10个云南地方猪种微卫星遗传多样性分析

doi:10.16431/j.cnki.1671-7236.2018.04.020

摘要/Abstract

摘要：

为阐明保山猪、迪庆藏猪、高贡黎山猪、丽江猪、明光小耳猪、滇南小耳猪、撒坝猪、大河猪、昭通猪、大河乌猪10个云南省优良地方猪种的群体遗传多样性和遗传结构，本试验参考ArkDB数据库中家猪14条染色体上的15对微卫星引物，对549个云南地方猪个体的耳组织样品进行了检测分析，计算各微卫星座位等位基因数（Na）、有效等位基因数（Ne）、Shannon's信息指数（I）、表观杂合度（Ho）、期望杂合度（He）、F-统计量（Fis、Fit、Fst）、基因流（Nm）、群体遗传距离等相关参数及多态信息含量（PIC），采用NTsys 2.10软件构建聚类树，并采用STRUCTRUE 2.3.3软件评估群体遗传结构。结果显示：15个微卫星座位共检测到293个等位基因，各座位等位基因数在5~38个之间，平均等位基因数为19个，平均有效等位基因数8.3682个；10个云南地方猪群体的Shannon多样性、表观杂合度、期望杂合度和多态信息含量分别在1.4374~2.0317、0.6389~0.7756、0.7021~0.8281和0.6647~0.7993之间。各座位单个群体内近交系数（Fis）、总群体近交系数（Fit）、群体间遗传分化系数（Fst）的变化范围分别为-0.0678~0.4594、0.0618~0.5567和0.0713~0.1801；群体间Fst平均值为0.1101，处于中度遗传分化状态，有11.01%的遗传变异来自于群体间，大部分遗传变异来自于群体内；每个座位基因流程度较高，变化范围在1.6392~3.2551之间，平均值为2.0214。基于Nei氏遗传距离构建UPGMA系统发生树显示，高黎贡山猪与迪庆藏猪聚为一支，并与丽江猪、保山猪和明光小耳猪聚为一大支，其结果得到了STRUCTURE分析的验证。综上所述，10个云南地方猪种遗传多样性丰富，群体内有近交现象，群体间处于中度遗传分化，存在着一定的基因交流。

关键词: 云南地方猪种; 微卫星标记; 遗传多样性; 遗传结构

Abstract:

Baoshan pig,Diqing Tibetan pig,Gaoli Gongshan pig,Lijiang pig,Mingguang Small-ear pig,Diannan Small-ear pig,Saba pig,Dahe pig,Zhaotong pig and Dahe Black pig are ten local pig breeds with excellent breed characteristics in Yunnan province,China.To assess their genetic diversity and genetic structure,a total of 549 unrelated ear tissue samples from the ten indigenous pig breeds were genotyped using 15 fluorescence-labeled microsatellite DNA markers of 14 chromosomes in the ArkDB database.The number of alleles (Na),effective allele number (Ne),Shannon's information index (I),apparent heterozygosity (Ho),expected heterozygosity (He), F-statistics(Fis,Fit,Fst),gene flow (Nm),population genetic distance and other related parameters and polymorphic information content (PIC) were determined,cluster tree was built by NTsys 2.10,and STRUCTRUE 2.3.3 software was used to evaluate the genetic structure of the population.The results showed that the Na of 15 microsatellite loci was 293,ranging from 5 to 38 alleles per locus.The mean number of alleles and effective number of alleles per locus were found to be 19 and 8.3682,respectively.The average Shannon's information index,observed heterozygosity,expected heterozygosity and polymorphism information content of 10 indigenous pig populations ranged from 1.4374 to 2.0317,0.6389 to 0.7756,0.7021 to 0.8281,0.6647 to 0.7993,respectively.The average inbreeding coefficient within accessions (Fis) and overall inbreeding coefficient (Fit) per locus ranged from -0.0678 to 0.4594 and 0.0618 to 0.5567,respectively.The moderate degree of genetic differentiation index (Fst) ranged from 0.0713 to 0.1801 with an average of 0.1101,which demonstrated that approximately 11.01% of genetic variations were among populations and 88.99% of genetic differences were within populations.The high level of gene flow at each locus was discovered from 1.6392 to 3.2551,with a mean Nm of 2.0214.The phylogenetic relationships of pig breeds were constructed using UPGMA method based on Nei's genetic distance.The UPGMA dendrogram showed that the Gaoli Gongshan pig and Diqing Tibetan pig jointed as one cluster.And then joined with Baoshan pig,Lijiang pig and Mingguang Small-ear pig breeds as a big group.STRUCTURE analysis confirmed the analysis result observed in the UPGMA tree.The study indicated that the genetic diversity was abundant in ten Yunnan local pig breeds.There were close inbreeding phenomenon in the ten breeds.The level of genetic differentiation among populations was moderately,with a certain amount of gene flow.

