广东省现有5个地方猪种基于SNP芯片的遗传多样性分析
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摘要
本研究以广东省现有的5个地方猪品种为对象,利用SNP芯片进行SNP分型,对比欧洲野猪、亚洲野猪以及4个西方商业猪种,对广东省现有地方猪品种的遗传多样性、遗传距离以及群体结构进行分析。结果表明:两广小耳花猪、大花白猪和蓝塘猪的遗传多样性低于西方商业猪种以及粤东黑猪和梅花猪;广东省地方猪与亚洲野猪遗传距离较近,与西方猪种遗传距离较远;作为大花白猪一个类群的梅花猪与大花白猪遗传距离较远,主成分分析以及Structure分析表明梅花猪与大花白猪遗传差异较大,梅花猪具有独特的遗传结构并存在西方猪血液的渗入;粤东黑猪与西方猪种遗传距离较近,粤东黑猪也存在西方猪种血液的渗入。综上所述,两广小耳花猪、大花白猪和蓝塘猪的遗传多样性较低,梅花猪和粤东黑猪存在西方猪种血液的渗入。
The analyse of genetic diversity, genetic distance and population structure of the five Cantoness indigenous pig breeds were performed using SNP chip. The European, Asian wild boars and four commercial pig breeds were included in this study as controls. The results showed that XE, DHB, and LT pigs are low in genetic diversity compared with the western commercial pig breed, YDH and MH pig; Cantonese indigenous pig breeds had near genetic distance with Asian wild boars and large with western pig breeds; The MH pig, which was a subpopulation of DHB pig, has large genetic distance with the DHB, principal components analysis and STRUCTURE analysis showed the genetic difference between the two breeds, the MH pig has its special genetic structure and genetic introgression from the Western pigs was observed; The YDH pig has near genetic distance with the western pig breeds, genetic introgression from the Western pigs was also observed in the YDH pig. In conclusion, the XE, DHB, and LT pigs are low in genetic diversity, genetic introgression from the Western pigs was also observed both in MH and YDH pig.
The analyse of genetic diversity, genetic distance and population structure of the five Cantoness indigenous pig breeds were performed using SNP chip. The European, Asian wild boars and four commercial pig breeds were included in this study as controls. The results showed that XE, DHB, and LT pigs are low in genetic diversity compared with the western commercial pig breed, YDH and MH pig; Cantonese indigenous pig breeds had near genetic distance with Asian wild boars and large with western pig breeds; The MH pig, which was a subpopulation of DHB pig, has large genetic distance with the DHB, principal components analysis and STRUCTURE analysis showed the genetic difference between the two breeds, the MH pig has its special genetic structure and genetic introgression from the Western pigs was observed; The YDH pig has near genetic distance with the western pig breeds, genetic introgression from the Western pigs was also observed in the YDH pig. In conclusion, the XE, DHB, and LT pigs are low in genetic diversity, genetic introgression from the Western pigs was also observed both in MH and YDH pig.
引文
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[3]唐立群,肖层林,王伟平.SNP分子标记的研究及其应用进展[J].中国农学通报,2012,28(12):154-158.
[4]Ai H,Huang L S,Ren J.Genetic diversity,linkage disequilibrium and selection signatures in chinese and Western pigs revealed by genome-wide SNP markers[J].PLoS One,2013,8(2):e56001.
[5]Makina S O,Muchadeyi F C,Marlek鰏ter E V,et al.Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel[J].Front Genet,2014,5:333.
[6]于辉,刘荣辉,李华,等.猪5个群体SLA微卫星遗传多样性[J].遗传,2012,34(11):1427-1433.
[7]刘德武,杨关福,李加琪,等.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,2002,33(1):18-22.
[8]张冬杰,刘娣,何鑫淼,等.中国地方猪品种的遗传多样性与聚类分析[J].畜牧与兽医,2015,47(10):1-4.
[9]Goedbloed D J,Megens H J,Van H P,et al.Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations[J].Mol Ecol,2013,22(3):856-866.
[10]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 Human Genet,2007,81(3):559-575.
[11]Szpiech Z A,Jakobsson M,Rosenberg N A.ADZE:a rarefaction approach for counting alleles private to combinations of populations[J].Bioinformatics,2008,24(21):2498-2504.
[12]Tamura K,Dudley J,Nei M,et al.MEGA4:molecular evolutionary genetics analysis(MEGA)software version 4.0[J].Mol Biol Evol,2007,24(8):1596-1599.
[13]Yang J,Lee S H,Goddard M E,et al.GCTA:a tool for genome-wide complex trait analysis[J].Am J Human Genet,2011,88(1):76-82.
[14]Pritchard J K,Stephens M,Donnelly P.Inference of population structure using multilocus genotype data[J].Genetics,2000,155(2):945-959.
[15]Traspov A,Deng W,Kostyunina O,et al.Population structure and genome characterization of local pig breeds in Russia,Belorussia,Kazakhstan and Ukraine[J].Genet Sel Evol,2016,48(1):57.
[16]胡鸿惠,彭国良,肖正中.梅花猪品种资源的保护与遗传保种研究探讨[J].中国畜牧兽医,2015(4):1004-1008.