藏系绵羊群体遗传多样性及遗传结构分析
|
摘要
旨在从分子层面对藏区绵羊群体进行群体关系研究。本试验选取西藏、青海、甘肃、云南和四川5个地区的20个藏系绵羊群体共384个个体进行Affymetrix Ovine 600K芯片扫描分型,基于杂合度和近交系数分析藏系绵羊群体的遗传多样性,并通过PCA、NJ-tree和STRUCTURE分析藏系绵羊的群体聚类情况。结果发现,西藏浪卡子绵羊的观测杂合度最低(0.235 0),近交系数最高(0.279 6);青海山谷型藏羊的观测杂合度最高(0.323 4),近交系数最低(0.009 0)。遗传结构分析结果显示,西藏和云南地区藏系绵羊能够单独聚成一支,而青海、甘肃和四川地区的草地型绵羊混乱聚集在一起。结果表明,西藏和云南地区藏系绵羊的遗传多样性普遍低于青海、甘肃和四川地区的藏系绵羊,且西藏和云南地区的藏系绵羊基本能保持地域特异性,而青海、甘肃和四川地区的草地型绵羊在遗传距离和群体结构中差异不大。
This experiment was conducted to study population relationship of Tibetan sheep at the molecular level. A total of 384 individuals from 20 Tibetan sheep populations from 5 regions including Tibet, Qinghai, Gansu, Yunnan and Sichuan were selected for Affymetrix Ovine 600K chip scanning. The genetic diversity of Tibetan sheep populations was analyzed based on heterozygosity and inbreeding coefficient, and the population clustering of Tibetan sheep was analyzed by PCA, NJ-tree and STRUCTURE. The results showed that the observed heterozygosity of Tibet Langkazi sheep was the lowest(0.235 0) and the inbreeding coefficient was the highest(0.279 6). The observed heterozygosity of Qinghai valley type Tibetan sheep was the highest(0.323 4) and the inbreeding coefficient was the lowest(0.009 0). The results of genetic structure analysis showed that Tibetan sheep in Tibet and Yunnan could be gathered together alone, while grassland sheep in Qinghai, Gansu and Sichuan were clustered together in confusion. The results indicate that the genetic diversity of Tibetan sheep in Tibet and Yunnan is generally lower than that of Tibetan sheep in Qinghai, Gansu and Sichuan. Tibetan sheep in Tibet and Yunnan can maintain regional specificity, while grassland sheep in Qinghai, Gansu and Sichuan regions have little difference in genetic distance and population structure.
This experiment was conducted to study population relationship of Tibetan sheep at the molecular level. A total of 384 individuals from 20 Tibetan sheep populations from 5 regions including Tibet, Qinghai, Gansu, Yunnan and Sichuan were selected for Affymetrix Ovine 600K chip scanning. The genetic diversity of Tibetan sheep populations was analyzed based on heterozygosity and inbreeding coefficient, and the population clustering of Tibetan sheep was analyzed by PCA, NJ-tree and STRUCTURE. The results showed that the observed heterozygosity of Tibet Langkazi sheep was the lowest(0.235 0) and the inbreeding coefficient was the highest(0.279 6). The observed heterozygosity of Qinghai valley type Tibetan sheep was the highest(0.323 4) and the inbreeding coefficient was the lowest(0.009 0). The results of genetic structure analysis showed that Tibetan sheep in Tibet and Yunnan could be gathered together alone, while grassland sheep in Qinghai, Gansu and Sichuan were clustered together in confusion. The results indicate that the genetic diversity of Tibetan sheep in Tibet and Yunnan is generally lower than that of Tibetan sheep in Qinghai, Gansu and Sichuan. Tibetan sheep in Tibet and Yunnan can maintain regional specificity, while grassland sheep in Qinghai, Gansu and Sichuan regions have little difference in genetic distance and population structure.
