基于SNP芯片的盆周山地猪保种群体保种效果评估

doi:10.7668/hbnxb.20192586

摘要/Abstract

摘要：

为了更好地保护和利用盆周山地猪这一遗传资源,利用猪50K SNP芯片,对盆周山地猪保种群内所含的152头健康种猪进行了SNP检测,利用Plink软件计算群体的多态性标记比例、期望杂合度、观测杂合度,SNeP(V1.1)软件计算有效群体含量;利用Plink软件构建状态同源(IBS)矩阵,Gamatrix(V2)软件构建基因组关系G矩阵;利用Mega X(V10.0)分析盆周山地猪保种群家系结构;利用Plink软件计算每个样本的连续性纯合片段(ROH)个数和长度,并计算基于ROH的近交系数。结果表明,整个盆周山地猪保种群体的多态性标记比例为0.660 1,有效群体含量为7.4头;群体期望杂合度为0.289 2、观测杂合度为0.294 7;群体平均IBS遗传距离为(0.234 1± 0.027 3),公猪的平均IBS距离为(0.228 0±0.033 5);现有群体大致可分为5个包含公猪的家系和1个不含公猪的家系,家系A和D的公猪数量相对较少;在盆周山地猪保种群中共发现ROH片段3 737个,含21~25个ROH的个体数量占比最多(32.24%),ROH长度在100~200 Mb的个体数量占比最多(42.11%),群体平均近交系数为0.085。综上所述,盆周山地猪保种群体遗传多样性较丰富,但部分个体间存在较大的近交风险,群体家系较少,个别家系内公猪个体数量少,存在血统流失风险。

关键词: 盆周山地猪, 50K SNP芯片, 保种群体, 遗传结构, 保种效果

Abstract:

The aim of this study was to better understand the Penzhoushandi pigs.The 50K SNP chip was used to analyze the SNPs in 152 healthy adult Penzhoushandi pigs conserved population.The proportion of polymorphism markers,expected heterozygosity and observed heterozygosity were calculated by Plink software and the effective size of conserved population was calculated by SNeP(V1.1)software.The IBS distance matrix was analysed by Plink software and the genomic relationship G matrix was analyzed by Gamatrix(V2)software.The Mega X(V10.0)software was used to analysis the family structure of conserved population.The numbers and length of ROHs and inbreeding coefficient based on ROHs of each sample were calculated by Plink software.The results showed that the proportion of polymorphism markers was 0.660 1 and the effective size of conserved population was 7.4.The expected heterozygosity and observed heterozygosity were 0.289 2 and 0.294 7.The average IBS genetic distance of whole group was(0.234 1±0.027 3),and the average IBS genetic distance of boars was(0.228 0±0.033 5).The whole conserved group could be divided into 5 families with boars and 1 family without boars. The size of boars in family A and D was relatively small. A total of 3 737 ROHs,gatherring in individuals with the most ROHs by 21-25(32.24%)numbers and 100-200 Mb length(42.11%),were founded in the Penzhoushandi pigs conserved population.The average inbreeding coefficient of conserved population was 0.085.In general,the genetic diversity of the Penzhoushandi pigs conserved population was relatively rich,but there was also existing a risk of inbreeding among some individuals. The families in the conserved population were relatively less,and the number of boars in some families was small. Thus,there was a risk of ancestry loss in this families. Therefore,selection and breeding measures should be strengthened or extra ancestry should be introduced to ensure the long-term preservation of the genetic diversity of Penzhoushandi pigs.

Key words: Penzhoushandi pigs, 50K SNP chip, Conserved population, Genetic structures, Conservation effect

龙熙, 柴捷, 陈力, 潘红梅, 张亮, 陈四清, 郭宗义, 张廷焕. 基于SNP芯片的盆周山地猪保种群体保种效果评估[J]. 华北农学报, 2022, 37(S1): 358-365. doi: 10.7668/hbnxb.20192586.

