应用微卫星标记分析中国地方鸡种的遗传变异

利用 8个微卫星位点对中国 9个地方鸡种和 1个引进品种进行了遗传检测。计算出了各品种的平均杂合度、平均多态信息含量 (PIC)及品种间的遗传距离 ,并进行了系统聚类。结果表明 :8个微卫星位点上共检测到了5 4个等位基因 ,每个位点上平均为 6 .75个。各位点平均多态信息含量为 0 .5 0 71～ 0 .74 34,均表现出了高度多态性。各群体平均杂合度较高 ,为 0 .5 5 6 4～ 0 .7135 ,说明我国地方鸡种有着较丰富的遗传多样性。地方鸡种间的遗传距离相对较远 ,10个鸡种共分为三大类。研究结果对我国鸡种资源的评估、保存和预测杂种优势具有一定的指导意义     

Variation of 423G>T in the Agouti Gene Exon 4 in Indigenous Chinese Goat Breeds

The Agouti gene plays an important role in pigment synthesis in domestic animals. A transversion of 423G>T recognized by BanII was found after a fragment (178 bp) of the goat Agouti gene exon 4 was amplified and sequenced. To investigate its genetic effect and diversity, 677 individuals from 12 indigenous Chinese goat breeds and one imported goat breed from South Africa (Boer goat) were analyzed by PCR-RFLP. Two alleles, T and G, and three genotypes, TT, TG, and GG, were detected. Allele T had a higher frequency in most goat breeds and, combined with the coat color phenotype, is believed to be responsible for the black phenotype or to be linked with the causative site in the goat. The results also indicate that the 423G>T transversion showed lower genetic diversity in goat breeds with black coat color in China. Genetic differentiation among the 13 goat populations was 0.2023. The clustering of populations based on the 423G>T site was basically consistent with the variation of coat color.     

Assessing genetic diversity in Italian goat populations using AFLP® markers

Amplified fragment length polymorphism (AFLP) markers were used to investigate the genetic variation in a sample of seven goat (Capra hircus) populations. A total of 210 individuals (30 per population) were analysed using seven selected AFLP primer combinations that produced 219 clear polymorphisms. Four autochthonous goat breeds (Bionda dell'Adamello, Frisa, Orobica and Verzaschese), two primary populations, one from the Lombardy Alps (Val di Livo) and the other from Sardinia island (Sarda) and a reference cosmopolitan breed (Saanen) were included in the analysis. The expected heterozygosity (Het) did not differ significantly among breeds (range 0.21-0.24). No breed specific markers were identified. The variability at AFLP loci was largely maintained within breeds, as indicated by the coefficient of genetic differentiation (Gst) value (0.11). Dice similarities calculated between pairs of individuals belonging to the same or to different breeds largely overlapped. Bootstrapping on markers indicated that the coefficient of variation (CV) of the genetic indexes tested decreases only marginally by adding markers over 100 AFLPs. Cluster analysis based on standard genetic distance between breeds indicates that Sarda is the most distant population, while Bionda, Frisa, Verzaschese and Val di Livo seem to be highly related populations. Interestingly, Saanen is closer than Orobica to the other four goat populations of the Lombardy Alps. Principal co-ordinates analysis based on Dice similarities confirms these observations. Genetic diversity of the goat populations investigated confirms what is expected on the basis of their geographical location. Results from Orobica are not correlated with geographical distances and may reflect undocumented migrations and gene flows and identify an original genetic resource.     

Genetic diversity and population structure in multiple Chinese goat populations using a SNP panel

Information about genetic diversity and population structure among goat breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of goat breeds. Here, we measured genetic diversity and population structure in multiple Chinese goat populations, namely, Nanjiang, Qinggeda, Arbas Cashmere, Jining Grey, Luoping Yellow and Guangfeng goats. A total of 193 individuals were genotyped for about 47 401 autosomal single nucleotide polymorphisms (SNPs). We found a high proportion of informative SNPs, ranging from 69.5% in the Luoping Yellow to 93.9% in the Jining Grey goat breeds with an average mean of 84.7%. Diversity, as measured by expected heterozygosity, ranged from 0.371 in Luoping Yellow to 0.405 in Jining Grey goat populations. The average estimated pair‐wise genetic differentiation (F_ST) among the populations was 8.6%, ranging from 0.2% to 16% and indicating low to moderate genetic differentiation. Principal component analysis, genetic structure and phylogenetic tree analysis revealed a clustering of six Chinese goat populations according to geographic distribution. The results from this study can contribute valuable genetic information and can properly assist with within‐breed diversity, which provides a good opportunity for sustainable utilization of and maintenance of genetic resource improvements in the Chinese goat populations.     

