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Prescreening of large-effect markers with multiple strategies improves the accuracy of genomic prediction

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Journal of Integrative Agriculture 2024年第5期23卷 1634-1643页

作者： Keanning Li Bingxing An Mang Liang Tianpeng Chang Tianyu Deng Lili Du Sheng Cao Yueying Du Hongyan Li Lingyang Xu Lupei Zhang Xue Gao Junya LI Huijiang Gao Laboratory of Molecular Biology and Bovine Breeding Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijing 100193China Shaanxi Key Laboratory of Molecular Biology for Agriculture College of Animal Science and TechnologyNorthwest A&F UniversityYangling712100China College of Computer and Information Engineering Tianjin Agricultural UniversityTianjin 300384China College of Animal Science and Technology Qingdao Agricultural UniversityQingdao 266109China Tongliao Animal Agriculture Development Service Center Tongliao 028000China

Presently,integrating multi-omics information into a prediction model has become a ameliorate strategy for genomic selection to improve genomic prediction ***,we set the genomic and transcriptomic data as the training population data,using BSLMM,TWAS,and eQTL mapping to prescreen features according to |β_(b)|>0,top 1%of phenotypic variation explained(PVE),expression-associated single nucleotide polymorphisms(eSNPs),and egenes(false discovery rate(FDR)genomic prediction.

关键词： multi-omics data features prescreening eQTL mapping Huaxi cattle genomic selection

Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks

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Journal of Animal Science and Biotechnology 2024年第5期15卷 1832-1850页

作者： Daoliang Lan Wei Fu Wenhui Ji Tserang‑Donko Mipam Xianrong Xiong Shi Ying Yan Xiong Peng Sheng Jiangping Ni Lijun Bai Tongling Shan Xiangdong Kong Jian Li Ministry of Education of Key Laboratory of Qinghai‑Tibetan Plateau Animal Genetic Resource and Utilization Southwest Minzu UniversityChengduChina College of Animal&Veterinary sciences Southwest Minzu UniversityChengduChina Institute of Qinghai‑Tibetan Plateau Southwest Minzu UniversityChengduChina Jiguang Gene Biotechnology Co. Ltd.NanjingChina Chengdu Genepre Technology Co. Ltd.ChengduChina Shanghai Veterinary Research Institute Chinese Academy of Agricultural SciencesShanghaiChina

Background The genetic diversity of yak,a key domestic animal on the Qinghai-Tibetan Plateau(QTP),is a vital resource for domestication and breeding *** study presents the first yak pangenome obtained through the de novo assembly of 16 yak *** We discovered 290 Mb of nonreference sequences and 504 new *** pangenome-wide presence and absence variation(PAV)analysis revealed 5,120 PAV-related genes,highlighting a wide range of variety-specific genes and genes with varying frequencies across yak *** component analysis(PCA)based on binary gene PAV data classified yaks into three new groups:wild,domestic,and ***,we pro-posed a‘two-haplotype genomic hybridization model'for understanding the hybridization patterns among breeds by integrating gene frequency,heterozygosity,and gene PAV data.A gene PAV-GWAS identified a novel gene(Bos-Gru3G009179)that may be associated with the multirib trait in Jinchuan ***,an integrated transcrip-tome and pangenome analysis highlighted the significant differences in the expression of core genes and the muta-tional burden of differentially expressed genes between yaks from high and low *** analysis across multiple species revealed that yaks have the most unique differentially expressed m RNAs and lnc RNAs(between high-and low-altitude regions),especially in the heart and lungs,when comparing high-and low-altitude *** The yak pangenome offers a comprehensive resource and new insights for functional genomic studies,supporting future biological research and breeding strategies.

关键词： High-and low-altitude Novel genes Pangenome PAV-GWAS Yak

Viromes of Haemaphysalis longicornis reveal different viral abundance and diversity in free and engorged ticks

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Virologica Sinica 2024年第2期39卷 194-204页

作者： Jian Xiao Xuan Yao Xuhua Guan Jinfeng Xiong Yaohui Fang Jingyuan Zhang You Zhang Abulimiti Moming Zhengyuan Su Jiayin Jin Yingying Ge Jun Wang Zhaojun Fan Shuang Tang Shu Shen Fei Deng Key Laboratory of Virology and Biosafety and National Virus Resource Center Wuhan Institute of VirologyChinese Academy of SciencesWuhan430071China Hubei Provincial Center for Disease Control and Prevention Wuhan430070China University of Chinese Academy of sciences Beijing101408China Hubei Jiangxia Laboratory Wuhan430200China Xinjiang Key Laboratory of Vector-borne Infectious Diseases Urumqi830002China Current address:Department of Medical Laboratory The Second Affiliated HospitalHainan Medical UniversityHaikou57000China

