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Intergeneric chromosome-specific painting reveals differential chromosomal transmission from Tripidium arundinaceum in sugarcane progeny

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Journal of Integrative Agriculture 2024年第11期23卷 3751-3762页

作者： Fan Yu Zehuai Yu Jin Chai Xikai Yu Chen Fu Xinwang Zhao Hailong Chang Jiawei Lei Baoshan Chen Wei Yao Muqing Zhang Jiayun Wu Qinnan Wang Zuhu Deng State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangxi Key Laboratory for Sugarcane Biology College of AgricultureGuangxi UniversityNanning 530004China National Engineering Research Center for Sugarcane Fujian Agriculture and Forestry UniversityFuzhou 350002China Institute of Nanfan&Seed Industry Guangdong Academy of SciencesGuangzhou 510316China Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture and Rural Affairs/Fujian Agriculture and Forestry UniversityFuzhou 350002China

Sugarcane has recently attracted increasing attention for its potential as a source of sugar and bioethanol,so increasing its yield is essential to ensure the sugar security and bioenergy *** hybridization is a highly efficient method to produce new genetic variants of crop plants,particularly those species with high ploidy such as sugarcane(Saccharum spp.).Tripidium arundinaceum exhibits many desirable agronomic traits,and has been widely studied to produce hybrids with improved stress tolerance and other characteristics in sugarcane ***,the genetic relationship between *** and Saccharum species,and the individual *** chromosomal compositions in sugarcane hybrids are still *** we used whole-genome single-nucleotide polymorphisms(SNPs)to ascertain the phylogenetic relationships between these species and found that *** is more closely related to Saccharum than Sorghum,in contrast to the previous narrow genetic analyses using chloroplast ***,oligonucleotide(oligo)-based chromosome-specific painting derived from Saccharum officinarum was able to distinctly identify the chromosomes of *** developed the oligo-genomic in situ hybridization(GISH)system for the first time,to unveil the novel chromosome translocations and the transmission of individual *** chromosomes in sugarcane ***,we discovered that the chromosomal transmission of *** exhibited several different inheritance modes,including n,2n,and over 2n in the BC1 *** inheritance patterns may have resulted from first division restitution(FDR)or FDR+nondisjunction of a chromosome with the sister chromatids in the second meiosis division/second division restitution(FDR+NSC/SDR)model during *** results will be of substantial benefit for the further selection of *** chromosomes for sugarcane genetic improvement.

关键词： sugarcane Tripidium arundinaceum chromosome painting Oligo-FISH chromosomal transmission

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gene-knockout by iSTOP enables rapid reproductive disease modeling and phenotyping in germ cells of the founder generation

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Science China(Life Sciences) 2024年第5期67卷 1035-1050页

作者： Yaling Wang Jingwen Chen Xueying Huang Bangguo Wu Peng Dai Feng Zhang Jinsong Li Lingbo Wang State Key Laboratory of Genetic Engineering Shanghai Key Laboratory of Metabolic Remodeling and HealthInstitute of Metabolism and Integrative BiologyFudan UniversityShanghai 200438China Institute of Reproduction and Development Obstetrics and Gynecology HospitalFudan UniversityShanghai 200011China NHC Key Lab of Reproduction Regulation(Shanghai Institute for Biomedical and Pharmaceutical Technologies) School of PharmacyFudan UniversityShanghai 200433China Shanghai Key Laboratoryof Maternal and Fetal Medicine Clinical and Translational Research Center of Shanghai First Maternity and Infant HospitalFrontier Science Center for Stem Cell ResearchSchoolof Life Sciences and TechnologyTongji UniversityShanghai 200092China State Key Laboratory of Cell Biology CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai 200031China

Cytosine base editing achieves C·G-to-T·A substitutions and can convert four codons(CAA/CAG/CGA/TGG)into STOP-codons(induction of STOP-codons,iSTOP)to knock out genes with reduced *** enables direct phenotyping in founders’somatic cells,but it remains unknown whether this works in founders’germ cells so as to rapidly reveal novel genes for ***,we initially establish that iSTOP in mouse zygotes enables functional characterization of known genes in founders’germ cells:Cfap43-iSTOP male founders manifest expected sperm features resembling human“multiple morphological abnormalities of the flagella”syndrome(i.e.,MMAF-like features),while oocytes of Zp3-iSTOP female founders have no zona *** further illustrate iSTOP’s utility for dissecting the functions of unknown genes with Ccdc183,observing MMAF-like features and male infertility in Ccdc183-iSTOP founders,phenotypes concordant with those of Ccdc183-KO *** ultimately establish that CCDC183 is essential for sperm morphogenesis through regulating the assembly of outer dynein arms and participating in the intra-flagellar *** study demonstrates iSTOP as an efficient tool for direct reproductive disease modeling and phenotyping in germ cells of the founder generation,and rapidly reveals the essentiality of Ccdc183 in fertility,thus providing a time-saving approach for validating genetic defects(like nonsense mutations)for human infertility.