LONG Xi, CHAI Jie, CHEN Li, PAN Hongmei, ZHANG Liang, CHEN Siqing, GUO Zongyi, ZHANG Tinghuan. Evaluation of the Conservation Effect in Penzhoushandi Conserved Population Based on SNP Chip[J]. Acta Agriculturae Boreali-Sinica, 2022, 37(S1): 358-365. doi: 10.7668/hbnxb.20192586.

http://www.hbnxb.net/CN/Y2022/V37/IS1/358

图/表 6

图1 基于IBS遗传距离矩阵的亲缘关系分析可视化结果每一个小方格代表第一个到最后一个样本两两之间的遗传距离值,该值越大越接近红色,即2个个体的遗传距离越大,反之亦然。

Fig.1 Visualization results of genetic relationship analysis based on IBS distance matrix Each small square represents the genetic distance value between two pairs from the first sample to the last one, the larger the value,the closer it is to red,that is,the larger the genetic distance between two individuals,vice versa.

图2 基于G矩阵的亲缘关系分析可视化结果图每一个小方格代表两两样本之间的基因组亲缘关系值,方格填充颜色越接近红色表示该值越大,即2个个体亲缘关系越近。

Fig.2 Visualization results of genetic relationship analysis based on G matrix Each small square represents the value of the relationship between two pairs from the first sample to the last one, the larger the value,the closer it is to red,that is,the closer relationship between two individuals.

图3 盆周山地猪保种群公猪聚类分析

Fig.3 Cluster analysis results of boars in the Penzhoushandi pig sconserved population

图4 盆周山地猪个体ROH片段个数分布

Fig.4 Distribution of ROH number in Penzhoushandi pigs

图5 盆周山地猪个体ROH长度分布

Fig.5 Distribution of ROH length in Penzhoushandi pigs

表1 盆周山地猪群体近交系数分布比例

Tab.1 Distribution ratio of inbreeding coefficient in Penzhoushandi pigs population

近交系数 Inbreeding coefficient	百分比/% Percentage
≥0.5	0
0.25~0.50	0
0.125~0.250	17.11
0.062 5~0.125 0	51.97
≤0.062 5	30.92

