Maternal origins,population structure and demographic history of ten Chinese indigenous goat breeds from Yunnan

Yunnan as a frontier zone that connects China with South and Southeast Asia, has 11 well‐recognized goat breeds. However, the knowledge about maternal origins, population structure and demographic history of Chinese indigenous goats from Yunnan is limited. In this study, we analysed a 481‐bp fragment of first hypervariable segment (HVSI) of the mitochondrial DNA (mtDNA) control region sequences of 749 individuals from 10 Yunnan indigenous goat breeds, of which 556 sequences were newly determined. There were 110 polymorphic sites that defined 158 haplotypes among all sequences. The haplotype and nucleotide diversity of these breeds ranged from 0.782 ± 0.079 to 0.982 ± 0.015 and from 0.028 ± 0.003 to 0.043 ± 0.005, respectively. Phylogenetic analysis identified two lineages A and B, of which the lineage A had higher frequency (68.1%) and distributed in all Yunnan breeds. We combined previously reported sequences with our sequences belonging to the lineage B and detected two subclades B1 and B2, in which the B1 subclade shared individuals from Eastern Asia, Southeast Asia and Southern Asia. Given higher level of diversity and more unique haplotypes, the B2 subclade probably originated from Southwestern China. The haplotype network, analysis of molecular variance (AMOVA) and a Mantel test revealed no significant phylogeographic structuring among Yunnan goat breeds. This can be explained by high gene flow and genetic admixture among these breeds from different geographic regions in Yunnan. Additionally, both the lineages A and B reflected different demographic histories. This study will provide a scientific basis for the conservation and utilization of Yunnan indigenous goats.     

基于线粒体DNA D-loop区序列分析中国及新西兰奶山羊遗传进化关系

[目的]分析我国地方培育奶山羊品种与国外引进品种的遗传进化关系。[方法]以4个国内奶山羊品种（文登奶山羊、关中奶山羊、崂山奶山羊、雅安奶山羊）和3个新西兰引进奶山羊品种（阿尔卑斯奶山羊、吐根堡奶山羊、萨能奶山羊）为研究对象,采集33只个体的外周血样本,提取血液基因组DNA,利用PCR法扩增线粒体DNA（mitochondrial DNA,mtDNA）D-loop区全长序列,对测序获得的序列进行生物信息学分析,探究不同奶山羊品种的遗传多样性及进化关系。[结果]7个品种奶山羊的mtDNA D-loop区中A、T碱基含量高于G、C碱基含量。共检测到82个多态位点,25个单一多态位点,55个简约信息位点。各品种单倍型多样度（Hd）范围为0.905~1.000,核苷酸多样度（Pi）范围为0.001 51~0.013 32;共存在26种单倍型,文登奶山羊和萨能奶山羊各有5个单倍型,阿尔卑斯奶山羊有4个单倍型,崂山奶山羊、吐根堡奶山羊、关中奶山羊、雅安奶山羊各有3个单倍型;各品种核苷酸平均差异数（K_XY）范围为6.400 00~38.450 00,核苷酸歧异度（D_XY）范围为0.005 79~0.034 76,遗传分化系数（G_ST）范围为0.000 00~0.186 05,遗传分化指数（F_ST）范围为0.231 56~0.971 52。品种间系统发育树表明,文登奶山羊和崂山奶山羊聚为一支;关中奶山羊与3种新西兰奶山羊遗传距离较近,从遗传学角度证实了关中奶山羊由国外奶山羊与地方品种经杂交选育而成;雅安奶山羊与其他品种遗传距离最远。[结论]中国奶山羊存在2个支系起源且未发现群体扩张;中国培育奶山羊品种含有较多的国外奶山羊血统;文登奶山羊与崂山奶山羊亲缘关系较近,雅安奶山羊在遗传进化中可能存在地域隔离。     

Genetic diversity of Chinese domestic goat based on the mitochondrial DNA sequence variation

The aim of this study was to characterize the genetic diversity of domestic goat in China. For this purpose, we determined the sequence of the mitochondrial DNA (mtDNA) control region in 72 individuals of the Yangtze River delta white goat, and reanalysed 723 published samples from 31 breeds/populations across China. All goat haplotypes were classified into four haplogroups (A–D) previously described. The phylogenetic pattern that emerged from the mtDNA control region sequence was confirmed by the analysis of the entire cytochrome b sequence of eight goats representative of the four haplogroups. It appeared that in Chinese domestic goat, haplogroups A and B were dominant and distributed in nearly all breeds/populations, while haplogroups C and D were only found in seven breeds/populations. Four breeds/populations contained all four haplogroups. When grouping the breeds/populations into five geographic groups based on their geographic distributions and ecological conditions, the southern pasturing area had the highest diversity whereas the northern farming area had the lowest diversity. 84.29% and 11.37% of the genetic variation were distributed within breeds and among breeds within the ecologically geographical areas, respectively; only 4% of genetic variation was observed among the five geographic areas. We speculate that the traditional seasonal pastoralism, the annual long-distance migrations that occurred in the past, and the commercial trade would account for the observed pattern by having favoured gene flows.     

