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The Crop Journal 2024年第3期12卷 866-879页

作者： Haozhe Tan Binghui Tang Mengling Sun Qiulu Yin Yizan Ma Jianying Li Pengcheng Wang Zhonghua Li Guannan Zhao Maojun Wang Xianlong Zhang Chunyuan You Lili Tu National Key laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070HubeiChina Cotton research Institute Shihezi Academy of Agriculture ScienceShihezi 832000XinjiangChina

Cotton fiber is one of the main raw materials for the textile *** recent years,many cotton fiber quality QTL have been identified,but few were applied in *** this study,a genome wide association study(GWAS)of fiber-quality traits in 265 upland cotton breeding intermediate lines(GhBreeding),combined with genome-wide selective sweep analysis(GSSA)and genomic selection(GS),revealed 25 *** of these QTL were ignored by only using *** CRISPR/Cas9 mutants of GhMYB_D13 had shorter fiber,which indicates the credibility of QTL to a certain *** these QTL were verified in other cotton natural populations,5 stable QTL were found having broad potential for application in ***,among these 5 stable QTL,superior genotypes of 4 showed an enrichment in most improved new varieties widely cultivated *** findings provide insights for how to identify more QTL through combined multiple genomic analysis to apply in breeding.

关键词： Cotton fiber quality breeding GWAS Genome-wide selective sweep analysis genomic selection InDel markers

Multi-omics Approach Reveals Influenza-A Virus Target Genes Associated genomic,Clinical and Immunological Characteristics in Cancers

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Biomedical and Environmental Sciences 2024年第7期37卷 698-715页

作者： Jiaojiao Wang Yong Liao Pinglian Yang Weile Ye Yong Liu Chunxia Xiao Weixiong Liao Chunbo Chen Zhiping Liu Zunnan Huang Center of Scientific research Department of CardiologyMaoming People’s HospitalMaoming 525000GuangdongChina Department of Pharmacy Maoming People’s HospitalMaoming 525000GuangdongChina State Key laboratory of Bioactive Molecules and Druggability Assessment Jinan UniversityGuangzhou 510632GuangdongChina Guangdong Province Key laboratory of Pharmacodynamic Constituents of TCM and New Drugs research College of PharmacyJinan UniversityGuangzhou 510632GuangdongChina Key laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University Key Laboratory of Computer-Aided Drug Design of Dongguan CityKey Laboratory for Research and Development of Natural Drugs of Guangdong ProvinceSchool of PharmacyGuangdong Medical UniversityDongguan 523808GuangdongChina Department of Critical Care Medicine Maoming People’s HospitalMaoming 525000GuangdongChina

Objective To examine the precise function of influenza A virus target genes(IATGs)in *** Using multi-omics data from the TCGA and TCPA datasets,33 tumor types were evaluated for *** expression in cancer cells was analyzed using transcriptome *** number variation(CNV)was assessed using GISTICS ***’s analysis was used to correlate mRNA expression with methylation *** was used for the enrichment ***’s correlation analysis was used to examine the association between IATG mRNA expression and *** ImmuCellAI algorithm was used to calculate the infiltration scores of 24 immune cell *** In 13 solid tumors,IATG mRNA levels were atypically *** for UCS,UVM,KICH,PCPG,THCA,CHOL,LAMI,and MESO,most cancers contained somatic IATG *** main types of CNVs in IATGs are heterozygous amplifications and *** most tumors,IATG mRNA expression is adversely associated with ***-PCR demonstrated that EGFR,ANXA5,CACNA1C,CD209,UVRAG were upregulated and CLEC4M was downregulated in KIRC cell lines,consistent with the TCGA and GTEx *** genomic changes and clinical characteristics of IATGs were identified,which may offer fresh perspectives linking the influenza A virus to cancer.