中国绒山羊遗传多样性现状和系统发生关系的微卫星分析

为了调查中国绒山羊遗传资源现状, 作者应用联合国粮农组织和国际家畜研究所推荐的19对微卫星引物并结合荧光PCR技术, 对9个中国地方产绒山羊群体和1个西非山羊品种进行了遗传多样性检测。14个微卫星座位在10个山羊群体中显示为高度多态, 可作为山羊遗传多样性分析的有效标记。多态信息含量和遗传杂合度等数据表明: 目前中国地方产绒山羊群体的遗传多样性较为丰富, 并且大部分保种场较好地保存了这些地方资源。采用非加权配对算术平均法构建的聚类图和采用主成分分析法得到的散点图均显示, 中国山羊与西非山羊为不同的2类; 中国产绒山羊中河谷山羊、河西绒山羊与其他山羊的遗传距离较远; 其他山羊又大致分为2类: 一类由辽宁绒山羊、新疆山羊、柴达木山羊、陕北山羊组成, 另一类由内蒙古绒山羊组成。此研究结果为开展我国地方绒山羊种质特性研究及资源保护和利用提供了科学依据。     

Genetic variability and bottleneck studies in Zalawadi, Gohilwadi and Surti goat breeds of Gujarat (India) using microsatellites

Indian goat breeds are recognized as an invaluable component of the world's goat genetic resources. Microsatellite pairs were chosen from the list suggested by International Society for Animal Genetics (ISAG) and amplified in two multiplexes (Set-I: 7 microsatellites and Set-II: 11 microsatellites) for automated fluorescence genotyping to assess bottleneck and analyze genetic variability and genetic distances within and between three goat breeds viz. Zalawadi, Gohilwadi and Surti. The observed number of alleles ranged from 4 (Oar JMP-29) to 15 (ILSTS-030 and -034) with a total of 178 alleles and mean of 9.89 alleles across the three breeds. The overall heterozygosity, PIC and Shannon index values were 0.61, 0.60 and 1.50 indicating high genetic diversity. The maximum observed heterozygosity was found in Gohilwadi and minimum in Surti goat breed. The Nei's standard genetic distance was minimum between Zalawadi and Gohilwadi, and maximum between Gohilwadi and Surti. Non-significant heterozygote excess on the basis of IAM, TPM and SMM models, as revealed from Wilcoxon sign-rank tests, along with a normal ‘L’-shaped distribution of mode-shift test, indicated no bottleneck in Zalawadi and Gohilwadi goat populations, whereas mild bottleneck in the recent past for Surti breed. This research on goat genetic diversity in Gujarat state provides valuable information on Zalawadi, Gohilwadi and Surti goat genetic resources, and will assist in developing a national plan for the conservation and utilization of indigenous goat breeds.     

Genetic diversity in Swiss goat breeds based on microsatellite analysis

Genetic diversity in eight Swiss goat breeds was estimated using PCR amplification of 20 bovine microsatellites on 20-40 unrelated animals per breed. In addition, the Creole breed from the Caribbean and samples of Ibex and Bezoar goat were included. A total of 352 animals were tested. The bovine microsatellites chosen amplified well in goat. The average heterozygosity within population was higher in domestic goat (0.51-0.58) than in Ibex (0.17) and Bezoar goat (0.19). Twenty-seven per cent of the genetic diversity in the total population could be attributed to differences between the populations. However, with the exclusion of Ibex from the total population, this proportion dropped to 17%. Principal component analysis showed that all Swiss goat breeds are closely related, whereas the Creole breed, Ibex and Bezoar goat are clearly distinct from all eight Swiss breeds.     

Genetic diversity and patterns of population structure in Creole goats from the Americas

Biodiversity studies are more efficient when large numbers of breeds belonging to several countries are involved, as they allow for an in‐depth analysis of the within‐ and between‐breed components of genetic diversity. A set of 21 microsatellites was used to investigate the genetic composition of 24 Creole goat breeds (910 animals) from 10 countries to estimate levels of genetic variability, infer population structure and understand genetic relationships among populations across the American continent. Three commercial transboundary breeds were included in the analyses to investigate admixture with Creole goats. Overall, the genetic diversity of Creole populations (mean number of alleles = 5.82 ± 1.14, observed heterozygosity = 0.585 ± 0.074) was moderate and slightly lower than what was detected in other studies with breeds from other regions. The Bayesian clustering analysis without prior information on source populations identified 22 breed clusters. Three groups comprised more than one population, namely from Brazil (Azul and Graúna; Moxotó and Repartida) and Argentina (Long and shorthair Chilluda, Pampeana Colorada and Angora‐type goat). Substructure was found in Criolla Paraguaya. When prior information on sample origin was considered, 92% of the individuals were assigned to the source population (threshold q ≥ 0.700). Creole breeds are well‐differentiated entities (mean coefficient of genetic differentiation = 0.111 ± 0.048, with the exception of isolated island populations). Dilution from admixture with commercial transboundary breeds appears to be negligible. Significant levels of inbreeding were detected (inbreeding coefficient > 0 in most Creole goat populations, P < 0.05). Our results provide a broad perspective on the extant genetic diversity of Creole goats, however further studies are needed to understand whether the observed geographical patterns of population structure may reflect the mode of goat colonization in the Americas.     