参考文献 38

[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 genetic resources in China pigs[M]. Beijing: China Agriculture Press, 2011.
[2]	孙嘉栋, 孙晓凤, 李兰, 沈伟, 程顺峰. 干细胞技术在地方猪种质资源保护中的应用前景[J]. 生物技术通报, 2020, 36(8):228-234. doi:10.13560/j.cnki.biotech.bull.1985.2020-0014. doi: 10.13560/j.cnki.biotech.bull.1985.2020-0014
	Sun J D, Sun X F, Li L, Shen W, Cheng S F. Application prospects of stem cell technology in the protection of indigenous porcine germplasm resources[J]. Biotechnology Bulletin, 2020, 36(8):228-234.
[3]	潘五岳. 浅谈地方猪遗传资源保护与利用[J]. 兽医导刊, 2020(14):21.
	Pan W Y. Talking about the protection and utilization of local pig genetic resources[J]. Veterinary Orientation, 2020(14):21.
[4]	朱丹, 陈四清, 郭宗义, 何朝勇, 郭恒翠, 李兴桂. 盆周山地猪保种选育初报[J]. 畜禽业, 2020, 31(9):6-7,10. doi:10.19567/j.cnki.1008-0414.2020.09.003. doi: 10.19567/j.cnki.1008-0414.2020.09.003
	Zhu D, Chen S Q, Guo Z Y, He C Y, Guo H C, Li X G. Preliminary report on the conservation and breeding of Penzhoushandi pigs[J]. Livestock and Poultry Industry, 2020, 31(9):6-7,10.
[5]	Jeffreys A J, Wilson V, Thein S L. Hypervariable minisatellite regions in human DNA[J]. Nature, 1985, 314(6006):67-73. doi:10.1038/314067a0. doi: 10.1038/314067a0 URL
[6]	吴丰春, 魏泓, 甘世祥. 贵州小型香猪群体遗传结构的RAPD分析[J]. 第三军医大学学报, 2000, 22(12):1162-1165. doi:10.16016/j.1000-5404.2000.12.016. doi: 10.16016/j.1000-5404.2000.12.016
	Wu F C, Wei H, Gan S X. RAPD analysis on genetic construction of Guizhou miniature pig population[J]. Acta Academiae Medicine Militaris Tertiae, 2000, 22(12):1162-1165.
[7]	李崇奇, 常青, 陈建琴, 张保卫, 朱立峰, 周开亚. 东北亚地区野猪种群mtDNA遗传结构及系统地理发生[J]. 动物学报, 2005, 51(4):640-649. doi:10.3969/j.issn.1674-5507. doi: 10.3969/j.issn.1674-5507
	Li C Q, Chang Q, Chen J Q, Zhang B W, Zhu L F, Zhou K Y. Population structure and phylogeography of the wild boar Sus scrofa in Northeast Asia based on mitochondrial DNA control region variation analysis[J]. Acta Zoologica Sinica, 2005, 51(4):640-649.
[8]	Ron M, Domochovsky R, Golik M, Seroussi E, Ezra E, Shturman C, Weller J I. Analysis of vaginal swabs for paternity testing and marker-assisted selection in cattle[J]. Journal of Dairy Science, 2003, 86(5):1818-1820. doi:10.3168/jds.S0022-0302(03)73767-9. doi: 10.3168/jds.S0022-0302(03)73767-9 pmid: 12778592
[9]	Nechtelberger D, Kaltwasser C, Stur I, Meyer J N, Brem G, Mueller M, Mueller S. DNA microsatellite analysis for parentage control in Austrian pigs[J]. Animal Biotechnology, 2001, 12(2):141-144. doi:10.1081/ABIO-100108340. doi: 10.1081/ABIO-100108340 pmid: 11808629
[10]	林丽, 王志刚, 刘榜, 李拥军, 赵小丽, 杨述林, 樊斌, 李奎, 肖炜. 利用5个多态蛋白(酶)位点分析6个地方猪品种的遗传结构[J]. 华中农业大学学报, 2001, 20(6):511-515. 10.3321/j.issn:1000-2421.2001.06.001.
	Lin L, Wang Z G, Liu B, Li Y J, Zhao X L, Yang S L, Fan B, Li K, Xiao W. Analysis of genetic structure of six Chinese indigenous pig breeds using five serum protein(enzyme)loci[J]. Journal of Huazhong Agricultural, 2001, 20(6):511-515.
[11]	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. doi:10.3969/j.issn.1000-6850.2012.12.028. doi: 10.3969/j.issn.1000-6850.2012.12.028