关键词： genomic changes Immune microenvironment Prognosis Drug resistance Experimental validation

Transmission restriction and genomic evolution co-shape the genetic diversity patterns of influenza A virus

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Virologica Sinica 2024年第4期39卷 525-536页

作者： Xiao Ding Jingze Liu Taijiao Jiang Aiping Wu State Key laboratory of Common Mechanism research for Major Diseases Suzhou Institute of Systems MedicineChinese Academy of Medical Sciences&Peking Union Medical CollegeSuzhou215123China Key laboratory of Pathogen Infection Prevention and Control(Peking Union Medical College) Ministry of EducationBeijing100730China Guangzhou National laboratory Guangzhou510006China State Key laboratory of Respiratory Disease The Key Laboratory of Advanced Interdisciplinary Studies CenterThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510030China

Influenza A virus(IAV)shows an extensive host range and rapid genomic variations,leading to continuous emergence of novel viruses with significant antigenic variations and the potential for cross-species *** causes global pandemics and seasonal flu outbreaks,posing sustained threats ***,studying all IAVs'evolutionary patterns and underlying mechanisms is crucial for effective prevention and *** developed FluTyping to identify IAV genotypes,to explore overall genetic diversity patterns and their restriction *** groups isolates based on genetic distance and phylogenetic relationships using whole genomes,enabling identification of each isolate's *** distinct genetic diversity patterns were observed:one genotype domination pattern comprising only H1N1 and H3N2 seasonal influenza subtypes,multi-genotypes cocirculation pattern including majority avian influenza subtypes and swine influenza H1N2,and hybrid-circulation pattern involving H7N9 and three H5 subtypes of influenza ***,the IAVs in multi-genotypes cocirculation pattern showed region-specific dominant genotypes,implying the restriction of virus transmission is a key factor contributing to distinct genetic diversity patterns,and the genomic evolution underlying different patterns was more influenced by host-specific *** summary,a comprehensive picture of the evolutionary patterns of overall IAVs is provided by the FluTyping's identified genotypes,offering important theoretical foundations for future prevention and control of these viruses.

关键词： Influenza A virus Genetic diversity Transmission Genetic pattern Genotype

Mapping the metabolic responses to oxaliplatin-based chemotherapy with in vivo spatiotemporal metabolomics

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Journal of Pharmaceutical Analysis 2024年第2期14卷 196-210页

作者： Mariola Olkowicz Khaled Ramadan Hernando Rosales-Solano Miao Yu Aizhou Wang Marcelo Cypel Janusz Pawliszyn Department of Chemistry University of WaterlooWaterlooONCanada Jagiellonian Centre for Experimental Therapeutics(JCET) Jagiellonian UniversityKrakowPoland Latner Thoracic Surgery research Laboratories Toronto General Hospital Research InstituteUniversity Health NetworkTorontoONCanada The Jackson laboratory JAX Genomic MedicineFarmingtonCTUSA Division of Thoracic Surgery Department of SurgeryUniversity Health NetworkUniversity of TorontoToronto Lung Transplant ProgramTorontoONCanada

Adjuvant chemotherapy improves the survival outlook for patients undergoing operations for lung metastases caused by colorectal cancer (CRC). However, a multidisciplinary approach that evaluates several factors related to patient and tumor characteristics is necessary for managing chemotherapy treatment in metastatic CRC patients with lung disease, as such factors dictate the timing and drug regimen, which may affect treatment response and prognosis. In this study, we explore the potential of spatial metabolomics for evaluating metabolic phenotypes and therapy outcomes during the local delivery of the anticancer drug, oxaliplatin, to the lung. 12 male Yorkshire pigs underwent a 3 h left lung in vivo lung perfusion (IVLP) with various doses of oxaliplatin (7.5, 10, 20, 40, and 80 mg/L), which were administered to the perfusion circuit reservoir as a bolus. Biocompatible solid-phase microextraction (SPME) microprobes were combined with global metabolite profiling to obtain spatiotemporal information about the activity of the drug, determine toxic doses that exceed therapeutic efficacy, and conduct a mechanistic exploration of associated lung injury. Mild and subclinical lung injury was observed at 40 mg/L of oxaliplatin, and significant compromise of the hemodynamic lung function was found at 80 mg/L. This result was associated with massive alterations in metabolic patterns of lung tissue and perfusate, resulting in a total of 139 discriminant compounds. Uncontrolled inflammatory response, abnormalities in energy metabolism, and mitochondrial dysfunction next to accelerated kynurenine and aldosterone production were recognized as distinct features of dysregulated metabolipidome. Spatial pharmacometabolomics may be a promising tool for identifying pathological responses to chemotherapy.

