利用可变窗口F_(ST)方法检测不同尾型呼伦贝尔羊尾部脂肪沉积相关基因
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摘要
旨在挖掘控制绵羊尾型的候选基因,揭示绵羊尾部脂肪沉积机理。本研究利用呼伦贝尔羊两个不同尾型品系的288个个体,其中大尾羊142只和小尾羊146只,基于Illumina Ovine SNP 600KSNP芯片数据计算全基因组单点F_(ST)值。通过三次光滑样条估计方法确定可变窗口大小和数量,构建W统计量并进行统计检验,鉴定选择区段和注释相关基因。结果,在基因组范围内共确定了23 144个可变窗口,其中区间最大的窗口位于chr12:35 241 750~43 798 950bp处,其大小为8.56 Mb,并包含775个SNPs。经检测发现,27个窗口达到极显著水平(P<0.001),并鉴定了337个候选基因,其中22个是与已发现的脂肪代谢相关的基因。通过GO分析发现,这些候选基因主要富集在细胞内组成成分、有机氮化合物代谢过程以及小分子代谢过程等条目。通过可变窗口F_(ST)法能够有效检测到受选择的基因与绵羊尾部脂肪沉积相关。这些基因可以作为绵羊尾型选育的候选基因,为培育短尾绵羊提供重要依据。
The aims of this study were to reveal the genetic mechanism of fat deposition in the tail of sheep,and to explore the candidate genes involved in sheep tail fat.A total of 288 individuals from two lines of Hulun Buir sheep with different tail types were used to identify candidate genes controlling different tail types of sheep.These individuals included 142 fat-tailed and 146 thintailed sheep.The whole-genome single locus F_(ST) values were calculated based on the Illumina Ovine 600 KSNP genotype data.The cubic smoothing spline method was used to define the numbers and sizes of variable windows.A total of 23 144 variable windows were identified within the whole genome.The largest window with 775 SNPs was located at chr12:35 241 750-43 798 950 bp,with a size of 8.56 Mb.The W statistic was constructed to detect the windows with selection signature.Twenty-seven of variable windows reached extremely significant level(P<0.001).After annotation,these windows harbored 337 candidate genes,of which 22 were related to thefat metabolism.Through GO analysis,these candidate genes were mainly enriched in the intracellular components,organonitrogen compound metabolic process and small molecule metabolic process.The F_(ST) method with variable windows was used to effectively identify candidate genes associated with fat deposition in the tail of sheep.These genes can be used to breed a new sheep breed with small size.The results will provide an important reference for breeding short-tailed sheep.
The aims of this study were to reveal the genetic mechanism of fat deposition in the tail of sheep,and to explore the candidate genes involved in sheep tail fat.A total of 288 individuals from two lines of Hulun Buir sheep with different tail types were used to identify candidate genes controlling different tail types of sheep.These individuals included 142 fat-tailed and 146 thintailed sheep.The whole-genome single locus F_(ST) values were calculated based on the Illumina Ovine 600 KSNP genotype data.The cubic smoothing spline method was used to define the numbers and sizes of variable windows.A total of 23 144 variable windows were identified within the whole genome.The largest window with 775 SNPs was located at chr12:35 241 750-43 798 950 bp,with a size of 8.56 Mb.The W statistic was constructed to detect the windows with selection signature.Twenty-seven of variable windows reached extremely significant level(P<0.001).After annotation,these windows harbored 337 candidate genes,of which 22 were related to thefat metabolism.Through GO analysis,these candidate genes were mainly enriched in the intracellular components,organonitrogen compound metabolic process and small molecule metabolic process.The F_(ST) method with variable windows was used to effectively identify candidate genes associated with fat deposition in the tail of sheep.These genes can be used to breed a new sheep breed with small size.The results will provide an important reference for breeding short-tailed sheep.
引文
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[2]甘尚权,张伟,宋天增,等.X染色体一处新发现的SNP位点在脂尾(臀)、瘦尾绵羊群体中的多态检测及分析[J].西南农业学报,2013,26(5):2066-2070.GAN S Q,ZHANG W,SONG T Z,et al.Polymorphism detection and analysis of novel SNP on X chromosome between fat-tailed and thin-tailed sheep breeds[J].Southwest China Journal of Agricultural Sciences,2013,26(5):2066-2070.(in Chinese)
[3]刘真,王慧华,刘瑞凿,等.不同尾型绵羊全基因组选择信号检测[J].畜牧兽医学报,2015,46(10):1721-1732.LIU Z,WANG H H,LIU R Z,et al.Genome-wide detection of selection signatures of distinct tail types in sheep populations[J].Acta Veterinaria et Zootechnica Sinica,2015,46(10):1721-1732.(in Chinese)
[4]甘尚权,张伟,沈敏,等.绵羊X染色体59383635位点多态性与脂尾性状的相关性分析[J].遗传,2013,35(10):1209-1216.GAN S Q,ZHANG W,SHEN M,et al.Correlation analysis between polymorphism of the 59383635th locus on X chromosome and fat-tail trait in sheep[J].Hereditas,2013,35(10):1209-1216.(in Chinese)
[5]马云龙,张勤,丁向东.利用高密度SNP检测不同猪品种间X染色体选择信号[J].遗传,2012,34(10):1251-1260.MA Y L,ZHANG Q,DING X D.Detecting selection signatures on X chromosome in pig through high density SNPs[J].Hereditas,2012,34(10):1251-1260.(in Chinese)
[6]NIELSEN R.Molecular signatures of natural selection[J].Annu Rev Genet,2005,39:197-218.
