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Journal of Integrative Agriculture  2022, Vol. 21 Issue (6): 1830-1837    DOI: 10.1016/S2095-3119(21)63882-0
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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-ju1ZHANG 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

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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 FS 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.
Keywords:  mitochondrial DNA        genetic diversity        population structure        population expansion        phylogeny  
Received: 26 February 2021   Accepted: 21 December 2021

This research was funded by the Chongqing Natural Science Foundation (cstc2021jcyj-msxmX0013) and National Natural Science Foundation of China (31172195).

About author:  GUO Yi, E-mail:; GONG Ying, E-mail:; Correspondence E Guang-xin, Tel: +86-23-68250205, Fax: +86-23-68251192, E-mail: * These authors contributed equally to this study.

Cite this article: 

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. 2022. Investigation of Mitochondrial DNA genetic diversity and phylogeny of goats worldwide. Journal of Integrative Agriculture, 21(6): 1830-1837.

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