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A newly developed 20 K snp array reveals QTLs for disease resistance to Cryptocaryon irritans in tiger pufferfish (Takifugu rubripes)

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AQUACULTURE 2025年第Part2期595卷

作者： Li, Yangzhen Fraslin, Clemence Chi, Yong Mukiibi, Robert Hu, Yuanri Wang, Jialin Li, Weiguo Li, Weidong Houston, Ross D. Robledo, Diego Chen, Songlin Chinese Acad Fishery Sci Yellow Sea Fisheries Res Inst State Key Lab Mariculture Biobreeding & Sustainabl Qingdao 266071 Peoples R China Univ Edinburgh Roslin Inst Midlothian EH25 9RG England Tangshan Haidu Seafood Co Ltd Tangshan 063506 Peoples R China Huazhi Biotech Co Ltd Changsha 410125 Peoples R China Shanghai Ocean Univ Natl Demonstrat Ctr Expt Fisheries Sci Educ Shanghai 201306 Peoples R China Benchmark Genet Penicuik EH26 0GB England Univ Santiago de Compostela Dept Genet Santiago De Compostela 15706 Spain

This study describes the development and application of a 20 K single nucleotide polymorphism (snp) array in fugu (Takifugu rubripes). The main goal of this newly developed snp array is to enhance selective breeding practice via the incorporation of genomic information. Fugu is one of the economic aquaculture species and mainly threatened by parasite disease. The performance of the array was evaluated in a farmed pufferfish population challenged with Cryptocaryon irritans and benchmarked against whole-genome sequencing of a subset of the animals. The array showed very high call rates, consistency between technical replicates, and concordance with genome-resequencing data. Heritability estimates using pedigree and snp datasets demonstrated a significant genetic component of resistance to C. irritans, with heritability estimates ranging from 0.53 to 0.67, and prediction accuracies were significantly improved with the use of genomic data. Genome-wide association study identified two putative quantitative trait loci (QTLs) on chromosomes 3 and 17. Our findings suggest resistance to C. irritans can be rapidly increased in fugu populations by selective breeding, further expedited via the application of genetic markers. Therefore, they represent a valuable resource for selective breeding programmes aimed at enhancing disease resistance in fugu aquaculture.

关键词： snp array Heritability Genomic prediction GWAS QTL Selective breeding

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Development and evaluation of a 50 K snp array for blotched snakehead ( Channa maculata)

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AQUACULTURE 2025年 598卷

作者： Cui, Tongxin Liu, Haiyang Zhang, Jin Luo, Qing Fei, Shuzhan Chen, Kunci Zhao, Jian Ou, Mi Chinese Acad Fishery Sci Pearl River Fisheries Res Inst Key Lab Trop & Subtrop Fishery Resources Applicat Minist Agr & Rural Affairs Guangzhou 510380 Peoples R China Zhejiang Ocean Univ Sch Fishery Zhoushan 316022 Peoples R China Shanghai Ocean Univ Coll Fisheries & Life Sci Shanghai 201306 Peoples R China

snp arrays are potent tools for genetic typing, offering several advantages such as high throughput, costeffectiveness, and accuracy. They play a pivotal role in genetic studies, including genome selection and population genetics. The blotched snakehead ( Channa maculata) holds significant economic importance in China as a freshwater fish species. To facilitate genetic breeding research on this species, we developed a 50 K snp array named "Lixin-I" for genetic typing. We performed whole-genome resequencing on 748 blotched snakeheads from 18 populations, yielding 2,307,294 high-quality snps after quality control. From these data, we selected 50,000 snps evenly distributed throughout the genome, including snps previously associated with growth and sex traits from prior studies. Evaluation of the "Lixin-I" snp array on 150 blotched snakeheads showed a 96.00 % consistency rate with whole-genome resequencing and a 97.94 % call rate. Using this array, we genotyped 464 cultured blotched snakeheads and performed a genome-wide association analysis (GWAS) for weight trait. We successfully identified 13 snps associated with weight, located on three chromosomes. These results indicate that weight in blotched snakeheads is a complex trait regulated by multiple genes, providing valuable insights for the genetic analysis of growth traits. Furthermore, we conducted population genetic structure and genetic diversity analyses on seven wild blotched snakehead populations. These findings provide critical insights for the rational utilization and germplasm innovation of blotched snakehead genetic resources. In summary, the developed "Lixin-I" snp array is a high-quality genetic typing tool that effectively supports genetic breeding efforts in blotched snakeheads.

