猪重要性状全基因组关联分析的研究进展

doi:10.11843/j.issn.0366-6964.2015.06.001

摘要/Abstract

摘要：

全基因组关联分析（Genome-wide association study，GWAS）是在关联分析的基础上对全基因组范围内的遗传标记进行检测，以研究复杂疾病和性状遗传的一种有效方法。国内外许多研究人员针对猪重要性状展开GWAS，鉴定出大量单核苷酸多态性(Single nucleotide polymorphism，SNP)标记、数量性状基因座(Quantitative trait locus，QTL)和候选基因为猪育种提供必要的分子基础，同时有助于后续相关功能基因的研究和数量性状核苷酸(Quantitative trait nucleotide，QTN)的鉴定。本文主要对GWAS在猪重要性状上的研究进展进行综述，同时简单介绍猪重要性状QTN的研究进展。

Abstract:

Genome-wide association study (GWAS) is an effective method to detect complex diseases and traits genetics by the genetic markers in the range of the genome，based on association study.To find new SNPs，QTLs and candidate genes，researchers employ GWAS to study main traits in pigs.It is important to research on molecular genetics of pig breeding and study on related functional genes and QTNs.This review will provide reference for research progress of GWAS about important traits in pig.Furthermore，the paper introduces the research progress of QTN briefly.

中图分类号:

S813.1
S828

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.

ZHAO Qian，PU Ya-bin，GUAN Wei-jun，ZHAO Qian-jun，MA Yue-hui. Research Progress of Genome-wide Association Studies for Important Traits in Pig[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2015, 46(6): 873-881.

