喀喇昆仑-帕米尔地区山羊群体遗传多样性及系统发育分析

doi:10.16431/j.cnki.1671-7236.2024.06.028

摘要/Abstract

摘要： 【目的】明确喀喇昆仑-帕米尔地区山羊群体遗传多样性及系统发育情况,为山羊种质资源保存、发掘和利用提供理论依据。【方法】以分布于喀喇昆仑-帕米尔地区的山羊为研究对象,对其线粒体(mtDNA)非编码序列置换环(D-loop)区和细胞色素b(Cytb)基因序列进行PCR扩增并测序。利用Mega 7.0.26软件分析碱基组成,结合从GenBank中下载的山羊mtDNA D-loop区序列和Cytb基因序列绘制系统发育树,使用DNASP 5.10软件统计单倍型分布并进行中性检验,通过Network 10.2软件构建单倍型中介网络图。【结果】喀喇昆仑-帕米尔地区山羊mtDNA D-loop区序列和Cytb基因序列AT含量分别为60.1%和58.7%,AT含量均高于GC含量,具有碱基组成偏好性。D-loop区序列和Cytb基因分别存在163和84个SNPs位点,分别定义40、30种单倍型,单倍型多样性(Hd)分别为0.985和0.883,核苷酸多样性(Pi)分别为0.01570和0.00425。mtDNA D-loop区和Cytb基因的中性检验Tajima’s D值和Fu’s Fs值均＜0,显著偏离中性,核苷酸错配分布图呈现3个峰。系统发育树分析表明喀喇昆仑-帕米尔地区山羊包含4个支系,分别为A、B、C、G。【结论】喀喇昆仑-帕米尔地区山羊至少经历过3次群体扩张事件,遗传多样性丰富,西亚地区的山羊对其存在基因渗入,同域的北山羊对其没有遗传贡献。

关键词: 山羊; 喀喇昆仑-帕米尔地区; D-loop区; Cytb基因; 遗传多样性

Abstract: 【Objective】 This experiment was conducted to further clarify the genetic diversity and phylogeny of goat population in Karakoram-Pamir region,and to provide theoretical basis for the conservation,excavation and application of biological resources.【Method】 The mitochondrial (mtDNA) D-loop region and cytochrome b (Cytb) gene sequences were amplified by PCR and sequenced of goats in Karakoram-Pamir region.Mega 7.0.26 software was used to analyze the base composition and draw the phylogenetic tree by combining the D-loop region and Cytb gene of goats downloaded from GenBank,and DNASP 5.10 software was used to analyze haplotype distribution and neutral test,and haplotype media-joining network was constructed by Network 10.2 software.【Result】 The AT content in mtDNA D-loop region and Cytb gene sequences of goats in Karakoram-Pamir region was 60.1% and 58.7%,respectively,and the AT content was higher than the GC content,showing a preference for base composition.There were 163 SNPs in D-loop region and 84 SNPs in Cytb gene,and 40 and 30 haplotypes were defined,respectively,with haplotype diversity (Hd) of 0.985 and 0.883 and nucleotide diversity (Pi) of 0.01570 and 0.00425,respectively.The Tajima’s D value and Fu’s Fs value of mtDNA D-loop region and Cytb gene were all less than 0 by the neutrality test,and significantly deviate from neutrality.Phylogenetic tree analysis showed that goats in Karakoram-Pamir region were distributed in 4 lineages:A,B,C and G.【Conclusion】 Goats in Karakoram-Pamir region had experienced at least three population expansion events and had rich genetic diversity.There was gene infiltration from goats in Western Asia,while Capra ibexs in the same region had no genetic contribution.

Key words: goats; Karakoram-Pamir region; D-loop region; Cytb gene; genetic diversity

中图分类号:

S823.8

黄翔辉, 张天能, 尔孜古·木沙, 王玉涛. 喀喇昆仑-帕米尔地区山羊群体遗传多样性及系统发育分析[J]. 中国畜牧兽医, 2024, 51(6): 2533-2544.

HUANG Xianghui, ZHANG Tianneng, ARZUGUL·Musha, WANG Yutao. Genetic Diversity and Phylogenetic Analysis of Goat Population in Karakoram-Pamir Region[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(6): 2533-2544.