	Tang L Q, Xiao C L, Wang W P. Research and application progress of SNP markers[J]. Chinese Agricultural Science Bulletin, 2012, 28(12):154-158.
[12]	黄树文, 张哲, 陈赞谋, 袁晓龙, 李加琪, 张豪. 广东省现有5个地方猪种基于SNP芯片的遗传多样性分析[J]. 中国畜牧杂志, 2018, 54(6):33-37. doi:10.19556/j.0258-7033.2018-06-033. doi: 10.19556/j.0258-7033.2018-06-033
	Huang S W, Zhang Z, Chen Z M, Yuan X L, Li J Q, Zhang H. Genetic diversity analysis of five cantonese indigenous pigs based on SNP chip[J]. Chinese Journal of Animal Science, 2018, 54(6):33-37.
[13]	Liu B, Shen L Y, Guo Z X, Gan M L, Chen Y, Yang R L, Niu L L, Jiang D M, Zhong Z J, Li X W, Zhang S H, Zhu L. SNP-based analysis of the genetic structure of Liangshan pig population[J]. Asian-australasian Journal of Animal Sciences, 2021, 34(7):1105-1115. doi:10.5713/ajas.19.0884. doi: 10.5713/ajas.19.0884
[14]	王晨, 马宁, 郭春和, 袁仁强, 曾检华, 宋德清, 张惠文, 陈瑶生, 刘小红. 基于SNP芯片分析的蓝塘猪遗传群体结构[J]. 广东农业科学, 2018, 45(6):110-115,173. doi:10.16768/j.issn.1004-874X.2018.06.018. doi: 10.16768/j.issn.1004-874X.2018.06.018
	Wang C, Ma N, Guo C H, Yuan R Q, Zeng J H, Song D Q, Zhang H W, Chen Y S, Liu X H. Population structure of Lantang pig evaluated using SNP chip[J]. Guangdong Agricultural Sciences, 2018, 45(6):110-115,173.
[15]	Diao S Q, Huang S W, Xu Z T, Ye S P, Yuan X L, Chen Z M, Zhang H, Zhang Z, Li J Q. Genetic diversity of indigenous pigs from South China area revealed by SNP array[J]. Animals:an Open Access Journal from MDPI, 2019, 9(6):361. doi:10.3390/ani9060361. doi: 10.3390/ani9060361 URL
[16]	刘彬, 沈林園, 陈映, 李强, 廖坤, 郭芝忺, 张顺华, 朱砺. 基于SNP芯片分析青峪猪保种群体的遗传结构[J]. 畜牧兽医学报, 2020, 51(2):260-269. doi:10.11843/j.issn.0366-6964.2020.02.007. doi: 10.11843/j.issn.0366-6964.2020.02.007
	Liu B, Shen L Y, Chen Y, Li Q, Liao K, Guo Z X, Zhang S H, Zhu L. Analysis of genetic structure of conservation population in Qingyu pig based on SNP chip[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(2):260-269.
[17]	Xu P, Wang X P, Ni L G, Zhang W, Liu C L, Zhao X, Zhao X T, Ren J. Genome-wide genotyping uncovers genetic diversity,phylogeny,signatures of selection,and population structure of Chinese Jiangquhai pigs in a global perspective1[J]. Journal of Animal Science, 2019, 97(4):1491-1500. doi:10.1093/jas/skz028. doi: 10.1093/jas/skz028 URL
[18]	Wang Y P, Zhao X Y, Wang C, Wang W W, Zhang Q, Wu Y, Wang J Y. HD-SNP chip-based conservation genetic analysis of indigenous pig breeds from Shandong Province,China[J]. Asian-australasian Journal of Animal Sciences, 2021, 34(7):1123-1133. doi:10.5713/ajas.20.0339. doi: 10.5713/ajas.20.0339
[19]	Fan B, Wang Z G, Li Y J, Zhao X L, Liu B, Zhao S H, Yu M, Li M H, Chen S L, Xiong T A, Li K. Genetic variation analysis within and among Chinese indigenous swine populations using microsatellite markers[J]. Animal Genetics, 2002, 33(6):422-427. doi:10.1046/j.1365-2052.2002.00898.x. doi: 10.1046/j.1365-2052.2002.00898.x pmid: 12464016
