大白猪和通城猪全基因组选择性清扫分析

doi:10.3724/SP.J.1005.2012.01271

遗传 ›› 2012, Vol. 34 ›› Issue (10): 1271-1281.doi: 10.3724/SP.J.1005.2012.01271

大白猪和通城猪全基因组选择性清扫分析

李秀领¹, 杨松柏¹, 唐中林², 李奎², 刘榜¹, 樊斌¹

1. 华中农业大学, 农业动物遗传育种与繁殖教育部重点实验室, 武汉 430070 2. 中国农业科学院北京畜牧兽医研究所, 北京 100193

收稿日期:2012-06-18 修回日期:2012-08-17 出版日期:2012-10-20 发布日期:2012-10-25
通讯作者: 樊斌 E-mail:fanbin@mail.hzau.edu.cn
基金资助:
国家自然科学基金项目(编号：31072009), 教育部新世纪人才支持计划(编号：NCET-11-0646)和中央高校基本科研业务费专项资金(编号：2010PY008)资助

Genome-wide selective sweep analysis on Large White and Tong-cheng pigs

LI Xiu-Ling¹, YANG Song-Bai¹, TANG Zhong-Lin², LI Kui², LIU Bang¹, FAN Bin¹

1. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural Uni-versity, Wuhan 430070, China 2. Institute of Animal Science and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Beijing 100193, China

Received:2012-06-18 Revised:2012-08-17 Online:2012-10-20 Published:2012-10-25

摘要/Abstract

摘要： 长期的人工选择使猪的生产性能得到显著提高, 与选择相关的基因组区域也随之发生特定遗传变异表征(选择信号)。不同类型品种所受到选择强度不一, 选择信号亦不相同, 选择性清扫分析已逐渐成为选择信号的主要检测手段。文章基于商用型大白猪(n=45)和地方猪品种通城猪(n=45)的猪60K SNP芯片分型数据, 借助遗传分化系数Fst法进行选择信号检测分析。利用gPLINK软件设定质控标准, 共计34 304个SNPs被筛选出用于统计分析。使用Genepop软件包计算两个猪品种之间的遗传分化参数Fst, 所得Fst平均值为0.3209。选取Fst > 0.7036(即占总Fst值数目的1%), 共计344个SNPs被选择出来。SNP位置注释显示这些位点涉及到79个候选基因(Sus scrofa Build 9)。利用在线软件Ingenuity Pathway Analysis对候选基因的生物学通路进行网络分析, 发现它们多与生长繁殖及免疫应答有关, 如NCOA6、ERBB4、RUNX2和APOB等基因。研究结果为进行猪产肉、抗病等性状候选基因和致因突变深入挖掘提供了有益参考。

关键词: 选择性清扫, 选择信号, 遗传分化系数Fst, 网络分析, 猪

Abstract: The production performance of pigs has been significantly improved due to long-term artificial selection, and the specific variation characterizations (selection signatures) emerged from the selected genome regions. Different types of breeds are subjected to different selection intensities and had different selection signatures. Selective sweep analysis is one of major methods to detect the selection signatures. In this study, based on the 60K BeadChip genotyping data of both commercial Large White (n=45) and local Tongcheng pigs (n=45), genetic differentiation coefficient Fst was applied to detect the selection signatures. Using gPLINK software to set quality control standards, a total of 34 304 SNPs were selected for statistical analysis. Fst values between two breeds were estimated with Genepop package and the average Fst value was 0.3209. Setting Fst>0.7036 (1% of total number of Fst values) as selection threshold, 344 SNPs were obtained and SNP location annotation indicated that there were 79 candidate genes (Sus scrofa Build 9). Furthermore, network analysis was performed using Ingenuity Pathway Analysis and the preliminary results suggested that most genes were in-volved in growth, reproduction, and immune response, such as NCOA6, ERBB4, RUNX2, and APOB genes. The findings from this study will contribute to further identification of candidate genes and causal mutations implying for meat production and disease resistance in pig.

Key words: selective sweeps, selection signature, genetic differentiation coefficient Fst, pig, network analysis

李秀领，杨松柏，唐中林，李奎，刘榜，樊斌. 大白猪和通城猪全基因组选择性清扫分析[J]. 遗传, 2012, 34(10): 1271-1281.

LI Xiu-Ling, YANG Song-Bai, TANG Zhong-Lin, LI Kui, LIU Bang, FAN Bin. Genome-wide selective sweep analysis on Large White and Tong-cheng pigs[J]. HEREDITAS, 2012, 34(10): 1271-1281.

