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中国药理学通报 2015年第B11期31卷 219-219页

Aim Clopidogrel therapy is associated with a substantial variability in pharmacokinetics （PK） and pharmacodynamics （PD） responses. To date, known gene variants explain only a small proportion of the variabili- ty. A genome-wide association study （GWAS） was conducted to identify new genetic loci modifying PD responses to clopidogrel in Chinese patients with coronary heart disease （CHD）. The initial GWAS by combination analysis of PIL/PD included 115 patients with CHD. The PK validation included 31 patients with CHD and the metabolizing functional validation included 32 human liver tissues. We identified novel variants in two transporter genes （ rs12456693 in SLC14A2 and kgpl 1138762 in ABCA1 ） and in N6AMT1 （rs2254638） associated with not only clo- pidogrel on-treated P2Y12 reaction unit （PRU）（P 〈 1 × 10^-4） , but also plasma clopidogrel active metabolite H4 concentration （P 〈 1 × 10^-2）. The significant association between rs12456693, kgpl 1138762, or rs2254638 and PK parameters of clopidogrel （P 〈 1 × 10^-2） was observed in additional CHD patients. Further, the N6AMT1 rs2254638 T variant was found to be associated decreased activation of clopidogrel （P -3.86 × 10^-2）. The new variants in N6AMT1 and ABCA1, together with CYP2C19 ＊ 2, dramatically improve the predictability of PRU varia- bility to 37.7% compared with the published value of approximately 20%. The present study identifies novel genet- ic loci modifying PIL/PD responses to clopidogrel, which contributes to a better understanding of the absorption and metabolic mechanisms that influence PD responses to clopidogrel treatment.

关键词： Clopidogrel pharmacokinetics pharmacodynamics genome-wide association study

Association Mapping of Quantitative Trait Loci for Grain Size in Introgression Line Derived from Oryza rufipogon

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Rice science 2020年第3期27卷 246-254页

作者： Kashif HUSSAIN ZHANG Yingxing Workie ANLEY Aamir RIAZ Adil ABBAS MdHasanuzzaman RANI WANG Hong SHEN Xihong CAO Liyong CHENG Shihua Key Laboratory for Zhejiang Super Rice Research&State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China Southern Rice Research Institute Thatta Agriculture Research WingGovernment of SindhSindh 73130Pakistan Department of Plant Sciences University of GondarP.O.Box 196Ethiopia Bangladesh Institute of Nuclear Agriculture Dhaka 2202Bangladesh

Grain size is one of the critical agronomic traits governing grain yield and quality in ***,the underlying genetic mechanisms that control grain size in rice are poorly *** used an introgression line derived from Zhonghui 8015 and Oryza rufipogon *** introgression line was evaluated under two different environmental conditions to dissect the quantitative trait loci controlling grain ***-wide association study(GWAS)was performed using 28193 SNPs through a general linear model,and 56 significant SNPs on different loci associated with the 4 grain size traits were *** genes including GS3 and q GL3 showed substantial effects on grain length and *** new stable loci were identified with pleiotropic effects on grain ***,gene expression analyses,combined gene-based associations,and functional annotations permitted the shortlisting of important dominant genes including GS3 and q GL3.

关键词： grain size association mapping Oryza sativa Oryza rufipogon quantitative trait locus genome-wide association analysis

Association mapping of lignin response to Verticillium wilt through an eight-way MAGIC population in Upland cotton

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Journal of Integrative Agriculture 2023年第5期22卷 1324-1337页

作者： TIAN Xiao-min HAN Peng WANG Jing SHAO Pan-xia AN Qiu-shuang Nurimanguli AINI YANG Qing-yong YOU Chun-yuan LIN Hai-rong ZHU Long-fu PAN Zhen-yuan NIE Xin-hui Key Laboratory of Oasis Eco-agricultural Xinjiang Production and Construction Corps/Agricultural CollegeShihezi UniversityShihezi 832003P.R.China College of Informatics Huazhong Agricultural UniversityWuhan 430070P.R.China Cotton Research Institute Shihezi Academy of Agricultural SciencesShihezi 832011P.R.China National Key Laboratory of Crop Genetic Improvement/College of Plant Sciences&Technology Huazhong Agricultural UniversityWuhan 430070P.R.China