引文
[1] 薄吾成.试论藏羊渊源[J].西北农林科技大学学报:自然科学版,1986(2):79-82.BO W C.On the origin of Tibetan sheep[J].Journal of Northwest A&F University:Natural Science Edition,1986(2):79-82.(in Chinese)
[2] 向泽宇,王长庭.青藏高原藏羊遗传资源的现状,存在问题及对策[J].中国畜牧兽医文摘,2011,27(2):1-4.XIANG Z Y,WANG C T.Current status of genetic resources of Tibetan sheep in Qinghai-Tibet plateau,existing problems and countermeasures[J].Animal Husbandry and Veterinary Digesl of China,2011,27(2):1-4.(in Chinese)
[3] 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 Commisson of Animal Genetic Resources.Animal genetic resources in China sheep and goats[M].Beijing:China Agriculture Press,2011.(in Chinese)
[4] 徐琳娜,李国林.藏系绵羊遗传多样性的研究进展[J].畜牧兽医杂志,2012,31(4):56-58,60.XU L N,LI G L.Research progress on genetic diversity of Tibetan sheep[J].Journal of Animal Science and Veterinary Medicine,2012,31(4):56-58,60.(in Chinese)
[5] 孙晓萍,刘建斌,袁超,等.藏绵羊高海拔适应性及生产性能分析[J].今日畜牧兽医,2018,34(4):50-52.SUN X P,LIU J B,YUAN C,et al.Analysis of high altitude adaptability and production performance of Tibetan sheep[J].Today Animal Husbandry and Veterinary Medicine,2018,34(4):50-52.(in Chinese)
[6] 贾荣莉.高原藏羊肺组织学结构及特点[J].中国兽医科技,1997,27(2):43-44.JIA R L.Histological structure and characteristics of lung of Tibetan sheep on plateau[J].Chinese Veterinary Science,1997,27(2):43-44.(in Chinese)
[7] 王欣荣,吴建平.藏羊脑动脉系统结构特征与高原适应性研究[J].家畜生态学报,2013,34(8):36-40.WANG X R,WU J P.Study on structural features of the cerebral arterial system associatedwith plateau adaptability in Tibetan sheep[J].Acta Ecologae Animalis Domastici,2013,34(8):36-40.(in Chinese)
[8] 涂正超,张亚平.藏绵羊线粒体DNA遗传多样性研究[J].畜牧兽医学报,1998,29(2):132-135.TU Z C,ZHANG Y P.Mitochondrial DNA polymorphism in Zang sheep based on restriction endonuclease cleavage patterns[J].Acta Veterinaria et Zootechnica Sinica,1998,29(2):132-135.(in Chinese)
[9] 熊勇.藏系绵羊ZFX、ZFY基因片段的克隆测序及进化研究[D].成都:西南民族大学,2004.XIONG Y.Cloning,sequencing and evolution of ZFX and ZFY gene fragments of Tibetan sheep[D].Chengdu:Southwest Minzu University,2004.(in Chinese)
[10] 李祥龙,张增利,巩元芳,等.我国主要地方绵羊品种mtDNA D-loop区PCR-RFLP研究[J].遗传,2006,28(2):165-170.LI X L,ZHANG Z L,GONG Y F,et al.Study on mtDNA D-loop of Chinese main indigenous sheep breeds using PCR-RFLP[J].Hereditas,2006,28(2):165-170.(in Chinese)
[11] 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.
[12] WEI C H,WANG H H,LIU G,et al.Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds[J].BMC Genomics,2015,16:194.
[13] LV F H,AGHA S,KANTANEN J,et al.Adaptations to climate-mediated selective pressures in sheep[J].Mol Biol Evol,2014,31(12):3324-3343.
[14] YANG J,LI W R,LV F H,et al.Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments[J].Mol Biol Evol,2016,33(10):2576-2592.
[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] NEI M.Molecular population genetics and evolution[J].Front Biol,1975,40:198-199.