关键词： Channa maculata snp array Lixin-I GWAS Population genetic

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A high-resolution 20K snp array for comprehensive genotyping and genetic mapping in Nicotiana tabacum L.

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The Crop Journal 2025年第2期13卷 630-635页

作者： Shizhou Yu Zhixiao Yang Jie Zhang Linggai Cao Jie Liu Peng Lu Jiemeng Tao Jufen Wan Qingdong Zeng Tenghang Xu Peijian Cao Jingjing Jin Xueliang Ren Molecular Genetics Key Laboratory of China Tobacco Guizhou Academy of Tobacco ScienceGuiyang 550081GuizhouChina Beijing Life Science Academy Beijing 102200China China Tobacco Gene Research Center Zhengzhou Tobacco Research Institute of CNTCZhengzhou 450001HenanChina State Key Laboratory for Crop Stress Resistance and High-Efficiency Production Northwest A&F UniversityYangling 712100ShaanxiChina College of Agronomy and Biotechnology Hebei Normal University of Science and TechnologyQinhuangdao 066004HebeiChina

Nicotiana tabacum(2n=4x=48),an economically important non-food crop and a model plant for genetic studies,faces challenges in efficient genotyping of novel *** address this,we developed the Ta-LD-SC,a 20K snp Affymetrix Axiom array,based on resequencing data from 150 tobacco accessions.A total of 20,213 unique snps were carefully selected,achieving coverage of over 90%of the tobacco genome(Nitab4.5 and NtaSR1)with a uniform probe distribution,limiting density to no more than 5 snps per 200 *** array underwent extensive validation using 866 tobacco accessions(NP panel)and 288 F2 individuals from a cross between K326 and Oxford 26(GP panel).Performance metrics demonstrated its robustness,with high snp call rates(93.6%-99.8%),a low technical error rate(<1%),and a superior PolyHighResolution snp rate(79.79%)compared to other crop snp *** structure analysis of the NP panel revealed two major introductions of foreign germplasm that have significantly influenced the genetic diversity of Chinese tobacco *** the array,a genome-wide association study(GWAS)identified 62 genes linked to eight agronomic traits,and a high-density genetic map encompassing 4553 snps across 6606.08 cM was *** Ta-LD-SC array provides a valuable tool for rapid,high-quality genotyping offering supporting marker annotations that may benefit genetic research and breeding of tobacco.

关键词： Cultivated tobacco snp array Population structure Differentiation patterns Breeding and genetic improvement

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WDR6K, a designed snp array for the research and improvement of rice drought-resistance

PLANT STRESS

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PLANT STRESS 2025年 15卷

作者： Li, Ziming Wang, Lei Liu, Yi Ma, Xiaosong Zhang, Anning Luo, Zhi Yan, Ming Zhou, Liguo Chen, Liang Luo, Lijun Xia, Hui Huazhong Agr Univ Coll Plant Sci & Technol Wuhan 430070 Peoples R China South China Agr Univ Coll Agr Guangzhou 510642 Peoples R China Minist Agr & Rural Affairs Shanghai Agrobiol Gene Ctr Key Lab Grain Crop Genet Resources Evaluat & Utili Shanghai 201106 Peoples R China Huazhong Agr Univ Natl Key Lab Crop Genet Improvement Hubei Hongshan Lab Wuhan 430070 Peoples R China Huazhong Agr Univ Natl Ctr Plant Gene Res Wuhan 430070 Peoples R China

