中国驴种线粒体DNA D-loop多态性研究

利用Clustal W软件对我国5个家驴品种26个个体的mtDNA D—loop区399bp序列进行同源序列比对,共检测到核苷酸多态位点23个,只有转换1种类型,约占所测核苷酸的5．76％。以欧洲驴D—loop作对照,我国5个家驴品种D—loop区序列的平均核苷酸变异率为1．80％,其中凉州驴的平均核苷酸变异率为0．35％．云南驴为1．25％,关中驴为2．30％,新疆驴为2．91％,佳米驴为2．20％。家驴品种内与品种间mtDNA D—loop区序列歧异度分别为0．25％-5．01％和4．51％-5．51％,说明家驴品种间D—loop区序列多态性比较丰富。在所测家驴个体中,mtD NAD—loop序列由11种单倍型组成,单倍型比例为42．31％,表明我国家驴mtDNA遗传多态性正逐步丧失,需要加强其种质资源保护。引用GenBank中亚洲野驴和欧洲家驴的序列,构建了我国5个家驴品种的NJ分子系统树,首次从分子水平证实中国家驴可能起源于非洲野驴,而与亚洲野驴无关。     

我国部分黄牛品种线粒体D-loop区遗传多样性与起源分化

为了解我国地方黄牛品种线粒体DNA的遗传变异情况, 文章测定了16个地方黄牛品种206个个体线粒体D-loop区的全序列, 共检测到101个变异位点; 99种单倍型, 其中73种是普通牛单倍型, 26种是瘤牛单倍型; 平均核苷酸差异为22.6920, 单倍型多样度为0.9320, 核苷酸多样度为0.0227, 表明我国黄牛品种遗传多样性非常丰富。构建的NJ进化树显示16个品种来源于两大母系: 普通牛和瘤牛; 构建的Network图表明73种普通牛单倍型可以分为3大单倍型群; 26种瘤牛单倍型分为5种单倍型群, 推测我国瘤牛在迁移过程中, 至少经历了4次群体扩张事件。通过分析比较地方黄牛品种与内罗门牛共有的 H3单倍型, 发现其中只有16%的序列与内罗门牛的H3单倍型非常相似, 其余84%的序列均发生了鸟嘌呤变异, 推测这些变异很可能是我国瘤牛固有的变异。     

POPU金钱豹mtDNA ND5基因序列及其遗传变异

测定山西7个不同地域金钱豹9个体mtDNA ND5基因部分序列,结合GenBank下载的37条序列,进行遗传多样性分析,用豹属的狮Panthera leo和虎Panthera tigris作外群,构建其不同单倍型的NJ分子聚类关系。46条序列共产生18个单倍型,单倍型多样度和核苷酸多样度指数表明金钱豹的遗传多样性比较丰富,AMOVA分析显示其种群间出现显著的遗传分化。单倍型聚类分析表明,亚洲和非洲种群尽管有一定的分化,但其置信度很低,不足以形成各自独立的分支。     

POPULATION GENETIC DIVERSITY OF PANTHERA PARDUS BASED ON MTDNA ND5 GENE SEQUENCES

测定山西7个不同地域金钱豹9个体mtDNA ND5基因部分序列,结合GenBank 下载的37条序列,进行遗传多样性分析,用豹属的狮Panthera leo和虎Panthera tigris作外群,构建其不同单倍型的NJ分子聚类关系.46条序列共产生18个单倍型,单倍型多样度和核苷酸多样度指数表明金钱豹的遗传多样性比较丰富,AMOVA分析显示其种群间出现显著的遗传分化.单倍型聚类分析表明,亚洲和非洲种群尽管有一定的分化,但其置信度很低,不足以形成各自独立的分支.     

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

[目的]研究帕米尔盘羊对新疆地方家绵羊是否有遗传贡献。[方法]测定了盘羊、家绵羊75个体的细胞色素b基因全序列,分析其遗传多样性,计算不同群体间遗传距离,进而构建系统发生树。[结果]新疆地方绵羊中检测到43个多态位点,定义为23个单倍型,单倍型多样度(Hd)为0.889±0.00102,核苷酸多样度(Pi)为0.521%。新疆地方家绵羊群体可分为4个支系(A、B、C和D),其中支系D首次在新疆多浪羊群体中被检测到。[结论]系统发育分析表明,新疆绵羊有多个母系起源或经过多次驯化,摩弗伦羊是绵羊母系祖先之一。     