关键词： disease modeling infertility multiple morphological abnormalities of the flagella(MMAF) induction of STOP-codons(iSTOP CRISPR-STOP) sperm motility

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Identification of genomic regions and candidate genes underlying carotenoid accumulation in soybean using next-generation sequencing based bulk segregant analysis

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Journal of Integrative Agriculture 2025年第6期24卷 2063-2079页

作者： Berhane S.Gebregziabher Shengrui Zhang Jing Li Bin Li Junming Sun State Key Laboratory of Crop Gene Resources and Breeding/National Engineering Center for Crop Molecular Breeding Ministry of Agriculture and Rural Affairs/Key Laboratory of Soybean Biology (Beijing)/Institute of Crop Sciences Chinese Academy of Agricultural Sciences Crop Sciences Research Department Ethiopian Institute of Agricultural Research

The improvement of soybean seed carotenoid contents is very important due to the beneficial role of carotenoids in human health and nutrition. However, the genetic architecture underlying soybean carotenoid biosynthesis remains largely unknown. In the present study, we employed next generation sequencing-based bulked-segregant analysis to identify new genomic regions governing seed carotenoids in 1,551 natural soybean accessions. The genomic DNA samples of individual plants with extreme phenotypes were pooled to form two bulks with high(50 accessions) and low(50 accessions) carotenoid contents for Illumina sequencing. A total of 125.09 Gb of clean bases and 89.82% of Q30 were obtained, and the average alignment efficiency was 99.45% with an average coverage depth of 62.20× and 99.75% genome coverage. Based on the G prime statistic algorithm(G') method analysis, 16 candidate genomic loci with a total length 20.41 Mb were found to be related to the trait. Of these loci, the most significant regions displaying the highest elevated G' values were found in chromosome 06 at a position of 18.53–22.67 Mb, and chromosome 19 at genomic region intervals of 8.36–10.94, 12.06–13.79 and 18.45–20.26 Mb. These regions were then used to identify the key candidate genes. In these regions, 250 predicted genes were found and analyzed to obtain 90 significantly enriched(P<0.05) gene Ontology(GO) terms. Based on ANNOVAR analysis, 50 genes with non-synonymous and stopgained mutations were preferentially selected as potential candidate genes. Of those 50 genes, following their gene annotation functions and high significant haplotype variations in various environments,five genes were identified as the most promising candidate genes regulating soybean seed carotenoid accumulation, and they should be investigated in further functional validation studies. Collectively, understanding the genetic basis of carotenoid pigments and identifying genes underpinning carotenoid accumulation via a bulked

关键词： soybean (Glycine max L. Merrill) carotenoid bulk segregant analysis next-generation sequencing candidate genes

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Multi-omics for COVID-19:driving development of therapeutics and vaccines

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National Science Review 2023年第9期10卷 307-336页

作者： Mengyu Guo Muya Xiong Jinying Peng Tong Guan Haixia Su Yanyi Huang Cai-Guang Yang Yang Li Diana Boraschi Thanigaimalai Pillaiyar Guanbo Wang Chengqi Yi Yechun Xu Chunying Chen CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology of China State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences University of Chinese Academy of Sciences State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Biomedical Pioneering Innovation Centre Peking University Institute for Cell Analysis Shenzhen Bay Laboratory Peking-Tsinghua Center for Life Sciences Peking University College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular SciencesPeking University State Key Laboratory of Drug Research Centre for Chemical BiologyShanghai Institute of Materia MedicaChinese Academy of Sciences Laboratory of Immunology and Nanomedicine and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical ImmunomodulationShenzhen Institute of Advanced TechnologyChinese Academy of Sciences Institute of Biochemistry and Cell Biology National Research Council Institute of Pharmacy Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery Eberhard Karls University Tübingen Department of Chemical Biology and Synthetic and Functional Biomolecules Center College of Chemistry and Molecular Engineering Peking University GBA National Institute for Nanotechnology Innovation

The ongoing COVID-19 pandemic caused by SARS-CoV-2 has raised global concern for public health and *** development of therapeutics and vaccines to combat this virus is continuously ***-omics approaches,including genomics,transcriptomics,proteomics,metabolomics,epigenomics and metallomics,have helped understand the structural and molecular features of the virus,thereby assisting in the design of potential therapeutics and accelerating vaccine development for ***,we provide an up-to-date overview of the latest applications of multi-omics technologies in strategies addressing COVID-19,in order to provide suggestions towards the development of highly effective knowledge-based therapeutics and vaccines.