Haemaphysalis longicornis ticks,commonly found in East Asia,can transmit various pathogenic viruses,includingthe severe fever with thrombocytopenia syndrome virus(SFTSV)that has caused febrile diseases among humansin Hubei ***,understanding of the viromes of *** was limited,and the prevalence ofviruses among *** ticks in Hubei was not well *** study investigates the viromes of bothengorged(fed)and free(unfed)*** ticks across three mountainous regions in Hubei Province from 2019to ***-sequencing analysis identified viral sequences that were related to 39 reference viruses belonging tounclassified viruses and seven RNA viral families,namely Chuviridae,Nairoviridae,Orthomyxoviridae,Parvoviridae,Phenuiviridae,Rhabdoviridae,and *** abundance and diversity in these ticks were analysed,andphylogenetic characteristics of the Henan tick virus(HNTV),Dabieshan tick virus(DBSTV),Okutama tick virus(OKTV),and Jingmen tick virus(JMTV)were elucidated based on their full genomic *** demonstrated that DBSTV was the most common virus found in individual *** ticks(12.59%),followed by HNTV(0.35%),whereas JMTV and OKTV were not *** results improve our understanding of *** tick viromes in central China and highlight the role of tick feeding status and geographyin shaping the viral *** findings of new viral strains and their potential impact on public health raisethe need to strengthen surveillance efforts for comprehensively assessing their spillover potentials.

关键词： Ticks Virome Haemaphysalis longicornis Phylogenetic analysis Viral abundance and diversity

Circulating Tumor DNA as Biomarkers for CancerDetection

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genomics, Proteomics & Bioinformatics 2017年第2期15卷 59-72页

作者： Xiao Han Junyun Wang Yingli Sun CAS Key Laboratory of genomic and Precision Medicine China Gastrointestinal Cancer Research Center Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100101 China University of Chinese Academy of sciences Beijing 100049 China

Detection of circulating tumor DNAs(ct DNAs) in cancer patients is an important component of cancer precision medicine ct DNAs. Compared to the traditional physical and biochemical methods, blood-based ct DNA detection offers a non-invasive and easily accessible way for cancer diagnosis, prognostic determination, and guidance for treatment. While studies on this topic are currently underway, clinical translation of ct DNA detection in various types of cancers has been attracting much attention, due to the great potential of ct DNA as blood-based biomarkers for early diagnosis and treatment of cancers. ct DNAs are detected and tracked primarily based on tumorrelated genetic and epigenetic alterations. In this article, we reviewed the available studies on ct DNA detection and described the representative methods. We also discussed the current understanding of ct DNAs in cancer patients and their availability as potential biomarkers for clinical purposes. Considering the progress made and challenges involved in accurate detection of specific cell-free nucleic acids, ct DNAs hold promise to serve as biomarkers for cancer patients, and further validation is needed prior to their broad clinical use.

关键词： Precision medicine Liquid biopsy Circulating tumor DNA Biomarker Clinical diagnosis Cell-free nucleic acids

A simple and efficient CRISPR/Cas9 system permits ultra-multiplex genome editing in plants

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The Crop Journal 2024年第2期12卷 569-582页

作者： Suting Wu Htin Kyaw Zhijun Tong Yirong Yang Zhiwei Wang Liying Zhang Lihua Deng Zhiguo Zhang Bingguang Xiao William Paul Quick Tiegang Lu Guoying Xiao Guannan Qin Xue'an Cui Biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijing 100081China Key Laboratory of Genetics Breeding and Multiple Utilization of CropsMinistry of EducationCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina Key Laboratory of Biological Breeding for Fujian and Taiwan Crops Ministry of Agriculture and Rural AffairsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina Key Laboratory of Agro-ecological Processes in Subtropical Region Institute of Subtropical AgricultureChinese Academy of SciencesChangsha 410125HunanChina School of Biosciences The University of SheffieldFirth CourtWestern BankSheffield S102TNUK Key Laboratory of Tobacco Biotechnological Breeding National Tobacco Genetic Engineering Research CenterYunnan Academy of Tobacco Agricultural SciencesKunming 650021YunnanChina