华东地区地方鸡品种mtDNA控制区遗传多样性

为了探明我国华东地区地方鸡品种的遗传多样性和群体遗传结构,追溯其母系起源和进化过程,利用PCR技术扩增了11个地方鸡品种的线粒体DNA(mtDNA)控制区(D-loop)序列,并结合NCBI数据库中已发表的红色原鸡(Gallus gallus)D-loop区全序列,分析了它们的遗传多样性与亲缘关系,构建了11个品种与红色原鸡系统发生邻接树。结果表明:11个地方品种mtDNA D-loop区全长为1,231或1,232 bp,其中1,231 bp的序列有196条,1,232 bp的序列有123条,经过比对发现,两者在859 bp处存在单碱基缺失。11个地方品种319个个体共计检测到变异位点37个,总体单倍型多样度核苷酸多样度和平均核苷酸差异分别为0.901±0.009、0.00573±0.000001和6.833。按照鸡mtDNA单倍型分类通用标准,共包含35种单倍型,可以分为A、B、C和E共4个分支(单倍型群),分别包括11、10、9和5个单倍型。中介网络图中11个鸡品种也很明显地分成了4个支系,分别含有100、118、47和54条序列。系统发育树分为4个大枝,海南亚种(G.gallus jabouillei)自成一枝;C单倍型群与4个亚种的红色原鸡聚为一枝;E单倍型群与2个亚种红色原鸡聚为一枝;A和B单倍型群只与滇南亚种(G.gallus spadiceus)聚为一枝。11个品种中,除了狼山和丝羽乌骨鸡2个标准化品种外,都有很高的遗传多样性,可开发选择潜力很大。没有发现线粒体品种特异性DNA序列。华东地区地方品种至少有4个母系起源,部分品种可能受到了欧美高产品系的渗入。     

广西3个猪种线粒体DNA D-loop序列遗传多样性及系统进化研究

本研究旨在了解广西石头猪、德保猪和隆林猪的起源、群体遗传结构和亲缘关系。通过PCR扩增和测序技术获得3个群体61个个体的线粒体D-loop序列,采用DNASP 5.0进行多态性分析,MEGA 6.0计算各品种间的遗传距离及构建系统发育树。结果显示,3个猪种mtDNA D-loop区全长1 124~1 325 bp,石头猪和德保猪的中间重复序列变异仅存在A型,隆林猪存在A型和B型;石头猪mtDNA D-loop区8个多态性位点归纳出10种单倍型,德保猪8个多态性位点归纳出5种单倍型,隆林猪11个多态性位点归纳出9种单倍型;3种猪单倍型多样度分别为0.857、0.81和0.917,核算多样度分别为0.002 29、0.002 9和0.002 83。石头猪和德保猪可能有相同的母源血统,隆林猪可能有2种母系起源;3个品种猪单倍型多样性较为丰富,但核苷酸多样性匮乏,亟需进行科学保护。     

TYR基因外显子1的序列变异

为了分析家猪与野猪的遗传多样性及起源,测定了来自１２个中国地方家猪品种、３个欧洲引进猪品种以及8个中国野猪和2个越南野猪共36个个体的酪氨酸酶基因（TYR）外显子1的序列,共检出６个单核苷酸多态性位点（SNPs）,且这6个位点的变异均为同义突变,根据这些变异可将酪氨酸酶基因DNA序列归结为４种单倍型。结合已发表的数据,构建了简约中介网络图。 在网络图中,单倍型TYR*2主要为欧洲家猪与欧洲野猪和三条亚洲家猪染色体。大部分亚洲家猪和野猪共享单倍型TYR*1,表明这是一个亚洲类型的单倍型;同时也有部分欧洲家猪与野猪携带这一单倍型。 而单倍型TYR*3和TYR*4为本研究检测到的稀有单倍型,这两种单倍型主要由中国家猪与亚洲野猪组成。这种网络图结构支持家猪的欧洲和亚洲独立起源学说,同时也表明相当部分的欧洲家猪品种受到亚洲猪的基因渗透,而少量中国家猪和日本野猪也受到了欧洲猪的基因渗透。     

中国部分牦牛品种线粒体DNA遗传多态性研究

采用DNA测序技术首次测定了中国5个牦牛品种(类群)35个个体线粒体DNA控制区(D loop)全序列,结果表明:牦牛线粒体DNA控制区全序列长度为891～895bp,T、C、A、G4种核苷酸的含量分别为28.5%、25.3%、32.5%、13.7%。检测到55个变异位点,约占分析位点总数的6.16%,核甘酸变异类型有转换、颠换、插入/缺失4种。确定了24种单倍型,单倍型H4和H6为中国牦牛的主体单倍型,各单倍型在品种间分布不平衡,所测定的5个牦牛品种(类群)单倍型多样度平均为0.9697±0.0180,说明我国牦牛D loop单倍型类型丰富。牦牛品种内各序列平均核苷酸差异数为10.936,核苷酸多样度为1.231%;牦牛品种间核苷酸分歧度(Dxy)约为0.760%～2.155%,品种间双参数距离范围为0.000～0.029,表明我国牦牛遗传多态性丰富。对D环序列变异的分子方差分析和单倍型网络关系图的结果表明:我国牦牛品种间出现显著的遗传分化,牦牛单倍型网络关系图聚为2个聚类簇,表明我国牦牛有2个母系来源,或者有2个主要的驯化地点。     

