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A novel candidate gene CLN8 regulates fat deposition in avian

Journal of Animal Science and Biotechnology 2023年第5期14卷 1895-1908页

作者： Xiaoqin Li Fan Zhang Yunxiao Sun Dandan Sun Fangxi Yang Yongtong Liu Zhuocheng Hou National Engineering Laboratory for Animal breeding and Key Laboratory of Animal Genetics and breeding College of Animal Science and TechnologyMARAChina Agricultural UniversityNo.2 Yuanmingyuan West RdBeijing 100193China beijing nankou duck breeding inc Beijing 100076China

Background The fat deposition has a crucial role in animal meat flavor,and fat deposition-related traits are vital for breeding in the commercial duck *** fat-related traits are typical complex phenotypes,which need a large amount of data to analyze the genetic *** In this study,we performed a new phenotypic analysis of fat traits and genotyped whole-genome varia-tions for 1,246 ducks,and combed with previous GWAS data to reach 1,880 ducks for following *** carcass composition traits,subcutaneous fat weight(SFW),subcutaneous fat percentage(SFP),abdominal fat weight(AFW),abdominal fat percentage(AFP)and the body weight of day 42(BW42)for each duck were *** identified a set of new loci that affect the traits related to fat deposition in *** these loci,ceroid-lipofuscinosis,neuronal 8(CLN8)is a novel candidate gene controlling fat *** investigated its novel function and regulation in avian *** significant SNPs(the most significant SNP,P-value=21.37E-12)and a single haplotype were detected in the upstream of CLN8 for subcutaneous fat ***,luciferase assay demonstrated that 5 linked SNPs in the upstream of the CLN8 gene significantly decreased the transcriptional activity of ***,ATAC-seq analysis showed that transcription factor binding sites were identified in a region close to the haplotype.A set of luciferase reporter gene vectors that contained different deletion fragments of the CLN8 promoter were con-structed,and the core promoter area of CLN8 was finally identified in the-1,884/-1,207 bp region of the 5′flanking sequences,which contains adipogenesis-related transcription factors binding ***,the over-expression of CLN8 can remarkably facilitate adipocyte differentiation in *** with these,the global transcriptome profiling and functional analysis of the over-expressed CLN8 in the cell line further revealed that the lipid biosynthetic process durin

关键词： Avian Adipogenesis CLN8 SNP Transcription regulation

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The phased chromosome-scale genome of yellowhorn sheds light on the mechanism of petal color change

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Horticultural Plant Journal 2023年第6期9卷 1193-1206页

作者： Quanxin Bi Mengke Wang Jiang Li Jinmin Lian Yongchao Niu Yifan Cui Xiaojuan Liu Haiyan Yu Libing Wang State Key Laboratory of Tree Genetics and breeding Research Institute of ForestryChinese Academy of ForestryBeijing 100091China Biozeron Shenzhen Inc.ShenzhenGuangzhouGuangdong 518000China

Yellowhorn(Xanthoceras sorbifolium), especially its varieties, is the red petal yellowhorn(X. sorbifolium var. purpurea), an important tree species with great ornamental value, and its flower petals change color throughout the flowering period. In this study, we mainly focused on the mechanism of the petal color change with transcriptomics and metabolomics data. A phased chromosome-scale assembly of the red petal yellowhorn genome was generated using the PacBio high-fidelity reads, Illumina short reads, and Phase genomics Proximo Hi-C data. The final de novo assembly yielded 533.67 Mb with a contig N50 of 5.42 Mb, and 27 501 protein-coding genes were predicted. Notably, an alternate haplotig assembly was also obtained. Furthermore, a variation database for the alleles within the genome was constructed. Subsequently, the expression pattern of flower pigmentation-related genes and allelic expression imbalance events were investigated. Apart from 6 genes involved in the anthocyanin biosynthesis pathway regulated by the activation of 15 MYB-bHLH-WD40s, the increased expression of senescencerelated gene 1(SRG1) and 2-oxoglutarate-dependent dioxygenase(DIOX5) might also result in decreasing content of lutein and increasing abundance of(E/Z)-phytoene, cyanidin-3-O-rutinoside, and cyanidin-3-O-sambubioside. These changes in genes and metabolites were most likely related to the petal color change in red petal yellowhorn. This phased chromosome-scale genome assembly provides more accurate genomic information for future molecular breeding and facilitates allele function studies of the red petal yellowhorn.