参考文献

[1] Giuffra E, Kijas JMH, Amarger V, Carlborg Ö, Jeon JT, Andersson L. The origin of the domestic pig: independent domestication and subsequent introgression. Genetics, 2000, 154(4): 1785-1791.
[2] Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG. Recent and ongoing selection in the human genome. Nat Rev Genet, 2007, 8(11): 857-868.
[3] Hudson RR, Kreitman M, Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics, 1987, 116(1): 153-159.
[4] Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 1989, 123(3): 585-595.
[5] Fu YX, Li WH. Statistical tests of neutrality of mutations. Genetics, 1993, 133(3): 693-709.
[6] Fay JC, Wu CI. Hitchhiking under positive Darwinian selection. Genetics, 2000, 155(3): 1405-1413.
[7] Li WH, Wu CI, Luo CC. A new method for estimating synonymous and nonsynonymous rates of nucleotide sub-stitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol, 1985, 2(2): 150-174.
[8] McDonald JH, Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature, 1991, 351(6328): 652-654.
[9] Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Cooper R, Kwiatkowski D, Ward R, Lander ES. Detecting recent positive selection in the human genome from hap-lotype structure. Nature, 2002, 419(6909): 832-837.
[10] Lewontin RC, Krakauer J. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics, 1973, 74(1): 175-195.
[11] Wright S. Isolation by distance. Genetics, 1943, 28(2): 114-138.
[12] Karlsson EK, Baranowska I, Wade CM, Salmon Hillbertz NH, Zody MC, Anderson N, Biagi TM, Patterson N, Piel-berg GR, Kulbokas EJ 3rd, Comstock KE, Keller ET, Mesirov JP, von Euler H, Kämpe O, Hedhammar Å, Lander ES, Andersson G, Andersson L, Lindblad-Toh K. Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet, 2007, 39(11): 1321-1328.
[13] Pariset L, Joost S, Marsan PA, Valentini A, Econogene Consortium (EC). Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean. BMC Genet, 2009, 10: 7.
[14] Wahlberg P, Carlborg Ö, Foglio M, Tordoir X, Syvänen AC, Lathrop M, Gut IG, Siegel PB, Andersson L. Genetic analysis of an F₂ intercross between two chicken lines divergently selected for body-weight. BMC Genomics, 2009, 10(1): 248.
[15] Flori L, Fritz S, Jaffrézic F, Boussaha M, Gut I, Heath S, Foulley JL, Gautier M. The genome response to artificial selection: a case study in dairy cattle. PloS One, 2009, 4(8): e6595.
[16] Kijas JW, Lenstra JA, Hayes B, Boitard S, Porto Neto LR, San Cristobal M, Servin B, McCulloch R, Whan V, Giet-zen K, Paiva S, Barendse W, Ciani E, Raadsma H, McE-wan J, Dalrymple B; International Sheep Genomics Con-sortium Members. Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol, 2012, 10(2): e1001258.
[17] Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet, 2007, 81(3): 559-575.
[18] Rousset F. GENEPOP’007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour, 2008, 8(1): 103-106.
[19] Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution, 1984, 38(6): 1358-1370.
[20] Wright S. Evolution and the Genetics of Populations. Volume 4. Variability Within and Among Natural Popula-tions. Chicago: University of Chicago Press, 1978.
[21] Herbst RS. Review of epidermal growth factor receptor biology. Int J Radiat Oncol Biol Phys, 2004, 59(2): 21-26.
[22] Short TH, Rothschild MF, Southwood OI, McLaren DG, de Vries A, van der Steen H, Eckardt GR, Tuggle CK, Helm J, Vaske DA, Mileham AJ, Plastow GS. Effect of the estrogen receptor locus on reproduction and production traits in four commercial pig lines. J Anim Sci, 1997, 75(12): 3138-3142.
[23] Davies G, Jiang WG, Mason MD. The interaction between beta-catenin, GSK3beta and APC after motogen induced cell-cell dissociation, and their involvement in signal transduction pathways in prostate cancer. Int J Oncol, 2001, 18(4): 843-847.
[24] Livolsi A, Busuttil V, Imbert V, Abraham RT, Peyron JF. Tyrosine phosphorylation-dependent activation of NF- kappa B. Requirement for p56 LCK and ZAP-70 protein tyrosine kinases. Eur J Bio-chem, 2001, 268(5): 1508-1515.
[25] Pearson G, Robinson F, Beers-Gibson T, Xu BE, Karandi-kar M, Berman K, Cobb MH. Mitogen-activated protein (MAP) kinase pathways: regulation and physiological functions. Endocr Rev, 2001, 22(2): 153-183.
[26] Dong C, Davis RJ, Flavell RA. Map kinases in the immune response. Annu Rev Immunol, 2002, 20: 55-72.
[27] Song G, Ouyang GL, Bao SD. The activation of Akt/PKB signaling pathway and cell survival. J Cell Mol Med, 2005, 9(1): 59-71.
