运用四种线性模型对京海黄鸡上市体重进行全基因组关联分析

doi:10.11843/j.issn.0366-6964.2014.07.004

畜牧兽医学报 ›› 2014, Vol. 45 ›› Issue (7): 1053-1059.doi: 10.11843/j.issn.0366-6964.2014.07.004

运用四种线性模型对京海黄鸡上市体重进行全基因组关联分析

樊庆灿¹，王金玉^1*，张跟喜¹，唐莹¹，张涛¹，顾玉萍²，施会强²

（1.扬州大学动物科技学院，扬州 225009； 2.江苏京海禽业集团有限公司，南通 226103）

收稿日期:2014-01-25 出版日期:2014-07-23 发布日期:2014-07-21
通讯作者: 王金玉，教授，主要从事动物遗传育种研究，Tel：0514-87979075，E-mail：jywang@yzu.edu.cn
作者简介:樊庆灿(1986-)，男，山东菏泽人，博士生，主要从事动物遗传育种与繁殖研究，E-mail：378728593@qq.com
基金资助:
国家肉鸡产业技术体系（nycytx-42-G1-05）；江苏省研究生创新工程（CXLX12_0930）；江苏省高校自然科学基金（12KJB230003）

A Genome-wide Association Study of Market Weight Using Four Statistic Models in Jinghai Yellow Chicken

FAN Qing-can¹，WANG Jin-yu^1*，ZHANG Gen-xi¹，TANG Ying¹，ZHANG Tao¹，GU Yu-ping²，SHI Hui-qiang²

(1.College of Animal Science and Technology，Yangzhou University，Yangzhou 225009，China；2.Jiangsu Jinghai Poultry Industry Group CD.，LTD.，Nantong 226103，China)

Received:2014-01-25 Online:2014-07-23 Published:2014-07-21

摘要/Abstract

摘要：

旨在使用4种模型对京海黄鸡的16周龄体重进行全基因组关联分析（GWAS）。试验以京海黄鸡母鸡为试验材料，通过60KSNP芯片分型，并使用2种线性回归模型和广义线性模型（GLM）、混合线性模型（MLM）4种模型对基因型数据和京海黄鸡16周龄体重进行关联分析。结果表明，虽然4种模型识别出的显著SNPs（P<0.05）数目不同，但各有优缺点。此外，本研究共识别20个与京海黄鸡上市体重关联显著的SNPs（P<0.05）。这些SNPs主要分布于1、4、19、25和Z染色体上，其中，1号染色体50.6～53.6 Mb和Z染色体33.6～44.8 Mb区域是显著SNPs（P<0.05）分布较为集中的区域。另外还有部分显著SNPs（P<0.05）位于之前报道的影响鸡生长性状的QTL内。最后，本研究还找到了17个候选基因，同时还探讨了FAM184B、NCAPG和NLK的功能，所有的这些结果将促进鸡生长性状标记的研究。

关键词: 京海黄鸡, 上市体重, GWAS, GLM, MLM

Abstract:

The aim of this study was to conduct a genome-wide association study (GWAS) using four statistic models to identify the single nucleotide polymorphisms (SNP) associated with 16-week-old body weight of Jinghai Yellow chicken.60KSNP chips and four statistic models was applied to analyze the associations between different genotypes and body weight at the age of 16 weeks (BW16).The four models included two line regression models，generalized linear model (GLM) and mixed liner model (MLM).The result showed that although the numbers of significant SNPs (P<0.05) identified by the four models were different，each of them had its merits.Therefore，different models should be selected for different purpose in practice.Twenty significant SNPs (P<0.05) affecting on BW16 were identified.They located on chromosome 1，4，19，25 and Z，respectively.And the regions of 50.6-53.6 Mb on chromosome 1 and 33.6-44.8 Mb on chromosome Z were the concentrated areas containing more significant SNPs.Moreover，some of the significant SNPs (P<0.05) located in the quantitative trait loci (QTLs) in previous papers reported.Finally，17 candidate genes were identified and the functions of FAM184B，NCAPG and NLK were discussed.All these present results would benefit the researches of chicken molecular markers.

Key words: Jinghai Yellow chicken, market weight, GWAS, GLM, MLM

中图分类号:

S831.2

樊庆灿，王金玉，张跟喜，唐莹，张涛，顾玉萍，施会强. 运用四种线性模型对京海黄鸡上市体重进行全基因组关联分析[J]. 畜牧兽医学报, 2014, 45(7): 1053-1059.

FAN Qing-can，WANG Jin-yu，ZHANG Gen-xi，TANG Ying，ZHANG Tao，GU Yu-ping，SHI Hui-qiang. A Genome-wide Association Study of Market Weight Using Four Statistic Models in Jinghai Yellow Chicken[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2014, 45(7): 1053-1059.

