微卫星标记对12个中外牛品种群体遗传结构的研究

选用联合国粮农组织(FAO)和国际动物遗传学会(ISAG)推荐的12对微卫星引物, 采用荧光标记–多重PCR技术, 检测了9个中国地方黄牛品种和3个外来牛品种的遗传多样性。利用等位基因频率计算出各群体的平均遗传杂合度(H)、多态信息含量(PIC)和群体间的DA及DS遗传距离。基于DA遗传距离, 用UPGMA法进行聚类分析, 结果12个中外牛品种被聚为4类: Ⅰ类属于南方黄牛品种, 包括恩施牛、黎平牛、昭通牛和川南山地牛; Ⅱ类属于中原黄牛品种, 包括郏县红牛、早胜牛和平陆山地牛; Ⅲ类属于北方黄牛, 包括延边牛和长白地方牛; Ⅳ类属于外来牛品种, 包括西门塔尔牛、夏洛来牛和德国黄牛。研究结果为中国地方牛品种的保护和利用提供了理论依据。     

采用微卫星标记分析13个中外牛品种的遗传变异和品种间的遗传关系

本研究应用联合国粮农组织(FAO)和国际动物遗传学会(ISAG)推荐的10对微卫星引物,结合荧光–多重PCR技术,检测了10个中国地方黄牛品种和3个外来牛品种的基因型。通过计算基因频率、多态信息含量和遗传杂合度,以Nei’s遗传距离和Nei’s标准遗传距离为基础,采用非加权组对算术平均聚类法构建了聚类图,分析了13个牛品种的群体内遗传变异和群体间遗传关系。并以聚类分析和群体结构分析为基础,将13个中外黄牛品种分为三类:Ⅰ类属于普通黄牛品种,包括延边牛、沿江牛、长白地方牛、蒙古牛、阿勒泰白头牛、哈萨克牛、复州牛和西藏牛;Ⅱ类属于含有瘤牛血统的黄牛品种,包括日喀则驼峰牛和阿沛甲咂牛;Ⅲ类属于外来牛品种,包括德国黄牛、西门塔尔牛和夏洛来牛。研究结果为加强我国地方黄牛品种种质特性研究以及地方牛品种资源的保护与利用提供了科学的依据。     

Genetic diversity measures of local European beef cattle breeds for conservation purposes

This study was undertaken to determine the genetic structure, evolutionary relationships, and the genetic diversity among 18 local cattle breeds from Spain, Portugal, and France using 16 microsatellites. Heterozygosities, estimates of Fst, genetic distances, multivariate and diversity analyses, and assignment tests were performed. Heterozygosities ranged from 0.54 in the Pirenaica breed to 0.72 in the Barrosã breed. Seven percent of the total genetic variability can be attributed to differences among breeds (mean F_st = 0.07; P < 0.01). Five different genetic distances were computed and compared with no correlation found to be significantly different from 0 between distances based on the effective size of the population and those which use the size of the alleles. The Weitzman recursive approach and a multivariate analysis were used to measure the contribution of the breeds diversity. The Weitzman approach suggests that the most important breeds to be preserved are those grouped into two clusters: the cluster formed by the Mirandesa and Alistana breeds and that of the Sayaguesa and Tudanca breeds. The hypothetical extinction of one of those clusters represents a 17% loss of diversity. A correspondence analysis not only distinguished four breed groups but also confirmed results of previous studies classifying the important breeds contributing to diversity. In addition, the variation between breeds was sufficiently high so as to allow individuals to be assigned to their breed of origin with a probability of 99% for simulated samples.     

Genetic diversity and population structure of indigenous yellow cattle breeds of China using 30 microsatellite markers

Twenty-seven domesticated yellow cattle breeds of China and three introduced cattle breeds were analysed by means of 30 microsatellite markers to determine the level of genetic variation within and among populations as well as the population structure. In all, 480 microsatellite alleles were observed across the 30 breeds with the mean number of alleles per locus of 9.093 for native breeds and 6.885 for the three introduced breeds. Mean F -statistics (0.08) for Chinese native cattle breeds implied that 92% of the total genetic variation was from genetic differentiation within each breed and 8% of the genetic variation existed among breeds. A phylogenetic tree was constructed based on Nei's genetic distances, and three clusters were obtained. According to the tree, the three introduced breeds were distinct from the 27 native breeds. The indigenous cattle breeds were divided into two clusters, one cluster including five humpless breeds and the other cluster containing 22 humped breeds. This study identifies multiple origins of yellow cattle of China from Bos taurus and Bos indicus . Furthermore, population structure analysis implies that there are possibly five independent original domestications for yellow cattle in China. Four of five origins were four different Bos indicus types, mainly in areas of the Chang Jiang, the Zhu Jiang River basin, the Yellow River and the Huai River basin. The other origin was for Bos taurus type of Mongolian descent, mainly located in Northwestern China, the Mongolian plateau and Northeastern China or north of the Great Wall.     