[20]	Wang S H, Zhang C, Shang M, Wu X G, Cheng Y X. Genetic diversity and population structure of native mitten crab(Eriocheir sensu stricto)by microsatellite markers and mitochondrial COI gene sequence[J]. Gene, 2019, 693:101-113. doi:10.1016/j.gene.2018. 12.083. doi: 10.1016/j.gene.2018. 12.083 URL
[21]	Charoensook R, Gatphayak K, Brenig B, Knorr C. Genetic diversity analysis of Thai indigenous pig population using microsatellite markers[J]. Asian-australasian Journal of Animal Sciences, 2019, 32(10):1491-1500. doi:10.5713/ajas.18.0832. doi: 10.5713/ajas.18.0832 pmid: 31010994
[22]	Kharzinova V R, Zinovieva N A. The pattern of genetic diversity of different breeds of pigs based on microsatellite analysis[J]. Vavilovskii Zhurnal Genetiki i Selektsii, 2020, 24(7):747-754. doi:10.18699/VJ20.669. doi: 10.18699/VJ20.669 pmid: 33738391
[23]	Múñoz M, Bozzi R, García-Casco J, Nuñez Y, Ribani A, Franci O, et al. Genomic diversity,linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip[J]. Scientific Reports, 2019, 9(1):13546. doi:10.1038/s41598-019-49830-6. doi: 10.1038/s41598-019-49830-6 URL
[24]	Wang X P, Zhang H, Huang M, Tang J H, Yang L J, Yu Z Q, Li D S, Li G X, Jiang Y C, Sun Y X, Wei S D, Xu P, Ren J. Whole-genome SNP markers reveal conservation status,signatures of selection,and introgression in Chinese Laiwu pigs[J]. Evolutionary Applications, 2021, 14(2):383-398. doi:10.1111/eva.13124. doi: 10.1111/eva.13124 URL
[25]	Lee S H, Seo D W, Cho E S, Choi B H, Kim Y M, Hong J K, Han H D, Jung Y B, Kim D J, Choi T J, Lee S H. Genetic diversity and ancestral study for Korean native pigs using 60K SNP chip[J]. Animals, 2020, 10(5):760. doi:10.3390/ani10050760. doi: 10.3390/ani10050760 URL
[26]	白小青, 范首君, 王金勇, 刘文, 郭宗义, 何道领, 陈四清, 王可甜, 付文贵, 陈磊, 赵久刚, 蓝静, 张亮. 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, Liu W, Guo Z Y, He D L, Chen S Q, Wang K T, Fu W G, Chen L, Zhao J G, Lan J, Zhang L. Genetic diversity of five native pig breeds of Chongqing based on microsatellite DNA markers[J]. Acta Veterinaria et Zootechnica Sinica, 2010, 41(12):1515-1522.
[27]	蔡春波, 张雪莲, 张万峰, 杨阳, 高鹏飞, 郭晓红, 李步高, 曹果清. 运用SNP芯片评估马身猪保种群体的遗传结构[J]. 畜牧兽医学报, 2021, 52(4):920-931. doi:10.11843/j.issn.0366-6964.2021.04.008. doi: 10.11843/j.issn.0366-6964.2021.04.008
	Cai C B, Zhang X L, Zhang W F, Yang Y, Gao P F, Guo X H, Li B G, Cao G Q. Evaluation of genetic structure in Mashen pigs conserved population based on SNP chip[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(4):920-931.
[28]	Barbato M, Orozco-ter Wengel P, Tapio M, Bruford M W. SNeP:a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data[J]. Frontiers in Genetics, 2015, 6:109. doi:10.3389/fgene.2015.00109. doi: 10.3389/fgene.2015.00109 pmid: 25852748
[29]	孙浩, 王振, 张哲, 肖倩, 徐忠, 张向喆, 杨红杰, 朱满兴, 薛明, 刘晓辉, 张文俊, 郑友民, 王起山, 潘玉春. 基于基因组测序数据的梅山猪保种现状分析[J]. 上海交通大学学报(农业科学版), 2017, 35(4):65-70. doi:10.3969/J.ISSN.1671-9964.2017.04.011. doi: 10.3969/J.ISSN.1671-9964.2017.04.011