参考文献

［1］张跟喜.边鸡遗传多样性及Myostatin基因对生长和繁殖性状的遗传效应研究［D］.扬州：扬州大学，2010.
［2］葛玉洋，李琦华，樊月圆，等.单核苷酸多态性在鸡生长发育中的应用［J］.安徽农业科学，2013，41(8):3395-3396.
［3］MCCARTHY M I，ABECASIS G R，CARDON L R，et al.Genome-wide association studies for complex traits：consensus，uncertainty and challenges ［J］.Nat Rev Genet，2008，9(5):356-369.
［4］HARDY J，SINGLETON A.Genome wide association studies and human diseases ［J］.Eng J Med，2009，360:1759-1768.
［5］LIU Y Z，WILSON S G，WANG L，et al.Identification of PLCL1 gene for hip bone size variation in females in a genome-wide association study ［J］.PLoS ONE，2008，3(9):e3160.
［6］LIU Y Z，PEI Y F，LIU J F，et al.Powerful bivariate genome-wide association analyses suggest the SOX6 gene influencing both obesity and osteoporosis phenotypes in males ［J］.PLoS ONE，2009，4(8):e6827.
［7］XIONG D H，LIU X G，GUO Y F，et al.Genome-wide association and follow-up replication studies identifiedADAMTS18 and TGFBR3 as bone mass candidate genes in different ethnic groups ［J］.Am J Hum Genet，2009，84(3):388-398.
［8］PURCELL S，NEALE B，TODD-BROWN K，et al.PLINK：A tool set for whole-genome association and population -based linkage analyses ［J］.Am J Hum Genet，2007，81(3)：559-575.
［9］胡耀东.鸡H/L和SRBC遗传选择及部分抗病性状的全基因组关联分析［D］.成都：四川农业大学，2012.
［10］NICODEMUS K K，LIU W L，CHASE G A，et al.Comparison of type I error for multiple test corrections in large single-nucleotide polymorphism studies using principal components versus haplotype blocking algorithms ［J］. BMC Genet，2005，6(suppl 1):S78.
［11］吴丹，刘冉冉，赵桂苹，等.鸡体质量性状基因的全基因组关联研究［J］.畜牧兽医学报，2012，43（12）：1887-1896.
［12］XIE L，LUO C，ZHANG C，et al.Genome-wide association study identified a narrow chromosome 1 region associated with chicken growth traits ［J］.PLoS ONE，2012，7(2):e30910.
［13］GU X，FENG C，MA L，et al.Genome-wide association study of body weight in chicken F2 resource population ［J］. PLoS ONE，2011，6:e21872.
［14］LIU W，LI D，LIU J，et al.A genome-wide SNP scan reveals novel loci for egg production and quality traits in white leghorn and brown-egg dwarf layers ［J］.PLoS ONE，2011，6(12):e28600.
［15］LINDHOLM-PERRY A K，SEXTEN A K，KUEHN L A，et al.Association，effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake，gain，meat and carcass traits in beef cattle ［J］. BMC Genet，2011，12:103.
［16］SORANZO N，RIVADENEIRA F，CHINAPPEN-HORSLEY U，et al.Meta- analysis of genome-wide scans for human adult stature identifies novel loci and associations with measures of skeletal frame size ［J］.PLoS Genet，2009，5：e1000445.
［17］EBERLEIN A，TAKASUGA A，SETOGUCHI K,et al.Dissection of genetic factors modulating fetal growth in cattle indicates a substantial role of the non-SMC condensin I complex，subunit G (NCAPG) gene ［J］.Genetics，2009，183(3):951-964.
［18］PAUSCH H，FLISIKOWSKI K，JUNG S，et al.Genome-wide association study identifies two major loci affecting calving ease and growth-related traits in cattle ［J］.Genetics，2011，187:1289-1297.
［19］SETOGUCHI K，FURUTA M，HIRANO T，et al.Cross-breed comparisons identified a critical 591 kb region for bovine carcass weight QTL (CW-2) on chromosome 6 and the Ile-442-Met substitution in NCAPG as a positional candidate ［J］.BMC Genet，2009，10：43.
［20］SETOGUCHI K，WATANABE T，WEIKARD R，et al.The SNP c.1326T>G in the non-SMC condensin I complex，subunit G (NCAPG) gene encoding a p.Ile442Met variant is associated with an increase in body frame size at puberty in cattle ［J］.Anim Genet，2011，42(6)：650-655.

［21］GLENSKE K，BRANDT H，ERHARDT G.Association of the Ile-442-Met substitution in NCAPG with birth weight in German Angus and German Simmental cattle ［J］.Arc Tierzucht, 2011，54(1)：104-106.
［22］OHKAWARA B，SHIRAKABE K，HYODO-MIURA J，et al.Role of the TAK1-NLK-STAT3 pathway in TGF-beta-mediated mesoderm induction ［J］.Genes Dev，2004，18:381-386.
［23］ISHITANI T，NINOMIYA-TSUJI J，NAGAI S，et al.The TAK1-NLK-MAPK-related pathway antagonizes signal-ling between beta-catenin and transcription factor TCF ［J］. Nature，1999，399：798-802.
［24］KORTENJANN M，NEHLS M，SMITH A J，et al.Abnormal bone marrow stroma in mice deficient for Nemo-like kinase，Nlk ［J］.Eur J Immunol，2001，31:3580-3587.
［25］MIRKOVIC I，CHARISH K，GORSKI S M，et al.Drosophila nemo is an essential gene involved in the regulation of programmed cell death ［J］.Mech Dev，2002，119：9-20.

