不同尾型绵羊全基因组选择信号检测
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摘要
为研究不同尾型绵羊群体遗传分化程度,检测全基因组选择信号,以挖掘不同尾型绵羊重要性状相关的候选基因。本研究基于蒙古羊(短脂尾)和藏羊(瘦尾)群体的Illumina Ovine SNP 50K芯片分型数据,借助遗传分化系数FST法进行群体间选择信号检测,寻找选择信号区域内的重要基因,并对其中与脂肪代谢相关的基因PPARG、PDGFD在呼伦贝尔羊(大尾和小尾品系;肥尾)与藏羊(瘦尾)尾脂进行mRNA相对表达量研究。结果,(1)465个SNPs被选择,基因注释找到448个候选基因,筛选到50个与脂类代谢相关的基因,GO功能富集分析发现,主要富集在脂类生物合成过程、磷脂代谢、脂质结合等条目,此外发现4个基因(PPARG、RXRG、SLC27A2和ACSL6)富集到PPAR信号通路。(2)肥瘦尾之间,呼伦贝尔羊(大尾和小尾品系)PPARG和PDGFD基因表达量均显著高于藏羊(P<0.01),而大小肥尾之间,呼伦贝尔羊大尾品系PPARG基因表达量显著高于小尾品系(P<0.05),PDGFD基因表达量则无明显差异。通过FST法有效检测到受选择的基因,部分与绵羊重要性状相关,相对定量试验证明PPARG和PDGFD基因与尾部脂肪沉积密切相关,可以作为尾型选育的候选基因,为绵羊育种及改良提供重要参考。
This experiment was conducted to study genetic differentiation between 2sheep populations with distinct tail types by genome-wide detection of selection signatures and to search the candidate genes related to important traits of sheep.Based on the Illumina Ovine SNP 50 KBreadchip genotyping data of Mongolian sheep and Tibetan sheep,population differentiation index FST was adopted to detect the selection signatures,and to found the genes located in selection signature regions.Based on the tail adipose tissue of Hulun Buir sheep(fat-tailed sheep,include large fat-tailed sheep and small fat-tailed sheep)and Tibetan sheep(thin-tailed sheep),the relative expression study was adopted to explore the difference of gene relative expression level of PPARG and PDGFD,which were related to fat metabolism.This result showed that:(1)465selected SNPs were found,448 candidate genes were detected by gene annotation.And 50 genes related to lipid metabolism were selected from these candidate genes,the analysis of GO showed that these genes were related to lipid biosynthetic process,phospholipid metabolic process and lipid binding.In addition,4genes were found,PPARG,RXRG,SLC27A2 and ACSL6,and enriched into the PPAR signaling pathway.(2)The gene relative expression levels of PPARGand PDGFDfrom Hulun Buir sheep was significantly higher than that of Tibetan sheep(P<0.01),between fattailed and thin-tailed sheep,the gene relative expression level of PPARGfrom lager fat-tailed Hulun Buir sheep was significantly higher than that of small fat-tailed Hulun Buir sheep(P<0.05),but the gene relative expression level of PDGFD had no significant difference between lager fattailed and small fat-tailed Hulun Buir sheep.FST could be used to detect the genes with selection signatures and some of the candidate genes were related to important traits in sheep.PPARGand PDGFDgenes were proved to be closely related to tail fat deposition through the relative expression studies,these genes could be used as candidate genes for different tailed sheep breeding.This study can provide theoretical references for sheep breeding or breed improvement.
This experiment was conducted to study genetic differentiation between 2sheep populations with distinct tail types by genome-wide detection of selection signatures and to search the candidate genes related to important traits of sheep.Based on the Illumina Ovine SNP 50 KBreadchip genotyping data of Mongolian sheep and Tibetan sheep,population differentiation index FST was adopted to detect the selection signatures,and to found the genes located in selection signature regions.Based on the tail adipose tissue of Hulun Buir sheep(fat-tailed sheep,include large fat-tailed sheep and small fat-tailed sheep)and Tibetan sheep(thin-tailed sheep),the relative expression study was adopted to explore the difference of gene relative expression level of PPARG and PDGFD,which were related to fat metabolism.This result showed that:(1)465selected SNPs were found,448 candidate genes were detected by gene annotation.And 50 genes related to lipid metabolism were selected from these candidate genes,the analysis of GO showed that these genes were related to lipid biosynthetic process,phospholipid metabolic process and lipid binding.In addition,4genes were found,PPARG,RXRG,SLC27A2 and ACSL6,and enriched into the PPAR signaling pathway.(2)The gene relative expression levels of PPARGand PDGFDfrom Hulun Buir sheep was significantly higher than that of Tibetan sheep(P<0.01),between fattailed and thin-tailed sheep,the gene relative expression level of PPARGfrom lager fat-tailed Hulun Buir sheep was significantly higher than that of small fat-tailed Hulun Buir sheep(P<0.05),but the gene relative expression level of PDGFD had no significant difference between lager fattailed and small fat-tailed Hulun Buir sheep.FST could be used to detect the genes with selection signatures and some of the candidate genes were related to important traits in sheep.PPARGand PDGFDgenes were proved to be closely related to tail fat deposition through the relative expression studies,these genes could be used as candidate genes for different tailed sheep breeding.This study can provide theoretical references for sheep breeding or breed improvement.
