Genetic Breeding College of AgronomyJiangxi Agricultural UniversityNanchang 330045China

Amylose content(AC) is the main factor determining the palatability, viscosity, transparency, and digestibility of rice(Oryza sativa)grains. AC in rice grains is mainly controlled by different alleles of the Waxy(Wx) gene. The AP2/EREBP transcription factor OsEBP89 interacts with the MYC-like protein OsBP5 to synergistically regulate the expression of ***, we determined that the GLYCOGEN SYNTHASE KINASE 5(OsGSK5, also named SHAGGY-like kinase 41 [OsSK41]) inhibits the transcriptional activation activity of OsEBP89 in rice grains during amylose biosynthesis. The loss of OsSK41 function enhanced Wx expression and increased AC in rice grains. By contrast, the loss of function of OsEBP89 reduced Wx expression and decreased AC in rice grains. OsSK41 interacts with OsEBP89 and phosphorylates four of its sites(Thr-28,Thr-30, Ser-238, and Thr-257), which makes OsEBP89 unstable and attenuates its interaction with OsBP5. Wx promoter activity was relatively weak when regulated by the phosphomimicvariantOsEBP89E–OsBP5but relatively strong when regulated by the nonphosphorylatable variant OsEBP89A–***, OsSK41-mediated phosphorylation of OsEBP89 represents an additional layer of complexity in the regulation of amylose biosynthesis during rice grain development. In addition, our findings provide four possible sites for regulating rice grain AC via precise gene editing.

关键词： AP2/EREBP transcription factor endosperm amylose content GSK3-like family protein MYC-like protein OsSK41/OsGSK5 OsEBP89 OsBP5 rice grain

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CsWRKY11 cooperates with CsNPR1 to regulate SA-triggered leaf de-greening and reactive oxygen species burst in cucumber

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Molecular Horticulture 2024年第1期4卷 336-348页

作者： Dingyu Zhang Ziwei Zhu Bing Yang Xiaofeng Li Hongmei Zhang Hongfang Zhu Shanghai Key Laboratory of Protected Horticultural Technology Horticultural Research InstituteShanghai Academy of Agricultural Sciences1000 Jinqi RoadShanghai 201403China State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture School of Life SciencesFudan UniversityShanghai 200438China

Salicylic acid(SA)is a multi-functional phytohormone,regulating diverse processes of plant growth and development,especially triggering plant immune responses and initiating leaf ***,the early SA signaling events remain elusive in most plant species apart from Arabidopsis,and even less is known about the multi-facet mechanism underlying SA-regulated ***,we report the identification of a novel regulatory module in cucumber,CsNPR1-CsWRKY11,which mediates the regulation of SA-promoted leaf senescence and ROS *** analyses demonstrate that under SA treatment,CsNPR1 recruits CsWRKY11 to bind to the promoter of CsWRKY11 to activate its expression,thus amplifying the primary SA ***,CsWRKY11 cooperates with CsNPR1 to directly regulate the expression of both chlorophyll degradation and ROS biosynthesis related genes,thereby inducing leaf de-greening and ROS *** study provides a solid line of evidence that CsNPR1 and CsWRKY11 constitute a key module in SA signaling pathway in cucumber,and gains an insight into the interconnected regulation of SA-triggered processes.

关键词： Salicylic acid CsNPR1 CsWRKY11 Chlorophyll degradation ROS burst

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Young Leaf White Stripe encodes a P-type PPR protein required for chloroplast development

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Journal of Integrative Plant Biology 2023年第7期65卷 1687-1702页

作者： Jie Lan Qibing Lin Chunlei Zhou Xi Liu Rong Miao Tengfei Ma Yaping Chen Changling Mou Ruonan Jing Miao Feng Thanhliem Nguyen Yulong Ren Zhijun Cheng Xin Zhang Shijia Liu Ling Jiang Jianmin Wan State Key Laboratory of Crop Genetics and Germplasm Enhancement Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing 210095China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

Pentatricopeptide repeat(PPR) proteins function in post-transcriptional regulation of organellar gene expression. Although several PPR proteins are known to function in chloroplast development in rice(Oryza sativa), the detailed molecular functions of many PPR proteins remain ***, we characterized a rice young leaf white stripe(ylws) mutant, which has defective chloroplast development during early seedling ***-based cloning revealed that YLWS encodes a novel P-type chloroplast-targeted PPR protein with 11 PPR motifs. Further expression analyses showed that many nuclear-and plastid-encoded genes in the ylws mutant were significantly changed at the RNA and protein levels. The ylws mutant was impaired in chloroplast ribosome biogenesis and chloroplast development under low-temperature conditions. The ylws mutation causes defects in the splicing of atpF, ndhA, rpl2,and rps12, and editing of ndhA, ndhB, and rps14transcripts. YLWS directly binds to specific sites in the atpF, ndhA, and rpl2 pre-mRNAs. Our results suggest that YLWS participates in chloroplast RNA group II intron splicing and plays an important role in chloroplast development during early leaf development.

关键词： chloroplast development PPR protein ribosome biogenesis RNA splicing

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