Identification of a new Y chromosome haplogroup in Spanish native cattle

The aim of this work was to perform a thorough analysis of the diversity of Y‐haplotypes in Spanish cattle. A total of 207 Bos taurus males were sampled across 25 European breeds, with a special focus on rare, local Spanish populations. Animals were genotyped with five Y‐specific microsatellites (INRA189, UMN0103, UMN0307, BM861 and BYM1), two indels (ZFY10 and USP9Y) and one SNP (UTY19). A new haplogroup, distinct from those described by Götherström et al. (2005), was identified and named Y1.2. Samples representing the three B. taurus Y‐haplogroups were genotyped for four additional Y chromosome SNPs (rs121919254, rs121919281, rs121919323 and rs137049553). Among these SNPs, only rs121919281 was informative in B. taurus and helped to confirm the new Y1.2 haplogroup. Analysis of a larger dataset of standardized haplotypes for 1507 individuals from 57 populations from Spain, other European countries and Africa showed the new Y1.2 haplogroup to be found exclusively in Spanish breeds. This finding reinforces the importance of local Spanish cattle as reservoirs of genetic diversity as well as the importance of the Iberian Peninsula in the history of cattle.     

Genetic diversity,introgression and relationships among West/Central African cattle breeds

Genetic diversity, introgression and relationships were studied in 521 individuals from 9 African Bos indicus and 3 Bos taurus cattle breeds in Cameroon and Nigeria using genotype information on 28 markers (16 microsatellite, 7 milk protein and 5 blood protein markers). The genotypes of 13 of the 16 microsatellite markers studied on three European (German Angus, German Simmental and German Yellow) and two Indian (Nelore and Ongole) breeds were used to assess the relationships between them and the African breeds. Diversity levels at microsatellite loci were higher in the zebu than in the taurine breeds and were generally similar for protein loci in the breeds in each group. Microsatellite allelic distribution displayed groups of alleles specific to the Indian zebu, African taurine and European taurine. The level of the Indian zebu genetic admixture proportions in the African zebus was higher than the African taurine and European taurine admixture proportions, and ranged from 58.1% to 74.0%. The African taurine breed, Muturu was free of Indian zebu genes while its counter Namchi was highly introgressed (30.2%). Phylogenic reconstruction and principal component analysis indicate close relationships among the zebu breeds in Cameroon and Nigeria and a large genetic divergence between the main cattle groups – African taurine, European taurine and Indian zebu, and a central position for the African zebus. The study presents the first comprehensive information on the hybrid composition of the individual cattle breeds of Cameroon and Nigeria and the genetic relationships existing among them and other breeds outside of Africa. Strong evidence supporting separate domestication events for the Bos species is also provided.     

婆罗门牛mtDNA D-loop变异及其遗传背景

对10头原种婆罗门牛mtDNAD-loop全序列912 bp测序,婆罗门牛遗传多样性丰富,检测到的9种单倍型兼有瘤牛(B.indicus)与普通牛(B.taurus)的遗传背景,核苷酸变异率为6.25 %,单倍型多态度为0.978±0.054 ,核苷酸多态度为0.014 30±0.008 68。所有单倍型聚为明显的两大分支,婆罗门牛的大部分单倍型为普通牛单倍型类群,并占绝对优势(90 %) ,仅Brah-6与亚洲瘤牛聚在一起,属于亚洲瘤牛线粒体单倍型,表明婆罗门牛的确是集亚洲瘤牛、欧洲普通牛等优良特性于一身(易产犊、产肉性能好、耐热与体表寄生虫等)的瘤牛品种之一。育种学家引种瘤牛的目的是改善当地牛的生产力与适应性,现代普通牛表现出明显又普遍的瘤牛渐渗现象。对现代的瘤牛品种而言,除亚洲瘤牛品种外,普通牛对其他瘤牛品种育成的贡献同样高。支持瘤牛(B.indicus)为独立驯化、起源于印度次大陆的假说。     

Mitochondrial genetic variation in European, African and Indian cattle populations

