JIA-2021-0354 利用线粒体D_Loop序列研究全世界山羊母系遗传多样性及系统发育分析

doi:10.1016/S2095-3119(21)63882-0

Journal of Integrative Agriculture ›› 2022, Vol. 21 ›› Issue (6): 1830-1837.DOI: 10.1016/S2095-3119(21)63882-0

所属专题：动物科学合辑Animal Science

• • 上一篇

JIA-2021-0354 利用线粒体D_Loop序列研究全世界山羊母系遗传多样性及系统发育分析

收稿日期:2021-02-26 接受日期:2021-12-21 出版日期:2022-06-01 发布日期:2021-12-21

Investigation of Mitochondrial DNA genetic diversity and phylogeny of goats worldwide

GUO Yi¹^*, GONG Ying¹^*, HE Yong-meng¹, YANG Bai-gao¹, ZHANG Wei-yi¹, CHEN Bo-er², HUANG Yong-fu¹, ZHAO Yong-ju¹, ZHANG Dan-ping³, MA Yue-hui⁴, CHU Ming-xing⁴, E Guang-xin¹

¹ College of Animal Science and Technology, Southwest University, Chongqing 400715, P.R.China
² Chongqing Agriculture and Rural Affairs Committee of Tongnan, Chongqing 402660, P.R.China
³ Dazhou Animal Husbandry Technology Extension Station, Dazhou 635299, P.R.China
⁴ Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China

Received:2021-02-26 Accepted:2021-12-21 Online:2022-06-01 Published:2021-12-21
About author:GUO Yi, E-mail: 3466813215@qq.com; GONG Ying, E-mail: 3480766351@qq.com; Correspondence E Guang-xin, Tel: +86-23-68250205, Fax: +86-23-68251192, E-mail: eguangxin@126.com * These authors contributed equally to this study.
Supported by:
This research was funded by the Chongqing Natural Science Foundation (cstc2021jcyj-msxmX0013) and National Natural Science Foundation of China (31172195).

摘要/Abstract

摘要：

本研究利用已公布的4165个来自于全世界196个品种的山羊线粒体D_Loop序列，进行核苷酸多样性、单倍型构建、单倍型多样性、群体系统发育学研究、中性检验及群体遗传距离等一系列遗传参数进行评估。在全部个体的401 bp片段长度的D_Loop区域内共鉴定得到301个多态位点，总体核苷酸多样性为0.03471；构建获得并构建2409个D_Loop单倍型，单倍型平均多样性为0.9983。系统发育分析表明，98.92%的单倍型被聚类为已知的6个山羊线粒体D_loop单倍型簇，其中单倍型A所占比例最大(86%)，D_Loop单倍型B簇在中国山羊中出现频率最高。中国西南地区山羊群体中发现了两个未知的D_Loop单倍型簇(Unknown I和Unknown II)。分子方差分析(AMOVA)和群体间成对差异(PiXY)研究结果表明，不同品种家养山羊间群体变异较小，群体遗传分化与地理分布不完全一致，表明群体间广泛存在遗传物质交流。中性检验(Tajima‘D和Fu’Fs检验)和错配分布研究结果表明，单倍型簇B、C和G存在群体扩张历史。较其他野羊，Capra aegagrus与家养山羊系统发育关系最为密切，并可能贡献于山羊A、B、C和F单倍群簇的驯化起源。本研究表明线粒体D_Loop单倍型B簇可能起源于中国或在山羊驯化早期已迁至中国，在中国西南地区山羊群体中两个未知的D_Loop单倍型簇的发现表明中国西南地区可能具有独特的山羊母系背景或驯化历史；Capra aegagrus是最可能的家养山羊野生祖先，并可能贡献于山羊A、B、C和F单倍群簇的驯化起源。本研究利用大样本量全世界山羊线粒体D_Loop序列数据集分析有助于更好的理解世界范围内山羊母系驯化起源及基因流动的历史变化，为进一步明确世界山羊群体迁徙的演变历史及种群系统发育定位提供了宝贵的理论依据。