云南水牛mtDNA D-loop遗传多样性研究

[目的] 探究云南3个水牛品种(德宏水牛、滇东南水牛、盐津水牛)的mtDNA D-loop区的遗传多样性与母系起源。[方法]采用PCR扩增、测序及生物信息学方法。[结果] 本研究共分析了215条云南水牛mtDNA D-loop全序列,检测到107个多态位点,定义了86种单倍型。结果表明,云南3个水牛品种的mtDNA遗传多样性非常丰富,其中,滇东南水牛的遗传多样性最高(Hd: 0.946±0.017,Pi: 0.0162±0.0018),盐津水牛的遗传多样性最低(Hd: 0.805±0.063,Pi: 0.0141±0.0031)。系统发育分析结果表明,在3个云南水牛品种中检测到2个主要支系(A和B支系及其亚支系)及一个稀有支系C,其中A支系为主要支系(79.07%),且经历了强烈的群体扩张。[结论] 云南3个水牛品种具有丰富的mtDNA遗传多样性,主要有A与B两个母系起源。     

四川7个地方山羊品种(类群)mtDNA遗传多样性研究

测定了四川7个地方山羊品种（类群）43个个体的mtDNA控制区全序列，结果表明：山羊mtDNA控制区全序列长度为1212bp或1213bp，A＋T含量（59．9％）明显高于G＋c含量（40．1％）。共检测到74个变异位点，序列均为中性突变，核苷酸多样度为1．686％，这些差异共定义了27种单倍型，单倍型多样度为0．966，遗传多样性较为丰富，品种（类群）间存在不同程度的遗传分化。7个地方山羊品种（类群）间的遗传距离变异范围为0．0017～0．0306。用MEGA软件的NJ法构建单倍型序列的系统发育无根树，结果表明四川地方山羊品种（类群）有两个母系来源，但是否就对应于角笋骨羊（Capra aegagrus）和捻角山羊（Capra falconeri）两个野生祖先，还有待于进一步研究。     

4个引进山羊品种mtDNA控制区序列变异和系统发生关系研究

本研究测定了四川4个引进山羊品种24个个体的线粒体控制区全序列,并从GenBank获得山羊属2个野山羊种的2每控制区序列。利用MEGA2．0软件构建分子系统发育无根树。序列分析表明:山羊控制区线粒体控制全序列长度为1 212bp或1 213 bp,A+T含量占59．9％,其中64个核苷酸位点存在变异(约占5．28％),核苷酸多样度为 1．731％,这些差异共定义了16种单倍型,单倍型多样性为0．913±0．048。安哥拉山羊、波尔山羊都有自己独特的单倍型,与其他品种间都没有共享类型。使用NJ法构建了系统发育树,结果表明:2个野山羊种中,角(?)羊与家养山羊的关系相对较近,4个家养山羊品种有2个母系来源,在4个家养山羊品种内部,安哥拉山羊的分化要比其他3个品种早。     

黄河下游同域山羊种群mtDNA D-环多态性及系统发育

对黄河下游7个山羊种群共59个个体的mtDNA D-环533 bp序列进行分析,发现59个多态位点,其中单一多态位点21个,简约信息位点38个,分别占全序列的11.7%、3.94%和7.13%。确定了37种单倍型,崂山奶山羊1个个体还发现了1处5碱基的缺失。各群体单倍型多样度为0.785 7~0.969 7,核苷酸多样度为1.27%~1.73%,遗传多样性较丰富。构建系统发育树将37种单倍型分为2个分支,由此推断黄河下游山羊资源至少具有2个母系起源,角猾羊与A类型聚为1支,7个群体具有角猾羊起源,未发现捻角山羊对7个群体有贡献的证据。错配分析表明,A类型经历过群体扩张,B类型未经历过群体扩张。并通过遗传距离分析了各群体的遗传分化。     