0
/ / 推荐

导出引用管理器 EndNote|Reference Manager|ProCite|BibTeX|RefWorks

链接本文: https://www.xmsyxb.com/CN/10.11843/j.issn.0366-6964.2015.06.001

https://www.xmsyxb.com/CN/Y2015/V46/I6/873

参考文献

［1］RISCH N，MERIKANGAS K.The future of genetic studies of complex human diseases［J］.Science，1996，273(5281)：1516-1517.
［2］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.
［3］WERNERSSON R，SCHIERUP M H，JØRGENSEN F G，et al.Pigs in sequence space：a 0.66X coverage pig genome survey based on shotgun sequencing［J］. BMC Genomics，2005，6：70.
［4］GROENEN M A，ARCHIBALD A L，UENISHI H，et al.Analyses of pig genomes provide insight into porcine demography and evolution［J］.Nature，2012，491(7424)：393-398.
［5］HIRSCHHORN J N，DALY M J.Genome-wide association studies for common diseases and complex traits［J］.Nat Rev Genet，2005，6(2)：95-108.
［6］严卫丽.复杂疾病全基因组关联研究进展—遗传统计分析［J］.遗传，2008，30(5)：543-549.
YAN W L.Genome-wide association study on complex diseases：genetic statistical issues［J］.Hereditas，2008，30(5)：543-549.(in Chinese)
［7］DO D N，STRATHE A B，OSTERSEN T，et al.Genome-wide association study reveals genetic architecture of eating behavior in pigs and its implications for humans obesity by comparative mapping［J］.PLoS ONE，2013，8(8)：e71509.
［8］DO D N，OSTERSEN T，STRATHE A B，et al.Genome-wide association and systems genetic analyses of residual feed intake，daily feed consumption，backfat and weight gain in pigs［J］.BMC Genet，2014，15(1)：27.
［9］DO D N，STRATHE A B，OSTERSEN T，et al.Genome-wide association and pathway analysis of feed efficiency in pigs reveal candidate genes and pathways for residual feed intake［J］.Front Genet，2014，5：307.
［10］ONTERU S K，GORBACH D M，YOUNG J M，et al.Whole genome association studies of residual feed intake and related traits in the pig［J］.PLoS ONE，2013，8(6)：e61756.
［11］CAI W，CASEY D S，DEKKERS J C M，et al.Selection response and genetic parameters for residual feed intake in Yorkshire swine［J］.J Anim Sci，2008，86（2）：287-298.
［12］YOUNG J M，CAI W，DEKKERS J C M，et al.Effect of selection for residual feed intake on feeding behavior and daily feed intake patterns in Yorkshire swine［J］.J Anim Sci，2011，89（3）：639-647.
［13］JUNG E J，PARK H B，LEE J B，et al.Genome-wide association analysis identifies quantitative trait loci for growth in a Landrace purebred population［J］.Anim Genet，2014，45(3)：442-444.
［14］DUIJVESTEIJN N，KNOL E F，MERKS J W M，et al.A genome-wide association study on androstenone levels in pigs reveals a cluster of candidate genes on chromosome 6［J］.BMC Genet，2010，11(1)：42.
［15］ROWE S J，KARACAÖREN B，KONINGD D，et al.Analysis of the genetics of boar taint reveals both single SNPs and regional effects［J］.BMC Genomics，2014，15：424.
［16］GRINDFLEK E，LIEN S，HAMLAND H，et al.Large scale genome-wide association and LDLA mapping study identifies QTLs for boar taint and related sex steroids［J］.BMC Genomics，2011，12：362.
［17］MA J，YANG J，ZHOU L，et al.Genome-wide association study of meat quality traits in a White Duroc× Erhualian F2 intercross and Chinese Sutai pigs［J］.PLoS ONE，2013，8(5)：e64047.
［18］YANG B，ZHANG W，ZHANG Z，et al.Genome-wide association analyses for fatty acid composition in porcine muscle and abdominal fat tissues［J］.PLoS ONE，2013，8(6)：e65554.
［19］LUO W，CHENG D，CHEN S，et al.Genome-wide association analysis of meat quality traits in a porcine Large White × Minzhu intercross population［J］.Int J Biol Sci，2012，8(4)：580-595.
［20］AMIN N，DUIJN C M，AULCHENKO Y S，et al.A genomic background based method for association analysis in related individuals［J］.PLoS ONE，2007，2(12)：e1274.
［21］LEE T，SHIN D，CHO S，et al.Genome-wide association study of integrated meat quality-related traits of the Duroc pig breed［J］.Asian-Austra J Anim Sci，2014，27(3) ：303-309
［22］PONSUKSILI S，MURANI E，TRAKOOLJUL N，et al.Discovery of candidate genes for muscle traits based on GWAS supported by eQTL-analysis［J］.Int J Biol Sci，2014，10(3)：327-337.
［23］WANG J Y，LUO Y R，FU W X，et al.Genome-wide association studies for hematological traits in swine［J］.Anim Genet，2013，44(1)：34-43.
［24］LU X，FU W X，LUO Y R，et al.Genome-wide association study for T lymphocyte subpopulations in swine［J］.BMC Genomics，2012，13(1)：488.
