实验用SPF大白猪和长白猪母系遗传结构分析
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摘要
无特定病原体(specific pathogen free, SPF)大白猪(Sus scrofa)和长白猪作为重要的实验动物,其遗传学质量控制研究十分必要。为分析实验用SPF大白猪、长白猪的线粒体DNA(mitochondrial DNA,mtDNA)控制区(displacement-loop region, D-loop区)遗传多样性,揭示其母系遗传结构,本研究提取SPF大白猪和长白猪基因组DNA,同时以我国地方品种巴马小型猪和融水小型猪为对照,应用PCR技术扩增其mtDNA D-loop区,进行测序比对。结果显示,107个样本中共检测到40个多态位点,分为13个单倍型,与地方品种相比,大白猪和长白猪单倍型数较少,分别含有3种和2种特有单倍型,只有1个共享单倍型H4。两猪群中各存在1个优势单倍型。单倍型多样度(Hd)分析,融水小型猪单倍型多样度最高(0.767),长白猪最低(0.429),大白猪和巴马小型猪分别为0.566和0.503。此外,中介网络关系图和系统进化树发现大白猪和长白猪与欧洲猪种亲缘关系较近。本研究表明实验用SPF大白猪和长白猪种群的单倍型数较少,各存在1个优势单倍型,遗传多样性低,具有清晰的母系遗传结构。研究结果有利于进一步的实验动物标准化以及遗传质量控制研究。
The genetic quality control research is very necessary for specific pathogen free(SPF) Yorkshire(Sus scrofa) and Landrace pig populations used as the important experimental animals. To analyze the genetic diversity of the mitochondrial DNA(mtDNA) displacement-loop region(D-loop region) and reveal the maternal genetic structure of experimental specific pathogen free(SPF) Yorkshire and Landrace population,genomic DNA of SPF Yorkshire and Landrace pigs were extracted, the mtDNA D-loop region was amplified by PCR, and the sequences were aligned. The local Bama miniature pigs and Rongshui miniature pigs were used as control. A total of 40 variable sites were identified in 107 samples, including 13 haplotypes. Comparedwith the local breeds, the fewer haplotypes were found in the Yorkshire and Landrace, which contained 3 and2 specific haplotypes, respectively, and one shared haplotype H4. There was one dominant haplotype in each of the two breeds. Analysis result of the haplotype diversity(Hd) showed that the Rongshui miniature pigs was the highest(0.767) and Landrace was the lowest(0.429). Yorkshire and Bama miniature pigs were 0.566 and0.503, respectively. In addition, the results of network and phylogenetic tree showed that the genetic relationship between Yorkshire and Landrace populations was closely related to European pig breeds. The study indicated that there was less haplotypes and lower genetic diversity in SPF Yorkshire and Landrace populations. Only one dominant haplotype for each breed was observed. This study will be beneficial for the further research of experimental animal standardization and genetic quality control.
The genetic quality control research is very necessary for specific pathogen free(SPF) Yorkshire(Sus scrofa) and Landrace pig populations used as the important experimental animals. To analyze the genetic diversity of the mitochondrial DNA(mtDNA) displacement-loop region(D-loop region) and reveal the maternal genetic structure of experimental specific pathogen free(SPF) Yorkshire and Landrace population,genomic DNA of SPF Yorkshire and Landrace pigs were extracted, the mtDNA D-loop region was amplified by PCR, and the sequences were aligned. The local Bama miniature pigs and Rongshui miniature pigs were used as control. A total of 40 variable sites were identified in 107 samples, including 13 haplotypes. Comparedwith the local breeds, the fewer haplotypes were found in the Yorkshire and Landrace, which contained 3 and2 specific haplotypes, respectively, and one shared haplotype H4. There was one dominant haplotype in each of the two breeds. Analysis result of the haplotype diversity(Hd) showed that the Rongshui miniature pigs was the highest(0.767) and Landrace was the lowest(0.429). Yorkshire and Bama miniature pigs were 0.566 and0.503, respectively. In addition, the results of network and phylogenetic tree showed that the genetic relationship between Yorkshire and Landrace populations was closely related to European pig breeds. The study indicated that there was less haplotypes and lower genetic diversity in SPF Yorkshire and Landrace populations. Only one dominant haplotype for each breed was observed. This study will be beneficial for the further research of experimental animal standardization and genetic quality control.
