猪的全基因组测序研究进展
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摘要
猪具有独特的生物学特征,在畜牧业生产和医学研究中占有重要地位。全基因组测序即de novo测序和全基因组重测序为解释猪的生物学特性和促进猪的分子育种发挥了重要作用。本文重点阐述全基因组测序在猪基因组学研究中的应用,分析全基因组测序技术及其在猪的全基因组测序工作中的优势和不足,并对未来猪的分子遗传育种研究工作进行展望。
Pigs have unique biological characteristics and occupy an important position in animal husbandry production and medical research. Whole-genome sequencing, de novo sequencing and whole-genome resequencing has been used in pigs to play an important role in explaining the biological characteristics of pigs and promoting molecular breeding in pigs. This paper focuses on the application of whole genome sequencing in pig genomics research, analyzes the whole genome sequencing technology and its advantages and disadvantages in pig genome sequencing, and prospects the future research work of pig molecular genetic breeding.
Pigs have unique biological characteristics and occupy an important position in animal husbandry production and medical research. Whole-genome sequencing, de novo sequencing and whole-genome resequencing has been used in pigs to play an important role in explaining the biological characteristics of pigs and promoting molecular breeding in pigs. This paper focuses on the application of whole genome sequencing in pig genomics research, analyzes the whole genome sequencing technology and its advantages and disadvantages in pig genome sequencing, and prospects the future research work of pig molecular genetic breeding.
引文
[1]Larson G,Dobney K,Albarella U,et al.Worldwide phylogeography of wild boar reveals multiple centers of pig domestication[J].Science,2005,307(5715):1618-1621.
[2]Ramosonsins S E,Burgospaz W,Manunza A,et al.Mining the pig genome to investigate the domestication process[J].Heredity,2014,113(6):471-484.
[3]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.
[4]Meurens F,Summerfield A,Nauwynck H,et al.The pig:a model for human infectious diseases[J].Trends Microbiol,2012,20(1):50-57.
[5]Sanger F,Nicklen S,Coulson A R.DNA sequencing with chainterminating inhibitors[J].Proc Natl Acad Sci U S A,1977,74(12):5463-5467.
[6]Aksyonov S A,Michael B,Bloom L B,et al.Multiplexed DNAsequencing-by-synthesis[J].Anal Biochem,2006,348(1):127-138.
[7]梁素芸,周正奎,侯水生.基于测序技术的畜禽基因组学研究进展[J].遗传,2017,39(4):276-292.
[8]Yue G D,Gao Q,Luo L H,et al.The application of high-throughput sequencing technology in plant and animal research[J].Scientia Sinica,2012,42(2):107-124.
[9]Fang X D,Mou Y L,Huang Z Y,et al.The sequence and anal-ysis of a Chinese pig genome[J].Gigascience,2012,1(1):16.
[10]Li M Z,Chen L,Tian S L,et al.Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies[J].Genome Res,2017,27(5):865-874.
[11]Stratton M.Genome resequencing and genetic variation[J].Nature Biotechnol,2008,26(1):65-66.
[12]Schuster S C.Next-generation sequencing transforms today’s biology[J].Nature Methods,2008,5(1):16-18.
[13]Li M Z,Tian S L,Carol K L,et al.Whole-genome sequencing of Berkshire(European native pig)provides insights into its origin and domestication[J].Sci Rep,2014,4:4678.
[14]Ai H S,Fang X D,Yang B,et al.Adaptation and possible an-cient interspecies introgression in pigs identified by whole-genome sequencing[J].Nature Genet,2015,47:217.
[15]Fu Y H,Li C C,Tang Q Z.Genomic analysis reveals selection in Chinese native black pig[J].Sci Rep,2016,6:36354.
[16]Molnár J,Nagy T,Stéger V,et al.Genome sequencing and analysis of Mangalica,a fatty local pig of Hungary[J].BMC Genomics,2014,15(1):761.
[17]Bosse M,Megens H J,Frantz L A,et al.Genomic analysis reveals selection for Asian genes in European pigs following humanmediated introgression[J].Nat Commun,2014,5:4392.