Abstract: Genetic diversity, population structure, and population expansion of goats worldwide (4 165 individuals from 196 breeds) were analyzed using published mitochondrial DNA (mtDNA) D_loop hypervariable region sequences. Results showed that 2 409 haplotypes and 301 polymorphic sites were present within the 401-bp length D_loop region, the nucleotide diversity (Pi) was 0.03471, and the haplotype diversity (Hd) was 0.9983. Phylogenetic analysis revealed that 98.92% of haplotypes were divided into six obvious clusters, consistent with the classification of the known mitochondrial haplogroups of goats. Haplogroup A accounted for the largest proportion (86%). Interestingly, two unknown divisions (Unknown I and Unknown II) were discovered from goats in Southwest China, suggesting that Southwest China has unique maternal haplogroups. Analysis of molecular variance (AMOVA) and the average number of pairwise differences between populations (PiXY) indicated that geographical variation was small but significant. Neutrality tests (Tajima’s D and Fu’s F_S tests) and mismatch distribution showed that haplogroups B, C, and G had expansion histories. In addition, the phylogenetic relationship between domestic and wild goats suggested that Capra aegagrus is the most likely wild ancestor and may have participated in the domestication of ancestral populations of A, B, C, and F haplogroups. A meta-analysis on the mtDNA sequences of goats from international databases was conducted to analyze goats’ genetic diversity, population structure, and matrilineal system evolution worldwide. The results may help further understand the domestication history and gene flow of goats worldwide.

Key words: mitochondrial DNA , genetic diversity , population structure , population expansion , phylogeny

. JIA-2021-0354 利用线粒体D_Loop序列研究全世界山羊母系遗传多样性及系统发育分析[J]. Journal of Integrative Agriculture, 2022, 21(6): 1830-1837.

GUO Yi, GONG Ying, HE Yong-meng, YANG Bai-gao, ZHANG Wei-yi, CHEN Bo-er, HUANG Yong-fu, ZHAO Yong-ju, ZHANG Dan-ping, MA Yue-hui, CHU Ming-xing, E Guang-xin. Investigation of Mitochondrial DNA genetic diversity and phylogeny of goats worldwide[J]. Journal of Integrative Agriculture, 2022, 21(6): 1830-1837.