［25］LU X，LIU J F，FU W X，et al.Genome-wide association study for Cytokines and immunoglobulin G in swine［J］.PLoS ONE，2013，8(10)：e74846.
［26］JUNG E J，PARKH B，LEE J B，et al.Genome-wide association study identifies quantitative trait loci affecting hematological traits in an F2 intercross between Landrace and Korean native pigs［J］.Anim Genet，2014，45(4)：534-541.
［27］FURLOTTE N A，ESKIN E，EYHERAMENDY S.Genome-wide association mapping with longitudinal data［J］.Genet Epidemiol，2012，36（5）：463-471.
［28］ZHANG Z，HONG Y，GAO J，et al.Genome-wide association study reveals constant and specific loci for hematological traits at three time stages in a White Duroc× Erhualian F₂ resource population［J］.PLoS ONE，2013，8(5)：e63665.
［29］CHEN C，YANG B，ZENG Z，et al.Genetic dissection of blood lipid traits by integrating genome-wide association study and gene expression profiling in a porcine model［J］.BMC Genomics，2013，14(1)：848.
［30］ZHANG F，ZHANG Z Y，YANX M，et al.Genome-wide association studies for hematological traits in Chinese Sutai pigs［J］.BMC Genet，2014，15：41.
［31］LUO W，CHEN S，CHENG D，et al.Genome-wide association study of porcine hematological parameters in a large White×Minzhu F2 resource population［J］.Int J Biol Sci，2012，8(6)：870-881.
［32］MANUNZA A，CASELLAS J，QUINTANILLA R，et al.A genome-wide association analysis for porcine serum lipid traits reveals the existence of age-specific genetic determinants［J］.BMC Genomics，2014，15：758.
［33］PREISSLER R，TETENS J，REINERS K，et al.A genome-wide association study to detect genetic variation for postpartum dysgalactia syndrome in five commercial pig breeding lines［J］.Anim Genet，2013，44(5)：502-508.
［34］RANGKASENEE N，MURANI E，BRUNNER R M，et al.Genome-wide association identifies TBX5 as candidate gene for osteochondrosis providing a functional link to cartilage perfusion as initial factor［J］.Front Genet，2013，4：78.
［35］ROUSSEAU S，IANNUCCELLI N，MERCAT M，et al.A genome-wide Association study points out the causal implication of SOX9 in the sex-reversal phenotype in XX pigs［J］.PLoS ONE，2013，8(11)：e79882.
［36］FU W X，LIU Y，LU X，et al.A genome-wide association study identifies two novel promising candidate genes affecting escherichia coli F4ab/F4ac susceptibility in swine［J］.PLoS ONE，2012，7(3)：e32127.
［37］THORNTON T，MCPEEK M S.ROADTRIPS：case-control association testing with partially or completely unknown population and pedigree structure［J］.Am J Hum Genet，2010，86(2)：172-184.
［38］KOGELMANL J，PANT S D，FREDHOL M M，et al.Systems genetics of obesity in an F2 pig model by genome-wide association，genetic network，and pathway analyses［J］.Front Genet，2014，5：214.
［39］ONTERU S K，FAN B，NIKKILA M T，et al.Whole-genome association analyses for lifetime reproductive traits in the pig［J］.J Anim Sci，2011，89(4)：988-995.
［40］ONTERU S K，FAN B，DU Z Q，et al.A whole-genome association study for pig reproductive traits［J］.Anim Genet，2012，43(1)：18-26.
［41］SCHNEIDER J F，REMPEL L A，SNELLING W M，et al.Genome-wide association study of swine farrowing traits.Part II：Bayesian analysis of marker data［J］.J Anim Sci，2012，90(10)：3360-3367.
［42］LOPES M S，BASTIAANSEN J，HARLIZIUS B，et al.A genome-wide association study reveals dominance effects on number of teats in pigs［J］.PLoS ONE，2014，9(8)：e105867.
［43］WANG L G，ZHANG L C，YAN H，et al.Genome-wide association studies identify the loci for 5 exterior traits in a Large White×Minzhu pig population［J］.PLoS ONE，2014，9(8)：e103766.
［44］REN J，MAO H，ZHANG Z，et al.A 6-bp deletion in the TYRP1 gene causes the brown colouration phenotype in Chinese indigenous pigs［J］.Heredity，2011，106(5)：862-868.
［45］CHO I C，ZHONG T，SEO B Y，et al.Whole-genome association study for the roan coat color in an intercrossed pig population between Landrace and Korean native pig［J］.Genes Genom，2011，33(1)：17-23.
［46］FONTANESI L，SCHIAVO G，GALIMBERTI G，et al.A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes［J］.BMC Genomics，2012，13：583.
［47］FAN B，ONTERU S K，DU Z Q，et al.Genome-wide association study identifies loci for body composition and structural soundness traits in pigs［J］.PLoS ONE，2011，6(2)：e14726.
［48］OKUMURA N，MATSUMOTO T，HAYASHI T，et al.Genomic regions affecting backfat thickness and cannon bone circumference identified by genome-wide association study in a Duroc pig population［J］.Anim Genet，2013，44(4)：454-457.