The development and maturation of the CRISPR/Cas genome editing system provides a valuable tool for plant functional genomics and genetic *** available genome-editing tools have a limited number of targets,restricting their application in genetic *** this study,we developed a novel CRISPR/Cas9 plant ultra-multiplex genome editing system consisting of two template vectors,eight donor vectors,four destination vectors,and one primer-design software *** combining the advantages of Golden Gate cloning to assemble multiple repetitive fragments and Gateway recombination to assemble large fragments and by changing the structure of the amplicons used to assemble sg RNA expression cassettes,the plant ultra-multiplex genome editing system can assemble a single binary vector targeting more than 40 genomic loci.A rice knockout vector containing 49 sg RNA expression cassettes was assembled and a high co-editing efficiency was *** plant ultra-multiplex genome editing system advances synthetic biology and plant genetic engineering.

关键词： CRISPR/Cas9 Multiplex genome editing Assembly system Plant

Clinical manifestations,diagnosis and long-term prognosis of adult autoimmune enteropathy:Experience from Peking Union Medical College Hospital

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World Journal of Gastroenterology 2024年第19期30卷 2523-2537页

作者： Mu-Han Li Ge-Chong Ruan Wei-Xun Zhou Xiao-Qing Li Sheng-Yu Zhang Yang Chen Xiao-Yin Bai Hong Yang Yu-Jie Zhang Peng-Yu Zhao Ji Li Jing-Nan Li Department of Gastroenterology Chinese Academy of Medical Sciences&Peking Union Medical College HospitalBeijing 100730China Department of Pathology Chinese Academy of Medical Scinences&Peking Union Medical College HospitalBeijing 100730China Department of Pathology Tianjin First Central HospitalNankai UniversityTianjin 300192China Affairs Office Chinese Academy of Medical Sciences&Peking Union Medical College Hospital(West campus)Beijing 100032China

BACKGROUND Autoimmune enteropathy(AIE)is a rare disease whose diagnosis and long-term prognosis remain challenging,especially for adult AIE *** To improve overall understanding of this disease’s diagnosis and *** We retrospectively analyzed the clinical,endoscopic and histopathological characteristics and prognoses of 16 adult AIE patients in our tertiary medical center between 2011 and 2023,whose diagnosis was based on the 2007 diagnostic *** Diarrhea in AIE patients was characterized by secretory *** common endoscopic manifestations were edema,villous blunting and mucosal hyperemia in the duodenum and *** blunting(100%),deep crypt lymphocytic infiltration(67%),apoptotic bodies(50%),and mild intraepithelial lymphocytosis(69%)were observed in the duodenal ***,there were other remarkable abnormalities,including reduced or absent goblet cells(duodenum 94%,ileum 62%),reduced or absent Paneth cells(duodenum 94%,ileum 69%)and neutrophil infiltration(duodenum 100%,ileum 69%).Our patients also fulfilled the 2018 diagnostic criteria but did not match the 2022 diagnostic criteria due to undetectable anti-enterocyte *** patients received glucocorticoid therapy as the initial medication,of which 14/16 patients achieved a clinical response in 5(IQR:3-20)*** were administered to 9 patients with indications of steroid dependence(6/9),steroid refractory status(2/9),or intensified maintenance medication(1/9).During the median of 20.5 months of followup,2 patients died from multiple organ failure,and 1 was diagnosed with non-Hodgkin’s *** cumulative relapse-free survival rates were 62.5%,55.6%and 37.0%at 6 months,12 months and 48 months,*** Certain histopathological findings,including a decrease or disappearance of goblet and Paneth cells in intestinal biopsies,might be potential diagnostic criteria for adult *** long-term prognosis is still unsatisfac

关键词： Autoimmune enteropathy Clinical manifestations Diagnostic criteria Pathological features Long-term prognosis

Classification of Sailboat Tell Tail Based on Deep Learning

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Journal of Ocean University of China 2024年第3期23卷 710-720页

作者： CHANG Xiaofeng YU Jintao GAO Ying DING Hongchen LIU Yulong YU Huaming Department of Physical Education Ocean University of ChinaQingdao 266100China College of Big Data Qingdao University of Science and TechnologyQingdao 266061China College of Oceanic and Atmospheric sciences Ocean University of ChinaQingdao 266100China

