广灵驴分子系谱的建立及群体遗传结构分析

doi:10.11843/j.issn.0366-6964.2022.02.007

摘要/Abstract

摘要： 旨在对广灵县优种驴场保种群体进行调查的基础上构建分子系谱，并对其种群的遗传结构进行分析。本研究采集保种群成年、体况良好的广灵驴（体重350~400 kg）颈静脉血10 mL（n=107），其中公驴13份，母驴94份，抗凝处理后提取全血DNA。采用12个微卫星标记进行荧光PCR扩增后，用ABI3730测序仪进行分型。分型结果采用Cervus 2.0和Pedigraph 2.4软件构建分子系谱，同时采用STRUCTURE2.3和Fstat软件计算群体遗传参数，采用R语言的hclust函数绘制7头公驴及其后代的系统发生NJ树（邻接树）。结果，对107头种驴进行了分子系谱构建，找到了30头子代的父亲和7头子代的母亲，系谱可靠性>90%；微卫星标记的平均观测杂合度（H_Obs）和多态信息含量（PIC）分别为0.676 5和0.593 9，标记遗传多样性较高；NJ树对7个公驴家系进行了聚类；群体分化系数（F_ST）为0.184，群体平均近交系数（F_IT）为0.033，群体内近交系数（F_IS）为-0.238，且群体处于哈代-温伯格平衡状态，存在很弱的近交。本研究建立了广灵驴保种群可靠性较高的分子系谱并对其遗传结构进行了分析，证明该群体遗传多态性较高，群体近交系数较低，处于较好的保种状态，具有较大的品种资源开发潜力。

关键词: 广灵驴, 微卫星标记, 分子系谱, 群体遗传结构, 多态性

Abstract: This study aimed to construct the molecular pedigree based on investigating of Guangling donkey population in breeding farm, and analyze its genetic structure. A total of 107 (including 13 males and 94 females) jugular vein blood of healthy adult donkey (body weight:350-400 kg) were collected, after condensant treatment, the DNA was extracted. After using 12 SSR markers for fluorescence PCR amplification, the products were genotyped on ABI3730 sequencing instrument. The molecular pedigree was constructed by Cervus 2.0 and Pedigraph 2.4 softwares, and the population genetic parameters were calculated by STRUCTURE2.3 and Fstat softwares. Moreover, the phylogenetic tree(NJ tree)of 7 male donkey and their offspring was established by hclust function of R software. In all, 107 donkey were included in the molecular pedigree and only 30 offspring were matched with their fathers, and 7 offspring were matched with their mothers, the reliance level of pedigree was higher than 90%. The H_Ob and PIC of SSR markers were 0.676 5 and 0.593 9, respectively. NJ phylogenetic tree included 7 male families, the F_ST of the current population was 0.184, the F_IT was 0.033, and F_IS was -0.238, the population was in Hardy-Weinberg equilibrium. This study constructed a high reliable molecular pedigree of Guangling donkey and analyzed its genetic structure. The results show that the Guangling donkey population has high genetic polymorphisms, with low inbreeding coefficient. Therefore, it is worthful to preserve the genetic information and develop its breed potentials.

Key words: Guangling donkey, microsatellite markers, molecular pedigree, population genetic structure, polymorphism

中图分类号:

S822.2

牛晓艳, 曹亮, 明世清, 李燕平, 詹海杰, 姜志广, 卫顺生, 张元庆. 广灵驴分子系谱的建立及群体遗传结构分析[J]. 畜牧兽医学报, 2022, 53(2): 391-401.

NIU Xiaoyan, CAO Liang, MING Shiqing, LI Yanping, ZHAN Haijie, JIANG Zhiguang, WEI Shunsheng, ZHANG Yuanqing. Construction of Molecular Pedigree and Analysis of Population Genetic Structure of Guangling Donkey[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(2): 391-401.

