基于GWAS后分析策略研究TRAPPC9基因对奶牛产奶性状的遗传效应

doi:10.11843/j.issn.0366-6964.2015.01.008

Abstract

Abstract:

Based on the result of the previous genome-wide association study(GWAS) for milk production traits in Beijing Chinese Holstein population，trafficking protein particle complex 9(TRAPPC9) as a novel candidate gene for milk production traits was confirmed in new Chinese Holstein population.Promoter，exon and GWAS’s significant region was amplified and sequenced by screening the DNA pools to select single nucleotide polymorphisms(SNP) and analyze their association with milk production traits of Chinese Holstein population.The association analysis showed that the genotypes of SNP1 had significant effect on protein percentage(PP) and lactose percentge(LP)(P<0.01)；the genotypes of SNP2 had significant effect on PP and LP(P<0.05)；the genotypes of SNP3 had significant effect on fat percent(FP) and PP(P<0.01)；the genotypes of SNP4 had significant effect on FP(P<0.01)；the genotypes of SNP5 had significant effect on FP and LP(P<0.05).The expression of TRAPPC9 also had significant effect on milk production traits，but the DNA methylation of promoter region of TRAPPC9 had no direct effect.In conclusion，TRAPPC9 gene can be considered as a molecular marker applied to Chinese Holstein marker-assisted selection.

CLC Number:

DONG Yi-chun，LIU Chao，WANG Xiao，WANG Ya-chun，ZHANG Yi，SUN Dong-xiao，ZHANG Sheng-li，ZHANG Qin，ZHANG Yuan，YU Ying. Confirming the Genetic Effects of Bovine TRAPPC9 on Milk Production Traits Based on Post-GWAS Strategies[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2015, 46(1): 60-68.