引文
高彩霞,辛畅,陈洪岩.2018.畜禽疫病防控用SPF猪的开发[J].实验动物与比较医学,38(04):245-249.(Gao C XXin C,Chen H Y.2018.Development of specific pathogen-free(SPF)pigs for prevention and control of livestock and poultry disease[J].Laboratory Animal and Comparative Medicine,38(04):245-249.)
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贺希文,高彩霞,姜骞,等.2015.加系SPF大白猪和长白猪群体遗传学分析[J].中国实验动物学报,23(6):551-556.(He X W,Gao C X,Jiang Q,et al.2015.Analysis of the pedigreed population genetics of SPF Yorkshire and Landrace pigs imported from Canada[J].Acta Laboratorium Animalis Scientia Sinica,23(6):551-556.)
黄树文,张哲,陈赞谋,等.2018.广东省现有5个地方猪种基于SNP芯片的遗传多样性分析[J].中国畜牧杂志(6):33-37.(Huang S W,Zhang Z,Chen Z M,et al2018.Genetic diversity analysis of five cantonese indigenous pigs based on SNP chip[J].Chinese Journal of Animal Science,(6):33-37.)
刘德武,杨关福,李加琪,等.2002,用RAPD标记分析6个品种猪的群体遗传结构[J].畜牧兽医学报,33(1):18-22.(Liu D W,Yang G F,Li J Q,et al.2002.Analysing genetic construction of six pig breeds using RAPD maker[J].Acta Veterinaria et Zootechnica Sinica,33(1):18-22.)
刘丽,赵生国,蔡原,等.2014.早胜牛及其杂交群体遗传多样性研究[J].农业生物技术学报,22(3):317-325.(Liu L,Zhao S G,Cai Y,et al.2014.The genetic diversity of Zaosheng Native cattle and associated crossbred population[J].Journal of Agricultural Biotechnology,22(3):317-325.)
刘艳,王珑.2011.浅述实验动物质量控制[J].中国公共卫生管理,(1):25-27.(Liu Y,Wang L.2011.Description of laboratory animal quality control[J].China Public Health Management,(1):25-27.)
陆超,郝林琳,程云云,等.2016.东北民猪线粒体DNA D-loop遗传多样性与母系起源研究[J].中国兽医学报,36(4):675-678.(Lu C,Hao L L,Cheng Y Y,et al.2016.Genetic diversity of mtDNA D-loop and maternal origin of Min Breeds[J].Chinese Journal of Veterinary Science,36(4):675-678.)
綦文晶,何剑雄,郭晓萍,等.2016.广西3个猪种线粒体DNA D-loop序列遗传多样性及系统进化研究[J].基因组学与应用生物学,35(9):2367-2374.(Qi W J,He JX,Guo X P,et al.2016.The genetic diversity and phylogenetic relationships among three guangxi pig breeds based on sequences of mtDNA D-loop[J].Genomics and Applied Biology,35(9):2367-2374.)
钱军,孙玉成.2011.实验动物与生物安全[J].中国比较医学杂志,21(10):15-19.(Qian J,Sun Y C.2011.Experimental animals and biosecurity[J].Chinese Journal of Comparative Medicine,21(10):15-19.)
权金强,高彩霞,江新杰,等.2017.SPF大白猪和长白猪群体生理生化特性分析[J].中国实验动物学报,25(2):160-165.(Quan J Q,Gao C X,Jiang X J,et al.2017.Analysis of physiological and biochemical characteristics of SPF Yorkshire and Landrace swine[J].Acta Laboratorium Animalis Scientia Sinica,25(2):160-165.
权金强,苟潇,赵生国.2015.云南地方猪种mtDNA D-loop区遗传多样性研究[J].四川农业大学学报,(4):422-428.(Quan J Q,Guo X,Zhao S G.2015.The genetic diversity of mitochondrial DNA D-loop in Yunnan native pigs[J].Journal of Sichuan Agricultural University,(4):422-428.)