参考文献 44

[1]	ROSSEL S,MARSHALL F,PETERS J,et al.Domestication of the donkey:timing,processes,and indicators[J].Proc Natl Acad Sci U S A,2008,105(10):3715-3720.
[2]	BLENCH R M,MACDONALD K C.The origins and development of African livestock:archaeology,genetics,linguistics and ethnography[M].London:University College London Press,2000.
[3]	WANG C F,LI H J,GUO Y,et al.Donkey genomes provide new insights into domestication and selection for coat color[J].Nat Commun,2020,11(1):6014.
[4]	BEJA-PEREIRA A,ENGLAND P R,FERRAND N,et al.African origins of the domestic donkey[J].Science, 2004, 304(5678):1781.
[5]	谢成侠.中国马驴品种志[M].上海:上海科学技术出版社,1987.XIE C X.Horse and ass breeds in China[M].Shanghai:Shanghai Scientific & Technical Publishers,1987.(in Chinese)
[6]	HAN H,CHEN N,JORDANA J,et al.Genetic diversity and paternal origin of domestic donkeys[J].Anim Genet,2017, 48(6):708-711.
[7]	HAN L,ZHU S B,NING C,et al.Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys[J].BMC Evol Biol,2014,14(1):246.
[8]	聂鸿瑶.广灵驴简介[J].辽宁畜牧兽医,1983(5):16-19.NIE H Y.Brief introduction of Guangling donkey[J].Liaoning Animal Husbandry and Veterinary Medicine,1983(5):16-19.(in Chinese)
[9]	梁全.广灵驴品种的保护与开发[J].中国畜牧业,2015(8):53-54.LIANG Q.Breed protection and development of Guangling donkey[J].China Animal Industry,2015(8):53-54.(in Chinese)
[10]	国家畜禽遗传资源委员会.中国畜禽遗传资源志-马驴驼志[M].北京:中国农业出版社,2011.National livestock and Poultry Genetic Resources Committee.Animal genetic resources in China horses,donkeys,camels[M].Beijing:China Agriculture Press,2011.(in Chinese)
[11]	闫俊峰.广灵驴特性和生长规律[J].农业技术与装备,2020(11):165-166.YAN J F.Characteristics and growth Law of Guangling donkey[J].Agricultural Technology & Equipment,2020(11):165-166.(in Chinese)
[12]	常洪.动物遗传资源学[M].北京:科学出版社,2009.CHANG H.Animal genetic resources[M].Beijing:Science Press,2009.(in Chinese)
[13]	GICQUEL E,BOETTCHER P,BESBES B,et al.Impact of conservation measures on demography and genetic variability of livestock breeds[J].Animal,2020,14(4):670-680.
[14]	张勇,肖礼华,陈祥,等.利用微卫星标记分析贵州地方鸡种的遗传多样性及亲缘关系[J].畜牧兽医学报, 2006,37(12):1274-1281.ZHANG Y,XIAO L H,CHEN X,et al.Analysis of genetic diversity and relationship among local chicken breeds in Guizhou by using microsatellites marker[J].Acta Veterinaria et Zootechnica Sinica,2006,37(12):1274-1281.(in Chinese)
[15]	王敏,张新浩,崔冉,等.利用微卫星标记鉴定德州驴亲子关系[J].中国畜牧兽医,2019,46(7):2003-2011.WANG M,ZHANG X H,CUI R,et al.Parentage testing of Dezhou Donkey with microsatellite marker[J].China Animal Husbandry & Veterinary Medicine,2019,46(7):2003-2011.(in Chinese)
[16]	NEI M.Molecular population genetics and evolution[M].New York:North-Holland Publishing Company,1975.
[17]	FRANKHAM R,BALLOU J D,BRISCOE D A.Introduction to conservation genetics[M].Cambridge:Cambridge University Press,2002.
[18]	纪志宾,王桂芝,王金凤,等.崂山奶山羊分子系谱的构建及家系遗传特征分析[J].中国农业科学,2011,44(13):2796-2807.JI Z B,WANG G Z,WANG J F,et al.Construction of molecular genealogy and analysis of family genetic characteristics in Laoshan dairy goat[J].Scientia Agricultura Sinica,2011,44(13):2796-2807.(in Chinese)
[19]	刘艳艳,谭晴晴,范阳阳,等.乌头驴和三粉驴微卫星遗传多态性分析[J].中国畜牧杂志,2017,53(1):44-50.LIU Y Y,TAN Q Q,FAN Y Y,et al.Genetic diversity analysis of Wutou Donkey and Sanfen Donkey[J].Chinese Journal of Animal Science,2017,53(1):44-50.(in Chinese)
[20]	杨虎,阿吉,王金富,等.新疆3个地方品种驴微卫星遗传分析[J].中国畜牧杂志,2008,44(1):8-10.YANG H,A J,WANG J F,et al.Genetic analysis of three ingenious breeds of Xinjiang Province[J].Chinese Journal of Animal Science,2008,44(1):8-10.(in Chinese)
[21]	JORDANA J,FERRANDO A,MIRÓ J,et al.Genetic relationships among American donkey populations:insights into the process of colonization[J].J Anim Breed Genet,2016,133(2):155-164.
[22]	ZENG L L,DANG R H,DONG H,et al.Genetic diversity and relationships of Chinese donkeys using microsatellite markers[J].Arch Anim Breed,2019,62(1):181-187.
[23]	DELL A,CURRY M,YARNELL K,et al.Genetic analysis of the endangered Cleveland Bay horse:a century of breeding characterised by pedigree and microsatellite data[J].PLoS One,2020,15(10):e0240410.