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References

［1］KAUFMAN L，FEIGENBAUM A，BI W，et al.A homozygous deletion of 8q24.3 including the NIBP gene associated with severe developmental delay，dysgenesis of the corpus callosum，and dysmorphic facial features ［J］.Am J Med Genet A，2010，152A(5):1268-1272.
［2］SACHER M，KIM Y G，LAVIE A，et al.The TRAPP complex：Insights into its architecture and function ［J］.Blackwell Munksgaard，2008，9:2032-2042.
［3］王晓铄，俞英.表观遗传对炎症的调控机制及其在奶牛乳房炎抗病育种中的应用前景［J］.遗传，2010，32(7):663-669.
WANG X S，YU Y.Regulation mechanisms of epigenetics on inflammation and its perspective on breeding for mastitis resistance in dairy cattle［J］.Hereditas(Beijing)，2010，32(7):663-669.（in Chinese）
［4］MIR A，KAUFMAN L，NOOR A，et al.Identification of mutations in TRAPPC9，which encodes the NIK- and IKK-beta-binding protein，in nonsyndromic autosomal-recessive mental retardation ［J］. Am J Hum Genet，2009，85(6)：909-915.
［5］PHILIPPE O，RIO M，CARIOUX A，et al.Combination of linkage mapping and microarray-expression analysis identifies NF-kappaB signaling defect as a cause of autosomal-recessive mental retardation ［J］. Am J Hum Genet, 2009，85(6):903-908.
［6］JIANG L，LIU J，SUN D，et al.Genome wide association studies for milk production traits in Chinese Holstein population ［J］.PLoS ONE，2010，5(10):e13661.
［7］齐超，谢岩，吴晓平，等.基于全基因组信息鉴定中国荷斯坦牛产奶性状基因及功能注释［J］.畜牧兽医学报，2012，43(6):872-877.
QI C，XIE Y，WU X P,et al.Identification and annotation of genes affecting milk production traits in Chinese Holstein based on GWAS［J］.Acta Veterinaria et Zootechnica Sinica，2012，43(6):872-877.（in Chinese）
［8］王晓，解小莉，王胜 ,等.中国荷斯坦牛乳房炎易感性及抗性的全基因组关联分析［J］.畜牧兽医学报，2013,44(12):1907-1912.
WANG X，XIE X L，WANG S，et al.Genome-wide association study for mastitis susceptibility and resistance in Chinese Holsteins［J］.Acta Veterinaria et Zootechnica Sinica，2013,44(12):1907-1912.（in Chinese）
［9］KLEIN R J，ZEISS C，CHEW E Y，et al.Complement factor H polymorphism in age-related macular degeneration ［J］.Science，2005，308(5720)：385-389.
［10］KIM A，BHAK J.Post-GWAS strategies ［J］.Genom Informat，2011，9(1):1-4.
［11］BASTIAANSEN J W M，BOVENHUIS H，WIJGA S，et al.Genome-wide association study for milk production and fat to protein ratio in dairy cattle ［C］.In：Proceedings of the 9th World Congress on Genetics Applied to Livestock Production.Leipzig，Germany，2010：270.
［12］SCHOPEN G C B，VISKER M H P W，KOKS P D，et al.Whole-genome association study for milk protein composition in dairy cattle ［J］.J Dairy Sci，2011，94(6)：3148-3158.
［13］MONTEIRO A N A，COETZEE G A，FREEDMAN M L，et al.Principles for the post-GWAS functional characterization of risk loci ［J］.Nat Prec，2010，doi:10.1038/npre.2010,5162.
［14］FREEDMAN M L，MONTEIRO A N A，GAYTHER S A，et al.Principles for the post-GWAS functional characterization of cancer risk loci ［J］.Nat Genet,2011,10(43):513-518.
［15］MAOUCHE S，SCHUNKERT H.Strategies beyond genome-wide association studies for atherosclerosis［J］.Arter，Throm，Vascular Biol，2012，32(2)：170-181.
［16］董易春.中国荷斯坦牛TRAPPC9基因效应分析及其功能初步验证［D］.北京:中国农业大学，2014.
DONG Y C.Genetic effect analysis and preliminary function confirmation of anti-mastitis related gene TRAPPC9［D］.Beijing:China Agricultural University,2014.（in Chinese）
［17］YU Y，ZHANG H，TIAN F，et al.Quantitative evaluation of DNA methylation patterns for ALVE and TVB genes in a neoplastic disease susceptible and resistant chicken model ［J］.PLoS ONE，2008，3(3):e1731.
［18］YU Y，ZHANG H，TIAN F，et al.An integrated epigenetic and genetic analysis of DNA methyltransferase genes(DNMTs) in tumor resistant and susceptible chicken lines ［J］.PLoS ONE，2008，3(7):e2672.
［19］SMITH T P，GROSSE W M，FREKING B A，et al.Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle ［J］.Genome Res，2001,11(4):626-630.
［20］HARHAY G P，SONSTEGARD T S，KEELE J W，et al.Characterization of 954 bovine full-CDS cDNA sequences ［J］.BMC Genomics，2005，6:166.
［21］董易春，刘超，王晓，等.中国荷斯坦奶牛TRAPPC9基因多态性及其与产奶性状和乳房炎抗性的相关分析［C］.第十七次全国动物遗传育种学术讨论会,2013.
DONG Y C,LIU C,WANG X,et al.Gene polymorphism and relevant analysis with milk production and mastitis resistance of TRAPPC9 in Chinese Holsteins［C］.17th National Symposium on Animal Genetics and Breeding Conference Proceedings,2013.（in Chinese）
［22］HU W H，PENDERGAST J S，MO X M，et al.NIBP，a novel NIK and IKK(beta)-binding protein that enhances NF-(kappa)B activation ［J］.J Biol Chem，2005，280(32):29233-29241.
［23］DAYEH T A，OLSSON A H，VOLKOV P，et al.Identification of CpG-SNPs associated with type 2 diabetes and differential DNA methylation in human pancreatic islets ［J］.Diabetologia，2013，56:1036-1046.
［24］WANG X S，ZHANG Y，HE Y H，et al.Aberrant promoter methylation of the CD4 gene in peripheral blood cells of mastitic dairy cows ［J］.Genet Mol Res：GMR，2013，12(4)：6228-6239.
［25］SENNER C E.The role of DNA methylation in mammalian development ［J］.Reprod Biomed Online，2011，22(6)：529-535.
［26］JONES P A，TAKAI D.The role of DNA methylation in mammalian epigenetics ［J］.Science,2001，293(5532)：1068-1070.
［27］ZAHOOR M A，YAMANE D，MOHAMED Y M，et al.Bovine viral diarrhea virus non-structural protein 5A interacts with NIK- and IKKbeta-binding protein ［J］.J Gen Virol, 2010，91(Pt 8):1939-1948.
［28］ABDUL-HADI A A.Immunological response of bovine mammary cell lines in mastitis and milk hygiene ［J］.Iraqi J Vet Med，2012，36(1):1-13.
［29］BOUTET P，SULON J，CLOSSET R，et al.Prolactin-induced activation of nuclear factor kappaB in bovine mammary epithelial cells：role in chronic mastitis ［J］.J Dairy Sci, 2007，90(1):155-164.
［30］BOULANGER D L，BUREAU F，MéLOTTE D，et al.Increased nuclear factor kappaB activity in milk cells of mastitis-affected cows ［J］. J Dairy Sci，2003，86(4):1259-1267.

Confirming the Genetic Effects of Bovine TRAPPC9 on Milk Production Traits Based on Post-GWAS Strategies

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