基于SNP芯片的云上黑山羊遗传结构分析
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摘要
为从分子水平对云上黑山羊遗传结构做出评价,本研究以云上黑山羊核心群母羊108只(来自7个育种核心场、10个群体)、育种素材云岭黑山羊和努比山羊各11和14只、对照组波尔山羊10只为试验动物,用Illumina公司Iselect Goat60k芯片技术在全基因组范围内进行单核苷酸多态性(SNP)分析,并运用GenAlEx 6.5、Cervus 3.0、SNPRelate、Plink 1.07、Mega 4.0进行遗传多样性参数统计计算、主成分分析和系统进化树构建。试验获得143个样本在48 116个SNPs位点上的分型结果,其中波尔山羊10个样本单独聚集,与云上黑山羊、努比山羊、云岭黑山羊存在较大的遗传距离,较小的遗传一致度和较小的基因流,在聚类进化树中显示为一个独立分支,这些结果与波尔山羊实际遗传背景完全一致,显示出它在本研究中的对照组作用,同时证明本研究方法可行、结果可靠;云上黑山羊108个样本具有高度一致性,在聚类系统树中这些样本聚为一个大簇,而努比山羊(14个)和云岭黑山羊(11个)的样本各自聚为一簇;UPGMA进化树显示,云上黑山羊与努比山羊关系较近,与云岭黑山羊关系稍远,这与云上黑山羊育种导血方案结果相一致。云上黑山羊新品种在基因组水平上可与其育种素材明显区分,在基因组层面已具备独立品种特点。
In order to evaluate the genetic structure in Yunshang Black goat at the molecular level,108 Yunshang Black goats from 10 families,11 Yunling Black goats,14 Nubian goats and 10 Boer goats(control group)were genotyped by Illumina Iselect Goat60 karray(SNP chip).Genetic diversity parameters statistics,principal component analysis and phylogenetic tree construction were performed by GenAlEx 6.5,Cervus 3.0,SNPRelate,Plink 1.07 and Mega 4.0.The typing results at 48 116 SNPs loci in 143 samples had been gotten.There was a great genetic distance between Boer goat and Yunshang Black goat,and a large genetic distance also existed between Boer goat and Nubian goat.Bore goat was displayed as an independent branch on the cluster tree.The results proofed the method of this study was practical and reliable.108 samples of Yunshang Black goats were high consistency,and these samples were clustered into a large cluster in the phylogenetic tree.The samples of Nubian goats(14)and Yunling Black goats(11)were clustered into a cluster.UPGMA evolution tree displayed that Yunshang Black goats were closely related toNubian goats,and had a little relationship with Yunling Black goats,which was consistent with the results of the breeding blood guide in Yunshang Black goat.Yunshang Black goat could be distinguished from the breeding material at the genomic level,which had genomic characteristics of an independent variety.
In order to evaluate the genetic structure in Yunshang Black goat at the molecular level,108 Yunshang Black goats from 10 families,11 Yunling Black goats,14 Nubian goats and 10 Boer goats(control group)were genotyped by Illumina Iselect Goat60 karray(SNP chip).Genetic diversity parameters statistics,principal component analysis and phylogenetic tree construction were performed by GenAlEx 6.5,Cervus 3.0,SNPRelate,Plink 1.07 and Mega 4.0.The typing results at 48 116 SNPs loci in 143 samples had been gotten.There was a great genetic distance between Boer goat and Yunshang Black goat,and a large genetic distance also existed between Boer goat and Nubian goat.Bore goat was displayed as an independent branch on the cluster tree.The results proofed the method of this study was practical and reliable.108 samples of Yunshang Black goats were high consistency,and these samples were clustered into a large cluster in the phylogenetic tree.The samples of Nubian goats(14)and Yunling Black goats(11)were clustered into a cluster.UPGMA evolution tree displayed that Yunshang Black goats were closely related toNubian goats,and had a little relationship with Yunling Black goats,which was consistent with the results of the breeding blood guide in Yunshang Black goat.Yunshang Black goat could be distinguished from the breeding material at the genomic level,which had genomic characteristics of an independent variety.