[7]HOLSINGER K E,WEIR B S.Genetics in geographically structured populations:defining,estimating and interpreting FST[J].Nat Rev Genet,2009,10(9):639-650.
[8]曾滔,赵福平,王光凯,等.基于群体分化指数FST的绵羊全基因组选择信号检测[J].畜牧兽医学报,2013,44(12):1891-1899.ZENG T,ZHAO F P,WANG G K,et al.Genome-wide detection of selection signatures in sheep populations with use of population differentiation index FST[J].Acta Veterinaria et Zootechnica Sinica,2013,44(12):1891-1899.(in Chinese)
[9]KIJAS J W,LENSTRA J A,HAYES B,et al.Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection[J].PLoS Biol,2012,10(2):e1001258.
[10]GORKHALI N A,DONG K Z,YANG M,et al.Genomic analysis identified a potential novel molecular mechanism for high-altitude adaptation in sheep at the Himalayas[J].Sci Rep,2016,6:29963.
[11]YUAN Z H,LIU E,LIU Z,et al.Selection signature analysis reveals genes associated with tail type in Chinese indigenous sheep[J].Anim Genet,2017,48(1):55-66.
[12]MOIOLI B,PILLA F,CIANI E.Signatures of selection identify loci associated with fat tail in sheep[J].J Anim Sci,2015,93(10):4660-4669.
[13]MORADI M H,NEJATI-JAVAREMI A,MORADISHAHRBABAK M,et al.Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition[J].BMC Genet,2012,13:10.
[14]任鑫亮,高雅英.呼伦贝尔羊的特性及饲养管理措施[J].畜牧与饲料科学,2012,33(3):122-123.REN X L,GAO Y Y.Characteristics of Hulun Buir Sheep and breeding management measures[J].Animal Husbandry and Feed Science,2012,33(3):122-123.(in Chinese)
[15]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.
[16]BROWNING B L,BROWNING S R.A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals[J].Am J Hum Genet,2009,84(2):210-223.
[17]WEIR B S,COCKERHAM C C.Estimating F-statistics for the analysis of population structure[J].Evolution,1984,38(6):1358-1370.
[18]BEISSINGER T M,ROSA G J M,KAEPPLER S M,et al.Defining window-boundaries for genomic analyses using smoothing spline techniques[J].Genet Sel Evol,2015,47(1):30.
[19]EDEN E,NAVON R,STEINFELD I,et al.GOrilla:a tool for discovery and visualization of enriched GO terms in ranked gene lists[J].BMC Bioinformatics,2009,10:48.
[20]R CORE TEAM.R:A language and environment for statistical computing[M].Vienna,Austria:the R Foundation,2015,14:12-21.
[21]LI J M,LU C L,CHENG M C,et al.Role of the DLGAP2gene encoding the SAP90/PSD-95-associated protein 2in schizophrenia[J].PLoS One,2014,9(1):e85373.
[22]李宏图,秦秀娟,乌恩巴雅尔,等.呼伦贝尔羊"短尾"品系的外形分析[J].中国草食动物,2006(S1):148-149.LI H T,QIN X J,WUEN B Y E,et al.Analysis of shape of short-tailed Hulun Buir sheep[J].China Herbivores,2006(S1):148-149.(in Chinese)
[23]XU S S,REN X,YANG G L,et al.Genome-wide association analysis identifies the genetic basis of fat deposition in the tails of sheep(Ovis aries)[J].Anim Genet,2017,48(5):560-569.
[24]SABIN M A,YAU S W,RUSSO V C,et al.Dietary monounsaturated fat in early life regulates IGFBP2:implications for fat mass accretion and insulin sensitivity[J].Obesity,2011,19(12):2374-2381.
[25]杨华,徐珍,左波.猪IGFBP2基因多态性及其与胴体、肉质性状的关联分析[J].中国畜牧杂志,2017,53(3):25-28.YANG H,XU Z,ZUO B.Polymorphism of IGFBP2gene and its association with carcass and meat quality traits in pigs[J].Chinese Journal of Animal Science,2017,53(3):25-28.(in Chinese)
[26]GENG T Y,SUTTER A,HARLAND M D,et al.SphK1mediates hepatic inflammation in a mouse model of NASH induced by high saturated fat feeding and initiates proinflammatory signaling in hepatocytes[J].J Lipid Res,2015,56(12):2359-2371.
[27]LIU Z J,GAN L,LIU G N,et al.Sirt1decreased adipose inflammation by interacting with Akt2and inhibiting mTOR/S6K1pathway in mice[J].J Lipid Res,2016,57(8):1373-1381.
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