[18]Frantz L A,Schraiber J G,Madsen O,et al.Evidence of longterm gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes[J].Nat Genet,201547(10):1141-1148.
[19]龙科任.利用基因组重测序鉴定巴克夏猪的人工选择痕迹[D].成都:四川农业大学,2015.
[20]Choi J W,Chung W H,Lee K T,et al.Whole-genome resequencing analyses of five pig breeds,including Korean wild and native,and three European origin breeds[J].DNA Res,2015,22(4):259-267.
[21]Li M Z,Tian S L,Jin L,et al.Genomic analyses identify dis-tinct patterns of selection in domesticated pigs and Tibetan wild boars[J].Nat Genet,2013,45:1431.
[22]Jensen-Seaman M,Furey T S,Payseur B A,et al.Comparative recombination rates in the rat,mouse,and human genomes[J].Genome Res,2004,14(4):528-538.
[23]Wang J,Zou H Y,Chen L,et al.Convergent and divergent genetic changes in the genome of Chinese and European pigs[J].Sci Rep2017,7(1):8662.
[24]Zhu Y L,Li W B,Yang B,et al.Signatures of selection and interspecies introgression in the genome of chinese domestic pigs[J].Genome Biol Evol,2017,9(10):2592-2603.
[25]Wang Z,Chen Q,Yang Y,et al.Genetic diversity and popul-ation structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data[J].Anim Genet,2015,46(6):697-701.
[26]Fan B,Wang Z G,Li Y J,et al.Genetic variation analysis within and among Chinese indigenous swine populations using microsatellite markers[J].Anim Genet,2002,33(6):422-427.
[27]Yang S L,Wang Z G,Liu B,et al.Genetic variation and relationships of eighteen Chinese indigenous pig breeds[J].Genet Sel Evol,2003,35(6):657-671.
[28]Ai H S,Huang L S,Ren J.Genetic diversity,linkage disequilibrium and selection signatures in chinese and Western pigs revealed by genome-wide SNP markers[J].PLoS One,2013,8(2):e56001.
[29]Herrero-Medrano J M,Megens H J,Groenen M A,et al.Wholegenome sequence analysis reveals differences in population management and selection of European low-input pig breeds[J].BMC Genomics,2014,15:601.
[30]Zhao P J,Li J H,Kang H M,et al.Structural Variant detection by large-scale sequencing reveals new evolutionary evidence on breed divergence between chinese and european pigs[J].Sci Rep,2016,6:18501.
[31]Moon S J,KimT H,Lee K T,et al.A genome-wide scan for signatures of directional selection in domesticated pigs[J].BMCGenomics,2015,16:130.
[32]Kristin D K,Jiang Y,Deanna C T,et al.ATRX partners with cohesin and MeCP2 and contributes to developmental silencing of imprinted genes in the brain[J].Dev Cell,2010,18(2):191-202.
[33]Sia G M,Clem R L,Huganir R L.The human language-associated gene SRPX2 regulates synapse formation and vocalization in mice[J].Science,2013,342(6161):987-991.
[34]Patrick S T,Raffaella S,Erin P,et al.A systematic,large-scale resequencing screen of X-chromosome coding exons in mental retardation[J].Nat Genet,2009,41(5):535-543.
[35]Xiao Q,Zhang Z,Sun H,et al.Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by sequencing data[J].Anim Genet,2017,48(5):596-599.
[36]Rubin C J,Megens H J,Barrio A M,et al.Strong signatures of selection in the domestic pig genome[J].Proc Natl Acad Sci,2012,109(48):19529.
[37]Raspa A.The genetics of the pig[J].Q Rev Biol,2011,36(25):390-425.
[38]Wang J,Zou H Y,Chen L,et al.Convergent and divergent genetic changes in the genome of Chinese and European pigs[J].Sci Rep2017,7(1):8662.
[39]Carol J B,Debra M K,Dale A B,et al.Mouse Tumor Biology(MTB):a database of mouse models for human cancer[J].Nucleic Acids Res,2015,43(Database issue):D818-824.