Mitochondrial DNA from representative animals of 13 different cattle breeds was assayed for restriction fragment length polymorphisms (RFLP) to determine phylogenetic relationships and levels of variation among breeds; 16 different mitotypes were found, described by 20 polymorphisms. Within these 16 mitotypes two major lineages were apparent: an Afro-European and an Asian type. These were found to differ at over 2.3% of sites surveyed. None of the mitotypes found in the Asian lineage was detectable in the Afro-European lineage and vice versa. Within each of the major mitotypes there were no further significant differences within or among breeds. Using rates of mitochondrial evolution estimated from other species, the two lineages were estimated to have diverged between 575000 and 1150000 years ago; well outside the 10000 years bp timeframe postulated by a single domestication hypothesis. The results presented are concordant with those generated in other studies and provide strong evidence for an independent domestication of Asian Bos indicus. Furthermore, the grouping of all African indicine populations within the clade containing all Bos taurus lineages points to the hybrid origins of the humped cattle of that continent.     

Mitochondrial DNA variation of Nigerian domestic helmeted guinea fowl

We analyzed genetic diversity of 215 mitochondrial DNA (mtDNA) D‐loop sequences from seven populations of domesticated helmeted guinea fowl (Numida meleagris) in Nigeria and compared that with results of samples collected in Kenya (n = 4) and China (n = 22). In total, 241 sequences were assigned to 22 distinct haplotypes. Haplotype diversity in Nigeria was 0.693 ± 0.022. The network grouped most matrilines into two main haplogroups: A and B. There was an absence of a geographic signal, and two haplotypes dominated across all locations with the exception of the Kebbi population in the northwest of the country; AMOVA also confirmed this observation (F_ST = 0.035). The low genetic diversity may be a result of recent domestication, whereas the lack of maternal genetic structure likely suggests the extensive genetic intermixing within the country. Additionally, the differentiation of the Kebbi population may be due to a certain demographic history and/or artificial selection that shaped its haplotype profile. The current data do not permit us to make further conclusions; therefore, more research evidence from genetics and archaeology is still required.     

Paternal origins of Chinese cattle

To determine the genetic diversity and paternal origin of Chinese cattle, 302 males from 16 Chinese native cattle breeds as well as 30 Holstein males and four Burma males as controls were analysed using four Y‐SNPs and two Y‐STRs. In Chinese bulls, the taurine Y1 and Y2 haplogroups and indicine Y3 haplogroup were detected in seven, 172 and 123 individuals respectively, and these frequencies varied among the Chinese cattle breeds examined. Y2 dominates in northern China (91.4%), and Y3 dominates in southern China (90.8%). Central China is an admixture zone, although Y2 predominates overall (72.0%). The geographical distributions of the Y2 and Y3 haplogroup frequencies revealed a pattern of male indicine introgression from south to north China. The three Y haplogroups were further classified into one Y1 haplotype, five Y2 haplotypes and one Y3 haplotype in Chinese native bulls. Due to the interplay between taurine and indicine types, Chinese cattle represent an extensive reservoir of genetic diversity. The Y haplotype distribution of Chinese cattle exhibited a clear geographical structure, which is consistent with mtDNA, historical and geographical information.     

Mitochondrial DNA variation of Salvelinus species found in Finland

Mitochondrial DNA (mtDNA) was purified from the Arctic charr, Salvelinus alpinus , the brook charr, Salvelinus fontinalis , and the lake charr, Salvelinus namaycush , and digested with restriction enzymes Ava II, Hinf I, Eco R V, Pst I and Xba I. Two Arctic charr samples were from natural populations and they represented two different morphotypes of Arctic charr. All other studied populations were hatchery maintained. Eight additional restriction enzymes and double digestions were employed to study morphotypes of Arctic charr. We distinguished two morphotypes with restriction enzyme Nci I. Sequence divergence among mtDNA types was 2.9–3.8% between S. alpinus and S. fontinalis , 3.4–4.6% between S. alpinus and S. namaycush , and 4.7–5.3% between S. fontinalis and S. namaycush . lntraspecific variation was lowest in Arctic charr, the average of nucleon diversity for three populations being 0.179, while for brook charr and for lake charr nucleon diversity was 0.334 and 0.550, respectively. According to the number of mtDNA types, it is obvious that introduction to Finland and hatchery propagation have not greatly affected the mtDNA variation of brook charr or lake charr.     