［49］张哲，贺金龙，邓熙，等.杜洛克猪生长性状全基因组关联分析［J］.广东农业科学，2014，14：139-143.
ZHANG Z，HE J L，DENG X，et al.Genome-wide association study for production traits in Duroc pig herd［J］.Guangdong Agricultural Sciences，2014，14：139-143.(in Chinese)
［50］BECKER D，WIMMERS K，LUTHER H，et al.A genome-wide association study to detect QTL for commercially important traits in Swiss Large White boars［J］.PLoS ONE，2013，8(2)：e55951.
［51］SANCHEZ M P，TRIBOUT T，IANNUCCELLI N，et al.A genome-wide association study of production traits in a commercial population of Large White pigs：evidence of haplotypes affecting meat quality［J］.Genet Sel Evol，2014，46(1)：12.
［52］FUJII J，OTSU K，ZORZATO F et al.Identification of a mutation in porcine ryanodine receptor associated with malignant hyperthermia［J］.Science，1991，253(5018)：448-451.
［53］VANLAERE A S，NGUYEN M，BRAUNSCHWEIG M，et al.A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig［J］.Nature，2003，425(6960)：832-836.
［54］KIM K S，LARSEN N，SHORT T，et al.A missense variant of the porcine melanocortin-4 receptor (MC4R) gene is associated with fatness，growth，and feed intake traits［J］.Mamm Genome，2000，11(2)：131-135.
［55］STRATZ P，WELLMAN N R，PREUS S S，et al.Genome-wide association analysis for growth，muscularity and meat quality in Pietrain pigs［J］.Anim Genet，2014，45(3)：350-356.
［56］MA J，YANG J，ZHOU L，et al.A splice mutation in the PHKG1 gene causes high glycogen content and low meat quality in pig skeletal muscle［J］.PLoS Genet，2014，10(10)：e1004710.
［57］REN J，DUAN Y，QIAO R，et al.A missense mutation in PPARD causes a major QTL effect on ear size in pigs［J］.PLoS Genet，2011，7(5)：e1002043.
［58］REN Z Q，WU W J，LIU W H，et al.Differential expression and effect of the porcine ANGPTL4 gene on intramuscular fat［J］.Genet Mol Res，2014，13(2)：2949-2958.
［59］LIU Z，SUN W，ZHAO Y，et al.The effect of variants in the promoter of BMPER on the intramuscular fat deposition in Longissimus dorsi muscle of pigs［J］.Gene，2014，542(2)：168-172.
［60］XU R X，WEI N，WANG Y，et al.Association of novel polymorphisms in lymphoid enhancer binding factor 1 (LEF-1) gene with number of teats in different breeds of pig［J］.Asian-Austra J Anim Sci，2014，27(9)：1254-1262.
［61］潘东东，李正帮，张维，等.全基因组关联研究综述［J］.应用概率统计，2014，30(1)：84-103.
PAN D D，LI Z B，ZHANG W，et al.The review of genome-wide association studies［J］.Chinese Journal of Applied Probability and Statistics，2014，30(1)：84-103.(in Chinese)
［62］王继英，王海霞，迟瑞宾，等.全基因组关联分析在畜禽中的研究进展［J］.中国农业科学，2013，46(4)：819-829.
WANG J Y，WANG H X，CHI R B，et al.Progresses in research of genome-wide association studies in livestock and poultry［J］.Scientia Agricultura Sinica，2013，46(4)：819-829.(in Chinese)
［63］NICODEMUS K K，LIU W，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.
［64］凃欣，石立松，汪樊，等.全基因组关联分析的进展与反思［J］.生理科学进展，2010，41(2)：87-94．
TU X，SHI L S，WANG F，et al.Genome-wide association study：advances，challenges and deliberation ［J］.Progress in Physiological Sciences，2010，41(2)：87-94.(in Chinese)
［65］权晟，张学军.全基因组关联研究的深度分析策略［J］.遗传，2011，33(2) ：100-108．
QUAN C，ZHANG X J.Research strategies for the next step of genome-wide association study［J］.Hereditas，2011，33(2)：100-108.(in Chinese)
本刊相关报道（以下文章由本刊网站www.xmsyxb.com可以免费下载查阅）：
1.兰蓉，朱兰，姚新荣，等.山羊产羔数全基因组关联分析［J］.畜牧兽医学报，2015,46(4):549-554.
LAN R，ZHU L，YAO X R，et al.Genome-wide association study of lambing number in goat［J］.Acta Veterinaria et Zootechnica Sinica，2015，46(4):549-554.
2.刘澳星，郭刚，王雅春，等.中国荷斯坦牛初产日龄遗传评估及全基因组关联分析［J］.畜牧兽医学报，2015,46(3):373-381.
LIU A X， GUO G， WANG Y C， et al.Genetic analysis and genome wide association studies for age at first calving in Chinese Holsteins［J］.Acta Veterinaria et Zootechnica Sinica，2015，46(3):373-381.
3.樊庆灿，王金玉，张跟喜，等.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 Q C，WANG J Y，ZHANG G X，et al.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.
4. 朱波,吴洋，齐欣，等.利用混合线性模型和BayesCPi进行QTL-MAS2011公共数据集的全基因组关联分析［J］.畜牧兽医学报，2014,45(5):692-698.
ZHU B，WU Y,QI X，et al.Genome-wide association analysis of the 15th QTL-MAS workshop data using mixed linear model and BayesCPi method［J］.Acta Veterinaria et Zootechnica Sinica，2014, 45(5):692-698.