Key words: Yunnan local pig breeds; microsatellite markers; genetic diversity; genetic structure

中图分类号:

S813

欧阳依娜, 江炎庭, 孙利民, 袁跃云, 李东江, 梁家充, 洪琼花. 10个云南地方猪种微卫星遗传多样性分析[J]. 《中国畜牧兽医》, 2018, 45(4): 992-1001.

OUYANG Yina, JIANG Yanting, SUN Limin, YUAN Yueyun, LI Dongjiang, LIANG Jiachong, HONG Qionghua. Genetic Diversity Analysis of Ten Yunnan Local Pig Breeds Using Microsatellite DNA Markers[J]. , 2018, 45(4): 992-1001.

参考文献

[1] 国家畜禽遗传资源委员会.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 Genetics Resources in China·Pigs[M].Beijing:China Agriculture Press,2011.(in Chinese)
[2] 云南省畜禽遗传资源委员会.云南省畜禽遗传资源志[M].昆明:云南科技出版社,2015. YUNNAN COMMISSION OF ANIMAL GENETIC RESOURCES.Animal Genetics Resources in Yunnan Province[M].Kunming:Yunnan Science and Technology Press,2015.(in Chinese)
[3] CORTÉS O,MARTINEZ A M,CAÑON J,et al.Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information[J].Heredity,2016,117(1):14-24.
[4] CHOI S K,LEE J E,KIM Y J,et al.Genetic structure of wild boar (Sus scrofa) populations from East Asia based on microsatellite loci analyses[J].BMC Genetics,2014,15(1):85-95.
[5] 王月月,刘雪雪,董坤哲,等.7种家养动物全基因组微卫星分布的差异研究[J].中国畜牧兽医,2015,42(9):2418-2426. WANG Y Y,LIU X X,DONG K Z,et al.Distribution difference of microsatellite in 7 domestic animals genomes[J].China Animal Husbandry & Veterinary Medicine,2015,42(9):2418-2426.(in Chinese)
[6] CHANDRA A,GRISHAM M P,PAN Y B.Allelic divergence and cultivar-specific SSR alleles revealed by capillary electrophoresis using fluorescence-labeled SSR markers in sugarcane[J].Genome,2014,57(6):363.
[7] 权金强,苟潇,赵生国.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,2015,33(4):422-428. QUAN J Q,GOU X,ZHAO S G.The genetic diversity of mitochondrial dna d-Loop in Yunnan native pigs[J].Journal of Sichuan Agricultural University,2015,33(4):422-428.(in Chinese)
[8] 董新星,杨婷,屈再久,等.云南高黎贡山猪微卫星DNA多态性分析[J].浙江畜牧兽医,2010,35(1):1-4. DONG X X,YANG T,QU Z J,et al.Polymorphism analysis of microsatellite DNA for Gaoli Gongshan pig from Yunnan[J].Zhejiang Journal Animal Science and Veterinary Medicine,2010,35(1):1-4.(in Chinese)
[9] 霍金龙,苗永旺,霍海龙,等.明光小耳猪遗传多样性分析[J].畜牧兽医学报,2009,40(2):272-279. HOU J L,MIAO Y W,HUO H L,et al.Analysis of genetic diversity of Mingguang Small-ear pig[J].Chinese Journal of Animal and Veterinary Sciences,2009,40(2):272-279.(in Chinese)
[10] 霍金龙,霍海龙,苗永旺,等.大河猪76个STR基因座的遗传多态性[J].动物学研究,2009,30(1):105-108. HOU J L,HUO H L,MIAO Y W,et al.Genetic diversity of 76 STR loci in the Dahe pig[J].Zoological Research,2009,30(1):105-108.(in Chinese)
[11] 张亚妮,张恩平,吴迪,等.两个藏猪类群微卫星DNA遗传多样性的研究[J].西北农林科技大学学报(自然科学版),2004,32(6):23-26. ZHANG Y N,ZHANG E P,WU D,et al.Microsatellite DNA genetic diversity study on two pig populations[J].Journal of Northwest A & F University (Natural Science Edition),2004,32(6):23-26.(in Chinese)