The tell tail is usually placed on the triangular sail to display the running state of the air flow on the sail *** is of great significance to make accurate judgement on the drift of the tell tail of the sailboat during sailing for the best sailing *** it is difficult for sailors to keep an eye for a long time on the tell sail for accurate judging its changes,affected by strong sunlight and visual *** this case,we adopt computer vision technology in hope of helping the sailors judge the changes of the tell tail in ease with *** paper proposes for the first time a method to classify sailboat tell tails based on deep learning and an expert guidance system,supported by a sailboat tell tail classification data set on the expert guidance system of interpreting the tell tails states in different sea wind conditions,including the feature extraction *** the expression capabilities that vary with the computational features in different visual tasks,the paper focuses on five tell tail computing features,which are recoded by an automatic encoder and classified by a SVM *** experimental samples were randomly divided into five groups,and four groups were selected from each group as the training set to train the *** remaining one group was used as the test set for *** highest resolution value of the ResNet network was 80.26%.To achieve better operational results on the basis of deep computing features obtained through the ResNet network in the *** method can be used to assist the sailors in making better judgement about the tell tail changes during sailing.

关键词： tell tail sailboat classification deep learning

The biosynthesis of asiaticoside and madecassoside reveals tandem duplication-directed evolution of glycoside glycosyltransferases in the Apiales

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Plant Communications 2024年第10期5卷 166-179页

作者： Xiaoyang Han Jingyi Zhao Hong Zhou Xuan Zhou Zixin Deng Zhenhua Liu Yi Yu Department of Gastroenterology Zhongnan Hospital of Wuhan UniversityHubei Clinical Center and Key Laboratory of Intestinal and Colorectal DiseaseSchool of Pharmaceutical SciencesWuhan UniversityWuhan 430071China Joint Center for Single Cell Biology School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China State Key Laboratory of Non-Food Biomass and Enzyme Technology Guangxi Academy of SciencesNanning 530007China

Certain plant species within the Apiales order accumulate triterpenoid saponins that feature a distinctive glucose-glucose-rhamnose(G-G-R)sugar chain attached at the C-28 position of the pentacyclic triterpene *** recently,the genomic basis underlying the biosynthesis and evolution of this sugar chain has remained *** this study,we identified two novel glycoside glycosyltransferases(GGTs)that can sequentially install the sugar chain’s second D-glucose and third L-rhamnose during the biosynthesis of asiaticoside and madecassoside,two representative G-G-R sugar chain-containing triterpenoid saponins produced by Centella *** assays revealed the remarkable substrate promiscuity of the two GGTs and the key residues crucial for sugar-donor selectivity of the glucosyltransferase and rhamnosyl*** further identified syntenic tandem gene duplicates of the two GGTs in the Apiaceae and Araliaceae families,suggesting a well-conserved genomic basis underlying sugar chain assembly that likely has evolved in the early ancestors of the Apiales ***,expression patterns of the two GGTs in pierced leaves of *** were found to be correlated with the production of asiaticoside and madecassoside,implying their involvement in host defense against herbivores and *** work sheds light on the biosynthesis and evolution of complex saponin sugars,paving the way for future engineering of diverse bioactive triterpenoids with unique glycoforms.

关键词： triterpenoid saponin glycoside glycosyltransferases biosynthesis asiaticoside madecassoside Centella asiatica

The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

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Molecular Plant 2024年第5期17卷 725-746页

作者： Tingting Shi Xinxin Zhang Yukang Hou Changfu Jia Xuming Dan Yulin Zhang Yuanzhong Jiang Qiang Lai Jiajun Feng Jianju Feng Tao Ma Jiali Wu Shuyu Liu Lei Zhang Zhiqin Long Liyang Chen Nathaniel R.Street Par K.Ingvarsson Jianquan Liu Tongming Yin Jing Wang Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengduSichuanChina College of Horticulture and Forestry Tarim UniversityAlar 843300China Umea Plant Science Centre Department of Plant PhysiologyUmea UniversityUmeaVasterbottenSweden Linnean Centre for Plant Biology Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural SciencesUppsalaSweden The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China Nanjing Forestry UniversityNanjingJiangsuChina

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary ***,among the world’s most widely distributed and cultivated trees,exhibit extensive phenotypic diversity and environmental *** this study,we present a genus-level super-pangenome comprising 19 Populus genomes,revealing the likely pivotal role of private genes in facilitating local environmental and climate *** the integration of pangenomes with transcriptomes,methylomes,and chromatin accessibility mapping,we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures,notably CG methylation in gene-body *** comparative genomic analyses have enabled the identification of 142202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive *** have experimentally validated a∼180-bp presence/absence variant affecting the expression of the CUC2 gene,crucial for leaf serration ***,we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome(http://***).Together,the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

关键词： Populus pangenomes whole-genome duplication structural variation genome evolution