猪VRTN基因SINE转座子插入多态与生长和繁殖性状的关联分析
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摘要
椎骨发育相关基因(vertebrae development associated, VRTN)是动物椎骨发育的重要调控基因,研究表明猪(Sus scrofa domesticus)VRTN基因中存在一个短散在重复序列(short interspersed repeated sequence, SINE)的插入多态,该多态可能与猪的脊椎数关联。本研究通过PCR检测、性状关联分析和生物信息学分析等研究了SINE插入多态在不同品种间的分布及其对猪生长和繁殖性状的影响。结果表明,引入品种SINE+频率高于培育猪种和中国地方猪种,大白猪SINE+/+个体100 kg体重日龄显著高于SINE-/-个体(P<0.05),大白猪SINE+/+个体眼肌面积显著低于SINE-/-个体(P<0.05)。产活仔数等繁殖性状与SINE插入多态无显著关联。经与表达序列标签(expressed sequence tag, EST)等数据库序列比对未发现SINE与VRTN基因形成融合转录本。本研究表明VRTN基因中SINE插入多态可能与猪生长速度和瘦肉率有关联,此结果为该分子标记在猪分子育种中的应用提供了参考。
The VRTN(vertebrae development associated) gene is an important regulatory gene for animal vertebrae development. Studies have shown that there is a short interspersed repeated sequence(SINE)insertion polymorphism in the VRTN gene of the porcine(Sus scrofa domesticus), which may be associated with the number of pig spines. In this study, the distribution of SINE insertion polymorphism in different pig breeds and its effects on growth and reproduction traits of pigs were studied by PCR detection, polymorphism correlation and bioinformatics analysis. The results showed that the frequency of SINE+in introduced breeds was higher than that of cultivated pig breeds and Chinese local pig breeds. The age at 100 kg body weight of SINE+/+pigs of Yorkshire was significantly higher than that of SINE-/-pigs(P<0.05), and the SINE+/+ pigs loin eye muscle area was significantly lower than that of SINE-/-pigs(P<0.05). There was no significant association between reproductive traits such as live litter size and SINE insertion polymorphism. SINE and VRTN genes were not found to form a fusion transcript after comparison with expressed sequence tag(EST).This study demonstrated that SINE insertion polymorphism in VRTN gene may be associated with pig growth rate and lean meat rate, which provided a reference for the application of this molecular marker in pig molecular breeding.
The VRTN(vertebrae development associated) gene is an important regulatory gene for animal vertebrae development. Studies have shown that there is a short interspersed repeated sequence(SINE)insertion polymorphism in the VRTN gene of the porcine(Sus scrofa domesticus), which may be associated with the number of pig spines. In this study, the distribution of SINE insertion polymorphism in different pig breeds and its effects on growth and reproduction traits of pigs were studied by PCR detection, polymorphism correlation and bioinformatics analysis. The results showed that the frequency of SINE+in introduced breeds was higher than that of cultivated pig breeds and Chinese local pig breeds. The age at 100 kg body weight of SINE+/+pigs of Yorkshire was significantly higher than that of SINE-/-pigs(P<0.05), and the SINE+/+ pigs loin eye muscle area was significantly lower than that of SINE-/-pigs(P<0.05). There was no significant association between reproductive traits such as live litter size and SINE insertion polymorphism. SINE and VRTN genes were not found to form a fusion transcript after comparison with expressed sequence tag(EST).This study demonstrated that SINE insertion polymorphism in VRTN gene may be associated with pig growth rate and lean meat rate, which provided a reference for the application of this molecular marker in pig molecular breeding.
引文
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Borchers N.,Reinsch.N,Kalm.E,2004.The number of ribs and vertebrae in a Piétrain cross:Variation,heritability and effects on performance traits[J].Journal of Animal Breeding&Genetics,121(6):392-403.
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Dall'Olio.S.,Scotti.E,Fontanesi.L.et.al.2014.Analysis of the 227 bp short interspersed nuclear element(SINE)insertion of the promoter of the myostatin(MSTN)gene in different horse breeds[J].Veterinaria Italiana,50(3):193-197.
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Fan Y.,Xing Y,Zhang Z et al.2013.A further look at porcine chromosome 7 reveals VRTN variants associated with vertebral number in Chinese and western pigs[J].PloSOne,8(4):e62534.
