基于祖源分析的猪遗传成分鉴定

doi:10.16431/j.cnki.1671-7236.2020.02.026

摘要/Abstract

摘要： 解析不同品牌猪肉的遗传成分对商业品牌的保护，防伪溯源及中国地方猪种的改良和开发具有重要参考价值。从市场上选取4种不同来源的猪肌肉组织通过全基因组重测序，并结合已发表的59头猪的数据，对其祖先成分进行分析，推测它们祖先可能的来源及其各祖先成分的含量。利用线粒体基因组数据判断4头猪的母系来源，揭示可能的母系来源。59头参考个体包含12个品种，分别是杜洛克猪、长白猪、大白猪、皮特兰猪、二花脸猪、金华猪、姜曲海猪、梅山猪、巴马香猪、陆川猪、五指山猪和香猪。将12个品种划分为商品猪、中国东部猪和中国南方猪。研究中，利用ADMIXTURE和RFMix软件分别对4头测试个体进行祖先成分的评估。设定4头测试个体的祖先群体为3类时，发现其中一头含有54.8%的商品猪成分和45.2%的中国南方猪成分，另一头含有81.3%的商品猪成分，而剩下的两头含有的商品猪成分占到97.0%以上。设定祖先群体为12类时，发现其中一头含有64.8%的杜洛克猪成分和35.2%的陆川猪成分；另一头含有的祖先成分比较复杂，长白猪的含量为22.5%，大白猪的含量为27.6%，五指山猪的含量为8.6%，二花脸猪的含量为5.5%，梅山猪、姜曲海猪和巴马香猪的含量均在1.2%左右；而剩余两头猪的祖先成分主要是杜洛克猪、长白猪、大白猪和皮特兰猪。另外，线粒体的祖源判断提示其中一头猪的母系来源可能是陆川猪或相近地方品种的母猪。通过常用的祖源分析方法对4头猪进行祖先血统成分的估计，发现4头猪的遗传成分各不相同，并能清晰地知道不同个体中祖先成分及占比。该研究结果证明通过祖源分析的方法可以估算每个测试个体的遗传成分来源。使用祖源成分作为遗传特征，可为品牌猪肉的鉴定和品牌保护提供重要的遗传学参考，也可以为中国地方猪品种的保护、开发提供指导和参考。

关键词: 猪; SNP; 线粒体DNA; 群体结构; 祖先成分

Abstract: It is great reference value to analyze traceability the genetic components of different brands of pork for the protection of commercial brands,traceability and the improvement and development of local pig breeds in China.Four kinds of pig muscle tissues from different sources were selected from the market and the whole genome was resequenced..Combined with the published data of 59 pigs,the ancestral components were analyzed to speculate the possible sources of their ancestors and the contents of their ancestral components.In addition,mitochondrial genomic data were used to determine the maternal origin of four pigs and reveal the possible maternal origin.The 59 reference individuals included 12 breeds,Duroc,Landrace,Largewhite,Pietrain,Erhualian,Jinhua,Jiangquhai,Meishan,Bamaxiang,Luchaun,Wuzhishan and Xiang pigs respectively.The 12 breeds were divided into commercial pig,Eastern pig and Southern pig.In the study,four individuals were evaluated for their ancestral components using the software of ADMIXTURE and RFMix.The results showed that one of the four tested individuals contained 54.8% of commercial pig ingredients and 45.2% of Southern China pig ingredients,the other contained 81.3% of commercial pig ingredients,while the remaining two contained more than 97.0% of commercial pig ingredients.When the ancestral group was set as 12 groups,it was found that one of them contained 64.8% Duroc and 35.2% Luchuan pig;the other contained more complex ancestral components,including 22.5% Landrace,27.6% Large White,8.6% Wuzhishan,5.5% Erhualian,Meishan,Jiangquhai and Bama Xiang;the remaining were about 1.2%.The ancestors of the remaining two pigs were mainly Duroc,Large White and Pietran.In addition,the progeny judgment of mitochondria suggested that the maternal origin of one pig might be from Luchuan or similar local breeds.Through the commonly used method of ancestral analysis,the ancestral components of four pigs were estimated,and find that the genetic components of four pigs were different,and the ancestral components and proportion of different individuals were found.The results showed that the genetic component sources of each test individual could be estimated by the method of ancestral analysis.Using ancestral components as genetic characteristics could provided important genetic reference for brand pork identification and brand protection,as well as guidance and reference for the protection and development of local pig breeds in China.

Key words: pig; SNP; mtDNA; population structure; genetic component

中图分类号:

卜李那, 彭业博, 张春媛, 刘洋秀, 赵毅强. 基于祖源分析的猪遗传成分鉴定[J]. 中国畜牧兽医, 2020, 47(2): 544-553.

BU Lina, PENG Yebo, ZHANG Chunyuan, LIU Yangxiu, ZHAO Yiqiang. A Ancestry Analysis of Genetic Components of Pigs[J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(2): 544-553.