[1]	常天鹏, 夏江威, 宝金山, 金生云, 朱波, 徐凌洋, 陈燕, 张路培, 高雪, 李俊雅, 高会江. 利用两种统计模型对中国肉用西门塔尔牛屠宰性状的全基因组关联分析[J]. 畜牧兽医学报, 2018, 49(4): 833-840.
[2]	常天鹏, 夏江威, 宝金山, 金生云, 朱波, 徐凌洋, 陈燕, 张路培, 高雪, 李俊雅, 高会江. 利用两种统计模型对中国肉用西门塔尔牛屠宰性状的全基因组关联分析[J]. 畜牧兽医学报, 2018, 49(4): 833-840.
[3]	王杰, 刘璐, 刘杰, 赵桂苹, 刘冉冉, 郑麦青, 文杰. 基于通路分析方法诠释肉鸡体重性状全基因组关联研究[J]. 畜牧兽医学报, 2017, 48(5): 810-817.
[4]	王杰, 刘璐, 刘杰, 赵桂苹, 刘冉冉, 郑麦青, 文杰. 基于通路分析方法诠释肉鸡体重性状全基因组关联研究[J]. 畜牧兽医学报, 2017, 48(5): 810-817.
[5]	张涛，樊庆灿，张向前，张跟喜，王金玉，顾玉萍. 京海黄鸡体组成性状的全基因组关联分析[J]. 畜牧兽医学报, 2015, 46(9): 1502-1514.
[6]	张涛，樊庆灿，张向前，张跟喜，王金玉，顾玉萍. 京海黄鸡体组成性状的全基因组关联分析[J]. 畜牧兽医学报, 2015, 46(9): 1502-1514.
[7]	赵谦，浦亚斌，关伟军，赵倩君，马月辉. 猪重要性状全基因组关联分析的研究进展[J]. 畜牧兽医学报, 2015, 46(6): 873-881.
[8]	赵谦，浦亚斌，关伟军，赵倩君，马月辉. 猪重要性状全基因组关联分析的研究进展[J]. 畜牧兽医学报, 2015, 46(6): 873-881.
[9]	王文浩，张涛，王金玉，张跟喜，樊庆灿，陈学森，韩鲲鹏，王永娟. 京海黄鸡新城疫和传染性支气管炎抗病性状的全基因组关联分析[J]. 畜牧兽医学报, 2015, 46(2): 196-203.
[10]	王文浩，张涛，王金玉，张跟喜，樊庆灿，陈学森，韩鲲鹏，王永娟. 京海黄鸡新城疫和传染性支气管炎抗病性状的全基因组关联分析[J]. 畜牧兽医学报, 2015, 46(2): 196-203.
[11]	孙明明，林雨鑫，戴国俊，张菁菁，张跟喜，谢恺舟，王金玉，顾玉萍，王永娟. 柔嫩艾美耳球虫感染对京海黄鸡不同组织中Zyxin、CD4和TNFRSF1A 基因mRNA表达的影响[J]. 畜牧兽医学报, 2014, 45(8): 1369-1374.
[12]	孙明明，林雨鑫，戴国俊，张菁菁，张跟喜，谢恺舟，王金玉，顾玉萍，王永娟. 柔嫩艾美耳球虫感染对京海黄鸡不同组织中Zyxin、CD4和TNFRSF1A 基因mRNA表达的影响[J]. 畜牧兽医学报, 2014, 45(8): 1369-1374.
[13]	樊庆灿，王金玉，张跟喜，唐莹，张涛，顾玉萍，施会强. 运用四种线性模型对京海黄鸡上市体重进行全基因组关联分析[J]. 畜牧兽医学报, 2014, 45(7): 1053-1059.
[14]	唐莹,王金玉,张跟喜,樊庆灿,陈学森,张涛,魏岳,施会强. Myf5基因8个SNPs位点与京海黄鸡生长和繁殖性状的关联分析[J]. 畜牧兽医学报, 2014, 45(6): 863-870.
[15]	唐莹,王金玉,张跟喜,樊庆灿,陈学森,张涛,魏岳,施会强. Myf5基因8个SNPs位点与京海黄鸡生长和繁殖性状的关联分析[J]. 畜牧兽医学报, 2014, 45(6): 863-870.

运用四种线性模型对京海黄鸡上市体重进行全基因组关联分析

A Genome-wide Association Study of Market Weight Using Four Statistic Models in Jinghai Yellow Chicken

PDF

可视化

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

本文评价