参考文献

Ahmed S, Grobler P, Madisha T, Kotze A. 2017. Mitochondrial D-loop sequences reveal a mixture of endemism and immigration in Egyptian goat populations. Mitochondrial DNA (Part A, DNA Mapping, Sequencing, and Analysis), 8, 711–716.
Al-Araimi N A, Gaafar O M, Costa V, Neira A L, Al-Atiyat R M, Beja-Pereira A. 2017. Genetic origin of goat populations in Oman revealed by mitochondrial DNA analysis. PLoS ONE, 12, e0190235.
Bruford M W, Bradley D G, Luikart G. 2003. DNA markers reveal the complexity of livestock domestication. Nature Reviews Genetics, 4, 900–910.
Cai Y, Fu W, Cai D, Heller R, Zheng Z, Wen J, Li H, Wang X, Alshawi A, Sun Z, Zhu S, Wang J, Yang M, Hu S, Li Y, Yang Z, Gong M, Hou Y, Lan T, Wu K, et al. 2020. Ancient genomes reveal the evolutionary history and origin of cashmere-producing goats in China. Molecular Biology and Evolution, 37, 2099–2109.
Chen S Y, Su Y H, Wu S F, Sha T, Zhang Y P. 2005. Mitochondrial diversity and phylogeographic structure of Chinese domestic goats. Molecular Phylogenetics and Evolution, 37, 804–814.
Colli L, Lancioni H, Cardinali I, Olivieri A, Capodiferro M R, Pellecchia M, Rzepus M, Zamani W, Naderi S, Gandini F, Vahidi S M, Agha S, Randi E, Battaglia V, Sardina M T, Portolano B, Rezaei H R, Lymberakis P, Boyer F, Coissac E, et al. 2015. Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability. BMC Genomics, 16, 1115.
Deng J, Feng J, Li L, Zhong T, Wang L, Guo J, Ba G, Song T, Zhang H. 2018. Polymorphisms, differentiation, and phylogeny of 10 Tibetan goat populations inferred from mitochondrial D-loop sequences. Mitochondrial DNA (Part A: DNA Mapping, Sequencing, and Analysis), 29, 439–445.
Drummond J, Rambaut A, Shapiro B, Pybus O G. 2005. Bayesian coalescent inference of past 484 population dynamics from molecular sequences. Molecular Biology and Evolution, 22, 1185–1192.
E G X, Hong Q H, Zhao Y J, Ma Y H, Chu M X, Zhu L, Huang Y F. 2019. Genetic diversity estimation of Yunnan indigenous goat breeds using microsatellite markers. Evolutionary Ecology, 9, 5916–5924.
E G X, Zhao Y J, Chen L P, Ma Y H, Chu M X, Li X L, Hong Q H, Li L H, Guo J J, Zhu L, Han Y G, Gao H J, Zhang J H, Jiang H Z, Jiang C D, Wang G F, Ren H X, Jin M L, Sun Y Z, Zhou P, et al. 2018. Genetic diversity of the Chinese goat in the littoral zone of the Yangtze River as assessed by microsatellite and mtDNA. Ecology and Evolution, 8, 5111–5123.
Fantazi K, Migliore S, Kdidi S, Racinaro L, Tefiel H, Boukhari R, Federico G, Lo Presti V D, Gaouar S B S, Vitale M. 2018. Analysis of differences in prion protein gene (PRNP) polymorphisms between Algerian and Southern Italy’s goats. International Journal of Agriculture Sciences, 17, 578–585.
Fu Y X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915–925.
Ghernouti N, Bodinier N, Ranebi M, Maftah D, Petit D, Gaouar S B S. 2017. Control region of mtDNA identifies three migration events of sheep breeds in Algeria. Small Ruminant Research, 155, 66–71.
Guo H W, Li C, Wang X N. 2017. Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds. British Poultry Science, 58, 490–497.
Hammer S E, Schwammer H M, Suchentrunk F. 2008. Evidence for introgressive hybridization of captive markhor (Capra falconeri) with domestic goat: Cautions for reintroduction. Biochemical Genetics, 46, 216–226.
Huang Y F, Chen L P, Zhao Y J, Zhang H, Na R S, Zhao Z Q, Zhang J H, Jiang C D, Ma Y H, Sun Y W, E G X. 2016. Complete mitochondrial genome of Chuanzhong black goat in southwest of China (Capra hircus). Mitochondrial DNA (Part A: DNA Mapping, Sequencing, and Analysis), 27, 3063–3064.
Joshi M B, Rout P K, Mandal A K, Tyler-Smith C, Singh L, Thangaraj K. 2004. Phylogeography and origin of Indian domestic goats. Molecular Biology and Evolution, 21, 454–462.
Ju Y, Liu H, He J, Wang L, Xu J, Liu H, Dong Y, Zhang R, Zhao P, Xing X. 2020. Genetic diversity of Aoluguya Reindeer based on D-loop region of mtDNA and its conservation implications. Gene, 733, 144271.
Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1874.
Li M, Jin L, Ma J, Tian S, Li R, Li X. 2016. Detecting mitochondrial signatures of selection in wild Tibetan pigs and domesticated pigs. Mitochondrial DNA (Part A: DNA Mapping, Sequencing, and Analysis), 27, 747–752.