参考文献

[1] 国家畜禽资源遗传资源委员会.中国畜禽遗传资源志猪志[M].北京:中国农业出版社,2011. CHINA NATIONAL COMMISSION of ANIMAL GENETIC RESOURCES.Animal Genetic Resources in China:Pigs[M].Beijing:China Agriculture Press,2011.(in Chinese)
[2] 余群莲,鲁兴容,黄明发,等.土猪和国外引进猪肉质性状差异[J].肉类工业,2014,9:20-22. YU Q L,LU X R,HUANG M F,et al.Difference of meat quality trait between local pig and imported pig[J].Meat Industry,2014,9:20-22.(in Chinese)
[3] 余德谦.土猪生产发展现状与展望[J].广东畜牧兽医科技,2012,5:13-14. YU D Q,The present situation and prospect of the development of native pig production[J].Guangdong Journal of Animal and Veterinary Science,2012,5:13-14.(in Chinese)
[4] 陈其美,葛长利,董彬.中国地方猪种种质资源的保护与利用[J].中国猪业,2013,S2:160-163. CHEN Q M,GE C L,DONG B.Protection and utilization of pig genetic reources of Chinese indigenous breeds[J].Chinese Swine Industry,2013,S2:160-163.(in Chinese)
[5] 郭源梅,李龙云,赖昭胜,等.中国地方猪种利用现状与展望[J].江西农业大学学报,2017,3:427-435. GUO Y M,LI L Y,LAI Z S,et al.Present status and prospect of utilization of indigenous pig breeds in China[J].Acta Agriculture Universitatis Jiangxiensis,2017,3:427-435.(in Chinese)
[6] PIERRON D,HEISKE M,RAZAFINDRAZAKA H,et al.Strong selection during the last millennium for African ancestry in the admixed population of Madagascar[J].Nature Communications,2018,9(1):932.
[7] WANG Y,LU D,CHUNG Y J,et al.Genetic structure,divergence and admixture of Han Chinese,Japanese and Korean populations[J].Hereditas,2018,155:19.
[8] CHEN N,HUANG J,ZULFIQAR A,et al.Population structure and ancestry of Qinchuan cattle[J].Animal Genetics,2018,49(3):246-248.
[9] PILOT M,GRECO C,VONHOLDT B M,et al.Widespread,long-term admixture between grey wolves and domestic dogs across Eurasia and its implications for the conservation status of hybrids[J].Evolutionary Applications,2018,11(5):662-680.
[10] MONZON J,KAYS R,DYKHUIZEN D E.Assessment of coyote-wolf-dog admixture using ancestry-informative diagnostic SNPs[J].Molecular Ecology,2014,23(1):182-197.
[11] LU M,LEWIS C M,TRAYLOR M.Pharmacogenetic testing through the direct-to-consumer genetic testing company 23andMe[J].BMC Medical Genomics,2017,10(1):47.
[12] KULYNYCH J,GREELY,H T.Clinical genomics,big data,and electronic medical records:reconciling patient rights with research when privacy and science collide[J].Journal of Bioscience and Bioengineering,2017,4(1):94-132.
[13] CHEN N,CAI Y,CHEN Q,et al.Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia[J].Nature Communications,2018,9(1):2337.
[14] LIANG Z,BU L,QIN Y,et al.Selection of optimal ancestry informative markers for classification and ancestry proportion estimation in pigs[J].Frontiers in Genetics,2019,10:183.
[15] DELANEAU O,COULONGES C,ZAGURY J F.Shape-IT:new rapid and accurate algorithm for haplotype inference[J].BMC Bioinformatics,2008,9:540.
[16] PURCELL S,NEALE B,TODD-BROWN K,et al.PLINK:A tool set for whole-genome association and population-based linkage analyses[J].American Journal of Human Genetics,2007,81(3):559-575.
[17] PATTERSON N,PRICE A L,REICH D.Population structure and eigen analysis[J].PLoS Genetics,2006,2(12):e190.
[18] FELSENSTEIN J.Evolutionary trees from DNA sequences:A maximum likelihood approach[J].Journal of Molecular Evolutio,1981,17(6):368-376.
[19] ALEXANDER D H,NOVEMBRE J,LANGE K.Fast model-based estimation of ancestry in unrelated individuals[J].Genome Research,2009,19(9):1655-1664.
[20] MAPLES B K,GRAVEL S,KENNY E E,et al.RFMix:A discriminative modeling approach for rapid and robust local-ancestry inference[J].American Journal of Human Genetics,2013,93(2):278-288.
[21] 周永娜,刘华淼,鞠妍,等.牛、羊、马及鹿科动物母系起源和父系起源研究进展[J].特产研究,2017,4:52-57. ZHOU Y N,LIU H M,JU Y,et al.Research progress on maternal and paternal origin of cattle,sheep,horse and cervidae[J].Special Wild Econimic Animal and Plant Research,2017,4:52-57.(in Chinese)
[22] DING J,SIDORE C,BUTLER T J,et al.Assessing mitochondrial DNA variation and copy number in lymphocytes of~2,000 sardinians using tailored sequencing analysis tools[J].PLoS Genetics,2015,11(7):e1005306.
[23] GUINDON S,GASCUEL O.A simple,fast,and accurate algorithm to estimate large phylogenies by maximum likelihood[J].Systematic Biology,2003,52(5):696-704.