Mitochondrial DNA variation in European populations of Silurus glanis

Mitochondrial DNA diversity of 13 wild Silurus glanis populations (covering the entire range of the species) and eight hatchery populations was investigated. PCR-RFLP analysis of four regions of mitochondrial DNA (cytochrome b, control region, ND-5/6) was used. Nineteen haplotypes were found. Thirteen of them were private. The proportion of total genetic diversity attributable to population differentiation was almost 80%. Despite the existence of significant differentiation between populations for mtDNA variation, no consistent pattern of geographic structuring was revealed and nucleotide divergence among S. glanis populations was low. These phenomena are discussed with regard to the impact of glaciation events. The domesticated stocks show less genetic diversity than natural ones, possibly due to their mode of management. Analysis of three European catfish species S. glanis, S. aristotelis and Silurus triostegus (sampled in the Euphrates river) revealed several endonucleases which produced restriction phenotypes diagnostic for the three species.     

Mitochondrial DNA sequence variation within and between tuna Thunnus species and its application to species identification

Restriction analysis detected two types of bigeye tuna (α and β); the α type was in the majority in the Atlantic but nearly absent in the Indo-Pacific. The β type shared a larger number of restriction sites with other species than the conspecific β type, but bigeye-specific nucleotide substitutions with a novel diagnostic restriction profile were found. Although the nucleotide sequence difference between Atlantic and Pacific sub-species of the northern bluefin tuna was nearly the largest among species, individuals possessing the Atlantic type of mtDNA were found at very low frequency in the Pacific and vice versa. Previous RFLP markers were found to be diagnostic for the other five species (albacore, blackfin, longtail, southern bluefin and yellowfin tunas). Genetic information is provided to discriminate all Thunnus species regardless of their origin and to identify the ocean of capture in the northern bluefin and bigeye tunas.     

Genetic variation in two conserved local Romanian pig breeds using type 1 DNA markers

Analysis of the genetic variation of an endangered population is an important component for the success of conservation. Animals from two local Romanian pig breeds, the Mangalitsa and Bazna, were analysed for variation at a number of genetic loci using PCR-based DNA tests. Polymorphism was assessed at loci which 1) are known to cause phenotypic variation, 2) are potentially involved in trait differences or 3) are putative candidate genes. The traits considered are disease resistance, growth, coat colour, meat quality and prolificacy. Even though the populations are small and the markers are limited to specific genes, we found significant differences in five of the ten characterised loci. In some cases the observed allele frequencies were interesting in relation to gene function and the phenotype of the breed. These breeds are part of a conservation programme in Romania and marker information may be useful in preserving a representative gene pool in the populations. The use of polymorphisms in type 1 (gene) markers may be a useful complement to analysis based on anonymous markers.     

Origins and genetic diversity of New World Creole cattle: inferences from mitochondrial and Y chromosome polymorphisms

The ancestry of New World cattle was investigated through the analysis of mitochondrial and Y chromosome variation in Creoles from Argentina, Brazil, Mexico, Paraguay and the United States of America. Breeds that influenced the Creoles, such as Iberian native, British and Zebu, were also studied. Creoles showed high mtDNA diversity (H = 0.984 ± 0.003) with a total of 78 haplotypes, and the European T3 matriline was the most common (72.1%). The African T1a haplogroup was detected (14.6%), as well as the ancestral African‐derived AA matriline (11.9%), which was absent in the Iberian breeds. Genetic proximity among Creoles, Iberian and Atlantic Islands breeds was inferred through their sharing of mtDNA haplotypes. Y‐haplotype diversity in Creoles was high (H = 0.779 ± 0.019), with several Y1, Y2 and Y3 haplotypes represented. Iberian patrilines in Creoles were more difficult to infer and were reflected by the presence of H3Y1 and H6Y2. Y‐haplotypes confirmed crossbreeding with British cattle, mainly of Hereford with Pampa Chaqueño and Texas Longhorn. Male‐mediated Bos indicus introgression into Creoles was found in all populations, except Argentino1 (herd book registered) and Pampa Chaqueño. The detection of the distinct H22Y3 patriline with the INRA189‐90 allele in Caracú suggests introduction of bulls directly from West Africa. Further studies of Spanish and African breeds are necessary to elucidate the origins of Creole cattle, and determine the exact source of their African lineages.     