Water-saving and drought-resistance rice (WDR) integrates many green characters (e.g., drought resistance, water/nutrient use efficiency, direct seeding, etc.) from upland rice into the elite paddy rice. The molecular designed breeding is a promising breeding technology for WDR based on the high-throughput genotyping. Therefore, an efficient and low-cost genotyping tool for WDR breeding, which is suitable in the foreground selection of drought resistance and other green traits, is required. In this study, we designed a snp array named as WDR6K with special strategies in loci selection. WDR6K contains 5895 snp/InDel loci distributes evenly across the rice genome. Compared with other rice 6K snp arrays, WDR6K possesses a high proportion (>90.0 %) of missense snps without apparent loss of polymorphism. Moreover, WDR6K possesses considerable amount (similar to 41.0 %) of upland-lowland differentiated loci, by which we can identify and utilize genetic resources of upland rice. WDR6K refers to 5001 genes, including hundreds of known genes of green characters required by WDR. These genes are related to rice drought resistance as indicate by the GO/KEGG enrichments and their greater expression responses to drought, osmotic, and oxidative stresses and abscisic acid. Furthermore, WDR6K shall be closely associated with drought resistance as it contains 922 drought resistance contributing loci, which can facilitate the foreground selection for drought resistance. Finally, developed by the liquid phase genotyping by pinpoint sequencing of captured targets technology, WDR6K is low-cost and flexible for further version updates to add markers. Therefore, WDR6K has great prospective in the molecular designed breeding of WDR.

关键词： snp array Water-saving and drought-resistance rice Molecular designed breeding Foreground selection

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snp array-based whole genome homozygosity mapping as the first step to a molecular diagnosis in patients with Charcot-Marie-Tooth disease

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JOURNAL OF NEUROLOGY 2012年第3期259卷 515-523页

作者： Fischer, Carina Trajanoski, Slave Papic, Lea Windpassinger, Christian Bernert, Guenther Freilinger, Michael Schabhuettl, Maria Arslan-Kirchner, Mine Javaher-Haghighi, Poupak Plecko, Barbara Senderek, Jan Rauscher, Christian Loescher, Wolfgang N. Pieber, Thomas R. Janecke, Andreas R. Auer-Grumbach, Michaela Med Univ Graz Dept Internal Med Div Endocrinol & Metab A-8010 Graz Austria Med Univ Graz Med Res Ctr A-8010 Graz Austria Med Univ Graz Inst Human Genet A-8010 Graz Austria Preyersches Kinderspital Vienna Austria Med Univ Vienna Dept Pediat & Adolescent Med Vienna Austria Hannover Med Sch Inst Human Genet D-30623 Hannover Germany Amedes MVZ Hamburg Hamburg Germany Med Univ Graz Dept Neuropediat A-8010 Graz Austria Rhein Westfal TH Aachen Inst Human Genet Aachen Germany Rhein Westfal TH Aachen Inst Neuropathol Aachen Germany Christian Doppler Klin Dept Neuropediat Salzburg Austria Innsbruck Med Univ Dept Neurol Innsbruck Austria Innsbruck Med Univ Dept Pediat 2 Innsbruck Austria

Considerable non-allelic heterogeneity for autosomal recessively inherited Charcot-Marie-Tooth (ARCMT) disease has challenged molecular testing and often requires a large amount of work in terms of DNA sequencing and data interpretation or remains unpractical. This study tested the value of snp array-based whole-genome homozygosity mapping as a first step in the molecular genetic diagnosis of sporadic or ARCMT in patients from inbred families or outbred populations with the ancestors originating from the same geographic area. Using 10 K 2.0 and 250 K Nsp Affymetrix snp arrays, 15 (63%) of 24 CMT patients received an accurate genetic diagnosis. We used our Java-based script eHoPASA CMT-easy Homozygosity Profiling of snp arrays for CMT patients to display the location of homozygous regions and their extent of marker count and base-pairs throughout the whole genome. CMT4C was the most common genetic subtype with mutations detected in SH3TC2, one (p.E632Kfs13X) appearing to be a novel founder mutation. A sporadic patient with severe CMT was homozygous for the c.250G > C (p.G84R) HSPB1 mutation which has previously been reported to cause autosomal dominant dHMN. Two distantly related CMT1 patients with early disease onset were found to carry a novel homozygous mutation in MFN2 (p.N131S). We conclude that snp array-based homozygosity mapping is a fast, powerful, and economic tool to guide molecular genetic testing in ARCMT and in selected sporadic CMT patients.