[17] PATTERSON N,PRICE A L,REICH D.Populationstructure and eigenanalysis[J].PLoS Genet,2006,2(12):e190.
[18] PRICE A L,PATTERSON N J,PLENGE R M,et al.Principal components analysis corrects for stratification in genome-wide association studies[J].Nat Genet,2006,38(8):904-909.
[19] TAMURA K,PETERSON D,PETERSON N,et al.MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Mol Biol Evol,2011,28(10):2731-2739.
[20] KIM J J,VERDU P,PAKSTIS A J,et al.Use of Autosomal loci for clustering individuals and populations of East Asian origin[J].Hum Genet,2005,117(6):511-519.
[21] ALEXANDER D H,NOVEMBRE J,LANGE K.Fastmodel-based estimation of ancestry in unrelated individuals[J].Genome Res,2009,19(9):1655-1664.
[22] 晁燕,祁世荣,张延生.青海藏系绵羊高原型与山谷型类群的遗传多样性和分化研究[J].黑龙江畜牧兽医,2016(11):102-104.CHAO Y,QI S R,ZHANG Y S.Studyon genetic diversity and differentiation of Tibetan sheep plateau and valley types in Qinghai[J].Heilongjiang Animal Science and Veterinary Medicine,2016(11):102-104.(in Chinese)
[23] INTARAPANICH A,SHAW P J,ASSAWAMAKIN A,et al.Iterative Pruning PCA improves resolution of highly structured populations[J].BMC Bioinform,2009,10:382.
[24] 王荣鑫,马森,张才骏,等.青海藏系绵羊九项生理参数测定[J].青海畜牧兽医学院学报,1987(1):24-28,39.WANG R X,MA S,ZHANG C J,et al.Determination of nine physiological parameters of Tibetan sheep in Qinghai[J].Journal of Qinghai College of Animal Science and Veterinary Medicine,1987(1):24-28,39.(in Chinese)
[25] 甘肃省畜牧厅.甘肃省畜禽品种志[M].兰州:甘肃人民出版社,1986.Chief Editor of Gansu Animal Husbandry Department.Records of domestic animal and fowl breeds of Gansu Province[M].Lanzhou:Gansu People's Publishing House,1986.(in Chinese)
[26] 李沐森,郭文场.藏羊的类型分布及生活习性[J].特种经济动植物,2016(3):5-8.LI M S,GUO W C.Types,distribution and living habits of Tibetan sheep[J].Special Economic Animal and Plant,2016(3):5-8.(in Chinese)
[27] 吉金凤,祁红霞,何文,等.乔科羊产肉性能测定分析[J].畜牧兽医杂志,2007,26(1):82-83.JI J F,QI H X,HE W,et al.Determination and analysis of meat performance of Qiaoke sheep[J].Journal of Animal Science and Veterinary Medicine,2007,26(1):82-83.(in Chinese)
[28] 李昕,常明华,全晓毅,等.欧拉羊杂交改良高原型藏羊效果分析[J].中国畜牧兽医文摘,2015,31(1):55,73.LI X,CHANG M H,QUAN X Y,et al.Effect analysis of plateau Tibetan sheep improved by Oula sheep hybridization[J].Chinese Journal of Animal Husbandry and Veterinary Medicine,2015,31(1):55,73.(in Chinese)
[29] 杨晓军,赵有璋.藏系绵羊遗传多样性及其品种(系)分化的研究[J].中国草食动物,2006,26(4):19-22.YANG X J,ZHAO Y Z.Study on the genetic diversity and the breeds differentiation of Tibet sheep[J].China Herbivore Science,2006,26(4):19-22.(in Chinese)
[30] 徐琳娜.甘肃青海藏系绵羊群体遗传多样性的微卫星分析[D].兰州:甘肃农业大学,2010.XU L N.Analysis on genetic diversity in Tibet sheep populations in Gansu and Qinghai Provinces by microsatellite markers[D].Lanzhou:Gansu Agricultural University,2010.(in Chinese)