关键词： Xanthoceras sorbifolium var.purpurea Phased genome Metabolomics Transcriptomics Petal color

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Resequencing 250 Soybean Accessions:New Insights into Genes Associated with Agronomic Traits and Genetic Networks

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Genomics, Proteomics & Bioinformatics 2022年第1期20卷 29-41页

作者： Chunming Yang Jun Yan Shuqin Jiang Xia Li Haowei Min Xiangfeng Wang Dongyun Hao Key Laboratory for Agricultural Biotechnology of Jilin Provincial Institute of Agricultural BiotechnologyJilin Academy of Agricultural Sciences(JAAS)Jilin 130033China Frontiers Science Center for Molecular Design breeding College of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100094China Key Laboratory of Molecular Cytogenetics and Genetic breeding of Heilongjiang Province College of Life Science and TechnologyHarbin Normal UniversityHarbin 150025China BioTrust Technology inc. Beijing 100094China

The limited knowledge of genomic diversity and functional genes associated with the traits of soybean varieties has resulted in slow progress in *** this study,we sequenced the genomes of 250 soybean landraces and cultivars from China,America,and Europe,and investigated their population structure,genetic diversity and architecture,and the selective sweep regions of these *** novel agronomically important genes were identified,and the effects of functional mutations in respective genes were *** candidate genes GSTT1,GL3,and GSTL3 associated with the isoflavone content,CKX3 associated with yield traits,and CYP85 A2 associated with both architecture and yield traits were *** phenotype-gene network analysis revealed that hub nodes play a crucial role in complex phenotypic *** study describes novel agronomic trait-associated genes and a complex genetic network,providing a valuable resource for future soybean molecular breeding.

关键词： Agronomic trait GWAS Network Resequence Soybean

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Transcriptomics of Chinese Sapium Sebiferum(L.)Roxb seed to reveal key enzymes involved in oil accumulation

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Oil Crop Science 2020年第3期5卷 107-113页

作者： Yanyan Yu Yun Liu College of Life Science and Technology Beijing University of Chemical TechnologyBeijingChina beijing Zest Bridge Media Technology inc. BeijingChina

Chinese Sapium sebiferum(L.)Roxb has great potential to emerge as a promising biodiesel resource plant due to abundant oil content in ***,the unavailability of transcriptomic and genomic data impedes the progress of application in biodiesel *** analysis will help to further exploit tallow and kernel oil utilization in industry and facilitate molecular-breeding-based genetic improvement of *** hiseq 2000 sequencing platform was used to perform de novo transcriptome assembly and gene expression analyses of seeds from three strains in three developmental stages.A total of 188,254 unigenes over 200 bp were assembled with average length of 699 *** transcriptic unigenes were functionally assigned by GO and KEGG *** was used to identify differentially expressed unigenes of five cDNA *** genes endcoding enzymes related to fatty acid metabolism were ***-PCR was employed to confirm five key enzymes involved in fatty acid and triacylglycerol *** study provided comprehensive gene expression information of Chinese *** seed at transcriptional *** transcriptome data will facilitate high-oil-content genetic cultivation of ***,which will further exploit tallow and kernel oil utilization in biodiesel industry.

关键词： Sapium sebiferum(L.)Roxb Transcriptome Differentially expressed analysis Lipid metabolism

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Long-term,multidomain analyses to identify the breed and allelic effects in MSTN-edited pigs to overcome lameness and sustainably improve nutritional meat production

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Science China(Life Sciences) 2022年第2期65卷 362-375页

作者： Ziyao Fan Zhiguo Liu Kui Xu Tianwen Wu Jinxue Ruan Xinmin Zheng Shideng Bao Yulian Mu Tad Sonstegard Kui Li State Key Laboratory of Animal Nutrition Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijing 100193China Hubei Key Laboratory of Animal Embryo Engineering and Molecular breeding Hubei Institute of Animal Science and Veterinary MedicineHubei Academy of Agricultural SciencesWuhan 430064China Department of Stem Cell Biology and Regenerative Medicine Lerner Research InstituteCleveland ClinicCleveland OH 44195USA Acceligen inc. Eagan MN 55121USA

Beef and mutton production has been aided by breeding to integrate allelic diversity for myostatin(MSTN),but a lack of diversity in the MSTN germplasm has limited similar advances in pig ***,insurmountable challenges with congenital lameness and a dearth of data about the impacts of feed conversion,reproduction,and meat quality in MSTN-edited pigs have also currently blocked ***,in a largest-to-date evaluation of multiple MSTN-edited pig populations,we demonstrated a practical alternative edit-site-based solution that overcomes the major production obstacle of hindlimb *** also provide long-term and multidomain datasets for multiple breeds that illustrate how MSTN-editing can sustainably increase the yields of breed-specific lean meat and the levels of desirable lipids without deleteriously affecting feed-conversion rates or litter *** from establishing a new benchmark for the data scale and quality of genome-edited animal production,our study specifically illustrates how gene-editing site selection profoundly impacts the phenotypic outcomes in diverse genetic back-grounds.