[40]Xiao L,Florez S,Wang J B,et al.Dact2 represses PITX2transcriptional activation and cell proliferation through Wnt/betacatenin signaling during odontogenesis[J].PLoS One,2013,8(1):e54868.
[41]Andersson L.Melanocortin receptor variants with phenotypic effects in horse,pig,and chicken[J].Ann N Y Acad Sci,2003,994:313-318.
[42]LüM D,Han X M,Ma Y F,et al.Genetic variations associated with six-white-point coat pigmentation in Diannan small-ear pigs[J].Sci Rep,2016,6:27534.
[43]Wang C,Wang H Y,Zhang Y,et al.Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs[J].Mol Ecol Resour,2015,15(2):414-424.
[2]Ramosonsins S E,Burgospaz W,Manunza A,et al.Mining the pig genome to investigate the domestication process[J].Heredity,2014,113(6):471-484.
[3]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.
[4]Meurens F,Summerfield A,Nauwynck H,et al.The pig:a model for human infectious diseases[J].Trends Microbiol,2012,20(1):50-57.
[5]Sanger F,Nicklen S,Coulson A R.DNA sequencing with chainterminating inhibitors[J].Proc Natl Acad Sci U S A,1977,74(12):5463-5467.
[6]Aksyonov S A,Michael B,Bloom L B,et al.Multiplexed DNAsequencing-by-synthesis[J].Anal Biochem,2006,348(1):127-138.
[7]梁素芸,周正奎,侯水生.基于测序技术的畜禽基因组学研究进展[J].遗传,2017,39(4):276-292.
[8]Yue G D,Gao Q,Luo L H,et al.The application of high-throughput sequencing technology in plant and animal research[J].Scientia Sinica,2012,42(2):107-124.
[9]Fang X D,Mou Y L,Huang Z Y,et al.The sequence and anal-ysis of a Chinese pig genome[J].Gigascience,2012,1(1):16.
[10]Li M Z,Chen L,Tian S L,et al.Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies[J].Genome Res,2017,27(5):865-874.
[11]Stratton M.Genome resequencing and genetic variation[J].Nature Biotechnol,2008,26(1):65-66.
[12]Schuster S C.Next-generation sequencing transforms today’s biology[J].Nature Methods,2008,5(1):16-18.
[13]Li M Z,Tian S L,Carol K L,et al.Whole-genome sequencing of Berkshire(European native pig)provides insights into its origin and domestication[J].Sci Rep,2014,4:4678.
[14]Ai H S,Fang X D,Yang B,et al.Adaptation and possible an-cient interspecies introgression in pigs identified by whole-genome sequencing[J].Nature Genet,2015,47:217.
[15]Fu Y H,Li C C,Tang Q Z.Genomic analysis reveals selection in Chinese native black pig[J].Sci Rep,2016,6:36354.
[16]Molnár J,Nagy T,Stéger V,et al.Genome sequencing and analysis of Mangalica,a fatty local pig of Hungary[J].BMC Genomics,2014,15(1):761.
[17]Bosse M,Megens H J,Frantz L A,et al.Genomic analysis reveals selection for Asian genes in European pigs following humanmediated introgression[J].Nat Commun,2014,5:4392.
[18]Frantz L A,Schraiber J G,Madsen O,et al.Evidence of longterm gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes[J].Nat Genet,201547(10):1141-1148.
[19]龙科任.利用基因组重测序鉴定巴克夏猪的人工选择痕迹[D].成都:四川农业大学,2015.
[20]Choi J W,Chung W H,Lee K T,et al.Whole-genome resequencing analyses of five pig breeds,including Korean wild and native,and three European origin breeds[J].DNA Res,2015,22(4):259-267.
[21]Li M Z,Tian S L,Jin L,et al.Genomic analyses identify dis-tinct patterns of selection in domesticated pigs and Tibetan wild boars[J].Nat Genet,2013,45:1431.