引文
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[2]国家畜禽遗传资源委员会.中国畜禽遗传资源志·羊志[M].北京:中国农业出版社,2011.China National Commission of Animal Genetic Resources.Animal Genetic Resources in China.Sheep and Goat[M].Beijing:Chinese Agricultural Press,2011.(in Chinese)
[3]MEGENS H J,CROOIJMANS R P,SAN CRISTOBAL M,et al.Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples:differences in microsatellite variation between two areas of domestication[J].GSE,2008,40(1):103-128.
[4]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):33-42.MA Y L,ZHANG Q,DING X D,et al.Detecting selection signatures on X chromosome in pig through high density SNPs[J].Hereditas,2012,34(10):33-42.(in Chinese)
[5]许忠能.生物信息学[M].北京:清华大学出版社,2008.XU Z N.Bioinformatics[M].Beijing:Tsinghua University Press,2008.(in Chinese)
[6]THORNTON K R,JENSEN J D.Controlling the false-positive rate in multilocus genome scans for selection[J].Genetics,2007,175(2):737-750.
[7]AKEY J M,ZHANG G,ZHANG K,et al.Interrogating a high-density SNP map for signatures of natural selection[J].Genome Res,2002,12(12):1805-1814.
[8]AMARAL A J,FERRETTI L,MEGENS H J,et al.Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA[J].PLoS ONE,2011,6(4):e14782.
[9]FLORI L,FRITZ S,JAFFREZIC F,et al.The genome response to artificial selection:a case study in dairy cattle[J].PLoS ONE,2009,4(8):e6595.
[10]GU J,ORR N,PARK S D,et al.A genome scan for positive selection in thoroughbred horses[J].PLoS ONE,2009,4(6):e5767.
[11]KARLSSON E K,BARANOWSKA I,WADE C M,et al.Efficient mapping of mendelian traits in dogs through genome-wide association[J].Nat Genet,2007,39(11):1321-1328.
[12]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.
[13]PARISET L,JOOST S,MARSAN P A,et al.Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean[J].BMC Genet,2009,10:7.
[14]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.
[15]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)
[16]WEIR B S,HILL W G.Estimating F-statistics[J].Ann Rev Genet,2002,36:721-750.
[17]HUA X,WU J,GOLDSTEIN J L,et al.Structure of the human gene encoding sterol regulatory element binding protein-1(SREBF1)and localization of SREBF1and SREBF2to chromosomes 17p11.2and22q13[J].Genomics,1995,25(3):667-673.
[18]TONTONOZ P,HU E,SPIEGELMAN B M.Stimulation of adipogenesis in fibroblasts by PPAR gamma2,a lipid-activated transcription factor[J].Cell,1994,79(7):1147-1156.
[19]TONTONOZ P,KIM J,GRAVES R,et al.ADD1:a novel helix-loop-helix transcription factor associated with adipocyte determination and differentiation[J].Mol Cell Biol,1993,13(8):4753-4759.
[20]ARTEMENKO Y,GAGNON A,AUBIN D,et al.Anti-adipogenic effect of PDGFis reversed by PKC inhibition[J].J Cell Physiol,2005,204(2):646-653.
[21]HOLMSTRM T E,MATTSSON C L,FLTING J M,et al.Differential signalling pathways for EGF versus PDGF activation of Erk1/2 MAP kinase and cell proliferation in brown pre-adipocytes[J].Exp Cell Res,2008,314(19):3581-3592.
[22]LAROCHELLE W J,JEFFERS M,MCDONALD W F,et al.PDGF-D,a new protease-activated growth factor[J].Nat Cell Biol,2001,3(5):517-521.
[23]LEWONTIN R C,KRAKAUER J.Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms[J].Genetics(Print),1973,74(1):175-195.
[24]CAVALLI-SFORZA L L.Population structure and human evolution[J].Proc Royal Soc London.Series B:Biol Sci,1966,164:362-379.
[25]李秀领,杨松柏,唐中林,等.大白猪和通城猪全基因组选择性清扫分析[J].遗传,2012,34(10):53-63.LI X L,YANG S B,TANG Z L,et al.Genome-wide selective sweep analysis on Large White and Tongcheng pigs[J].Hereditas,2012,34(10):53-63.(in Chinese)
[26]刘喜冬,王志鹏,樊惠中,等.基于高密度SNP标记的肉牛人工选择痕迹筛查[J].遗传,2012,34(10):86-95.LIU X D,WANG Z P,FAN H Z,et al.Artificial selection for cattle based on high-density SNP markers[J].Hereditas,2012,34(10):86-95.(in Chinese)
[27]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.Genomewide 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)
[28]ZHANG M,SU Y Q,SUGIURA K,et al.Estradiol promotes and maintains cumulus cell expression of natriuretic peptide receptor 2(NPR2)and meiotic arrest in mouse oocytes in vitro[J].Endocrinology,2011,152(11):4377-4385.
[29]DOYLE L A,YANG W,ABRUZZO L V,et al.A multidrug resistance transporter from human MCF-7breast cancer cells[J].Proc Natl Acad Scie USA,1998,95(26):15665-15670.
[30]OLSEN H G,NILSEN H,HAYES B,et al.Genetic support for a quantitative trait nucleotide in the ABCG2gene affecting milk composition of dairy cattle[J].BMC Genet,2007,8:32.
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