Genetic phylogeography and maternal lineages of 18 Chinese black goat breeds

To understand the origin and genetic phylogeography of Chinese black goats, variations of mitochondrial DNA were characterised with 394 goats from 18 breeds, including 91 new individuals from regions poorly studied until now. Comparison of a 481-bp segment revealed a total of 192 haplotypes with 141 variable sites. The haplotype and nucleotide diversities ranged from 0.782?±?0.079 to 1.000?±?0.020 and from 0.009?±?0.001 to 0.045?±?0.006, respectively, indicating a relatively high genetic diversity in Chinese black goats. Phylogenetic analyses identified five haplogroups (A, B₁, B₂, C and D). The dominant haplogroups A, B₁ and B₂ were distributed in most of breeds, while the haplogroups C and D were only presented in the breeds located in north or northwest of China. Analysis of molecular variance and multidimensional scaling plot of F _ST analyses indicated no obvious geographic structure among breeds. Furthermore, the migration rates revealed that a wide range of gene flow or gene exchange occurred among breeds, which may result in the weak geographic structure of Chinese black goats. Population expansion analysis based on mismatch distribution indicated that two expansion events in Chinese black goats occurred at 10 and 28 mutational time units. Finally, our findings indicate the multiple maternal origins of Chinese black goats and more gene flow (female-mediated) which occurred during their domestic and breeding histories.     

Genetic diversity of Chinese indigenous goat breeds based on microsatellite markers

Eighteen microsatellites were used to investigate the genetic diversity and differentiation of eight Chinese indigenous goat breeds. The results indicated that there is a significant difference of genetic diversity between different loci. Chinese indigenous goat breeds have similar genetic diversity to other Asian goats, but with lower Fst. The clustering of individuals and populations showed that Chinese indigenous goat breeds might have originated from two ancestral populations. The genetic differentiation between populations is consistent with the results of archaeology, mtDNA and RAPD.     

Polymorphism and evolutionary profile of mitochondrial DNA control region inferred from the sequences of Pakistani goats

Complete mitochondrial DNA (mtDNA) control region of 30 Pakistani domestic goats was sequenced to investigate the genetic diversity and organization. Twenty‐two new haplotypes were observed and all were classified into mt‐lineage A. Phylogenetic analysis revealed two distinct clusters in mt‐lineage A, A1 and A2. A 17 bp deletion and a 76 bp insertion were detected in the L‐domain and observed 10 and one animals, respectively, in 232 Pakistani domestic goats. These remarkable deletion/insertion events would be useful to investigate mtDNA diversity within the highly divergent mt‐lineage A. In analysis of the control region feature, the caprine mtDNA was A/T rich as observed for other artiodactyls. Four conserved regions, Block A in the L domain, the C‐domain, Block B and CSB1 in the R domain, were defined as well as in the other species.     

Mitochondrial DNA diversity and the origin of Chinese indigenous sheep

Large-scale mitochondrial DNA (mtDNA) D-loop sequences data from previous studies were investigated to obtain genetic information which contributes to a better understanding of the genetic diversity and history of modern sheep. In this study, we analyzed mtDNA D-loop sequences of 963 individuals from 16 Chinese indigenous breeds that distributed seven geographic regions. Phylogenetic analysis showed that all three previously defined haplogroups A, B, and C were found in all breeds among different regions except in Southwest China mountainous region, which had only the A and B haplogroups. The weak phylogeographic structure was observed among Chinese indigenous sheep breeds distribution regions and this could be attributable to long-term strong gene flow among regions induced by the human migration, commercial trade, and extensive transport of sheep. The estimation of demographic parameters from mismatch analyses showed that haplogroups A and B had at least one demographic expansion of indigenous sheep in China.     

利用mtDNA细胞色素b分析贵州山羊的系统发育

试验选取贵州山羊4个群体(共55只),设计引物对其mtDNA细胞色素b基因片段进行测序,测序结果与GenBank报道的8个山羊品种mtDNA细胞色素b基因进行比对分析。结果发现,在55只贵州山羊中有11个变异位点,其中转换10次,T/G颠换1次;10种单倍型中有7种单倍型为1个群体独享,3种单倍型为多个群体共享。4个山羊类群间存在较近的亲缘关系,既是独立的类群,其间也存在基因交流,其中贵州黑山羊和贵州麻羊的亲缘关系最近,与贵州白山羊的亲缘关系次之,与贵州小香羊的亲缘关系最远。从山羊品种间遗传距离构建的邻接树可见,贵州4个山羊类群均起源于镰刀状角羊骨羊。     