Lignin metabolism plays a pivotal role in plant defense against pathogens and is always positively correlated as a response to pathogen infection. Thus, understanding resistance genes against plant pathogens depends on a genetic analysis of the lignin response. This study used eight Upland cotton lines to construct a multi-parent advanced generation intercross(MAGIC) population(n=280), which exhibited peculiar characteristics from the convergence of various alleles coding for advantageous traits. In order to measure the lignin response to Verticillium wilt(LRVW), the artificial disease nursery(ADN) and rotation nursery(RN) were prepared for MAGIC population planting in four environments. The stem lignin contents were collected, and the LRVW was measured with the lignin value of ADN/RN in each environment, which showed significant variations. We employed 9 323 high-quality single-nucleotide polymorphism(SNP) markers obtained from the Cotton-SNP63K array for genotyping the MAGIC population. The SNPs were distributed through the whole genome with 4.78 SNP/Mb density, ranging from 1.14(ChrA06) to 10.08(ChrD08). In addition, a genome-wide association study was performed using a Mixed Linear Model(MLM) for LRVW. Three stable quantitative trait loci(QTLs), qLRVW-A04, qLRVW-A10, and qLRVW-D05, were identified in more than two environments. Two key candidate genes, Ghi_D05G01046 and Ghi_D05G01221, were selected within the QTLs through the combination of variations in the coding sequence, induced expression patterns, and function annotations. Both genes presented nonsynonymous mutations in coding regions and were strongly induced by Verticillium dahliae. Ghi_D05G01046 encodes a leucine-rich extensin(LRx) protein involved in Arabidopsis cell wall biosynthesis and organization. Ghi_D05G01221 encodes a transcriptional co-repressor novel interactor of novel interactor of jasmonic acid ZIM-domain(JAZ–NINJA), which functions in the jasmonic acid(JA) signaling pathway. In summary, t

关键词： genome-wide association study lignin response MAGIC population Upland cotton Verticillium wilt

Genomic and mitochondrial evidence of ancient isolations and extreme introgression in the four-lined snake

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Current Zoology 2020年第1期66卷 99-111页

作者： Evanthia THANOU Panagiotis KORNILIOS Petros LYMBERAKIS Adam D.LEACHE Department of Biology University of WashingtonSeattleWAUSA The Molecular Ecology Backshop LoutrakiGreece Institute of Evolutionary Biology(CSIC-Universitat Pompeu Fabra) BarcelonaSpain Natural History Museum of Crete University of CreteIrakleioGreece

Comparing mitochondrial and genomic phylogenies is an essential tool for investigating speciation processes,because each genome carries different inheritance properties and evolutionary ***,mitonuclear discordance may arise from ecological adaptation,historic isolation,population size changes,and sex-biased *** related taxa are expected to experience gene flow;however,this may not be true for insular populations or populations isolated in *** four-lined snake Elaphe quatuorlineata has a fragmented distribution,separating populations of the Italian and Balkan Peninsulas,whereas several insular Aegean populations of significantly smaller body size(Cyclades island group and Skyros Island,Greece)are currently considered distinct *** constructed the species-tree phylogeny of this species utilizing genome-wide single nucleotide polymorphisms and a gene-tree based on complete cytochrome b sequences,aiming to detect convergence and discrepancies between biparentally and maternally inherited *** structuring,phylogenetic patterns and migration events among geographically defined lineages supported our hypothesis of isolation in multiple *** biogeographical barriers did not restrict subsequent dispersal,extensive genetic exchange occurred between mainland Balkan *** process has led to the mitochondrial sweep of an ancestral mitolineage that survived only in peripheral(East Greece)and insular populations(North Cyclades and Skyros).The Central Cyclades represent an ancient lineage for both molecular markers that emerged almost 3.3 *** their distinct morphology,insular *** populations should be the future focus of an extensive sampling,especially since the mitonuclear discordance observed in this species could be related to ecological adaptations,such as the island-dwarfism phenomenon.