[24]	MCCUE M E,BANNASCH D L,PETERSEN J L,et al.A high density SNP array for the domestic horse and extant Perissodactyla:utility for association mapping,genetic diversity,and phylogeny studies[J].PLoS Genet,2012,8(1):e1002451.
[25]	MCCOY A M,MCCUE M E.Validation of imputation between equine genotyping arrays[J].Anim Genet,2014,45(1):153.
[26]	SCHUBERT M,JÓNSSON H,CHANG D,et al.Prehistoric genomes reveal the genetic foundation and cost of horse domestication[J].Proc Natl Acad Sci U S A,2014,111(52):E5661-E5669.
[27]	PETERSEN J L,MICKELSON J R,COTHRAN E G,et al.Genetic diversity in the modern horse illustrated from genome-wide SNP data[J].PLoS One,2013,8(1):e54997.
[28]	SCHAEFER R J,SCHUBERT M,BAILEY E,et al.Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds[J].BMC Genomics,2017,18(1):565.
[29]	FAWCETT J A,SATO F,SAKAMOTO T,et al.Genome-wide SNP analysis of Japanese Thoroughbred racehorses[J].PLoS One,2019,14(7):e0218407.
[30]	HAUSWIRTH R,HAASE B,BLATTER M,et al.Mutations in MITF and PAX3 cause "splashed white" and other white spotting phenotypes in horses[J].PLoS Genet,2012,8(4):e1002653.
[31]	NOLTE W,THALLER G,KUEHN C.Selection signatures in four German warmblood horse breeds:tracing breeding history in the modern sport horse[J].PLoS One,2019,14(4):e0215913.
[32]	AVILA F,MICKELSON J R,SCHAEFER R J,et al.Genome-wide signatures of selection reveal genes associated with performance in American Quarter Horse subpopulations[J].Front Genet,2018:9:249.
[33]	GURGUL A,JASIELCZUK I,SEMIK-GURGUL E,et al.A genome-wide scan for diversifying selection signatures in selected horse breeds[J].PLoS One,2019,14(1):e0210751.
[34]	王杰,王永,许期树,等.微卫星DNA在高原型藏山羊亲子鉴定中的应用研究[J].西南民族大学学报:自然科学版,2010,36(1):74-79.WANG J,WANG Y,XU Q S,et al.The application of microsatellite DNA in paternity testing for Tibetan goats[J].Journal of Southwest University for Nationalities:Natural Science Edition,2010,36(1):74-79.(in Chinese)
[35]	李成渤,王桂芝,纪志宾,等.崂山奶山羊微卫星标记与泌乳性状的相关分析[J].中国农业科学,2009,42(10):3639-3646.LI C B,WANG G Z,JI Z B,et al.Correlation analysis between microsatellite markers and milk performance traits in Laoshan Dairy Goat[J].Scientia Agricultura Sinica,2009,42(10):3639-3646.(in Chinese)
[36]	马建岗,路兴中.关于用Nei氏标准遗传距离推算畜禽分化时间的探讨[J].遗传,1992,14(3):37-39.MA J G,LU X Z.Discussion about estimating the time of divergence between animals with Nei's standard genetic distance[J].Hereditas,1992,14(3):37-39.(in Chinese)
[37]	WRIGHT S.Evolution and the genetics of Populations.Vol. 4.Variability within and among natural populations[M]. Chicago:University of Chicago Press,1978:35-49.
[38]	雷初朝,陈宏,杨公社,等.中国驴种线粒体DNA D-loop多态性研究[J].遗传学报,2005,32(5):481-486.LEI C Z,CHEN H,YANG G S,et al.Study on mitochondrial DNA D-loop polymorphism in Chinese donkeys[J].Acta Genetica Sinica,2005,32(5):481-486.(in Chinese)
[39]	雷初朝,陈宏,王德解,等.关中驴线粒体DNA D-loop多态性分析[J].中国畜牧杂志,2004,40(4):10-12.LEI C Z,CHEN H,WANG D J,et al.Analysis on Polymorphism of mtDNA D-loop Region in Guanzhong Donkey[J].Chinese Journal of Animal Science,2004,40(4):10-12.(in Chinese)
[40]	葛庆兰,雷初朝,蒋永青,等.中国家驴mtDNA D-loop遗传多样性与起源研究[J].畜牧兽医学报,2007,38(7):641-645.GE Q L,LEI C Z,JIANG Y Q,et al.Mitochondrial DNA D-loop genetic diversity and origin of chinese domestic donkeys[J].Acta Veterinaria et Zootechnica Sinica,2007,38(7):641-645.(in Chinese)
[41]	王全喜,陈建兴,闵令江,等.中国家驴品种遗传多样性及母系起源研究[J].内蒙古农业大学学报,2012,33(2):7-11.WANG Q X,CHEN J X,MIN L J,et al.Genetic Civersith and maternal origin of Chinese donkey breeds[J].Journal of Inner Mongolia Agricultural University,2012,33(2):7-11.(in Chinese)
[42]	XIA X,YU J,ZHAO X,et al.Genetic diversity and maternal origin of Northeast African and South American donkey populations[J].Anim Genet,2019,50(3):266-270.
[43]	ÖZKAN VNAL E,ÖZDIL F,KAPLAN S,et al.Phylogenetic relationships of Turkish indigenous donkey populations determined by mitochondrial DNA D-loop region[J].Animals,2020,10(11):1970.
[44]	MA X Y,NING T,ADEOLA A C,et al.Potential dual expansion of domesticated donkeys revealed by worldwide analysis on mitochondrial sequences[J].Zool Res,2020,41(1):51-60.