Mitochondrial DNA diversity of Anatolian indigenous domestic goats

Anatolia has been an important region for civilizations and agricultural revolution as a major domestication centre for livestock species. Goats (Capra hircus) were among the earliest domesticated animals in this region. In this study, genetic diversity of Anatolian goat breeds was characterized by comparison of mitochondrial DNA hypervariable region 1. A total of 295 individuals, including 99 Anatolian Black goats, 96 Angora goats and 100 Kilis goats, were used. Haplogroup A was found to be the dominant haplogroup in all three breeds. The highest haplogroup diversity, including haplogroups A, B2, C and G, was observed in the Anatolian Black breed. Haplogroup D was only observed in Kilis and Angora goats. Haplogroup G was found in Angora and Anatolian Black breeds. The Anatolian goat breeds had high genetic diversity values and a weak phylogeographical structure. The nucleotide diversity values were found to be higher than those in previously studied goat breeds. The fact that Anatolia is a domestication centre and its geographical position as a junction of trade routes may have caused the higher genetic diversity of Anatolian goat breeds.     

Genetic Diversity of Mitochondrial DNA D-loop Sequences in Huili Black Goat

To explore the genetic diversity and origin for genetic resource protection of Huili Black goat, the mitochondrial DNA (mtDNA) D-loop was investigated. mtDNA D-loop sequences of 41 goats were analyzed by PCR, sequencing techniques, and biological information and the phylogenetic trees were constructed. The mtDNA sequences of the Huili Black goat ranged from 1211 to 1213 bp, and 2 sequences were 1211 bp, 29 sequences 1212 bp, and 10 sequences 1213 bp. The content of A+T (60.1%) was higher than one of G+C (39.9%). There were 9 haplotypes, and the haplotype diversity was 0.842+0.00368. The nucleotide diversity was 0.01542+0.00034. The phylogenetic analysis showed that Huili Black goat was distributed in a branch, and were closed to Jianchang Black goat, Chengdu Ma goat, Jintang Black goat, Guizhou White goat, Guizhou Black goat, but they were less related to Capra falconeri. Huili Black goats had rather abundant genetic diversity, and were greatly affected by other goat breeds in history.     

D‐loop sequence mitochondrial DNA variability of Sarda goat and other goat breeds and populations reared in the Mediterranean area

To provide useful knowledge on goat breed origin and history, we studied the mitochondrial DNA (mtDNA) of 69 goats from five different breeds, Camosciata delle Alpi, Maltese, Nubian, Saanen and Sarda, and one population, the Tunisian. All goats analysed displayed a moderate haplotype and nucleotide diversity. The highest was in the Sarda – the autochthonous breed reared in Sardinia. On the basis of mtDNA control region sequences, animals showed a high genetic haplotype diversity, 35 haplotypes were each represented by a single sequence and only a few haplotypes were shared among the animals. New haplotypes of goats reared in the Mediterranean area were identified and the majority of Italian goats belonged to haplogroup A. This result confirmed worldwide distribution and diversity of haplogroup A.     

唐古拉山牦牛群体的母系遗传多样性及遗传结构分析

[目的]从分子水平上探究青海省唐古拉山牦牛群体的母系遗传多样性、群体遗传结构及其遗传背景。[方法] 对52头唐古拉山牦牛个体mtDNA D-loop区序列进行测定后,使用生物信息学软件分析确定其核苷酸变异位点和单倍型数目,计算单倍型多样度和核苷酸多样度大小,并进行系统发育分析。[结果] 在619 bp唐古拉山牦牛D-loop区序列分析中,排除2处插入（缺失）后共检测到31处多态位点,包括单一多态位点5处和简约信息位点26处。根据序列间核苷酸变异共确定了13种单倍型,单倍型多样度和核苷酸多样度分别为0.821±0.043和0.007±0.004。与我国其他18个家牦牛品种和野牦牛相比,唐古拉山牦牛群体单倍型多样度和核苷酸多样度值均较低,表明该群体遗传变异较为贫乏,母系遗传多样性水平较低。以美洲野牛为外群,邻接法（即NJ法）构建的系统发育树结果显示：唐古拉山牦牛群体13种单倍型分布在A、B、C、D和E五种单倍型组中,且聚为2个大的母系分支（即I和II）,支系Ⅰ占比为77%,提示唐古拉山牦牛由2个母系支系组成,拥有2个母系起源且以支系Ⅰ为主。 [结论] 唐古拉山牦牛母系遗传多样性水平较低,由2个母系支系组成,以支系Ⅰ为主,推测其有2个母系起源。     