关键词： MSTN-edited pigs multidomain evaluation genetic background editing strategy

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A comprehensive analysis of immunoglobulin heavy chain genes in the Bactrian camel(Camelus bactrianus)

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Frontiers of Agricultural Science and Engineering 2015年第3期2卷 249-259页

作者： Zuoxiang LIANG Tao WANG Yi SUN Wenlong YANG Zhihong LIU Jing FEI Ying GUO Qingwei MA Qingjie PAN Liming REN Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong College of Animal Science and TechnologyQingdao Agricultural UniversityQingdao 266109China State Key Laboratory of Agrobiotechnology China Agricultural UniversityBeijing 100193China Laboratory of Animal Molecular Genetics College of Animal Science and Veterinary MedicineShandong Agricultural UniversityTaian 271018China Key Laboratory of Animal Genetics Breeding and ReproductionInner Mongolia Agricultural UniversityHohhot 010018China Bioyong Technology inc. Beijing 100080China

Heavy chain only antibodies(HCAbs)represent a rare type of antibody that is devoid of light chains and the CH1 domain that have been reported in cartilaginous fish and *** analyzing transcript data and genome sequences,we conducted a comprehensive analysis of Bactrian camel immunoglobulin heavy chain *** on the transcript data,oneμgene,fiveγgenes,oneαgene and oneεgene were ***,the variable region of HCAbs(VHH)and the conventional antibodies(VH)sequences associated with theγ3,γ1a/b andμgenes were *** on these genome sequences,seven DH,six JH,μ,γ2a,γ2c,α,andεgenes and a portion of aγ3 gene were *** Kozak sequences within different VH families were found in our analysis,and the variability index differed between the VHH3 and VH3 *** analysis of the constant regions of the camelid immunoglobulin genes indicates that these genes appeared before the evolutionary divergence of Bactrian camels and dromedaries.

关键词： Bactrian camel heavy-chain antibodies VHH γ3

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Systematic identification of wheat spike developmental regulators by integrated multiomics, transcriptional network, GWAS, and genetic analyses

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Molecular Plant 2024年第3期17卷 438-459页

作者： Xuelei Lin Yongxin Xu Dongzhi Wang Yiman Yang Xiaoyu Zhang Xiaomin Bie Lixuan Gui Zhongxu Chen Yiliang Ding Long Mao Xueyong Zhang Fei Lu Xiansheng Zhang Cristobal Uauyo Xiangdong Fu Jun Xiao Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Nanjing Agricultural University NanjingJiangsu 210095China Key Laboratory of Crop Biology College of Life SciencesShandong Agricultural UniversityTaianShandong 271018China Department of Life Science Tcuni Inc.ChengduSichuan 610000China John Innes Centre Norwich Research ParkNorwich NR47UHUK Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China CAS-JIC Centre of Excellence for Plant and Microbial Science(CEPAMS) Institute of Genetics and Developmental BiologyCASBeijing 100101China

The spike architecture of wheat plays a crucial role in determining grain number,making it a key trait for optimization in wheat breeding *** this study,we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages,revealing co-ordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering *** constructed a core transcriptional regulatory network(TRN)that drives wheat spike formation and experimentally validated a multi-layer regulatorymodule involving TaSPL15,TaAGLG1,and *** integrating the TRN with genome-wide association studies,we identified 227 transcription factors,including 42 with known functions and 185 with unknown *** investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time,such as TaMYC2-A1,TaMYB30-A1,and *** particular interest,TaMYB30-A1,downstream of and repressed by WFzP,was found to regulate fertile spikelet ***,the excellent haplotype of TaMYB30-A1,which contains a C allele at the WFzP binding site,was enriched during wheat breeding improvement in China,leading to improved agronomic ***,we constructed a free and open access Wheat Spike Multi-Omic Database(http://39.***.48.156:8800/#/).Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development,with practical value forwheat breeding.