[12] 萨姆布鲁克J,拉塞尔D W.分子克隆实验指南(第3版)[M].北京:科学出版社,2002. SAMBROCK J,RUSSEL D W.Molecular Cloning:A Laboratory Manual (Third edition)[M].Beijing:Science Press,2002.(in Chinese)
[13] YEH F C,YANG R,BOYLE T.POPGENE Version 1.32 Microsoft Windows-Based Freeware for Population Genetic Analysis[M].Edmonton:University of Alberta,1999.
[14] EVANNO G,REGNAUT S,GOUDET J.Detecting the number of clusters of individuals using the software STRUCTURE:A simulation study[J].Molecular Ecology,2005,14(8):2611-2620.
[15] FRANKHAM R,BALLOU J D,BRISCOE D A.Introduction to Conservation Genetics[M].Cambridge:Cambridge University Press,2002.
[16] 陈祥,丁玫,许厚强,等.贵州5个地方猪品种微卫星标记的遗传多样性[J].中国畜牧杂志,2015,51(7):1-5. CEHN X,DING M,XU H Q,et al.Genetic diversity of microsatellite markers in five domestic pig breeds in Guizhou province[J].Chinese Journal of Animal Science,2015,51(7):1-5.(in Chinese)
[17] 孙俊丽,张冰,潘天彪,等.基于微卫星位点研究7个广西地方猪种的遗传关系[J].西南农业学报,2016,29(6):1475-1480. SUN J L,ZHANG B,PAN T B,et al.Genetic diversity of seven Guangxi local pig breeds assessed with microsatellite markers[J].Southwest China Journal of Agricultural Sciences,2016,29(6):1475-1480.(in Chinese)
[18] MONTENEGRO M,LLAMBÍ S,CASTRO G,et al.Genetic characterization of Uruguayan Pampa Rocha pigs with microsatellite markers[J].Genetics and Molecular Biology,2015,38(1):48-54.
[19] 章学东,李庆海,童训权,等.淳安花猪保种群种质结构分析与比较[J].浙江农业学报,2015,27(7):1154-1159. ZHANG X D,LI Q H,TONG X Q,et al.Germplasm structure analysis and comparison of conservation population of Chun'an spotted pigs[J].Acta Agriculturae Zhejiangensis,2015,27(7):1154-1159.(in Chinese)
[20] PHAM L D,DO D N,NAM L Q,et al.Molecular genetic diversity and genetic structure of vietnamese indigenous pig populations[J].Journal of Animal Breeding and Genetics,2014,131(5):379-386.
[21] SAHOO N R,NESA N,NASKAR S,et al.Microsatellite and mitochondrial diversity analysis of native pigs of Indo-Burma biodiversity hotspot[J].Animal Biotechnology,2016,27(1):52-59.
[22] 白小青,范首君,王金勇,等.5个重庆地方猪种遗传多样性的微卫星分析[J].畜牧兽医学报,2010,41(12):1515-1522. BAI X Q,FAN S J,WANG J Y,et al.Genetic diversity of five native pig breeds of Chongqing based on microsatellite DNA markers[J].Chinese Journal of Animal and Veterinary Sciences,2010,41(12):1515-1522.(in Chinese)
[23] 江燕,钟晓琳,王明民,等.南阳黑猪与栾川黑猪的种群遗传关系研究[J].家畜生态学报,2013,34(5):11-15. JIANG Y,ZHONG X L,WANG M M,et al.Genetic relationship between Nanyang Black pig and Luanchuan Black pig[J].Journal of Domestic Animal Ecology,2013,34(5):11-15.(in Chinese)
[24] BOTSTEIN D,WHITE R L,SKOLNICK M,et al.Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J].American Journal of Human Genetics,1980,32(3):314-331.
[25] LI X,YANG S,TANG Z,et al.Genome-wide scans to detect positive selection in Large White and Tongcheng pigs[J].Animal Genetics,2014,45(3):329-339.
[26] WRIGHT S.Evolution in mendelian population[J].Genetics,1931,16(2):97-159.