关键词： COVID-19 SARS-CoV-2 multi-omics antibodies small-molecule drugs vaccines

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Growth,ROS Markers,Antioxidant Enzymes,Osmotic Regulators and Metabolic Changes in Tartary Buckwheat Subjected to Short Drought

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Phyton-International Journal of Experimental Botany 2023年第1期92卷 35-54页

作者： Yan Wan Yuan Liang Xuxiao Gong Jianyong Ouyang Jingwei Huang Xiaoyong Wu Qi Wu Changying Liu Xueling Ye Xiaoning Cao Gang Zhao Liang Zou Dabing Xiang Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural AffairsSichuan Engineering&Technology Research Center of Coarse Cereal IndustrializationCollege of Food and Biological EngineeringChengdu UniversityChengdu610106China School of Preclinical Medicine Chengdu UniversityChengdu610106China Center for Agricultural Genetic Resources Research Shanxi Agricultural UniversityTaiyuan030031China

Tartary buckwheat(Fagopyrum tataricum)is an important pseudocereal feed crop with medicinal and nutritional *** is one of the main causes of reduced growth and yield in these *** investigated the growth,physiological,and metabolic responses of the widely promoted Tartary buckwheat variety Chuan Qiao No.1 to polyethylene glycol(PEG)-mediated drought *** significantly decreased shoot length,shoot biomass and relative water *** length,malondialdehyde content,electrolyte leakage,activities of superoxide dismutase,peroxidase,catalase and amylase,and contents of soluble sugar,soluble protein and proline were increased by PEG-mediated *** metabolomics analysis identified 32 core metabolites in seedlings subjected to PEG-mediated drought,16 of which increased—including quercetin,isovitexin,cyanidin 3-O-beta-D-glucoside,L-arginine,and glycerophosphocholine,while the other 16 decreased—including 3-methoxytyramine,2,6-diaminopimelic acid,citric acid,UDP-alpha-D-glucose,adenosine,*** 32 core metabolites were enriched in 29 metabolic pathways,including lysine biosynthesis,citrate(TCA)cycle,anthocyanin biosynthesis,and aminoacyl-tRNA *** them,taurine and hypotaurine metabolism,flavor and flavor biosynthesis,indole alkaline biosynthesis,and alanine,aspartate and glutamate metabolism were the four main metabolic pathways affected by *** findings provide new insights into the physiological and metabolic response mechanisms of Tartary buckwheat to drought stress.

关键词： Tartary buckwheat drought untargeted metabolomics analysis metabolic pathway physiological response

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Exercise-induced microbial changes in preventing type 2 diabetes

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Science China(Life Sciences) 2024年第5期67卷 892-899页

作者： Ting Yao Hui Wang Kaiqing Lin Ruwen Wang Shanshan Guo Peijie Chen Hao Wu Tiemin Liu Ru Wang School of Exercise and Health Shanghai Frontiers Science Research Base of Exercise and Metabolic HealthShanghai University of SportShanghai 200438China Department of Physiology and Pathophysiology School of Basic Medical SciencesXi’an Jiaotong University School of MedicineXi’an 710061China Shanghai Key Laboratory of Metabolic Remodeling and Health Institute of Metabolism&Integrative BiologyFudan UniversityShanghai 200433China State Key Laboratory of Genetic Engineering Human Phenome InstituteFudan Microbiome Centerand Department of Bariatric and Metabolic SurgeryHuashan HospitalFudan UniversityShanghai 201203China State Key Laboratory of Genetic Engineering Department of Endocrinology and MetabolismHuman Phenome Instituteand School of Life SciencesZhongshan HospitalFudan UniversityShanghai 200032China

The metabolic benefits associated with long-term physical activity are well appreciated and growing evidence suggests that it involves the gut *** we re-evaluated the link between exercise-induced microbial changes and those associated with prediabetes and *** found that the relative abundances of substantial amounts of diabetes-associated metagenomic species associated negatively with physical fitness in a Chinese athlete students *** additionally showed that those microbial changes correlated more with handgrip strength,a simple but valuable biomarker suggestive of the diabetes states,than maximum oxygen intake,one of the key surrogates for endurance ***,the causal relationships among exercise,risks for diabetes,and gut microbiota were explored based on mediation *** propose that the protective roles of exercise against type 2 diabetes are mediated,at least partly,by the gut microbiota.