[2] 向泽宇,王长庭.青藏高原藏羊遗传资源的现状,存在问题及对策[J].中国畜牧兽医文摘,2011,27(2):1-4.XIANG Z Y,WANG C T.Current status of genetic resources of Tibetan sheep in Qinghai-Tibet plateau,existing problems and countermeasures[J].Animal Husbandry and Veterinary Digesl of China,2011,27(2):1-4.(in Chinese)
[3] 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 Commisson of Animal Genetic Resources.Animal genetic resources in China sheep and goats[M].Beijing:China Agriculture Press,2011.(in Chinese)
[4] 徐琳娜,李国林.藏系绵羊遗传多样性的研究进展[J].畜牧兽医杂志,2012,31(4):56-58,60.XU L N,LI G L.Research progress on genetic diversity of Tibetan sheep[J].Journal of Animal Science and Veterinary Medicine,2012,31(4):56-58,60.(in Chinese)
[5] 孙晓萍,刘建斌,袁超,等.藏绵羊高海拔适应性及生产性能分析[J].今日畜牧兽医,2018,34(4):50-52.SUN X P,LIU J B,YUAN C,et al.Analysis of high altitude adaptability and production performance of Tibetan sheep[J].Today Animal Husbandry and Veterinary Medicine,2018,34(4):50-52.(in Chinese)
[6] 贾荣莉.高原藏羊肺组织学结构及特点[J].中国兽医科技,1997,27(2):43-44.JIA R L.Histological structure and characteristics of lung of Tibetan sheep on plateau[J].Chinese Veterinary Science,1997,27(2):43-44.(in Chinese)
[7] 王欣荣,吴建平.藏羊脑动脉系统结构特征与高原适应性研究[J].家畜生态学报,2013,34(8):36-40.WANG X R,WU J P.Study on structural features of the cerebral arterial system associatedwith plateau adaptability in Tibetan sheep[J].Acta Ecologae Animalis Domastici,2013,34(8):36-40.(in Chinese)
[8] 涂正超,张亚平.藏绵羊线粒体DNA遗传多样性研究[J].畜牧兽医学报,1998,29(2):132-135.TU Z C,ZHANG Y P.Mitochondrial DNA polymorphism in Zang sheep based on restriction endonuclease cleavage patterns[J].Acta Veterinaria et Zootechnica Sinica,1998,29(2):132-135.(in Chinese)
[9] 熊勇.藏系绵羊ZFX、ZFY基因片段的克隆测序及进化研究[D].成都:西南民族大学,2004.XIONG Y.Cloning,sequencing and evolution of ZFX and ZFY gene fragments of Tibetan sheep[D].Chengdu:Southwest Minzu University,2004.(in Chinese)
[10] 李祥龙,张增利,巩元芳,等.我国主要地方绵羊品种mtDNA D-loop区PCR-RFLP研究[J].遗传,2006,28(2):165-170.LI X L,ZHANG Z L,GONG Y F,et al.Study on mtDNA D-loop of Chinese main indigenous sheep breeds using PCR-RFLP[J].Hereditas,2006,28(2):165-170.(in Chinese)
[11] 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.
[12] WEI C H,WANG H H,LIU G,et al.Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds[J].BMC Genomics,2015,16:194.
[13] LV F H,AGHA S,KANTANEN J,et al.Adaptations to climate-mediated selective pressures in sheep[J].Mol Biol Evol,2014,31(12):3324-3343.
[14] YANG J,LI W R,LV F H,et al.Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments[J].Mol Biol Evol,2016,33(10):2576-2592.
[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] NEI M.Molecular population genetics and evolution[J].Front Biol,1975,40:198-199.
[17] PATTERSON N,PRICE A L,REICH D.Populationstructure and eigenanalysis[J].PLoS Genet,2006,2(12):e190.