川中黑山羊和雷州山羊大小卵泡转录组学分析

试验旨在通过比较两个品种山羊大小卵泡的mRNA表达图谱来挖掘影响山羊卵泡发育的基因,为进一步阐述山羊卵泡发育机制提供数据基础。使用氯前列醇钠对川中黑山羊和雷州山羊进行同期发情处理,屠宰后采集卵巢并在体视显微镜下分离单个卵泡（大卵泡>6 mm;小卵泡<3 mm）,提取卵泡组织总RNA进行RNA-seq,利用生物信息学方法检测mRNA表达谱,筛选差异基因,并对其进行GO功能、KEGG通路富集分析。结果显示,川中黑山羊大小卵泡差异基因共4 451个,雷州山羊2 355个,二者共有差异基因1 771个。分析筛选出两个品种共有（INHBA、INHA、CYP19A1、KITLG、LHCGR和STAR）及各自特有（IGFBP6、BMP6和BMPR2）的已报道与卵泡发育相关的基因,此外还筛选出可能与这两种山羊繁殖性能相关的基因（GADD45B、TC2N和MSMO1）。GO功能分析显示,两个品种共有差异基因主要与各种物质的跨膜转运活性有关;KEGG通路分析显示,类固醇生成、细胞因子受体相互作用和cAMP信号通路在两个品种中均存在显著变化。类固醇生成过程中细胞色素P450代谢差异可能是川中黑山羊高产仔数的一个潜在因素。本研究结果为进一步探究山羊卵泡发育的基因功能及不同山羊品种繁殖性能差异提供参考。     

Y‐chromosomal variation of local goat breeds of Turkey close to the domestication centre

Genetic variations in chromosome Y are enabling researchers to identify paternal lineages, which are informative for introgressions and migrations. In this study, the male‐specific region markers, sex‐determining region‐Y (SRY), amelogenin (AMELY) and zinc finger (ZFY) were analysed in seven Turkish native goat breeds, Angora, Kilis, Hair, Honaml?, Norduz, Gürcü and Abaza. A SNP in the ZFY gene defined a new haplotype Y2C. All domestic haplogroups originate from Capra aegagrus, while the finding of Y1A, Y1B, Y2A and Y2C in 32, 4, 126 and 2 Turkish domestic goats, respectively, appears to indicate a predomestic origin of the major haplotypes. The occurrence of four haplotypes in the Hair goat and, in contrast, a frequency of 96% of Y1A in the Kilis breed illustrate that Y‐chromosomal variants have a more breed‐dependent distribution than mitochondrial or autosomal DNA. This probably reflects male founder effects, but a role in adaptation cannot be excluded.     

Mitochondrial DNA variation of indigenous goats in Narok and Isiolo counties of Kenya

Phylogenetic relationships among and genetic variability within 60 goats from two different indigenous breeds in Narok and Isiolo counties in Kenya and 22 published goat samples were analysed using mitochondrial control region sequences. The results showed that there were 54 polymorphic sites in a 481‐bp sequence and 29 haplotypes were determined. The mean haplotype diversity and nucleotide diversity were 0.981 ± 0.006 and 0.019 ± 0.001, respectively. The phylogenetic analysis in combination with goat haplogroup reference sequences from GenBank showed that all goat sequences were clustered into two haplogroups (A and G), of which haplogroup A was the commonest in the two populations. A very high percentage (99.90%) of the genetic variation was distributed within the regions, and a smaller percentage (0.10%) distributed among regions as revealed by the analysis of molecular variance (amova ). This amova results showed that the divergence between regions was not statistically significant. We concluded that the high levels of intrapopulation diversity in Isiolo and Narok goats and the weak phylogeographic structuring suggested that there existed strong gene flow among goat populations probably caused by extensive transportation of goats in history.     

中国地方猪种线粒体基因组遗传多样性及其系统发育分析

为从分子水平上探究中国地方猪种遗传多样性和分类地位,本试验采用生物信息学方法比较了6个类型共22个中国地方猪种的线粒体基因组全序列,分析了其多态性,并构建了6个类型猪种线粒体D-loop区单倍型的网络中介图以及基于线粒体D-loop序列、Cytb基因、完整编码区序列的系统进化树。结果表明,6个类型22个猪种中共检测到了144个多态位点,22种单倍型,说明地方猪种具有丰富的遗传多样性;地方猪线粒体基因组序列中核苷酸变异以转换为主,且Ti/Tv大于转换/颠换比临界值（2.0）,变异位点均符合中性突变。6个类型猪种间遗传距离均较小,且有共享单倍型。系统进化树结果表明,6种类型地方猪种主要聚为两个支系。表明线粒体D-loop序列及Cytb基因均可作为研究种内系统发育、起源进化的分子标记。