西藏藏猪遗传多样性研究

采用mt DNA D-loop作为分子标记,对西藏的4个藏猪群体(林芝、山南、昌都和日喀则)遗传多样性进行了研究。结果表明,西藏藏猪mt DNA D-loop高变区A+T含量(62.90%)明显高于G+C含量(37.1%),富含A和T,存在碱基偏倚性。在长度为435 bp的序列中,共检测到20个变异位点,界定了26个单倍型,单倍型多样度(Hd)为0.705±0.021,平均核苷酸差异数(k)为1.231,核苷酸多样度(Pi)为0.002 83。其中,Hd、k和Pi在昌都藏猪群体中最高,日喀则藏猪最低。此外,Hap1和Hap3单倍型是4个群体的共享单倍型,表明4个藏猪群体存在两个共同的母系祖先单倍型。     

Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication

Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.     

Cytochrome b Genetic Diversity and Maternal Origin of Chinese Domestic Donkey

To clarify the origin of Chinese domestic donkeys, we investigated the mitochondrial Cytb gene from 244 animals from 13 native breeds. We found 55 variable sites in the Cytb gene sequence and subsequently defined 58 haplotypes. Analysis of haplotypes in combination with Cytb sequences revealed two mitochondrial origins in Chinese domestic donkeys, phenotypically expressed by the Somalian and Nubian lineages. The Somalian lineage predominated in Chinese domestic donkey breeds. Five specific Cytb gene SNPs diagnostic of each of the lineages were found in this study: 225(T-C), 237(C-T), 915(C-T), 1014(C-T), and 1134(A-G) mutations. They effectively distinguish the Nubian from the Somalian lineage in the mtDNA Cytb gene. Both lineages are from Africa and thus support the African maternal origins of Chinese domestic donkeys. No obvious geographic structure was found in Chinese domestic donkey breeds, but the population showed abundant genetic diversity.     

Protamine P1 sequences in equids: comparison with even-toed animals

Protamine P1 amino acid sequences were determined from semen samples of the Przewalski horse, donkey, Somali wild ass, Grevy's zebra, and Grant's zebra (odd-toed perissodactyls), and compared with those of the domestic horse. Although the rate of amino acid variation of protamine P1 is known to be among the most rapidly diverging polypeptides, the equid sequences revealed only little variation. The sequence from the Przewalski horse was identical with that from the domestic horse. The other sequences differed from the corresponding sequences of the domestic and Przewalski horses in two positions-Ser29 was replaced by Cys and Gln32 was replaced by Arg. The presence of the Cys residue at position 29 in the protamine P1 from the zebras, the donkey, and the Somali wild ass may allow formation of one extra protamine disulfide bridge during chromosome condensation in these species. Comparison with protamines from various even-toed animals (artiodactyls) indicated amino acid changes specific for those but different from the equid sequences.     

The forgotten donkey's history. Remarks on African wild asses of the Giardino Zoologico in Rome and their relevance for Equus africanus (von Heuglin & Fitzinger, 1866) taxonomy and conservation

This paper reviews the history of African wild asses in the Giardino Zoologico of Rome, highlighting their relevance to taxonomy of Equus africanus (von Heuglin & Fitzinger, 1866). Specifically, it is demonstrated that the so-called Munich/Catskill stock of African wild ass originated from three animals imported in Rome from Eritrean Danakil in August 1932. Available evidence suggests that contrary to some recent statements, these ‘wild’ asses were not related to the Nubian wild ass and are better considered as the result of some intergradations between Somali wild asses and local Danakil donkeys.     

Genome-wide analysis reveals selection signatures for body size and drought adaptation in Liangzhou donkey

Liangzhou donkey is a domestic animal breed distributed on the edge of the Tengger Desert in Gansu Province of China. It has small body size and strong adaptability to dry environments. Here, we sequenced 10 Liangzhou donkey genomes and compared them to the 55 genomes of 8 representative donkey breeds worldwide. The population structure analysis revealed that Liangzhou donkey harboured the ancestry with the Asian domestic donkeys (0.863) and European domestic donkeys (0.137). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the genetic diversity in Liangzhou donkey. In addition, we analyzed the genetic basis of the small body size and drought adaptation of Liangzhou donkey by using F_st, θπ-ratio, XP-EHH, CLR and θπ methods. We found that the NCAPG-LCORL on chromosome 3 may be a candidate region for small body size trait of Liangzhou donkey. The CYP4A11 gene located on chromosome 5 showed strong sign of selection sweep. CYP4A11 can convert arachidonic acid into 19(S)-HETE, which can promote water reabsorption in renal tubule and enhance the ability of Liangzhou donkey to adapt to dry environment. These results contribute to a better understanding of the underlying population structure of Liangzhou donkeys and provides a valuable resource for future research on donkey breeding in response to climate change.     