Disclosing the origin and diversity of Omani cattle

Among all livestock species, cattle have a prominent status as they have contributed greatly to the economy, nutrition and culture from the beginning of farming societies until the present time. The origins and diversity of local cattle breeds have been widely assessed. However, there are still some regions for which very little of their local genetic resources is known. The present work aimed to estimate the genetic diversity and the origins of Omani cattle. Located in the south‐eastern corner of the Arabian Peninsula, close to the Near East, East Africa and the Indian subcontinent, the Sultanate of Oman occupies a key position, which may enable understanding cattle dispersal around the Indian Ocean. To disclose the origin of this cattle population, we used a set of 11 polymorphic microsatellites and 113 samples representing the European, African and Indian ancestry to compare with cattle from Oman. This study found a very heterogenic population with a markedly Bos indicus ancestry and with some degree of admixture with Bos taurus of African and Near East origin.     

中国17个黄牛品种mtDNA变异特征与多态性分析

中国黄牛品种资源丰富,尚有28个地方固有品种.为了进一步深入了解这些宝贵遗传资源,本研究通过mtDNA变异特征与多态性分析揭示这些来自中国不同地域地方黄牛的母系起源与分子系统学特征.在17个品种84个体的mtDNA D-loop全序列中,一共检测到了102个核苷酸替代突变位.由此定义的53个单倍型被类聚为2个明显的单倍群：普通牛和瘤牛.mtDNA D-loop全序列变异的第一个特征是转换发生的频率远高于颠换;第二个特征是缺失与替代突变共存;第三个特征是缺失突变率比较高.所有D-loop全序列的核苷酸多样性和单倍型多样性分别为0.026 78±0.000 50和0.919±0.027.普通牛D-loop单倍型在北方牛种群中占有优势(80%～100%),而瘤牛单倍型在南方牛种群中占有优势(42.9%～100%),2种不同单倍型在中原牛种群中的分布也存在差异.2种不同单倍型在中国不同地域17个黄牛品种中的差异性分布揭示出了瘤牛mtDNA基因在中国黄牛中自南而北、由高到低的流动模式,这种基因流动模式的形成可能是由历史事件、地理隔离以及气候环境差异等造成的.     

Estimation of breed contributions to present and future genetic diversity of 44 North Eurasian cattle breeds using core set diversity measures

Extinction of breeds threatens genetic diversity of livestock species. The need to conserve genetic diversity is widely accepted but involves in general two questions: (i) is the expected loss of diversity in a set of breeds within a defined future time horizon large enough to establish a conservation plan, and if so (ii) which breeds should be prioritised for such a conservation plan? The present study uses a marker assisted methodology to address these questions. The methodology combines core set diversity measures with a stochastic method for the estimation of expected future diversity and breed marginal diversities. The latter is defined as the change in the total diversity of all breeds caused by a one unit decrease in extinction probability of a particular breed. The stochastic method was validated by means of simulations. A large field data set consisting of 44 North Eurasian cattle breeds was analysed using simplified determined extinction probabilities. The results show that the expected loss of diversity in this set within the next 20 to 50 years is between 1 and 3% of the actual diversity, provided that the extinction probabilities which were used are approximately valid. If this loss is to be reduced, it is sufficient to include those three to five breeds with the highest marginal diversity in a conservation scheme.     

Mitochondrial DNA variation and GIS analysis confirm a secondary origin of geographical variation in the bushcricket Ephippiger ephippiger (Orthoptera: Tettigonioidea), and resurrect two subspecies

Geographic variation within species can originate through selection and drift in situ (primary variation) or from vicariant episodes (secondary variation). Most patterns of subspecific variation within European flora and fauna are thought to have secondary origins, reflecting isolation in refugia during Quaternary ice ages. The bushcricket Ephippiger ephippiger has an unusual pattern of geographical variability in morphology, behaviour and allozymes in southern France, which has been interpreted as reflecting recent primary origins rather than historical isolation. Re-analysis of this variation using Geographical Information Systems (GIS) suggests a possible zone of hybridization within a complex pattern of geographical variation. Here we produce a genetic distance matrix from restriction fragment length polymorphism (RFLP) bandsharing of an approximately 4.5 kb fragment of mitochondrial DNA (mtDNA), and compare this with predictions resulting from the GIS analysis. The mtDNA variation supports a postglacial origin of geographical variation. Partial Mantel test comparisons of genetic distances with matrices of geographical distance, relevant environmental characteristics and possible refugia show refugia to be the best predictors of genetic distance. There is no evidence to support isolation by distance. However, environmental contrasts do explain significant variation in genetic distance after allowing for the effect of refugial origin. Also, a neighbour-joining tree has a major division separating eastern and western forms. We conclude that the major source of variation within the species is historical isolation in glacial refugia, but that dispersal, hybridization and selection associated with environmental features has influenced patterns of mtDNA introgression. At least two valid subspecies can be defined.