引文
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[2]字品文,江炎庭,相德才,等.云南黑山羊羊肉品质的研究[J].中国草食动物科学,2017,37(5):21-25.ZI P W,JIANG Y T,XIANG D C,et al.Study on meat quality traits of Yunan Black goat[J].China Herbivore Science,2017,37(5):21-25.(in Chinese)
[3]江炎庭,王鹏,洪琼花,等.放牧补饲条件下云南黑山羊生长发育规律研究[J].家畜生态学报,2015,36(11):52-56.JIANG Y T,WANG P,HONG Q H,et al.Growth and development of Yunnan Black goat raising under the grazing plus supplementary feeding mode[J].Journal of Domestic Animal Ecology,2015,36(11):52-56.(in Chinese)
[4]许家磊,王宇,后猛,等.SNP检测方法的研究进展[J].分子植物育种,2015,13(2):475-482.XU J L,WANG Y,HOU M,et al.Progress detection methods of SNP[J].Molecular Plant Breeding,2015,13(2):475-482.(in Chinese)
[5]张清峰,秦巧梅.高密度SNP芯片及其对肉牛育种影响的研究进展[J].中国畜牧兽医,2011,38(10):122-124.ZHANG Q F,QIN Q M.High density SNP chip impacts beef cattle breeding[J].China Animal Husbandry&Veterinary Medicine,2011,38(10):122-124.(in Chinese)
[6]董园园,盛海辉,杨茜,等.一种新的基于单碱基延伸的SNP芯片技术[J].遗传,2009,31(4):439-444.DONG Y Y,SHENG H H,YANG Q,et al.A new SNP microarray technology based on single base extension[J].Hereditas,2009,31(4):439-444.(in Chinese)
[7]兰蓉,朱兰,姚新荣,等.山羊产羔数全基因组关联分析[J].畜牧兽医学报,2015,46(4):549-554.LAN R,ZHU L,YAO X R,et al.Genome-wide association analysis of lambing number in goat[J].Acta Veterinaria et Zootechnica Sinica,2015,46(4):549-554.(in Chinese)
[8]MARTIN P,PALHIERE I,TOSSER K G,et al.Heritability and genome-wide association mapping for supernumerary teats in French Alpine and Saanen dairy goats[J].Journal of Dairy Science,2016,99(11):8891-8900.
[9]袁泽湖,王慧华,胡师金,等.利用50K芯片数据分析中国11个地方绵羊群体的遗传结构[J].畜牧兽医学报,2016,47(5):899-908.YUAN Z H,WANG H H,HU S J,et al.Population structure analysis of Chinese indigenous sheep by 50Kchip data[J].Acta Veterinaria et Zootechnica Sinica,2016,47(5):899-908.(in Chinese)
[10]DONG Y,XIE M,JIANG Y,et al.Sequencing and automated whole-genome optical mapping of the genome of a domestic goat(Capra hircus)[J].Nature Biotechnology,2013,31(2):135-141.
[11]白俊艳,庞有志,张小辉,等.3个鹌鹑群体的微卫星标记多态性分析[J].中国畜牧兽医,2015,42(9):2444-2452.BAI J Y,PANG Y Z,ZHANG X H,et al.Polymorphism analysis of 3quail groups by using microsatellite marker[J].China Animal Husbandry&Veterinary Medicine,2015,42(9):2444-2452.(in Chinese)
[12]兰蓉,朱兰,伍红德,等.云南肉山羊黑色品系遗传结构的微卫星分析[J].中国草食动物科学,2012,s1:21-25.LAN R,ZHU L,WU H D,et al.The study on the genetic structure of Yunnan Black meat goat strain using microsatellite markers[J].China Herbivore Science,2012,s1:21-25.(in Chinese)
[13]李晓雨,张纪刚,狄冉,等.利用微卫星标记分析5个山羊品种的遗传多样性和进化关系[J].安徽农业大学学报,2015,42(4):520-528.LI X Y,ZHANG J G,DI R,et al.Genetic diversity and phylogenetic relationship of five goat breeds based on microsateuite markers[J].Journal of Anhui Agricultural University,2015,42(4):520-528.(in Chinese)
[14]陈蓉,王晓云,宋毓宁,等.基于SRAP和SNP分子标记的国内穿心莲遗传多样性分析[J].中国中药杂志,2014,39(23):4559-4565.CHEN R,WANG X Y,SONG Y N,et al.Genetic diversity analysis of Andrographis paniculatain China based on SRAP and SNP[J].China Journal of Chinese Materia Medica,2014,39(23):4559-4565.(in Chinese)
[15]于磊,刘炳舰,刘进贤.日本鳗鲡离散SNP标记筛选及群体遗传多样性分析[J].中国海洋大学学报(自然科学版),2018,4:37-47.YU L,LIU B J,LIU J X.Outlier SNPs development and preliminary genetic diversity analysis of Japanese Eel(Anguilla japonica)[J].Periodical of Ocean University of China,2018,48(4):37-47.(in Chinese)
[16]ALAIN V,DENIS M,MAGALI S C,et al.A review on SNP and other types of molecular markers and their use in animal genetics[J].Genetics Selection Evolution,2002,34(3):275-305.
[17]WU K,YANG M,LIU H,et al.Genetic analysis and molecular characterization of Chinese sesame(Sesamum indicum L.)cultivars using insertion-deletion(InDel)and simple sequence repeat(SSR)markers[J].BMC Genetics,2014,15(1):35.
[18]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.
[19]马克平.试论生物多样性的概念[J].生物多样性,1993,1(1):20-22.MA K P.On the concept of biodiversity[J].Biodiversity Science,1993,1(1):20-22.(in Chinese)
[20]FRANKHAM R,BALLOU J D,BRISCOE D A.Introduction to Conservation,Genetics[M].Cambridge:Cambridge University Press,2002.
[21]WRIGHT S.Evolution and the genetics of populations[J].Physiological&Biochemical Zoology,1968,8(1):1191-1192.
[22]WRIGHT S G.Evolution in mendelian population[J].Bulletin of Mathematical Biology,1990,52(1-2):241-295.
[23]NEI M.Genetic distance between populations[J].American Naturalist,1972,106:283-292.