Feschotte C.2008.Transposable elements and the evolution of regulatory networks[J].Nature Reviews Genetics,9(5):397-405.
Hirose K.,Mikawa S,Okumura.N.et al.2013.Association of swine vertnin(VRTN)gene with production traits in Duroc pigs improved using a closed nucleus breeding system[J].Animal Science Journal,84(3):213-221.
Huang J.,Zhang M,Ye R et al.2017.Effects of increased vertebral number on carcass weight in PIC pigs[J].Anima Science Journal,88(12).
Huang X,Lu G,Zhao Q et al.2008.Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice[J].Plant Physiology,148(1):25-40.
Jacques P.é.,Jeyakani J,Bourque G.2013.The majority of primate-specific regulatory sequences are derived from transposable elements[J].PLoS Genet,9(5):e1003504.
King J.W.B.,Roberts R.C.1960.Carcass length in the bacon pig;its association with vertebrae numbers and prediction from radiographs of the young pig[J].Anima Production,2(1):59-65.
Kramerov D.A.,Vassetzky N.S.2011.Origin and evolution of SINEs in eukaryotic genomes[J].Heredity,107(6)487-495.
Kunarso G,Chia N.Y.,Jeyakani J.et al.2010.Transposable elements have rewired the core regulatory network of human embryonic stem cells[J].Nature Genetics,42(7)631-634.
Lynch V.J.,Leclerc R.D.,May G.et al.2011.Transposonmediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals[J].Nature Genetics,43(11):1154-1159.
Mikawa S,Sato S,Morozumi T.et al.2011.Identification of a second gene associated with variation in vertebral number in domestic pigs[J].BMC Genetics,12,5.
Nakano H.,Sato S,Uemoto Y.et al.2015.Effect of VRTNgene polymorphisms on Duroc pig production and carcass traits,and their genetic relationships[J].Animal Science Journal,86(2):125-131.
Rebollo R,Romanish M.T.,Mager D.L.2012.Transposable elements:An abundant and natural source of regulatory sequences for host genes[J].The Annual Review of Genetics,46(1):21.
Rohrer G.A.,Dan J.N.,Wiedmann R.T.et al.2015.A study of vertebra number in pigs confirms the association of vertnin and reveals additional QTL[J].BMC Genetics,16(1):1-9.
Seibt K.M.,Wenke T.,Muders K..et al.2016.Short interspersed nuclear elements(SINEs)are abundant in Solanaceae and have a family-specific impact on gene structure and genome organization[J].Plant Journal,86(3):268.
Wang T,Zeng J,Lowe C.B.et al.2007.Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53[J].Proceedings of The National Academy of Sciences of the USA,104(47):18613-18618.
Witherspoon D.J.,Zhang Y,Xing.J.et al.2013.Mobile element scanning(ME-Scan)identifies thousands of novel Alu insertions in diverse human populations[J].Genome Research,23(7):1170-1181.
Xie D,Chen C.C,Ptaszek L.M.et al.2010.Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species[J].Genome Research,20(6):804-815.
Yang J.,Huang L,Yang M.et al.2016.Possible introgression of the VRTN mutation increasing vertebral number,carcass length and teat number from Chinese pigs into European pigs[J].Scientific Reports,6:19240.
Adams M.D,Susan E.C.,Robert A.H.et.al,2000.The genome sequence of Drosophila melanogaster[J].Science,287(5461):2185-2195.
Batzer M.A.,Stoneking M,Alegria-Hartman M.et.al.1994.African origin of human-specific polymorphic Alu insertions[J].Proceeding of the National Academy of Science of the USA,91(25):12288-12292.
Borchers N.,Reinsch.N,Kalm.E,2004.The number of ribs and vertebrae in a Piétrain cross:Variation,heritability and effects on performance traits[J].Journal of Animal Breeding&Genetics,121(6):392-403.
Bourque G,Leong B,Vega V.B.et al.2008.Evolution of the mammalian transcription factor binding repertoire via transposable elements[J].Genome Research,18(11):1752-1762.
Burgess.D.J.2013.Population genetics:Mobile elements across human populations[J].Nature reviews Genetics,14(6):370.
Clark.L.A.,Wahl.J.M.,Rees.C.A..et al.2006.Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog[J].Proceedings of the National Academy of Sciences of the USA,103(5):1376-1381.