关键词： Autosomal recessive CMT Homozygosity mapping snp array Hereditary neuropathies Gene

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snp array-based copy number and genotype analyses for preimplantation genetic diagnosis of human unbalanced translocations

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EUROPEAN JOURNAL OF HUMAN GENETICS 2012年第9期20卷 938-944页

作者： van Uum, Chris M. J. Stevens, Servi J. C. Dreesen, Joseph C. F. M. Drusedau, Marion Smeets, Hubert J. Hollanders-Crombach, Bertien de Die-Smulders, Christine E. M. Geraedts, Joep P. M. Engelen, John J. M. Coonen, Edith Maastricht Univ Med Ctr Dept Clin Genet NL-6202 AZ Maastricht Netherlands Maastricht Univ Sch Oncol & Dev Biol GROW NL-6202 AZ Maastricht Netherlands Maastricht Univ Med Ctr Dept Obstet & Gynaecol IVF Lab NL-6202 AZ Maastricht Netherlands

Preimplantation genetic diagnosis (PGD) for chromosomal rearrangements (CR) is mainly based on fluorescence in situ hybridisation (FISH). Application of this technique is limited by the number of available fluorochromes, the extensive preclinical work-up and technical and interpretative artefacts. We aimed to develop a universal, off-the-shelf protocol for PGD by combining single-nucleotide polymorphism (snp) array-derived copy number (CN) determination and genotyping for detection of unbalanced translocations in cleavage-stage embryos. A total of 36 cleavage-stage embryos that were diagnosed as unbalanced by initial PGD FISH analysis were dissociated (n=146) and amplified by multiple displacement amplification (MDA). snp CNs and genotypes were determined using snp array. Epstein-Barr Virus-transformed cell lines with known CR were used for optimising the genomic smoothing (GS) length setting to increase signal to noise ratio. snp CN analysis showed 23 embryos (64%) that were unbalanced in all blastomeres for the chromosomes involved in the translocation, 5 embryos (14%) that were normal or balanced in all blastomeres and 8 embryos (22%) that were mosaic. snp genotyping, based on analysis of informative snp loci with opposing homozygous parental genotypes, confirmed partial monosomies associated with inheritance of unbalanced translocation in surplus embryos. We have developed a universal MDA-snp array technique for chromosome CN analysis in single blastomeres. snp genotyping could confirm partial monosomies. This combination of techniques showed improved diagnostic specificity compared with FISH and may provide more reliable PGD analysis associated with higher embryo transfer rate. European Journal of Human Genetics (2012) 20, 938-944;doi:10.1038/ejhg.2012.27;published online 29 February 2012

关键词： preimplantation genetic diagnosis snp array chromosomal translocations whole-genome amplification genotyping blastomeres

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snp array genomic analysis of matched pairs of brain and liver metastases in primary colorectal cancer

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JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY 2023年第20期149卷 18173-18183页

作者： Brandt, Vivian-Pascal Holland, Heidrun Wallenborn, Marco Koschny, Ronald Frydrychowicz, Clara Richter, Mandy Holland, Lydia Nestler, Ulf Sander, Caroline Univ Hosp Leipzig Dept Neurosurg Leipzig Saxony Germany Univ Leipzig Saxonian Incubator Clin Translat SIKT Leipzig Saxony Germany Univ Hosp Heidelberg Interdisciplinary Endoscopy Ctr IEZ Dept Gastroenterol & Hepatol Heidelberg Baden Wuerttemb Germany Univ Med Leipzig Paul Flechsig Inst Neuropathol Leipzig Saxony Germany