[22]Jensen-Seaman M,Furey T S,Payseur B A,et al.Comparative recombination rates in the rat,mouse,and human genomes[J].Genome Res,2004,14(4):528-538.
[23]Wang J,Zou H Y,Chen L,et al.Convergent and divergent genetic changes in the genome of Chinese and European pigs[J].Sci Rep2017,7(1):8662.
[24]Zhu Y L,Li W B,Yang B,et al.Signatures of selection and interspecies introgression in the genome of chinese domestic pigs[J].Genome Biol Evol,2017,9(10):2592-2603.
[25]Wang Z,Chen Q,Yang Y,et al.Genetic diversity and popul-ation structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data[J].Anim Genet,2015,46(6):697-701.
[26]Fan B,Wang Z G,Li Y J,et al.Genetic variation analysis within and among Chinese indigenous swine populations using microsatellite markers[J].Anim Genet,2002,33(6):422-427.
[27]Yang S L,Wang Z G,Liu B,et al.Genetic variation and relationships of eighteen Chinese indigenous pig breeds[J].Genet Sel Evol,2003,35(6):657-671.
[28]Ai H S,Huang L S,Ren J.Genetic diversity,linkage disequilibrium and selection signatures in chinese and Western pigs revealed by genome-wide SNP markers[J].PLoS One,2013,8(2):e56001.
[29]Herrero-Medrano J M,Megens H J,Groenen M A,et al.Wholegenome sequence analysis reveals differences in population management and selection of European low-input pig breeds[J].BMC Genomics,2014,15:601.
[30]Zhao P J,Li J H,Kang H M,et al.Structural Variant detection by large-scale sequencing reveals new evolutionary evidence on breed divergence between chinese and european pigs[J].Sci Rep,2016,6:18501.
[31]Moon S J,KimT H,Lee K T,et al.A genome-wide scan for signatures of directional selection in domesticated pigs[J].BMCGenomics,2015,16:130.
[32]Kristin D K,Jiang Y,Deanna C T,et al.ATRX partners with cohesin and MeCP2 and contributes to developmental silencing of imprinted genes in the brain[J].Dev Cell,2010,18(2):191-202.
[33]Sia G M,Clem R L,Huganir R L.The human language-associated gene SRPX2 regulates synapse formation and vocalization in mice[J].Science,2013,342(6161):987-991.
[34]Patrick S T,Raffaella S,Erin P,et al.A systematic,large-scale resequencing screen of X-chromosome coding exons in mental retardation[J].Nat Genet,2009,41(5):535-543.
[35]Xiao Q,Zhang Z,Sun H,et al.Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by sequencing data[J].Anim Genet,2017,48(5):596-599.
[36]Rubin C J,Megens H J,Barrio A M,et al.Strong signatures of selection in the domestic pig genome[J].Proc Natl Acad Sci,2012,109(48):19529.
[37]Raspa A.The genetics of the pig[J].Q Rev Biol,2011,36(25):390-425.
[38]Wang J,Zou H Y,Chen L,et al.Convergent and divergent genetic changes in the genome of Chinese and European pigs[J].Sci Rep2017,7(1):8662.
[39]Carol J B,Debra M K,Dale A B,et al.Mouse Tumor Biology(MTB):a database of mouse models for human cancer[J].Nucleic Acids Res,2015,43(Database issue):D818-824.
[40]Xiao L,Florez S,Wang J B,et al.Dact2 represses PITX2transcriptional activation and cell proliferation through Wnt/betacatenin signaling during odontogenesis[J].PLoS One,2013,8(1):e54868.
[41]Andersson L.Melanocortin receptor variants with phenotypic effects in horse,pig,and chicken[J].Ann N Y Acad Sci,2003,994:313-318.
[42]LüM D,Han X M,Ma Y F,et al.Genetic variations associated with six-white-point coat pigmentation in Diannan small-ear pigs[J].Sci Rep,2016,6:27534.
[43]Wang C,Wang H Y,Zhang Y,et al.Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs[J].Mol Ecol Resour,2015,15(2):414-424.