盛中华,张哲,肖倩,等.2016.上海白猪(上系)遗传多样性和群体结构分析[J].农业生物技术学报,24(9):1293-1301.(Sheng Z H,Zhang Z,Xiao Q,et al.2016.Genetic diversity and population structure analysis of Shanghai White pig(Sus scrofa)[J].Journal of Agricultura Biotechnology,24(9):1293-1301.)
施赫赫,陈淦,刘科,等.2015.融水小型猪的实验动物化系列研究概述[J].中国比较医学杂志,(3):86-89.(Shi CC,Chen G,Liu K,et al.2015.Brief report of series study on Rongshui miniature pig as laboratory anima[J]Chinese Journal of Comparative Medicine,(3):86-89.)
王继英,郭建凤,孙守礼,等.2009.山东猪种mtDNA D-loop区部分序列遗传多样性及系统进化研究[J].畜牧兽医学报,40(6):792-799.(Wang J Y,Guo J F,Sun S L,e al.2009.The genetic diversity and phylogenetic relationships among pig breeds of Shandong province based on partial sequence of mtDNA D-loop region[J].Acta Veterinaria et Zootechnica Sinica,40(6):792-799.)
王亚楠.2015.9个中外猪品种全基因组选择区域及拷贝数变异分析[D].博士学位论文,华中农业大学,导师:刘榜,pp.22-81.(Wang Y N.2015.Genome-Wide analysis of selective regions and copy number variations among nine Chinese and Western pig breeds[D].Thesis for Ph D.Huazhong Agriculture University,Supervisor:Liu Bpp:22-81.)
徐嘉悦,施赫赫,王绪敏,等.2015.融水小型猪线粒体DNA结构和系统进化的分析[J].中国比较医学杂志,(3)28-34.(Xu J Y,Shi C C,Wang X M,et al.2015.Genomic and phylogenetic analysis of porcine mitochondrial genomes of Rongshui miniature pig[J].Chinese Journal of Comparative Medicine,(3):28-34.)
于萍,曹婷,施力光,等.2014.猪线粒体DNA研究应用进展[J].家畜生态学报,35(7):1-6.(Yu P,Cao T,Shi L G,e al.2014.Advances in research and application of porcine mitochondrial DNA[J].Acta Ecologiae Animalis Domastici,35(7):1-6.)
于萍,曹婷,施力光,等.2015.五指山猪线粒体控制区序列分析及遗传多样性研究[J].中国畜牧兽医,42(5)1222-1231.(Yu P,Cao T,Shi L G,et al.2015.Complete mitochondrial DNA D-loop sequence and genetic diversity of Wuzhishan pig[J].China Animal Husbandry&Veterinary Medicine,42(5):1222-1231.)
张冰,廖海洪,农素群,等.2015.广西5个猪种和国外3个猪种mtDNA D-loop序列遗传多样性及进化分析[J].中国畜牧兽医,42(7):1807-1815.(Zhang B,Liao H H,Nong S Q,et al.2015.The genetic diversity and phylogenetic relationships of five Guangxi pig breeds and three exotic pig breeds by analysis of mtDNA D-loop sequences[J].China Animal Husbandry&Veterinary Medicine,42(7):1807-1815.)
张冬杰,杨国伟,刘娣.2009.4个猪种线粒体DNA D-loop区PCR-RFLP分析[J].吉林农业大学学报,31(2):200-203.(Zhang D J,Yang G W,Liu Di.2009.PCR-RFLPanalysis of four porcine mitochondrial DNA D-loop[J].Journal of Jilin Agricultural University,31(2):200-203.)
张连峰.2011.我国常用实验动物资源的现状及对未来发展的思考[J].中国比较医学杂志,21(z1):39-44.(Zhang L F.2011.The current status of laboratory animal resources in China and reflections on its future development[J].Chinese Journal of Comparative Medicine,21(z1):39-44.)
Ai H,Huang L,Ren J.2013.Genetic diversity,linkage disequilibrium and selection signatures in Chinese and western pigs revealed by genome-wide SNP markers[J].PLoS One,8(2):e56001.
Kim K I,Lee J H,Li K,et al.2002.Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism[J].Animal Genetics,33(1):19-25.
Zhang J,Jiao T,Zhao S.2016.Genetic diversity in the mitochondrial DNA D-loop region of global swine(Sus scrofa)populations[J].Biochemical&Biophysical Research Communications,473(4):814-820.