关键词： Aegean Islands Elaphe quatuorlineata species-tree genome-wide SNPs mitochondrial introgression phylogeography refugia within refugia

Mapping quantitative trait loci using binned genotypes

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Journal of Genetics and Genomics 2019年第7期46卷 343-352页

作者： Wen Yao Guangwei Li Yanru Cui Yiming Yu Qifa Zhang Shizhong Xu National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan 430070 China Department of Botany and Plant Sciences University of California Riverside Riverside CA 92521 USA National Key Laboratory of Wheat and Maize Crop Science College of Life Sciences Henan Agricultural University Zhengzhou 450002 China College of Agronomy Hebei Agricultural University Baoding 071001 China

Precise mapping of quantitative trait loci(QTLs)is critical for assessing genetic effects and identifying candidate genes for quantitative *** and composite interval mappings have been the methods of choice for several decades,which have provided tools for identifying genomic regions harboring causal genes for quantitative ***,the concept was developed on the basis of sparse marker maps where genotypes of loci within intervals could not be ***,genomes of many organisms have been saturated with markers due to the new sequencing *** by sequencing usually generates hundreds of thousands of single nucleotide polymorphisms(SNPs),which often include the causal *** concept of interval no longer exists,prompting the necessity of a norm change in QTL mapping technology to make use of the high-volume genomic *** we developed a statistical method and a software package to map QTLs by binning markers into haplotype blocks,called *** new method detects associations of bins with quantitative *** borrows the mixed model methodology with a polygenic control from genome-wide association studies(GWAS)and can handle all kinds of experimental populations under the linear mixed model(LMM)*** tested the method using both simulated data and data from populations of *** results showed that this method has higher power than the current *** R package named binQTL is available from GitHub.

关键词： genome-wide association studies Linear mixed model Polygene Proximal contamination QTL mapping

Recent advances in RNA structurome

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Science China(Life Sciences) 2022年第7期65卷 1285-1324页

作者： Bingbing Xu Yanda Zhu Changchang Cao Hao Chen Qiongli Jin Guangnan Li Junfeng Ma Siwy Ling Yang Jieyu Zhao Jianghui Zhu Yiliang Ding Xianyang Fang Yongfeng Jin Chun Kit Kwok Aiming Ren Yue Wan Zhiye Wang Yuanchao Xue Huakun Zhang Qiangfeng Cliff Zhang Yu Zhou MOE Laboratory of Biosystems Homeostasis&Protection Innovation Center for Cell Signaling NetworkCollege of Life SciencesZhejiang UniversityHangzhou 310058China Key Laboratory of RNA Biology Institute of BiophysicsChinese Academy of SciencesBeijing 100101China Life Sciences Institute Zhejiang UniversityHangzhou 310058China State Key Laboratory of Plant Physiology and Biochemistry College of Life SciencesZhejiang UniversityHangzhou 310058China State Key Laboratory of Virology College of Life SciencesWuhan UniversityWuhan 430072China Beijing Advanced Innovation Center for Structural Biology School of Life SciencesTsinghua UniversityBeijing 100084China Stem Cell and Regenerative Biology Genome Institute of SingaporeA*STARSingaporeSingapore Department of Chemistry and State Key Laboratory of Marine PollutionCity University of Hong KongHong KongChina MOE Key Laboratory of Bioinformatics Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking Center for Life Sciences Beijing 100084China Department of Cell and Developmental Biology John Innes CentreNorwich Research ParkNorwich NR47UHUnited Kingdom Shenzhen Research Institute of City University of Hong Kong Shenzhen 518057China University of Chinese Academy of Sciences Beijing 100101China Key Laboratory of Molecular Epigenetics of the Ministry of Education Northeast Normal UniversityChangchun 130024China

RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the RNA structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 RNA genome. We also summarize the functionalities of RNA structures discovered in different regulatory layers-including RNA processing, transport, localization, and mRNA translation-across viruses, bacteria, animals, and plants. We review many versatile RNA structural elements in the context of different physiological and pathological processes(e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for RNA structural studies to map the RNA structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of RNA structures and functions for innovative applications.