关键词： Pulmonary metastases Colorectal cancer Adjuvant chemotherapy In vivo lung chemo-perfusion Solid-phase microextraction(SPME)microprobes Spatial metabolomics

A genomic association study revealing subphenotypes of childhood steroid-sensitive nephrotic syndrome in a larger genomic sequencing cohort

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Genes & Diseases 2024年第4期11卷 400-410页

作者： Han Chan Fenfen Ni Bo Zhao Huimin Jiang Juanjuan Ding Li Wang Xiaowen Wang Jingjing Cui Shipin Feng Xiaojie Gao Xueying Yang Huan Chi Hao Lee Xuelan Chen Xiaoqin Li Jia Jiao Daoqi Wu Gaofu Zhang Mo Wang Yupeng Cun Xiongzhong Ruan Haiping Yang Qiu Li Department of Nephrology Children's Hospital of Chongqing Medical UniversityNational Clinical Research Center for Child Health and DisordersMinistry of Education Key Laboratory of Child Development and DisordersChongqing Key Laboratory of PediatricsChongqing 400014China Department of Nephrology Shenzhen Children's HospitalShenzhenGuangdong 518034China Department of Nephrology Kunming Children's HospitalKunming Medical UniversityKunmingYunnan 650228China Department of Nephrology Wuhan Children's HospitalTongji Medical College of Huazhong University of Science and TechnologyWuhanHubei 430015China Department of Nephrology Chengdu Women and Children Central HospitalChengduSichuan 610073China Pediatric research Institute Ministry of Education Key Laboratory of Child Development and DisordersNational Clinical Research Center for Child Health and DisordersChina International Science and Technology Cooperation Base of Child Development and Critical DisordersChongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory DisordersChildren's Hospital of Chongqing Medical UniversityChongqing 400014China Department of Nephrology John Moorhead Research LaboratoryUniversity College London Medical SchoolRoyal Free CampusUniversity College LondonLondon NW32PFUnited Kingdom

Dissecting the genetic components that contribute to the two main subphenotypes of steroid-sensitive nephrotic syndrome(SSNS)using genome-wide association studies(GWAS)strategy is important for understanding the *** conducted a multicenter cohort study(360 patients and 1835 controls)combined with a GWAS strategy to identify susceptibility var-iants associated with the following two subphenotypes of ssNS:steroid-sensitive nephrotic syn-drome without relapse(SSNswR,181 patients)and steroid-dependent/frequent relapse nephrotic syndrome(SDNS/FRNS,179 patients).The distribution of two single-nucleotide poly-morphisms(SNPs)in ANKRD36 and ALPG was significant between SSNSWR and healthy controls,and that of two SNPs in GAD1 and HLA-DQA1 was significant between SDNS/FRNS and healthy ***,rs1047989 in HLA-DQA1 was a candidate locus for SDNS/FRNS but not for *** significant SNPs were observed between SSNSWR and SDNS/***,chromosome 2:171713702 in GAD1 was associated with a greater steroid dose(>0.75 mg/kg/d)upon relapse to first remission in patients with SDNS/FRNS(odds ratio=3.14;95%confidence interval,0.97-9.87;P=0.034).rs117014418 in APOL4 was significantly associated with a decrease in eGFR of greater than 20%compared with the baseline in SDNS/FRNS patients(P=0.0001).Protein-protein intersection network construction suggested that HLA-DQA1 and HLA-DQB1 function together through ***,SSNSWR belongs to non-HLA region-dependent nephropathy,and the HLA-DQA/DQB region is likely strongly associated with dis-ease relapse,especially in SDNS/*** study provides a novel approach for the GWAS strategy of SsNS and contributes to our understanding of the pathological mechanisms of SSNSWRandSDNS/FRNS.