关键词： gut microbiota body fat diabetes handgrip maximum oxygen intake

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Post-translational cleavage generates truncated IgY forms in the snake Elaphe taeniura

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Zoological research 2025年第2期46卷 277-284页

作者： Ming Zhang Long Hua Tang-Yuan Xie Tao Wang Li-Juan Du Di Yu Han-Wei Cao Jin-Cheng Zhong Geng-Sheng Cao Xiang Ding Hai-Tang Han Yao-Feng Zhao Tian Huang Key Laboratory of Qinghai-Xizang Plateau Animal Genetic Resource Reservation and Utilization Sichuan Province and Ministry of EducationSouthwest Minzu UniversityChengduSichuan 610041China Henan Province Livestock Gene Editing Biotechnology Breeding Engineering Center School of Life SciencesHenan UniversityKaifengHenan 475000China State Key Laboratory of Animal Biotech Breeding College of Biological SciencesNational Engineering Laboratory for Animal BreedingFrontiers Science Center for Molecular Design BreedingChina Agricultural UniversityBeijing 100193China Laboratory of Proteomics Institute of BiophysicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

While variable regions of immunoglobulins are extensively diversified by V(D)J recombination and somatic hypermutation in vertebrates,the constant regions of immunoglobulin heavy chains also utilize certain mechanisms to produce diversity,including class switch recombination(CSR),subclass differentiation,and alternative expression of the same *** species of birds,reptiles,and amphibians express a truncated isoform of immunoglobulin Y(IgY),termed IgY(ΔFc),which lacks theυCH3 andυCH4 *** Anseriformes,IgY(ΔFc)arises from alternative transcriptional termination sites within the sameυgene,whereas in some turtles,intact IgY and IgY(ΔFc)are encoded by distinct *** from the previously reported IgY(ΔFc)variants,this study identified a truncated IgY in the snake Elaphe taeniura,characterized by the loss of only a portion of the CH4 *** blotting and liquid chromatographytandem mass spectrometry confirmed that this truncated IgY is generated by post-translational cleavage at N338 within the IgY heavy chain constant(CH)***,both human and snake asparaginyl endopeptidase were shown to cleave snake IgY in *** findings reveal a novel mechanism for the production of shortened IgY forms,demonstrating that the immunoglobulin CH region undergoes diversification through distinct strategies across vertebrates.

关键词： Truncated IgY Post-translational cleavage Asparaginyl endopeptidase

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Peripheral actions and direct central-local communications of melanocortin 4 receptor signaling

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Journal of Sport and Health Science 2023年第1期12卷 45-51页

作者： Lei Li Jinye Liang Cong Zhang Tiemin Liu Chao Zhang Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalShanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghai 200092China Department of Biology University of IowaIowa CityIA 52242USA State Key Laboratory of Genetic Engineering Department of Endocrinology and Metabolismand School of Life SciencesZhongshan HospitalFudan UniversityShanghai 200032China

Melanocortin 4 receptor(MC4R),the most important monogenetic cause of human metabolic disorders,has been of great interest to many researchers in the field of energy homeostasis and public *** MC4R is a vital pharmaceutical target for maintaining controllable appetite and body weight for professional athletes,previous studies have mainly focused on the central,rather than the peripheral,roles of ***,the local expression of MC4R and its behavioral regulation remain *** an attempt to shed light on different directions for future studies of MC4R signaling,we review a series of recent and important studies exploring the peripheral functions of MC4R and the direct physiological interaction between peripheral organs and central MC4R neurons in this article.