关键词： RNA structurome high-throughput techniques genome-wide 3D structure RNA secondary structure SARS-CoV-2 decoding function

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Enhancer variants reveal a conserved transcription factor network governed by PU.1 during osteoclast differentiation

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Bone Research 2018年第1期6卷 83-94页

作者： Heather A.Carey Blake E.Hildreth III Jennifer A.Geisler Mara C.Nickel Jennifer Cabrera Sankha Ghosh Yue Jiang Jing Yan James Lee Sandeep Makam Nicholas A.Young Giancarlo R.Valiente Wael N.Jarjour Kun Huang Thomas J.Rosol Ramiro E.Toribio Julia F.Charles Michael C.Ostrowski Sudarshana M.Sharma Department of Cancer Biology and Genetics and Comprehensive Cancer Center The Ohio State University Wexner Medical Center College of Veterinary Medicine The Ohio State University Department of Biochemistry and Molecular Biology and Hollings Cancer Center Medical University of South Carolina Division of Rheumatology Immunology and Allergy Department of Medicine Brigham and Women’s Hospital and Harvard Medical School Division of Rheumatology and Immunology Department of Internal Medicine The Ohio State University Wexner Medical Center Department of Biomedical Informatics The Ohio State University Wexner Medical Center

genome-wide association studies(GWASs) have been instrumental in understanding complex phenotypic traits. However, they have rarely been used to understand lineage-specific pathways and functions that contribute to the trait. In this study, by integrating lineage-specific enhancers from mesenchymal and myeloid compartments with bone mineral density loci, we were able to segregate osteoblast-and osteoclast(OC)-specific functions. Specifically, in OCs, a PU.1-dependent transcription factor(TF)network was revealed. Deletion of PU.1 in OCs in mice resulted in severe osteopetrosis. Functional genomic analysis indicated PU.1 and MITF orchestrated a TF network essential for OC differentiation. Several of these TFs were regulated by cooperative binding of PU.1 with BRD4 to form superenhancers. Further, PU.1 is essential for conformational changes in the superenhancer region of Nfatc1. In summary, our study demonstrates that combining GWASs with genome-wide binding studies and model organisms could decipher lineage-specific pathways contributing to complex disease states.

关键词： genome-wide GWASs MITF

Ethnic differences in genetic polymorphism associated with irritable bowel syndrome

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World Journal of Gastroenterology 2020年第17期26卷 2049-2063页

作者： Qi-Yun Xiao Xiu-Cai Fang Xiao-Qing Li Gui-Jun Fei Department of Gastroenterology Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China

Genetic polymorphism is associated with irritable bowel syndrome(IBS)in terms of susceptibility and clinical *** studies have shown that genetic polymorphism might play a key role in the onset and progression of IBS by modulating components of its pathogenesis such as the gut-brain axis,gastrointestinal motility,inflammatory activity,and immune *** underlying pathophysiological mechanisms have not been fully clarified,the potential ethnic differences that are present in worldwide genetic studies of IBS deserve *** review surveyed numerous studies focusing on IBSassociated single nucleotide polymorphisms,and investigated the ethnic disparities revealed by *** results demonstrate the need for more attention on ethnic factors in IBS-related genetic *** ethnic backgrounds into accounts and placing emphasis on disparities potentially ascribed to ethnicity could help lay a solid and generalized foundation for transcultural,multi-ethnic,or secondary analyses in IBS,for example,a *** genetic studies considering ethnic factors are greatly needed to obtain a better understanding of the pathophysiological mechanisms of IBS and to improve the prevention,intervention,and treatment of this disease.