[24] LETUNIC I,BORK P.Interactive tree of life (iTOL) v3:An online tool for the display and annotation of phylogenetic and other trees[J].Nucleic Acids Research,2016,44(W1):W242-W245.
[25] LIU Y,NYUNOYA T,LENG S,et al.Softwares and methods for estimating genetic ancestry in human populations[J].Human Genomics,2013,7:1.
[26] POHJOISMAKI J,LAMPI S,DONNER J,et al.Origins and wanderings of the finnish hunting spitzes[J].PLoS One,2018,13(6):e0199992.
[27] NORRIS E T,WANG L,CONLEY A B,et al.Genetic ancestry,admixture and health determinants in Latin America[J].BMC Genomics,2018,19(S8):861.
[28] JINYOUNG B,YOUNGHUN H,GORLOV I P,et al.Ancestry inference using principal component analysis and spatial analysis:a distance-based analysis to account for population substructure[J].BMC Genomics,2017,18(1):789.
[29] YAO H B,WANG C C,WANG J,et al.Genetic structure of Tibetan populations in Gansu revealed by forensic STR loci[J].Scientific Reports,2017,7:41195.
[30] CHACONDUQUE J C,ADHIKARI K,FUENTESGUAJARDO M,et al.Latin Americans show wide-spread converso ancestry and imprint of local native ancestry on physical appearance[J].Nature Communications,2018,9(1):5388.
[31] FOSSOY F,SORENSON M D,LIANG W,et al.Ancient origin and maternal inheritance of blue cuckoo eggs[J].Nature Communications,2016,7(1):10272.
[32] MARIN J,ROMERO K,RIVERA R,et al.Y-chromosome and mtDNA variation confirms independent domestications and directional hybridization in South American camelids[J].Animal Genetics,2017,48(5):591-595.
[33] XIA X,YU J,ZHAO X,et al.Genetic diversity and maternal origin of Northeast African and South American donkey populations[J].Animal Genetics,2019,50(3):266-270.
[34] ZHANG T,LIU H,YANG L K,et al.The complete mitochondrial genome and molecular phylogeny of Lueyang black-bone chicken[J].British Poultry Science,2018,59(6):618-623.
[35] YANG L,KONG X,YANG S,et al.Haplotype diversity in mitochondrial DNA reveals the multiple origins of Tibetan horse[J].PLoS One,2018,13(7):e0201564.
[36] MA H,WU Y,XIANG H,et al.Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences[J].PeerJ,2018,6:e4896.
[37] SIMAO F,STROBL C,VULLO C,et al.The maternal inheritance of Alto Paraná revealed by full mitogenome sequences[J].Forensic Science International-genetics,2019,39:66-72.
[38] ABDELKAFY E M,AHMED S,ELKEREDY A,et al.Genetic and phenotypic characterization of the native rabbits in Middle Egypt[J].Veterinary World,2018,11(8):1120-1126.
[39] 李彩霞,贾竟,魏以梁,等.30个祖先信息位点的筛选及应用[J].遗传,2013,36(8):779-785. LI C X,JIA J,WEI Y L,et al.The selection of 30 ancestry informative markers and their application in ancestry inference[J].Hereditas, 2013,36(8):779-785.(in Chinese)
[40] ZENG X,CHAKRABORTY R,KING J L,et al.Selection of highly informative SNP markers for population affiliation of major US populations[J].International Journal of Legal Medicine,2016,130(2):341-352.
[41] YANG B,CUI L,PEREZ-ENCISO M,et al.Genome-wide SNP data unveils the globalization of domesticated pigs[J].Genetics Selection Evolution,2017,49(1):71.
[42] CHEN M,SU G,FU J,et al.Population admixture in Chinese and European Sus scrofa[J].Scientific Reports,2017,7(1):13178.
[43] AI H,FANG X,YANG B,et al.Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing[J].Nature Genetics,2015,47(3):217-225.
[44] 胡元品,李朝英.可乐猪品种资源现状及其开发利用[J].当代畜禽养殖业,2017,5:60. HU Y P,LI C Y.Present situation,development and utilization of KeLe pig genetic resources[J].Modern Animal Husbandry,2017(5):60.(in Chinese)
[45] 顾平生.云南地方猪种优良肉质的开发利用[J].云南畜牧兽医,2016,4:34-35. GU P S.Development and utilization of local pig excellent meat quality in Yunnan province[J].Yunnan Journal of Animal Science and Veterinary Medicine,2016,4:34-35.(in Chinese)
[46] 周传臣.民猪开发利用的方式及其意义[J].当代畜禽养殖业,2015,3:20. ZHOU C C.Methods and significance of development and utilization of Min pig[J].Modern Animal Husbandry,2015,3:20.(in Chinese)
[47] 赵旭庭,朱满兴,潘雨来,等.江苏地方猪遗传资源保护与开发利用[J].江苏农业科学,2018,46(19):187-189. ZHAO X T,ZHU M X,PAN Y L,et al.Protection,development and utilization of local pig genetic resources in Jiangsu province[J].Jiangsu Agricultural Sciences,2018,46(19):187-189.(in Chinese)