关键词： Body weight Energy homeostasis GPCR Melanocortin-4 receptor

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Efficient CRISPR/Cas9-mediated genome editing in sheepgrass(Leymus chinensis)

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Journal of Integrative Plant Biology 2023年第11期65卷 2416-2420页

作者： Zhelong Lin Lei Chen Shanjie Tang Mengjie Zhao Tong Li Jia You Changqing You Boshu Li Qinghua Zhao Dongmei Zhang Jianli Wang Zhongbao Shen Xianwei Song Shuaibin Zhang Xiaofeng Cao State Key Laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Genetics and Developmental BiologyThe Chinese Academy of SciencesBeijing 100101China Institute of Forage and Grassland Sciences Heilongjiang Academy of Agricultural SciencesHarbin 150086China State Key Laboratory of Plant Cell and Chromosome Engineering Center for Genome EditingInstitute of Genetics and Developmental BiologyThe Chinese Academy of SciencesBeijing 100101China

The lack of genome editing platforms has hampered efforts to study and improve forage crops that can be grown on lands not suited to other ***,we established efficient Agrobacterium-mediated clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease 9(Cas9)genome editing in a perennial,stress-tolerant forage grass,sheepgrass(Leymus chinensis).By screening for active single-guide RNAs(sg RNAs),accessions that regenerate well,suitable Agrobacterium strains,and optimal culture media,and co-expressing the morphogenic factor Ta WOX5,we achieved 11%transformation and 5.83%editing efficiency in *** out Teosinte Branched1(TB1)significantly increased tiller number and *** study opens avenues for studying gene function and breeding in sheepgrass.

关键词： Agrobacterium genetic transformation genome editing Lc TB1 sheepgrass

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Large-scale genomic and phenomic analyses of modern cultivars empower future rice breeding design

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分子植物（英文版） 2025年第4期18卷 651-668页

作者： Xiaoding Ma Hao Wang Shen Yan Chuanqing Zhou Kunneng Zhou Qiang Zhang Maomao Li Yaolong Yang Danting Li Peng Song Cuifeng Tang Leiyue Geng Jianchang Sun Zhiyuan Ji Xianjun Sun Yongli Zhou Peng Zhou Di Cui Bing Han Xin Jing Qiang He Wei Fang Longzhi Han State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Smartgenomics Technology Institute Tianjin 301700China Anhui Province Key Laboratory of Rice Germplasm Innovation and Molecular Improvement Rice Research InstituteAnhui Academy of Agricultural SciencesHefei 230031China Jilin Provincial Laboratory of Crop Germplasm Resources Rice Research InstituteJilin Academy of Agricultural SciencesChangchun 136100China Jiangxi Research Center of Crop Germplasm Resources National Engineering Laboratory for Rice(Nanchang)Rice Research InstituteJiangxi Academy of Agricultural SciencesNanchang 330200China State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 310006China Guangxi Key Laboratory of Rice Genetics and Breeding Rice Research InstituteGuangxi Academy of Agricultural SciencesNanning 530007China National Key Laboratory of Crop Genetic Improvement College of Plant Science & TechnologyHuazhong Agricultural UniversityWuhan 430070China Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation Ministry of AgricultureBiotechnology and Germplasm Resources InstituteYunnan Academy of Agricultural SciencesKunming 620205China Institute of Coastal Agriculture Hebei Academy of Agriculture and Forestry SciencesTangshan 063300China Institute of Crop Sciences Ningxia Academy of Agricultural and Forestry SciencesYinchuan 750002China

Modern cultivated rice plays a pivotal role in global food *** accounts for nearly 30％of the world's rice production and has developed numerous cultivated varieties over the past decades that are well adapted to diverse growing ***,the genomic bases underlying the phenotypes of these modern cultivars remain poorly characterized,limiting the exploitation of this vast resource for breeding specialized,regionally adapted *** this study,we constructed a comprehensive genetic variation map of modern rice using resequencing datasets from 6044 representative cultivars from five major rice-growing regions in *** genomic and phenotypic analyses of this diversity panel revealed regional preferences for specific genomic backgrounds and traits,such as heading date,biotic/abiotic stress resis-tance,and grain shape,which are crucial for adaptation to local conditions and consumer *** identified 3131 quantitative trait loci associated with 53 phenotypes across 212 datasets under various envi-ronmental conditions through genome-wide association ***,we cloned and functionally veri-fied a novel gene related to grain length,*** integrating multiple datasets,we developed RiceAt-las,a versatile multi-scale toolkit for rice breeding *** successfully utilized the RiceAtlas breeding design function to rapidly improve the grain shape of the Suigeng4 *** valuable resources enhance our understanding of the adaptability and breeding requirements of modern rice and can facilitate advances in future rice-breeding initiatives.

关键词： modern rice cultivars genomic bases rice-growing regions breeding design

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