关键词： wheat spike development epigenome TRN TaMYB30-A1 breeding selection

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Boosting wheat functional genomics via an indexed EMS mutant library of KN9204

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Plant Communications 2023年第4期4卷 58-76页

作者： Dongzhi Wang Yongpeng Li Haojie Wang Yongxin Xu Yiman Yang Yuxin Zhou Zhongxu Chen Yuqing Zhou Lixuan Gui Yi Guo Chunjiang Zhou Wenqiang Tang Shuzhi Zheng Lei Wang Xiulin Guo Yingjun Zhang Fa Cui Xuelei Lin Yuling Jiao Yuehui He Junming Li Fei He Xigang Liu Jun Xiao Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Ministry of Education Key Laboratory of Molecular and Cellular Biology Hebei Key Laboratory of Molecular and Cellular BiologyCollege of Life SciencesHebei Normal UniversityHebei Collaboration Innovation Center for Cell SignalingShijiazhuang 050024China Center for Agricultural Resources Research Institute of Genetics and Development BiologyChinese Academy of SciencesShijiazhuang 050022China University of Chinese Academy of Sciences Beijing 100049China Department of Life Science TcuniIncChengdu 610000China State Key Laboratory of Protein and Plant Gene Research Peking-Tsinghua Center for Life SciencesSchool of Life SciencesCenter for Quantitative BiologyPeking UniversityBeijing 100871China State Key Laboratory of Protein and Plant Gene Research School of Advanced Agricultural SciencesPeking-Tsinghua Center for Life SciencesPeking UniversityBeijing 100871China Plant Genetic Engineering Center of Hebei Province Institute of Biotechnology and Food ScienceHebei Academy of Agriculture and Forestry SciencesShijiazhuang 050051China Institute ofCereal and OilCrops Hebei Academy of Agriculture and Forestry SciencesLaboratory of CropGenetics andBreeding ofHebeiShijiazhuang 050035China Key Laboratory of Molecular Module-Based breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong College of AgricultureLudong UniversityYantai 264025China Centre of Excellence for Plant and Microbial Science(CEPAMS) JIC-CASBeijing 100101China

A better understanding of wheat functional genomics can improve targeted breeding for better agronomic traits and environmental ***,the lack of gene-indexed mutants and the low transformation efficiency of wheat limit in-depth gene functional studies and genetic manipulation for *** this study,we created a library for KN9204,a popular wheat variety in northern China,with a reference genome,transcriptome,and epigenome of different tissues,using ethyl methyl sulfonate(EMS)*** library contains a vast developmental diversity of critical tissues and transition *** capture sequencing of 2090 mutant lines using KN9204 genome-designed probes revealed that 98.79%of coding genes had mutations,and each line had an average of 1383 EMS-type *** identified new allelic variations for crucial agronomic trait-related genes such as Rht-D1,Q,TaTB1,and *** tested 100 lines with severemutations in 80 NAC transcription factors(TFs)under drought and salinity stress and identified 13 lines with altered *** analysis of three lines using transcriptome and chromatin accessibility data revealed hundreds of direct NAC targets with altered transcription patterns under salt or drought stress,including SNAC1,DREB2B,CML16,and ZFP182,factors known to respond to abiotic ***,we have generated and indexed a KN9204 EMS mutant library that can facilitate functional genomics research and offer resources for genetic manipulation of wheat.

关键词： wheat exome capture sequencing EMS mutagenesis functional genomics

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ABE-induced PDGFD start codon silencing unveils new insights into the genetic architecture of sheep fat tails

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Journal of Genetics and Genomics 2023年第12期50卷 1022-1025页

作者： Peter Kalds Shuhong Huang Shiwei Zhou Siyuan Xi Yumeng Fang Yawei Gao Kexin Sun Chao Li Bei Cai Yao Liu Yige Ding Qifang Kou Tad Sonstegard Bjöm Petersen Stephen Kemp Baohua Ma Jian-Lin Han Yulin Chen Xiaolong Wang International Joint Agriculture Research Center for Animal Bio-breeding Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal GeneticsBreeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi 712100China Department of Animal and Poultry Production Faculty of Environmental Agricultural SciencesArish UniversityEl-Arish 45511Egypt College of Veterinary Medicine Northwest A&F UniversityYanglingShaanxi 712100China Key Laboratory of Ruminant Molecular and Cellular breeding School of AgricultureNingxia UniversityYinchuanNingxia 750000China Ningxia Tianyuan Tan Sheep Farm HongsibuNingxia 751999China Acceligen inc. St.PaulMN 55104United States International Livestock Research Institute(ILRI) Nairobi 30709-00100Kenya International Livestock Research Institute(ILRI) Nairobi 30709-00100Kenya CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic ResourcesInstitute of Animal ScienceChinese Academy of Agricultural Sciences(CAAS)Beijing 100193China Key Laboratory of Livestock Biology Northwest A&F UniversityYanglingShaanxi 712100China Institute of Farm Animal Genetics Friedrich-Loeffler-lnstitutMarienseeNeustadt am Rubenberge 31535Germany

Sheep is an important livestock species raised globally to produce meat,milk,wool,and other *** the Neolithic Revolution,sheep were domesticated in the Fertile Crescent of Southwest Asia around 10,000 years ago(Chessa... 详细信息

关键词： products. globally raised

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