PurposeBrain metastasis formation is a rare and late event in colorectal cancer (CRC) patients and associated with poor survival. In contrast to other metastatic sites, the knowledge on chromosomal aberrations in brain metastases is very ***, we carried out single nucleotide polymorphism (snp) array analyses on matched primary CRC and brain metastases of four patients as well as on liver metastases of three *** metastases showed more chromosomal aberrations than primary tumors or liver metastases. Commonly occurring aberrations were gain of 8q11.1-q24.3 (primary CRC), gain of 13q12.13-q12.3 (liver metastases), and gain of 20q11.1-q13.33 (brain metastases). Furthermore, we found one copy-neutral loss of heterozygosity (cn-LOH) region on chromosome 3 in primary CRC, three cn-LOH regions in liver metastases and 23 cn-LOH regions in brain metastases, comprising 26 previously undescribed *** more frequent occurrence of cn-LOHs and subsequently affected genes in brain metastases shed light on the pathophysiology of brain metastasis formation. Further pairwise genetic analyses between primary tumors and their metastases will help to define the role of affected genes in cn-LOH regions.

关键词： Colorectal cancer Liver metastasis Brain metastasis snp array Chromosomal aberration Cn-LOH

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snp array as a Tool for Prenatal Diagnosis of Congenital Heart Disease Screened by Echocardiography: Implications for Precision Assessment of Fetal Prognosis

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RISK MANAGEMENT AND HEALTHCARE POLICY 2021年 14卷 345-355页

作者： Huang, Hailong Cai, Meiying Wang, Yan Liang, Bin Lin, Na Xu, Liangpu Fujian Med Univ Fujian Matern & Child Hlth Hosp Ctr Prenatal Diag Affiliated Hosp 18 Daoshan Rd Fuzhou 350001 Fujian Peoples R China Fujian Key Lab Prenatal Diag & Birth Defects Fuzhou 350001 Fujian Peoples R China

Objective: This study aimed to examine the effectiveness of the snp array for the prenatal diagnosis of congenital heart disease (CHD) screened by echocardiography. Patients and Methods: A total of 356 pregnant women with fetal congenital heart malformations revealed by echocardiography at the Center for Prenatal Diagnosis of Fujian Maternal and Children Hospital during the period from November 2016 through July 2019 were recruited. The fetuses were assigned into three cohorts, including 142 with a single cardiac malformation, 106 with multiple cardiac malformations and 108 with cardiac and extracardiac malformations. All fetuses underwent chromosomal karyotyping and snp array simultaneously, and the effectiveness of the snp array for the prenatal diagnosis of CHD was evaluated. Results: The overall prevalence of abnormal karyotypes was 9.3% among the 356 fetuses with CHD, and a higher proportion was found in fetuses with cardiac and extracardiac malformations (18.5%) than in those with single (5.6%) or multiple cardiac malformations (4.7%) (P<0.05). Consistent with karyotype analysis, snp array detected an additional 25 fetuses with pathogenic copy number variations (CNVs), seven with variant of unknown significance (VOUS) and seven with benign CNVs, and a lower proportion of abnormal CNV was found in fetuses with a single cardiac malformation (4.2%) than in those with multiple cardiac malformations (9.4%) or cardiac and extracardiac malformations (14.8%) (P<0.05). Among the 33 fetuses with chromosomal abnormality, postnatal follow-up showed termination of pregnancy in 25 with pathogenic CNVs, one with VOUS, and six with normal karyotypes and snp array findings but severe multiple malformations by ultrasonography. Conclusion: snp array increases the overall detection of abnormal CNVs by 9%, which improves the detection of CNVs associated with CHD. snp array may serve as a tool for prenatal diagnosis of CHD that facilitates the discovery of pathogenic genes associat

关键词： congenital heart disease snp array echocardiography prenatal diagnosis

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snp array and FISH findings in two pleomorphic hyalinizing angiectatic tumors

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CANCER GENETICS 2012年第12期205卷 673-676页

