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

Abstract

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.

CLC Number:

S831.2

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.

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References

［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.

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

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