关键词： Frequentrelapse Genome-wide association study Human leukocyte antigen region Steroid-sensitive nephrotic syndrome

Population genomic data reveal low genetic diversity,divergence and local adaptation among threatened Reeves's Pheasant(Syrmaticus reevesii)

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Avian research 2024年第1期15卷 1-11页

作者： Qi Lu Pengcheng Wang Jiang Chang De Chen Shenghan Gao Jacob Hoglund Zhengwang Zhang Ministry of Education Key laboratory for Biodiversity Science and Ecological Engineering College of Life SciencesBeijing Normal UniversityBeijing100875China Jiangsu Key laboratory for Biodiversity and Biotechnology College of Life SciencesNanjing Normal UniversityNanjing210023China State Key laboratory of Environmental Criteria and Risk Assessment Chinese Research Academy of Environmental SciencesBeijing100012China State Key laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing100101China Department of Ecology and Genetics Animal EcologyUppsala UniversityUppsalaSweden

Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened ***’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat *** is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened ***,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic ***,we identified candidate genes linked with adaptation across the current distribution of Reeves’s *** present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 *** also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those *** comparing with other threatened species,we found that Reeves’s Pheasants have low genetic *** of homozygosity suggest that the Shennongjia population has experienced serious *** demographic history results indicated that three populations experienced several declines during the glacial *** adaptative analysis among the populations identified 241 candidate genes under directional *** are involved in a large variety of processes,including the immune response and *** results suggest that the three populations should be considered as three different conservation *** current study provides genetic evidence for conserving the threatened Reeves’s Pheasant and provides genomic resources for global biodiversity management.

关键词： Conservation genetics Local adaptation Pheasant Whole-genome sequencing

Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize

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Journal of Integrative Agriculture 2024年第7期23卷 2178-2195页

作者： Peng Liu Langlang Ma Siyi Jian Yao He Guangsheng Yuan Fei Ge Zhong Chen Chaoying Zou Guangtang Pan Thomas Lübberstedt Yaou Shen State Key laboratory of Crop Gene Exploration and Utilization in Southwest China/Maize research Institute Sichuan Agricultural UniversityChengdu 611130China Department of Agronomy Iowa State UniversityAmesIA 50011USA

Genetic transformation has been an effective technology for improving the agronomic traits of ***,it is highly reliant on the use of embryonic callus(EC)and shows a serious genotype *** this study,we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline(MQ2Gpipe).Based on the induction rate of EC(REC),these inbred lines were categorized into three *** low-REC germplasms displayed more abundant genetic diversity than the high-REC *** integrating a genome-wide selective signature screen and region-based association analysis,we revealed 95.23 Mb of selective regions and 43 REC-associated *** variants had phenotypic variance explained values ranging between 21.46 and 49.46%.In total,103 candidate genes were identified within the linkage disequilibrium regions of these REC-associated *** genes mainly participate in regulation of the cell cycle,regulation of cytokinesis,and other functions,among which MYB15 and EMB2745 were located within the previously reported QTL for EC *** leaf area-associated variants with large effects were closely linked to several REC-related loci,implying a potential synergistic selection of REC and leaf size during modern maize breeding.

关键词： maize genetic transformation embryonic callus selective signal association analysis

genomic selection of eight fruit traits in pear

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Horticultural Plant Journal 2024年第2期10卷 318-326页

作者： Manyi Sun Mingyue Zhang Satish Kumar Mengfan Qin Yueyuan Liu Runze Wang Kaijie Qi Shaoling Zhang Wenjing Chang Jiaming Li Jun Wu College of Horticulture State Key Laboratory of Crop Genetics&Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjingJiangsu 210095China State Key laboratory of Crop Biology College of Horticulture Science and EngineeringShandong Agricultural UniversityTai'anShandong 271018China The New Zealand Institute for Plant and Food research Limited Private Bag 1401Havelock North 4157New Zealand Zhongshan Biological Breeding laboratory NanjingJiangsu 210014China

genomic selection (GS) has the potential to improve selection efficiency and shorten the breeding cycle in fruit tree breeding. In this study,we evaluated the effect of prediction methods, marker density and the training population (TP) size on pear GS for improving its performance and reducing cost. We evaluated GS under two scenarios:(1) five-fold cross-validation in an interspecific pear family;(2) independent validation. Based on the cross-validation scheme, the prediction accuracy (PA) of eight fruit traits varied between 0.33 (fruit core vertical diameter)and 0.65 (stone cell content). Except for single fruit weight, a slightly better prediction accuracy (PA) was observed for the five parametrical methods compared with the two non-parametrical methods. In our TP of 310 individuals, 2 000 single nucleotide polymorphism (SNP) markers were sufficient to make reasonably accurate predictions. PAs for different traits increased by 18.21%-46.98%when the TP size increased from 50to 100, but the increment was smaller (-4.13%-33.91%) when the TP size increased from 200 to 250. For independent validation, the PAs ranged from 0.11 to 0.45 using rrBLUP method. In summary, our results showed that the TP size and SNP numbers had a greater impact on the PA than prediction methods. Furthermore, relatedness among the training and validation sets, and the complexity of traits should be considered when designing a TP to predict the test panel.