关键词： Irritable bowel syndrome Ethnicity Genetic polymorphism Single nucleotide polymorphism genome-wide association Pathogenesis

Gastric precancerous lesions are associated with gene variants in Helicobacter pylori -susceptible ethnic Malays

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World Journal of Gastroenterology 2013年第23期19卷 3615-3622页

作者： Sathiya Maran Yeong Yeh Lee Shuhua Xu Nur-Shafawati Rajab Norhazrini Hasan Syed Hassan Syed Abdul Aziz Noorizan Abdul Majid Bin Alwi Zilfalil Human genome Center School of Medical Sciences Universiti Sains Malaysia16150 Kubang Kerian Malaysia Department of Medicine School of Medical Sciences Universiti Sains Malaysia16150 Kubang Kerian Malaysia Max Planck Independent Research Group on Population Genomics Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences200031 Shanghai China Department of Immunology School of Medical Sciences Universiti Sains Malaysia16150 Kubang Kerian Malaysia Department of Surgery School of Medical Sciences Universiti Sains Malaysia16150 Kubang Kerian Malaysia Department of Paediatrics School of Medical Sciences Universiti Sains Malaysia16150 Kubang Kerian Malaysia

AIM: To identify genes associated with gastric pre-cancerous lesions in Helicobacter pylori (H. pylori )susceptible ethnic Malays. METHODS: Twenty-three Malay subjects with H. pylori infection and gastric precancerous lesions identified during endoscopy were included as "cases". Thirtyseven Malay subjects who were H. pylori negative and had no precancerous lesions were included as "controls". Venous blood was collected for genotyping with Affymetrix 50K Xba1 kit. Genotypes with call rates 0.5 was considered as significant markers. RESULTS: Of the 23 H. pylori -positive subjects recruited, one sample was excluded from further analysis due to a low genotyping call rate. Of the 22 H. pylori positive samples, atrophic gastritis only was present in 50.0%, complete intestinal metaplasia was present in 18.25%, both incomplete intestinal metaplasia and dysplasia was present in 22.7%, and dysplasia only was present in 9.1%. SNPs rs9315542 (UFM1 gene), rs6878265 (THBS4 gene), rs1042194 (CYP2C19 gene) and rs10505799 (MGST1 gene) were significantly associated with atrophic gastritis, complete intestinal metaplasia, incomplete metaplasia with foci of dysplasia and dysplasia, respectively. Allele frequencies in "cases" vs "controls" for rs9315542, rs6878265, rs1042194 and rs10505799 were 0.4 vs 0.06, 0.6 vs 0.01, 0.6 vs 0.01 and 0.5 vs 0.02, respectively. CONCLUSION: Genetic variants possibly related to gastric precancerous lesions in ethnic Malays susceptible to H. pylori infection were identified for testing in subsequent trials.

关键词： Gastric precancerous lesions Gene polymorphisms genome-wide association Helicobacter pylori Malays

HLA class Ⅱ associated with outcomes of hepatitis B and C infections

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World Journal of Gastroenterology 2013年第33期19卷 5395-5401页

作者： Akihiro Tamori Norifumi Kawada Department of Hepatology Osaka city University Graduate School of Medicine

Several factors influence the clinical course of hepatitis B virus(HBV)and hepatitis C virus(HCV)*** human leukocyte antigen(HLA)system,the major histocompatibility complex(MHC)in humans,has been considered one of the most important host factors with respect to *** date,conventional genotyping studies have shown that HLA classⅡloci are mainly associated with spontaneous clearance of HBV and ***,the specific HLA locus associated with the outcomes of hepatitis virus infection remains unclear.A recent genome-wide association study(GWAS)using a comprehensive approach for human genotyping demonstrated single nucleotide polymorphisms(SNPs)associated with the outcomes of hepatitis virus *** of large numbers of cohorts revealed that several SNPs in both HLA-DPA1 and HLADPB1 loci are associated with persistent HBV infection in Asian *** date,however,few studies have focused on HLA-DP because polymorphisms of HLA-DP haplotype do not vary greatly as compared with other loci of *** are not enough studies to reveal the function of *** additionally detected candidate SNPs within HLA loci associated with chronic HBV or HCV hepatitis,hepatic fibrosis,and the development of hepatocellular *** results of one cohort were not always consistent with those of other *** solve several controversial issues,it is necessary to validate reported SNPs on HLA loci in global populations and to elucidate the HLA-allele-regulated molecular response to hepatitis virus infection.

关键词： Hepatitis B virus Hepatitis C virus Hepatocarcinogenesis Human leukocyte antigen genome-wide association studies Genotyping Persistent infection