作者： Mohajeri, Arezoo Kindblom, Lars-Gunnar Sumathi, Vaiyapuri P. Brosjo, Otte Magnusson, Linda Nilsson, Jenny Nord, Karolin H. Mertens, Fredrik Lund Univ Dept Clin Genet Univ & Reg Labs Skane Univ Hosp Lund Sweden Univ Birmingham Sch Med Dept Musculoskeletal Pathol & Orthopaed Oncol Royal Orthopaed Hosp NHS Fdn Trust Birmingham W Midlands England Univ Birmingham Sch Med Div Canc Studies Birmingham W Midlands England Karolinska Hosp Dept Orthoped S-10401 Stockholm Sweden

Pleomorphic hyalinizing angiectatic tumor (PHAT) is a rare soft tissue tumor of intermediate malignancy and uncertain cellular origin and lineage of differentiation. Although PHAT is still poorly characterized at the genetic level, there is a potential genetic overlap with two other soft tissue tumors: myxoinflammatory fibroblastic sarcoma (MIFS) and hemosiderotic fibrolipomatous tumor (HFLT);MIFS and HFLT share a characteristic t(1;10)(p22;q24) with breakpoints in the TGFBR3 locus on chromosome 1 and near the MGEA5 locus on chromosome 10. Recently, a PHAT with a similar t(1;10) was reported, suggesting a genetic link between MIFS/HFLT and PHAT. To ascertain whether PHAT is also associated with this translocation, two cases were subjected to single nucleotide polymorphism (snp) array and fluorescence in situ hybridization analyses. Neither PHAT showed a t(1;10) or other types of rearrangement of the TGFBR3 or MGEA5 loci. Both tumors showed imbalances in the snp array analysis, but none was shared. Thus, the results indicate that PHAT is genetically distinguishable from MIFS and HFLT, but further studies are needed to identify the salient genetic pathways involved in PHAT development.

关键词： Pleomorphic hyalinizing angiectatic tumor PHAT snp array FISH

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Improvement of three popular Indian groundnut varieties for foliar disease resistance and high oleic acid using SSR markers and snp array in marker-assisted backcrossing

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The Crop Journal 2020年第1期8卷 1-15页

作者： Yaduru Shasidhar Murali T.Variath Manish K.Vishwakarma Surendra S.Manohar Sunil S.Gangurde Manda Sriswathi Hari Kishan Sudini Keshavji L.Dobariya Sandip K.Bera Thankappan Radhakrishnan Manish K.Pandey Pasupuleti Janila Rajeev K.Varshney International Crops Research Institute for the Semi-Arid Tropics(ICRISAT) HyderabadIndia Department of Genetics Osmania UniversityHyderabadIndia Junagadh Agricultural University JunagadhIndia ICAR-Directorate of Groundnut Research JunagadhIndia

Foliar fungal diseases(rust and late leaf spot)incur large yield losses,in addition to the deterioration of fodder quality in groundnut *** oleic acid has emerged as a key market trait in groundnut,as it increases the shelf life of the produce/products in addition to providing health benefits to ***-assisted backcrossing(MABC)is the most successful approach to introgressing or pyramiding one or more traits using traitlinked *** used MABC to improve three popular Indian cultivars(GJG 9,GG 20,and GJGHPS 1)for foliar disease resistance(FDR)and high oleic acid content.A total of 22 BC3F4 and 30 BC2F4 introgression lines(ILs)for FDR and 46 BC3F4 and 41 BC2F4 ILs for high oleic acid were *** parent genome analysis using the 58 K Axiom_Arachis array identified several lines showing upto 94%of genome recovery among second and third backcross *** of these ILs revealed FDR scores comparable to the resistant parent,GPBD 4,and ILs with high(~80%)oleic acid in addition to high genome *** ILs provide further opportunities for pyramiding FDR and high oleic acid in all three genetic backgrounds as well as for conducting multi-location yield trials for further evaluation and release for cultivation in target regions of India.

关键词： Foliar disease resistance High oleic acid Late leaf spot Marker-assisted backcrossing snp array Background genome recovery

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