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. Ev

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]	吕娇, 龚一富, 章丽, 胡媛, 王何瑜. 基于WGCNA发掘缺磷、红光和黄光处理下三角褐指藻岩藻黄素合成关键基因[J]. 遗传, 2023, 45(3): 237-249.
[2]	李亚楠, 张贤君, 张宁, 梁雅琳, 张宇星, 招华兴, 李紫聪, 黄思秀. 过表达组蛋白H3K9me3去甲基化酶对猪克隆胚胎发育的影响[J]. 遗传, 2023, 45(1): 67-77.
[3]	高菲, 王煜, 杜嘉祥, 杜旭光, 赵建国, 潘登科, 吴森, 赵要风. 遗传修饰猪模型在生物医学及农业领域研究进展及应用[J]. 遗传, 2023, 45(1): 6-28.
[4]	唐湘薇, 楚丹, 颜赛娜, 尹艳飞, 卞桥, 翁波, 陈斌, 冉茂良. miR-191靶向BDNF基因通过激活PI3K/AKT信号通路促进猪未成熟支持细胞增殖[J]. 遗传, 2021, 43(7): 680-693.
[5]	周子文, 王雪, 丁向东. 基于高密度SNP标记估计群体间遗传关联[J]. 遗传, 2021, 43(4): 340-349.
[6]	彭定威, 李瑞强, 曾武, 王敏, 石翾, 曾检华, 刘小红, 陈瑶生, 何祖勇. 编辑MSTN半胱氨酸节基元促进两广小花猪肌肉生长[J]. 遗传, 2021, 43(3): 261-270.
[7]	魏强, 奥岩, 杨漫漫, 陈涛, 韩虎, 张兴举, 王然, 夏秋菊, 姜芳芳, 李勇. 利用全基因组重测序技术鉴定五指山猪GHR突变体转基因插入位点[J]. 遗传, 2021, 43(12): 1149-1158.
[8]	韩程程, 夏凯, 龚茹莹, 吴栩涵, 张蕾, 梁新乐. 适于检测非洲猪瘟病毒的点亮Spinach-p54 RNA适配体的设计及应用[J]. 遗传, 2021, 43(12): 1170-1178.
[9]	邢宝松, 王璟, 陈俊峰, 马强, 任巧玲, 张家庆, 张华, 滑留帅, 孙加节, 曹海. 去势和非去势公猪背最长肌circRNA差异表达分析[J]. 遗传, 2021, 43(11): 1066-1077.
[10]	周俊, 赵成成, 吴霄, 石俊松, 周荣, 吴珍芳, 李紫聪. 猪耳成纤维细胞转录组异质性及对核移植胚胎发育的潜在影响[J]. 遗传, 2020, 42(9): 898-915.
[11]	胡雅丽, 戴睿, 刘永鑫, 张婧赢, 胡斌, 储成才, 袁怀波, 白洋. 水稻典型品种日本晴和IR24根系微生物组的解析[J]. 遗传, 2020, 42(5): 506-518.
[12]	任巧玲, 张家庆, 陆东锋, 王璟, 陈俊峰, 马强, 白献晓, 郭红霞, 高彬文, 邢宝松. 乏情和发情初产母猪下丘脑-垂体-卵巢轴中lincRNAs表达谱比较分析[J]. 遗传, 2020, 42(4): 388-402.
[13]	杨岸奇, 陈斌, 冉茂良, 杨广民, 曾诚. 基因组选择在猪杂交育种中的应用[J]. 遗传, 2020, 42(2): 145-152.
[14]	王冰源, 牟玉莲, 李奎, 刘志国. 农业动物干细胞研究进展[J]. 遗传, 2020, 42(11): 1073-1080.
[15]	敖政, 陈祥, 吴珍芳, 李紫聪. 体细胞克隆猪发育异常研究进展[J]. 遗传, 2020, 42(10): 993-1003.