[28] Lee KS, Hong SH, Bae SC. Both the Smad and p38 MAPK pathways play a crucial role in RUNX2 expression following induction by trans-forming growth factor β and bone morphogenetic protein. Oncogene, 2002, 21(47): 7156-7163.
[29] Sasaki T, Irie-Sasaki J, Jones RG, Oliveira-dos-Santos AJ, Stanford WL, Bolon B, Wakeham A, Itie A, Bouchard D, Kozieradzki I, Joza N, Mak TW, Ohashi PS, Suzuki A, Pernninger JM. Function of PI3Kγ in thymocyte development, T cell activation, and neutrophil migration. Science, 2000, 287(5455): 1040-1046.
[30] Kraus C, Liehr T, Hülsken J, Behrens J, Birchmeier W, Grzeschik KH, Ballhausen WG. Localization of the human β-catenin gene (CTNNB1) to 3p21: a region im-plicated in tumor development. Genimics, 1994, 23(1): 272-274.
[31] Nguyen A, Rauch TA, Pfeifer GP, Hu VW. Global methy-lation profiling of lymphobastoid cell lines reveals epige-netic contributions to autism spectrum disorders and a novel autism candidate gene, RORA, whose protein product is reduced in autistic brain. FASEB J, 2010, 24(8): 3036-3051.
[32] Lin HM, Zhao L, Cheng SY. Cyclin D1 is a ligand-inde-pendent corepressor for thyroid hormone receptors. J Biol Chem, 2002, 277(32): 28733-28741.
[33] Bhawan J, Gonzalez-Serva A, Nehal K, Labadie R, Lu-frano L, Thorne EG, Gilchrest BA. Effects of tretinoin on photodamaged skin: a histologic study. Arch Dermatol, 1991, 127(5): 666-672.
[34] Huang FJ, Lin YL. Effects of retinoic acid on pre-implantation embryo development in mice. Chang Gung Med J, 2001, 24(11): 681-687.
[35] Florini JR, Ewton DZ, Coolican SA. Growth hormone and the lnsulin-like growth factor system in myogenesis. Endocr Rev, 1996, 17(5): 481-517.
[36] Baarsch MJ, Scamurra RW, Burger K, Foss DL, Mahes-waran SK, Murtaugh MP. Inflammatory cytokine expres-sion in swine experimentally infected with Actinoba-cillus pleuropneumoniae. Infect Immun, 1995, 63(9): 3587-3594.
[37] Darwich L, Balasch M, Plnan-Durán J, Segalés J, Do-mingo M, Mateu E. Cytokine profiles of peripheral blood mononuclear cells from pigs with postweaning multisys-temic wasting syndrome in response to mitogen, superan-tigen or recall viral antigens. J Gen Virol, 2003, 84(12): 3453-3457.
[38] Schlaepfer DD, Hunter T. Integrin signalling and tyrosine phosphorylation: just the FAKs? Trends Cell Biol, 1998, 8(4): 151-157.
[39] Wang WL, Li Q, Xu J, Cvekl A. Lens fiber cell differen-tiation and denucleation are disrupted through expression of the N-terminal nuclear receptor box of Ncoa6 and result in p53-dependent and p53-independent apop-tosis. Mol Biol Cell, 2010, 21(14): 2453-2468.
[40] Park JY, Su YQ, Ariga M, Law E, Jin SLC, Conti M. EGF-like growth factors as mediators of LH action in the ovulatory follicle. Science, 2004, 303(5658): 682-684.
[41] Carraway KL, Weber JL, Unger MJ, Ledesma J, Yu N, Gassmann M, Lai C. Neuregulin-2, a new ligand of ErbB3/ErbB4-receptor tyrosine kinases. Nature, 1997, 387(6632): 512-516.
[42] Li RW, Capuco AV. Canonical pathways and networks regulated by estrogen in the bovine mammary gland. Funct Integr Genomics, 2008, 8(1): 55-68.
[43] Bumsted-O’Brien KM, Hendrickson A, Haverkamp S, Ashery-Padan R, Schulte D. Expression of the homeodo-main transcription factor Meis2 in the embryonic and postnatal retina. J Comp Neurol, 2007, 505(1): 58-72.
[44] Tsimikas S. Oxidized low-density lipoprotein biomarkers in atherosclerosis. Curr Atheroscler Rep, 2006, 8(1): 55-61.
[45] Peterson MM, Mack JL, Hall PR, Alsup AA, Alexander SM, Sully EK, Sawires YS, Cheung AL, Otto M, Gresham HD. Apolipoprotein B is an innate barrier against invasive Staphylococcus aureus infection. Cell Host Mi-crobe, 2008, 4(6): 555-566.
[46] Cortesio CL, Wernimont SA, Kastner DL, Cooper KM, Huttenlocher A. Impaired podosome formation and inva-sive migration of macrophages from patients with a PSTPIP1 mutation and PAPA syndrome. Arthritis Rheum, 2010, 62(8): 2556-2558.
[47] Fang MY, Larson G, Ribeiro HS, Li N, Andersson L. Con-trasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genet, 2009, 5(1): e1000341.
[48] Akey JM, Zhang G, Zhang K, Jin L, Shriver MD. Interro-gating a high-density SNP map for signatures of natural selection. Genome Res, 2002, 12(12): 1805-1814.
[49] Innan H, Kim Y. Pattern of polymorphism after strong ar-tificial selection in a domestication event. Proc Natl Acad Sci USA, 2004, 101(29): 10667-10672.