姜骞,韩凌霞,司昌德,等.2017.SPF巴马小型猪的培育及应用[J].中国比较医学杂志,27(5):1-3.(Jiang Q,Han L X,Si C D,et al.2017.Breeding and application of SPF Bama miniature pig[J].Acta Laboratorium Animalis Scientia Sinica,27(5):1-3.)
贺希文,高彩霞,姜骞,等.2015.加系SPF大白猪和长白猪群体遗传学分析[J].中国实验动物学报,23(6):551-556.(He X W,Gao C X,Jiang Q,et al.2015.Analysis of the pedigreed population genetics of SPF Yorkshire and Landrace pigs imported from Canada[J].Acta Laboratorium Animalis Scientia Sinica,23(6):551-556.)
黄树文,张哲,陈赞谋,等.2018.广东省现有5个地方猪种基于SNP芯片的遗传多样性分析[J].中国畜牧杂志(6):33-37.(Huang S W,Zhang Z,Chen Z M,et al2018.Genetic diversity analysis of five cantonese indigenous pigs based on SNP chip[J].Chinese Journal of Animal Science,(6):33-37.)
刘德武,杨关福,李加琪,等.2002,用RAPD标记分析6个品种猪的群体遗传结构[J].畜牧兽医学报,33(1):18-22.(Liu D W,Yang G F,Li J Q,et al.2002.Analysing genetic construction of six pig breeds using RAPD maker[J].Acta Veterinaria et Zootechnica Sinica,33(1):18-22.)
刘丽,赵生国,蔡原,等.2014.早胜牛及其杂交群体遗传多样性研究[J].农业生物技术学报,22(3):317-325.(Liu L,Zhao S G,Cai Y,et al.2014.The genetic diversity of Zaosheng Native cattle and associated crossbred population[J].Journal of Agricultural Biotechnology,22(3):317-325.)
刘艳,王珑.2011.浅述实验动物质量控制[J].中国公共卫生管理,(1):25-27.(Liu Y,Wang L.2011.Description of laboratory animal quality control[J].China Public Health Management,(1):25-27.)
陆超,郝林琳,程云云,等.2016.东北民猪线粒体DNA D-loop遗传多样性与母系起源研究[J].中国兽医学报,36(4):675-678.(Lu C,Hao L L,Cheng Y Y,et al.2016.Genetic diversity of mtDNA D-loop and maternal origin of Min Breeds[J].Chinese Journal of Veterinary Science,36(4):675-678.)
綦文晶,何剑雄,郭晓萍,等.2016.广西3个猪种线粒体DNA D-loop序列遗传多样性及系统进化研究[J].基因组学与应用生物学,35(9):2367-2374.(Qi W J,He JX,Guo X P,et al.2016.The genetic diversity and phylogenetic relationships among three guangxi pig breeds based on sequences of mtDNA D-loop[J].Genomics and Applied Biology,35(9):2367-2374.)
钱军,孙玉成.2011.实验动物与生物安全[J].中国比较医学杂志,21(10):15-19.(Qian J,Sun Y C.2011.Experimental animals and biosecurity[J].Chinese Journal of Comparative Medicine,21(10):15-19.)
权金强,高彩霞,江新杰,等.2017.SPF大白猪和长白猪群体生理生化特性分析[J].中国实验动物学报,25(2):160-165.(Quan J Q,Gao C X,Jiang X J,et al.2017.Analysis of physiological and biochemical characteristics of SPF Yorkshire and Landrace swine[J].Acta Laboratorium Animalis Scientia Sinica,25(2):160-165.
权金强,苟潇,赵生国.2015.云南地方猪种mtDNA D-loop区遗传多样性研究[J].四川农业大学学报,(4):422-428.(Quan J Q,Guo X,Zhao S G.2015.The genetic diversity of mitochondrial DNA D-loop in Yunnan native pigs[J].Journal of Sichuan Agricultural University,(4):422-428.)
盛中华,张哲,肖倩,等.2016.上海白猪(上系)遗传多样性和群体结构分析[J].农业生物技术学报,24(9):1293-1301.(Sheng Z H,Zhang Z,Xiao Q,et al.2016.Genetic diversity and population structure analysis of Shanghai White pig(Sus scrofa)[J].Journal of Agricultura Biotechnology,24(9):1293-1301.)