Clintock.Mc.B.1930.A cytological demonstration of the location of an interchange between two non-homologous chromosomes of Zea Mays[J].Proceedings of the National Academy of Sciences of the USA,16(12):791-796.
Dall'Olio.S.,Scotti.E,Fontanesi.L.et.al.2014.Analysis of the 227 bp short interspersed nuclear element(SINE)insertion of the promoter of the myostatin(MSTN)gene in different horse breeds[J].Veterinaria Italiana,50(3):193-197.
Doolittle W.F.,Sapienza C.1980.Selfish genes,the phenotype paradigm and genome evolution[J].Nature,284(5757):601-603.
Duckworth J.E.,Holmes.W.1968.Selection for carcass length in Large White pigs[J].Animal Production,10(4):359-372.
Fan Y.,Xing Y,Zhang Z et al.2013.A further look at porcine chromosome 7 reveals VRTN variants associated with vertebral number in Chinese and western pigs[J].PloSOne,8(4):e62534.
Feschotte C.2008.Transposable elements and the evolution of regulatory networks[J].Nature Reviews Genetics,9(5):397-405.
Hirose K.,Mikawa S,Okumura.N.et al.2013.Association of swine vertnin(VRTN)gene with production traits in Duroc pigs improved using a closed nucleus breeding system[J].Animal Science Journal,84(3):213-221.
Huang J.,Zhang M,Ye R et al.2017.Effects of increased vertebral number on carcass weight in PIC pigs[J].Anima Science Journal,88(12).
Huang X,Lu G,Zhao Q et al.2008.Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice[J].Plant Physiology,148(1):25-40.
Jacques P.é.,Jeyakani J,Bourque G.2013.The majority of primate-specific regulatory sequences are derived from transposable elements[J].PLoS Genet,9(5):e1003504.
King J.W.B.,Roberts R.C.1960.Carcass length in the bacon pig;its association with vertebrae numbers and prediction from radiographs of the young pig[J].Anima Production,2(1):59-65.
Kramerov D.A.,Vassetzky N.S.2011.Origin and evolution of SINEs in eukaryotic genomes[J].Heredity,107(6)487-495.
Kunarso G,Chia N.Y.,Jeyakani J.et al.2010.Transposable elements have rewired the core regulatory network of human embryonic stem cells[J].Nature Genetics,42(7)631-634.
Lynch V.J.,Leclerc R.D.,May G.et al.2011.Transposonmediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals[J].Nature Genetics,43(11):1154-1159.
Mikawa S,Sato S,Morozumi T.et al.2011.Identification of a second gene associated with variation in vertebral number in domestic pigs[J].BMC Genetics,12,5.
Nakano H.,Sato S,Uemoto Y.et al.2015.Effect of VRTNgene polymorphisms on Duroc pig production and carcass traits,and their genetic relationships[J].Animal Science Journal,86(2):125-131.
Rebollo R,Romanish M.T.,Mager D.L.2012.Transposable elements:An abundant and natural source of regulatory sequences for host genes[J].The Annual Review of Genetics,46(1):21.
Rohrer G.A.,Dan J.N.,Wiedmann R.T.et al.2015.A study of vertebra number in pigs confirms the association of vertnin and reveals additional QTL[J].BMC Genetics,16(1):1-9.
Seibt K.M.,Wenke T.,Muders K..et al.2016.Short interspersed nuclear elements(SINEs)are abundant in Solanaceae and have a family-specific impact on gene structure and genome organization[J].Plant Journal,86(3):268.
Wang T,Zeng J,Lowe C.B.et al.2007.Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53[J].Proceedings of The National Academy of Sciences of the USA,104(47):18613-18618.
Witherspoon D.J.,Zhang Y,Xing.J.et al.2013.Mobile element scanning(ME-Scan)identifies thousands of novel Alu insertions in diverse human populations[J].Genome Research,23(7):1170-1181.
Xie D,Chen C.C,Ptaszek L.M.et al.2010.Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species[J].Genome Research,20(6):804-815.
Yang J.,Huang L,Yang M.et al.2016.Possible introgression of the VRTN mutation increasing vertebral number,carcass length and teat number from Chinese pigs into European pigs[J].Scientific Reports,6:19240.