	Sun H, Wang Z, Zhang Z, Xiao Q, Xu Z, Zhang X Z, Yang H J, Zhu M X, Xue M, Liu X H, Zhang W J, Zheng Y M, Wang Q S, Pan Y C. Exploring the current situation of conservation of Meishan pigs based on genome sequencing data[J]. Journal of Shanghai Jiao Tong University (Agricultural Science), 2017, 35(4):65-70.
[30]	吴林慧, 孙琦, 王荔茹, 张凯丽, 谢胜松, 李新云, 赵书红, 马云龙. 恩施黑猪基因组群体遗传学参数的估计与选择信号研究[J]. 畜牧兽医学报, 2019, 50(3):485-494. doi:10.11843/j.issn.0366-6964.2019.03.003. doi: 10.11843/j.issn.0366-6964.2019.03.003
	Wu L H, Sun Q, Wang L R, Zhang K L, Xie S S, Li X Y, Zhao S H, Ma Y L. A study of the population genetics parameters and selection signatures in Enshi black pig[J]. Acta Veterinaria et Zootechnica Sinica, 2019, 50(3):485-494.
[31]	CTraspov A, Deng W J, Kostyunina O, Ji J X, Shatokhin K, Lugovoy S, Zinovieva N, Yang B, Huang L S. Population structure and genome characterization of local pig breeds in Russia,Belorussia,Kazakhstan and Ukraine[J]. Genetics Selection Evolution, 2016, 48:16. doi:10.1186/s12711-016-0196-y. doi: 10.1186/s12711-016-0196-y URL
[32]	Liu C X, Li P H, Zhou W D, Ma X, Wang X P, Xu Y, Jiang N J, Zhao M R, Zhou T W, Yin Y Z, Yren J, Huang R H. Genome data uncover conservation status,historical relatedness and candidate genes under selection in chinese indigenous pigs in the Taihu Lake Region[J]. Frontiers in Genetics, 2020, 11:591. doi:10.3389/fgene.2020.00591. doi: 10.3389/fgene.2020.00591 URL
[33]	Sancristobal M, Chevalet C, HaleY C S, Joosten R, Rattink A P, Harlizius B, et al. Genetic diversity within and between European pig breeds using microsatellite markers[J]. Animal Genetics, 2006, 37(3):189-198. doi:10.1111/j.1365-2052.2005.01385.x. doi: 10.1111/j.1365-2052.2005.01385.x pmid: 16734675
[34]	Wang X, Cao H H, Geng S M, Li H B. Genetic diversity of 10 indigenous pig breeds in china by using microsatellite markers[J]. Asian Australasian Association of Animal Production Societies, 2004, 17(9):1219-1222. doi:10.5713/ajas.2004.1219. doi: 10.5713/ajas.2004.1219
[35]	张哲, 罗元宇, 李晴晴, 贺金龙, 高宁, 张豪, 丁向东, 张勤, 李加琪. 一种基于高密度遗传标记的亲子鉴定方法及其应用[J]. 遗传, 2014, 36(8):835-841. doi:10.3724/SP.J.1005.2014.0835. doi: 10.3724/SP.J.1005.2014.0835
	Zhang Z, Luo Y Y, Li Q Q, He J L, Gao N, Zhang H, Ding X D, Zhang Q, Li J Q. Developing and applying of a parentage identification approach based on high density genetic markers[J]. Hereditas, 2014, 36(8):835-841.
[36]	Banos G, Wiggans G R, Powell R L. Impact of paternity errors in cow identification on genetic evaluations and international comparisons[J]. Journal of Dairy Science, 2001, 84(11):2523-2529. doi:10.3168/jds.S0022-0302(01)74703-0. doi: 10.3168/jds.S0022-0302(01)74703-0 pmid: 11768094
[37]	余国春. 微卫星与SNP标记技术在猪亲子鉴定中的有效性研究[D]. 雅安: 四川农业大学, 2014.
	Yu G C. Effectiveness study of porcine paternity test based on microsatellite and SNP marked technology[D]. Yaan: Sichuan Agricultural University, 2014.
[38]	Ai H S, 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. doi:10.1371/journal.pone.0056001. doi: 10.1371/journal.pone.0056001

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