施赫赫,陈淦,刘科,等.2015.融水小型猪的实验动物化系列研究概述[J].中国比较医学杂志,(3):86-89.(Shi CC,Chen G,Liu K,et al.2015.Brief report of series study on Rongshui miniature pig as laboratory anima[J]Chinese Journal of Comparative Medicine,(3):86-89.)
王继英,郭建凤,孙守礼,等.2009.山东猪种mtDNA D-loop区部分序列遗传多样性及系统进化研究[J].畜牧兽医学报,40(6):792-799.(Wang J Y,Guo J F,Sun S L,e al.2009.The genetic diversity and phylogenetic relationships among pig breeds of Shandong province based on partial sequence of mtDNA D-loop region[J].Acta Veterinaria et Zootechnica Sinica,40(6):792-799.)
王亚楠.2015.9个中外猪品种全基因组选择区域及拷贝数变异分析[D].博士学位论文,华中农业大学,导师:刘榜,pp.22-81.(Wang Y N.2015.Genome-Wide analysis of selective regions and copy number variations among nine Chinese and Western pig breeds[D].Thesis for Ph D.Huazhong Agriculture University,Supervisor:Liu Bpp:22-81.)
徐嘉悦,施赫赫,王绪敏,等.2015.融水小型猪线粒体DNA结构和系统进化的分析[J].中国比较医学杂志,(3)28-34.(Xu J Y,Shi C C,Wang X M,et al.2015.Genomic and phylogenetic analysis of porcine mitochondrial genomes of Rongshui miniature pig[J].Chinese Journal of Comparative Medicine,(3):28-34.)
于萍,曹婷,施力光,等.2014.猪线粒体DNA研究应用进展[J].家畜生态学报,35(7):1-6.(Yu P,Cao T,Shi L G,e al.2014.Advances in research and application of porcine mitochondrial DNA[J].Acta Ecologiae Animalis Domastici,35(7):1-6.)
于萍,曹婷,施力光,等.2015.五指山猪线粒体控制区序列分析及遗传多样性研究[J].中国畜牧兽医,42(5)1222-1231.(Yu P,Cao T,Shi L G,et al.2015.Complete mitochondrial DNA D-loop sequence and genetic diversity of Wuzhishan pig[J].China Animal Husbandry&Veterinary Medicine,42(5):1222-1231.)
张冰,廖海洪,农素群,等.2015.广西5个猪种和国外3个猪种mtDNA D-loop序列遗传多样性及进化分析[J].中国畜牧兽医,42(7):1807-1815.(Zhang B,Liao H H,Nong S Q,et al.2015.The genetic diversity and phylogenetic relationships of five Guangxi pig breeds and three exotic pig breeds by analysis of mtDNA D-loop sequences[J].China Animal Husbandry&Veterinary Medicine,42(7):1807-1815.)
张冬杰,杨国伟,刘娣.2009.4个猪种线粒体DNA D-loop区PCR-RFLP分析[J].吉林农业大学学报,31(2):200-203.(Zhang D J,Yang G W,Liu Di.2009.PCR-RFLPanalysis of four porcine mitochondrial DNA D-loop[J].Journal of Jilin Agricultural University,31(2):200-203.)
张连峰.2011.我国常用实验动物资源的现状及对未来发展的思考[J].中国比较医学杂志,21(z1):39-44.(Zhang L F.2011.The current status of laboratory animal resources in China and reflections on its future development[J].Chinese Journal of Comparative Medicine,21(z1):39-44.)
Ai H,Huang L,Ren J.2013.Genetic diversity,linkage disequilibrium and selection signatures in Chinese and western pigs revealed by genome-wide SNP markers[J].PLoS One,8(2):e56001.
Kim K I,Lee J H,Li K,et al.2002.Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism[J].Animal Genetics,33(1):19-25.
Zhang J,Jiao T,Zhao S.2016.Genetic diversity in the mitochondrial DNA D-loop region of global swine(Sus scrofa)populations[J].Biochemical&Biophysical Research Communications,473(4):814-820.