[18] PRICE A L,PATTERSON N J,PLENGE R M,et al.Principal components analysis corrects for stratification in genome-wide association studies[J].Nat Genet,2006,38(8):904-909.
[19] TAMURA K,PETERSON D,PETERSON N,et al.MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Mol Biol Evol,2011,28(10):2731-2739.
[20] KIM J J,VERDU P,PAKSTIS A J,et al.Use of Autosomal loci for clustering individuals and populations of East Asian origin[J].Hum Genet,2005,117(6):511-519.
[21] ALEXANDER D H,NOVEMBRE J,LANGE K.Fastmodel-based estimation of ancestry in unrelated individuals[J].Genome Res,2009,19(9):1655-1664.
[22] 晁燕,祁世荣,张延生.青海藏系绵羊高原型与山谷型类群的遗传多样性和分化研究[J].黑龙江畜牧兽医,2016(11):102-104.CHAO Y,QI S R,ZHANG Y S.Studyon genetic diversity and differentiation of Tibetan sheep plateau and valley types in Qinghai[J].Heilongjiang Animal Science and Veterinary Medicine,2016(11):102-104.(in Chinese)
[23] INTARAPANICH A,SHAW P J,ASSAWAMAKIN A,et al.Iterative Pruning PCA improves resolution of highly structured populations[J].BMC Bioinform,2009,10:382.
[24] 王荣鑫,马森,张才骏,等.青海藏系绵羊九项生理参数测定[J].青海畜牧兽医学院学报,1987(1):24-28,39.WANG R X,MA S,ZHANG C J,et al.Determination of nine physiological parameters of Tibetan sheep in Qinghai[J].Journal of Qinghai College of Animal Science and Veterinary Medicine,1987(1):24-28,39.(in Chinese)
[25] 甘肃省畜牧厅.甘肃省畜禽品种志[M].兰州:甘肃人民出版社,1986.Chief Editor of Gansu Animal Husbandry Department.Records of domestic animal and fowl breeds of Gansu Province[M].Lanzhou:Gansu People's Publishing House,1986.(in Chinese)
[26] 李沐森,郭文场.藏羊的类型分布及生活习性[J].特种经济动植物,2016(3):5-8.LI M S,GUO W C.Types,distribution and living habits of Tibetan sheep[J].Special Economic Animal and Plant,2016(3):5-8.(in Chinese)
[27] 吉金凤,祁红霞,何文,等.乔科羊产肉性能测定分析[J].畜牧兽医杂志,2007,26(1):82-83.JI J F,QI H X,HE W,et al.Determination and analysis of meat performance of Qiaoke sheep[J].Journal of Animal Science and Veterinary Medicine,2007,26(1):82-83.(in Chinese)
[28] 李昕,常明华,全晓毅,等.欧拉羊杂交改良高原型藏羊效果分析[J].中国畜牧兽医文摘,2015,31(1):55,73.LI X,CHANG M H,QUAN X Y,et al.Effect analysis of plateau Tibetan sheep improved by Oula sheep hybridization[J].Chinese Journal of Animal Husbandry and Veterinary Medicine,2015,31(1):55,73.(in Chinese)
[29] 杨晓军,赵有璋.藏系绵羊遗传多样性及其品种(系)分化的研究[J].中国草食动物,2006,26(4):19-22.YANG X J,ZHAO Y Z.Study on the genetic diversity and the breeds differentiation of Tibet sheep[J].China Herbivore Science,2006,26(4):19-22.(in Chinese)
[30] 徐琳娜.甘肃青海藏系绵羊群体遗传多样性的微卫星分析[D].兰州:甘肃农业大学,2010.XU L N.Analysis on genetic diversity in Tibet sheep populations in Gansu and Qinghai Provinces by microsatellite markers[D].Lanzhou:Gansu Agricultural University,2010.(in Chinese)