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

大白猪和通城猪全基因组选择性清扫分析

Genome-wide selective sweep analysis on Large White and Tong-cheng pigs

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

[1]	莫健新,王豪强,黄广燕,蔡更元,吴珍芳,张献伟. 微生物源果胶酶在猪PK15细胞中异源表达及其酶学性质分析[J]. 遗传, 2019, 41(8): 736-745.
[2]	周李生, 赵为民, 涂枫, 吴云鹤, 任守文, 方晓敏. 猪乳头性状生理学和遗传学研究进展[J]. 遗传, 2019, 41(5): 384-390.
[3]	陈应坚,廖苑君,林帆,孙胜南,赵小蕾,覃继恒,饶绍奇. 基于转录组数据的网络分析挖掘鼻咽癌与口腔鳞癌的共享功能模块[J]. 遗传, 2019, 41(2): 146-157.
[4]	赵剑超, 柴壮, 郭诗萌, 刘忠华. 猪早期胚胎发育中SOX2基因启动子活性分析[J]. 遗传, 2019, 41(10): 950-961.
[5]	黄耀强,李国玲,杨化强,吴珍芳. 基因编辑猪在生物医学研究中的应用[J]. 遗传, 2018, 40(8): 632-646.
[6]	刘海龙, 谌阳, 高杨, 周玲, 韩晓松, 赵长志, 杨高娟, 陈毅龙, 杨慧, 谢胜松. 靶向miRNA前体不同类型sgRNA的丰度及特异性评估[J]. 遗传, 2018, 40(7): 561-571.
[7]	冉茂良, 董莲花, 翁波, 曹蓉, 彭馥芝, 高虎, 罗荟, 陈斌. miR-362靶向ZNF644基因调控猪未成熟支持细胞的增殖和凋亡[J]. 遗传, 2018, 40(7): 572-584.
[8]	黄万龙,张秀秀,李嫒,苗向阳. 利用RNA-seq技术筛选大白猪皮下和肌内脂肪组织差异表达基因[J]. 遗传, 2017, 39(6): 501-511.
[9]	黄娇娇, 曹春伟, 郑国民, 赵建国. 基因组编辑技术在猪遗传改良中的应用[J]. 遗传, 2017, 39(11): 1078-1089.
[10]	钟翠丽, 李国玲, 莫健新, 全绒, 王豪强, 李紫聪, 吴珍芳, 张献伟. 不同电转仪的电转参数、质粒用量和拓扑结构对猪胎儿成纤维细胞转染效率的影响[J]. 遗传, 2017, 39(10): 930-938.
[11]	张轲, 冯光德, 张宝云, 向伟, 陈龙, 杨芳, 储明星, 王凭青. 表观遗传标记在猪分子育种中的研究与应用前景[J]. 遗传, 2016, 38(7): 634-643.
[12]	潘章源, 贺小云, 王翔宇, 郭晓飞, 曹晓涵, 胡文萍, 狄冉, 刘秋月, 储明星. 家养动物选择信号研究进展[J]. 遗传, 2016, 38(12): 1069-1080.
[13]	李国玲, 钟翠丽, 倪生, 刘德武, 蔡更元, 李紫聪, 杨化强, 吴珍芳. 利用CRISPR/Cas9系统建立Xist基因敲除猪模型[J]. 遗传, 2016, 38(12): 1081-1089.
[14]	李利族, 韩丽鑫, 王金奎, 汪亮, 刘娣, 杨秀芹. 猪PILRA基因克隆及变异剪接体鉴定[J]. 遗传, 2015, 37(9): 926-931.
[15]	李智方, 冯冲, 纪慧丽, 石宁宁, 宋小凤, 赵勤丽, 龙川, 潘登科, 杨小淦. 绿色荧光蛋白在α-1,3半乳糖基转移酶敲除猪组织器官的表达分析[J]. 遗传, 2015, 37(12): 1211-1217.