参考文献

[1] GAO Y S,JIA X X,TANG X J,et al.The genetic diversity of chicken breeds from Jiangxi,assessed with BCDO2 and the complete mitochondrial DNA D-loop region[J].PLoS One,2017,12(3):e0173192.
[2] 郑竹清.世界山羊群体遗传结构及其野生近缘种基因渗入研究[D].杨凌:西北农林科技大学,2019. ZHENG Z Q.Population structure and genetic introgression from wild relatives in worldwide goat populations[D].Yangling:Northwest A&F University,2019.(in Chinese)
[3] 王存芳,曾庆勇,杜立新,等.线粒体DNA(mtDNA)的研究进展[J].动物科学和动物医学,2001,18(1):16-18. WANG C F,ZENG Q Y,DU L X,et al.Research progress of mitochondrial DNA (mtDNA)[J].Animal Science and Veterinary Medicine,2001,18(1):16-18.(in Chinese)
[4] 王世锋,蔡佳麒,沙晓娟,等.基于Cytb基因分析帕米尔盘羊和新疆地方家绵羊的系统发育[J].生物技术,2016,26(1):48-52. WANG S F,CAI J Q,SHA X J,et al.Phylogenetic study based on the Cytb gene of O.a.poloi and Xinjiang local sheep[J].Biotechnology,2016,26(1):48-52.(in Chinese)
[5] LI M,JIN L,MA J,et al.Detecting mitochondrial signatures of selection in wild Tibetan pigs and domesticated pigs[J].Mitochondrial DNA (Part A:DNA Mapping,Sequencing,and Analysis),2014,27(1):747-752.
[6] GUO H W,LI C,WANG X N.Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds[J].British Poultry Science,2017,58(5):490-497.
[7] TABATA R,KAWAGUCHI F,SASAZAKI S,et al.Phylogeographic analysis of Madagascan goats using mtDNA control region and SRY gene sequences[J].Zoological Science,2019,36(4):294-298.
[8] JU Y,LIU H,HE J,et al.Genetic diversity of Aoluguya Reindeer based on D-loop region of mtDNA and its conservation implications[J].Gene,2020,733:144271.
[9] CHENYAMBUGA S W,HANOTTE O,HIRBO J,et al.Genetic characterization of indigenous goats of Subsaharan Africa using microsatellite DNA markers[J].Asian-Australasian Journal of Animal Sciences,2004,17(4):445-452.
[10] 梁瑞圆,陈晓勇,孙洪新,等.五个地方绵羊种群mtDNA D-Loop区系统进化及遗传多样性分析[J].华北农学报,2018,33(1):135-142. LIANG R Y,CHEN X Y,SUN H X,et al.Phylogenety and genetic diversity of five local sheep breeds on mtDNA D-loop[J].Acta Agriculturae Boreali-Sinica,2018,33(1):135-142.(in Chinese)
[11] LUIKART G,GIELLY L,EXCOFFIER L,et al.Multiple maternal origins and weak phylogeographic structure in domestic goats[J].Proceedings of the National Academy of Sciences of the United States of America,2001,98(10):5927-5932.
[12] SULTANA S,MANNEN H,TSUJI S.Mitochondrial DNA diversity of Pakistani goats[J].Animal Genetics,2003,34(6):417-421.
[13] 贾永红,史宪伟,简承松,等.贵州四个山羊品种mtDNA多态性及起源分化[J].动物学研究,1999,20(2):88-92. JIA Y H,SHI X W,JIAN C S,et al.mtDNA polymorphism and origin differentiation of four goat breeds in Guizhou[J].Zoological Research,1999,20(2):88-92.(in Chinese)
[14] LI M H,ZHAO S H,BIAN C,et al.Genetic relationships among twelve Chinese indigenous goat populations based on microsatellite analysis[J].Genetics Selection Evolution,2002,34(6):729-744.
[15] 张乐超,刘月琴,段春辉,等.7个地方山羊品种遗传多样性及遗传结构分析[J].生物技术通报,2020,36(6):183-190. ZHANG L C,LIU Y Q,DUAN C H,et al.Analysis of genetic diversity and genetic structure in 7 local goat breeds[J].Biotechnology Bulletin,2020,36(6):183-190.(in Chinese)
[16] 王玉涛,戴志刚,杨世杰,等.东帕米尔高原盘羊分布与栖息地植被覆盖时空变化[J].生态学报,2016,36(1):209-217. WANG Y T,DAI Z G,YANG S J,et al.The distribution of Marco Polo sheep and their habitat vegetation dynamics in East Pamir[J].Acta Ecologica Sinica,2016,36(1):209-217.(in Chinese)
[17] 国家畜禽遗传资源委员会.中国畜禽遗传资源志·羊志[M].北京:中国农业出版社,2011. CHINA NATIONAL COMMISSION OF ANIMAL GENETIC RESOURCES.Animal Genetic Resources in China·Sheep and Goat[M].Beijing:China Agricultural Press,2011.(in Chinese)
[18] 杨心春,朱一笑,刘洪瑜,等.马鞍山地区白山羊线粒体DNA D-loop区和SRY基因的遗传进化分析[J].西北农林科技大学学报(自然科学版),2021,49(9):9-15. YANG X C,ZHU Y X,LIU H Y,et al.Genetic evolution analysis on mitochondrial DNAD-loop region and SRY gene of Maanshan White goat[J].Journal of Northwest A&F University (Natural Science Edition),2021,49(9):9-15.(in Chinese)