Liu R Y, Xia X L, Lei C Z, Zhang M Z, Chen H, Yang G S. 2006a. Genetic diversity of mitochondrial DNA D-loop sequences in cattle breeds in Guizhou. Hereditas (Beijing), 28, 279–284. (in Chinese)
Liu R Y, Yang G S, Lei C C. 2006b. The genetic diversity of mtDNA D-loop and the origin of Chinese goat. Acta Genetica Sinica, 33, 420–428.
Luikart G, Gielly L, Excoffier L, Vigne J D, Bouvet J, Taberlet P. 2001. Multiple maternal origins and weak phylogeographic structure in domestic goats. Proceedings of the National Academy of Sciences of the United States of America, 98, 5927–5932.
Naderi S, Rezaei H R, Pompanon F, Blum M G, Negrini R, Naghash H R, Balkiz O, Mashkour M, Gaggiotti O E, Ajmone-Marsan P, Kence A, Vigne J D, Taberlet P. 2008. The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. Proceedings of the National Academy of Sciences of the United States of America, 105, 17659–17664.
Naderi S, Rezaei H R, Taberlet P, Zundel S, Rafat S A, Naghash H R, el-Barody M A, Ertugrul O, Pompanon F, Econogene C. 2007. Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS ONE, 10, 1–12.
Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York.
Nei M, Li W H. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the United States of America, 76, 5269–5273.
Rogers A R, Harpending H. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552–569.
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio J C, Guirao-Rico S, Librado P, Ramos-Onsins S E, Sánchez-Gracia A. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution, 34, 3299–3302.
Sardina M T, Ballester M, Marmi J, Finocchiaro R, van Kaam J B, Portolano B, Folch J M. 2006. Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage. Animal Genetics, 37, 376–378.
Schneider S, Excoffier L, Laval G. 2010. Arlequin (version 3.5.1.2): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47–50.
Sharma R, Kishore A, Mukesh M, Ahlawat S, Maitra A, Pandey A K, Tantia M S. 2015. Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers. BMC Genetics, 16, 73.
Slatkin M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics, 139, 457–462.
Sultana S, Mannen H, Tsuji S. 2003. Mitochondrial DNA diversity of Pakistani goats. Animal Genetics, 34, 417–421.
Tabata R, Kawaguchi F, Sasazaki S, Yamamoto Y, Rakotondraparany F, Ratsoavina F M, Yonezawa T, Mannen H. 2019. Phylogeographic analysis of madagascan goats using mtDNA control region and SRY gene sequences. Zoological Science, 36, 294–298.
Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585–595.
Tarekegn G M, Tesfaye K, Mwai O A, Djikeng A, Dessie T, Birungi J, Osama S, Zergaw N, Alemu A, Achieng G, Tutah J, Mutai C, Njuguna J, Mwacharo J M. 2018. Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats. Ecology and Evolution, 8, 1543–1553.
Tefiel H, Ata N, Chahbar M, Benyarou M, Fantazi K, Yilmaz O, Cemal I, Karaca O, Boudouma D, Gaouar S B S. 2018. Genetic characterization of four Algerian goat breeds assessed by microsatellite markers. Small Ruminant Research, 160, 65–71.
Wu Y P, Guan W J, Zhao Q J, He X H, Pu Y B, Huo J H, Xie J F, Han J L, Rao S Q, Ma Y H. 2009. A fine map for maternal lineage analysis by mitochondrial hypervariable region in 12 Chinese goat breeds. Animal Science Journal, 80, 372–380.
Zeder M, Hesse B. 2000. The initial domestication of goats (Capra hircus) in the Zagros Mountains 10 000 years ago. Science, 287, 2254–2257.
Zhang J, Jiao T, Zhao S. 2016. Genetic diversity in the mitochondrial DNA D-loop region of global swine (Sus scrofa) populations. Biochemical and Biophysical Research Communications, 473, 814–820.
Zhang L C, Liu Y Q, Duan C H, Wang Y, Guo H X. 2020. Genetic diversity and genetic structure analysis of 7 local goat breeds. Biotechnology Bulletin, 36, 1–8. (in Chinese)
Zheng Z, Wang X, Li M, Li Y, Yang Z, Wang X, Pan X, Gong M, Zhang Y, Guo Y, Wang Y, Liu J, Cai Y, Chen Q, Okpeku M, Colli L, Cai D, Wang K, Huang S, Sonstegard T S, et al. 2020. The origin of domestication genes in goats. Science Advances, 6, 1–13.

JIA-2021-0354 利用线粒体D_Loop序列研究全世界山羊母系遗传多样性及系统发育分析

Investigation of Mitochondrial DNA genetic diversity and phylogeny of goats worldwide

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 0

编辑推荐

Metrics