Genetic diversity and maternal origin of Northeast African and South American donkey populations

To investigate the mtDNA variation and origin of maternal lineages in South American donkeys and to reassess the domestication of donkeys in northeast Africa, we analyzed sequences (489 bp of the D‐loop) from 323 domestic donkeys sampled from Peru, Brazil, Ethiopia and Egypt. Altogether, the 323 sequences displayed 53 different haplotypes (45 in Ethiopia, 14 in Egypt, eight in Peru and six in Brazil). Among the four populations, Egyptian donkeys possessed the highest haplotype diversity (0.910 ± 0.032), followed by Brazilian donkeys (0.879 ± 0.060). The Clade I haplotypes dominated in Peruvian donkeys (65%), whereas Clade II haplotypes dominated in Brazilian donkeys (67%). Estimates of F_ST values showed a high genetic differentiation between Peruvian and Brazilian donkey populations (F_ST = 0.4066), which could be explained by the complex introduction history of South American donkeys. Phylogeographic analysis indicates that northeast Africa could be the most probable domestication center for Clade I donkeys. Analysis of molecular variance confirmed a weak genetic structure in domestic donkey populations among four continents (Europe, Asia, Africa and South America).     

Genetic diversity and paternal origin of domestic donkeys

Numerous studies have been conducted to investigate genetic diversity, origins and domestication of donkey using autosomal microsatellites and the mitochondrial genome, whereas the male‐specific region of the Y chromosome of modern donkeys is largely uncharacterized. In the current study, 14 published equine Y chromosome‐specific microsatellites (Y‐STR) were investigated in 395 male donkey samples from China, Egypt, Spain and Peru using fluorescent labeled microsatellite markers. The results showed that seven Y‐STRs—EcaYP9, EcaYM2, EcaYE2, EcaYE3, EcaYNO1, EcaYNO2 and EcaYNO4—were male specific and polymorphic, showing two to eight alleles in the donkeys studied. A total of 21 haplotypes corresponding to three haplogroups were identified, indicating three independent patrilines in domestic donkey. These markers are useful for the study the Y‐chromosome diversity and population genetics of donkeys in Africa, Europe, South America and China.     

Retention of solute and particle markers in the digestive tract of captive Somali wild asses (<Emphasis Type="Italic">Equus africanus somaliensis</Emphasis>)

In contrast to the domestic horse, whose digestive physiology has been thoroughly investigated, knowledge on the digestive physiology of wild equids is scarce. Comparisons between the domestic horse and the domestic donkey suggest that wild asses might achieve higher digestibilities. This could derive from longer retention times or a greater difference in the mean retention time (MRT) of particles vs. fluid (the selectivity factor (SF)). Here, we measured MRT of a solute (fluid; MRT_solute) and a particle (<2 mm; MRT_particle) marker in five captive male Somali wild asses (Equus africanus somaliensis) fed a diet of 95% grass hay. At a mean dry matter intake of 94 ± 3 g kg^?0.75 day^?1, MRT_solute was 33.3 ± 5.4 h and MRT_particle 39.6 ± 3.9 h, resulting in a SF of 1.21 ± 0.14. For their food intake, Somali wild asses appeared to have slightly higher MRT_particle than expected based on domestic equid data, in contrast to Grevy zebras (Equus grevyi), potentially indicating higher capacities of the digestive tract. However, considering data on domestic horses, donkeys, and zebra, there was no evident difference in the SF of wild equids compared to domestic ones. Together with an absence of reported anatomical differences in the digestive tract of wild and domestic equids, the data suggest a general similarity in the digestive physiology of equid species that contrasts with the diversity in the digestive physiology of ruminants, and that might be one contributing factor to a lack of sympatric, niche-differentiated equid species.     

Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys

Donkey (Equus asinus) is an important livestock animal in China because of its draft and medicinal value. After a long period of natural and artificial selection, the variety and phenotype of donkeys have become abundant. We clarified the genetic and demographic characteristics of Chinese domestic donkeys and the selection pressures by analyzing 78 whole genomes from 12 breeds. According to population structure, most Chinese domestic donkeys showed a dominant ancestral type. However, the Chinese donkeys still represented a significant geographical distribution trend. In the selective sweep, gene annotation, functional enrichment, and differential expression analyses between large and small donkey groups, we identified selective signals, including NCAPG and LCORL, which are related to rapid growth and large body size. Our findings elucidate the evolutionary history and formation of different donkey breeds and provide theoretical insights into the genetic mechanism underlying breed characteristics and molecular breeding programs of donkey clades.