[19] 邓娟,张红平,巴贵,等.基于Cytb基因多态性研究西藏地区8个藏山羊群体遗传结构及母系起源[J].畜牧兽医学报,2018,49(1):65-74. DENG J,ZHANG H P,BA G,et al.Genetic structure and maternal origins of 8 Tibetan goat populations in Tibet inferred from Cytb gene diversity[J].Acta Veterinaria et Zootechnica Sinica,2018,49(1):65-74.(in Chinese)
[20] 李祥龙,张亚平,陈圣偶,等.山羊品种间线粒体DNA限制性片段长度多态性研究[J].动物学研究,1997,18(4):70-77. LI X L,ZHANG Y P,CHEN S O,et al. Mitochondrial DNA restriction fragment length polymorphism among goat breeds[J].Zoological Research,1997,18(4):70-77.(in Chinese)
[21] 刘益平,曹少先,傅泽红,等.中国部分山羊品种线粒体DNA D-loop序列遗传多样性分析[J].畜牧兽医学报,2007,38(4):313-320. LIU Y P,CAO S X,FU Z H,et al.Analyzing on mitochondrial DNA D-loop sequences genetic polymorphism of partial Chinese goat breeds[J].Acta Veterinaria et Zootechnica Sinica,2007,38(4):313-320.(in Chinese)
[22] 张红平.采用mtDNA序列研究中国家养山羊的遗传多样性与起源分化[D].成都:四川农业大学,2003. ZHANG H P.Study on the genetic variety,origin and divergence using mitochondrial DNA sequences of Chinese domestic goats[D].Chengdu:Sichuan Agricultural University,2003.(in Chinese)
[23] 闫益波,杜丽英,张伯池,等.山西太行黑山羊mtDNA D-Loop区遗传多样性分析[J].山西农业科学,2020,48(6):974-980. YAN Y B,DU L Y,ZHANG B C,et al.Genetic diversity analysis of mtDNA D-loop region in Shanxi Taihang Black goat[J].Journal of Shanxi Agricultural Sciences,2020,48(6):974-980.(in Chinese)
[24] 黄勤华.贵州四个山羊品种mtDNA Cytb基因多态性研究[D].贵阳:贵州大学,2008. HUANG Q H.Genetic diversity of mitochondrial DNA cytochrome b gene (Cytb) in four goat breeds in Guizhou[D].Guiyang:Guizhou University,2008.(in Chinese)
[25] GRANT W S,BOWEN B W.Shallow population histories in deep evolutionary lineages of marine fishes:Insights from sardines and anchovies and lessons for conservation[J].Journal of Heredity,1998,89(5):415-426.
[26] JOSHI M B,ROUT P K,MANDAL A K,et al.Phylogeography and origin of Indian domestic goats[J].Molecular Biology and Evolution,2004,21(3):454-462.
[27] NADERI S,REZAEI H R,TABERLET P,et al.Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity[J].PLoS One,2007,2(10):e1012.
[28] GUO Y,GONG Y,HE Y M,et al.Investigation of mitochondrial DNA genetic diversity and phylogeny of goats worldwide[J].Journal of Integrative Agriculture,2022,21(6):1830-1837.
[29] CHEN S Y,SU Y H,WU S F,et al.Mitochondrial diversity and phylogegraphic structure of Chinese domestic goats[J].Molecular Phylogenetics and Evolution,2005,37(3):804-814.
[30] 武艳平,关伟军,赵倩君,等.山羊线粒体DNA D-loop区部分序列变异位点分析[J].畜牧兽医学报,2008,39(8):1137-1141. WU Y P,GUAN W J,ZHAO Q J,et al.Analysis on partial sequence of mitochondrial DNA D-loop region variation position of goat[J].Acta Veterinaria et Zootechnica Sinica,2008,39(8):1137-1141.(in Chinese)
[31] 赵金艳,权凯,王俊,等.中部地区家养山羊线粒体遗传多样性与母系起源研究[J].中国畜牧杂志,2021,57(10):106-111. ZHAO J Y,QUAN K,WANG J,et al.Mitochondrial genetic diversity and maternal origin of domestic goats in Central China[J].Chinese Journal of Animal Science,2021,57(10):106-111.(in Chinese)
[32] 郝荣超,王国华,梁菲菲.中国南部和西北地区山羊mtDNA D-loop区遗传多样性及群体分化[J].农业生物技术学报,2017,25(2):258-266. HAO R C,WANG G H,LIANG F F.The genetic diversity of mtDNA D-loop and the differentiation of goats (Capra hircus) in South and Northwest of China[J].Journal of Agricultural Biotechnology,2017,25(2):258-266.(in Chinese)
[33] LI M.New evidence discovery for maternal lineage B of goats (Capra hircus) in Chinese tropical zone[J].Geophysical Research Letters,2013,28(24):4525-4528.
[34] 郝荣超,昝林森,刘丑生,等.中国部分家养山羊mtDNA D环区遗传多样性与进化[J].遗传,2008,30(9):1187-1194. HAO R C,ZAN L S,LIU C S,et al.Genetic diversity and origin of mitochondrial DNA D-loop region for some domestic goat breeds of China[J].Hereditas,2008,30(9):1187-1194.(in Chinese)