关键词： Pear Pyrus Prediction method TP size SNP marker number

Smart Breeding Platform:A web-based tool for high-throughput population genetics,phenomics,and genomic selection

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Molecular Plant 2024年第5期17卷 677-681页

作者： Huihui Li Xin Li Peng Zhang Yingwei Feng Junri Mi Shang Gao Lele Sheng Mohsin Ali Zikun Yang Liang Li Wei Fang Wensheng Wang Qian Qian Fei Gu Wenbin Zhou State Key laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100081China Nanfan research Institute CAASSanyaHainan 572024China DAMO Academy Alibaba GroupHangzhou 310023China Hupan Lab Hangzhou 310023China Yazhouwan National laboratory No.8 Huanjin RoadYazhou DistrictSanya CityHainan Province 572024China State Key laboratory of Rice Biology China National Rice Research InstituteHangzhouZhejiang 310006China

Dear Editor,In the era of big data and artificial intelligence,"smart breeding"has become a broad conceptual framework encompassing the paradigm shift of crop breeding to relying on analysis of high-throughput population genetics and phenomics data to conduct genomic selection,allowing identification and optimal use of the genetic potential in crop species(Xiao et al.,2022;Xu et al.,2022;Wang et al.,2023).Most existing tools for analyzing high-throughput breeding data require extensive computational power,complex installation processes,and command-line expertise and are therefore challenging and inconvenient for the majority of researchers and breeders(Brandies and Hogg,2021).

关键词： breeding artificial breed

genomic alterations in oral multiple primary cancers

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International Journal of Oral Science 2024年第1期16卷 145-153页

作者： Wen Wang Qian Wang Shiying Sun Pengfei Zhang Yuyu Li Weimin Lin Qiwen Li Xiao Zhang Zhe Ma Haiyan Lu Hebei Key laboratory of Stomatology Hebei Clinical Research Center for Oral DiseasesHebei Medical UniversityShijiazhuangChina Department of Orthodontics School and Hospital of StomatologyHebei Medical UniversityShijiazhuangChina State Key laboratory of Oral Diseases&National Center for Stomatology&National Clinical research Center for Oral Diseases&West China Hospital of Stomatology Sichuan UniversityChengduChina Department of Preventive Dentistry School and Hospital of StomatologyHebei Medical UniversityShijiazhuangHebeiChina

Oral squamous cell carcinoma (OSCC) is the predominant type of oral cancer, while some patients may develop oral multiple primary cancers (MPCs) with unclear etiology. This study aimed to investigate the clinicopathological characteristics and genomic alterations of oral MPCs. Clinicopathological data from patients with oral single primary carcinoma (SPC, n=202) and oral MPCs (n=34) were collected and compared. Copy number alteration (CNA) analysis was conducted to identify chromosomal-instability differences among oral MPCs, recurrent OSCC cases, and OSCC patients with lymph node metastasis. Whole-exome sequencing was employed to identify potential unique gene mutations in oral MPCs patients. Additionally, CNA and phylogenetic tree analyses were used to gain preliminary insights into the molecular characteristics of different primary tumors within individual patients. Our findings revealed that, in contrast to oral SPC, females predominated the oral MPCs (70.59%), while smoking and alcohol use were not frequent in ***, long-term survival outcomes were poorer in oral MPCs. From a CNA perspective, no significant differences were observed between oral MPCs patients and those with recurrence and lymph node metastasis. In addition to commonly mutated genes such as CASP8, TP53 and MUC16, in oral MPCs we also detected relatively rare mutations, such as HS3ST6 and RFPL4A. Furthermore, this study also demonstrated that most MPCs patients exhibited similarities in certain genomic regions within individuals, and distinct differences of the similarity degree were observed between synchronous and metachronous oral MPCs.

关键词： alterations metastasis oral