Polymorphisms in BMP-2 gene and their associations with growth traits in goats

BMPs plays an important role in skeletal development. In this study, PCR-SSCP and DNA sequencing methods were employed to screen the genetic variation of caprine BMP-2 gene in 299 goats from three breeds (Boer goat, Chinese Xuhuai white goat and Chinese Haimen goat). Three fragments of BMP-2 gene were investigated, only 3′ flanking region of BMP-2 gene showed polymorphism. The alignment between nucleotide sequences of AY714781.1 in GenBank and the sequencing results of three PCR products with different patterns revealed that there was one mutation (AY714781.1: g.A172G) in 3′ flanking region of BMP-2 gene, which constructed three genotypes (AA, AB, BB). The frequencies of allele A and genotype AA were dominant in all three breeds. Frequency of allele B in Haimen goat breed was significantly lower than that of the other two breeds. The genotype distributions were in good agreement with Hardy-Weinberg equilibrium (P>0.05) in each breed. The PIC (Polymorphism Information Content) values in three populations were 0.3261, 0.2558, 0.1663 for Boer goat, Xuhuai White goat and Haimen goat respectively. It was indicated that individuals of Boer goats with genotype BB were significantly higher than those of individuals with genotype AA in body trunk index (P<0.01). No polymorphism was detected in the exon3.     

Genetic profile of the locally developed Meatmaster sheep breed in South Africa based on microsatellite analysis

This report is on the development and genetic distinctiveness of the Meatmaster, a locally developed South African composite sheep breed. Genotypes of 175 Meatmaster sheep were compared to genotypes of 242 individuals from six putative parent breeds and an outgroup. All comparisons were based on 10 microsatellite loci. No significant breed-specific alleles were found for the Meatmaster or most of the parental breeds. Nevertheless, a Bayesian-based assignment test placed 69.4% of Meatmaster individuals in clusters distinct from the well-defined breed-specific clusters of the parent breeds. Population differentiation from R_ST values showed low differentiation among the four Meatmaster populations (0.004–0.028), higher values for pair-wise combinations of Meatmaster populations and the parent breeds (0.051–0.194), and the highest values among Meatmaster populations and the outgroup: Namakwa Afrikaner (0.237–0.301). Clustering in a dendrogram placed all Meatmaster populations in distinct clusters with strong bootstrap support (97%). Trends from a hierarchical analysis of total variation confirmed some distinctiveness in the Meatmaster, with 2.315% of total variation found among Meatmaster populations compared to 11.455% among breeds. High levels of heterozygosity and numbers of alleles in Meatmaster populations indicated good retention of genetic diversity during the potential bottleneck created by selection in its early history. Results are discussed with reference to genetic distinctiveness in this developing breed, the genetic contribution of the Damara as a common ancestor, conservation of genetic diversity and an application for future genetic management for the Meatmaster breed.     

江西省主要地方鸡种的RAPD分析及其群体遗传关系的研究

采用RAPD技术分析了南城黑鸡、余干五黑鸡、泰和乌骨鸡、东乡绿壳蛋鸡、崇仁麻鸡、宁都三黄鸡、广丰白耳黄鸡和万载康乐黄鸡等8个江西地方鸡种、1个培育鸡种--景德黄鸡以及1个外来鸡种--以色列隐性白羽鸡基因组池DNA的多态性,经OPERONA,B,C,D,G5组100种随机引物扩增筛选,14种引物获得了33个多态标记.各品种间的遗传距离指数的计算结果和UPGMA聚类关系图表明:在10个鸡种间,南城黑鸡和余干五黑鸡的遗传距离最近,两者有着极密切的亲缘关系.据此认为这两个鸡群可视为同一品种的两个地方系.此外,广丰白耳黄鸡和景德黄鸡也表现出较密切的亲缘关系,这与景德黄鸡在培育过程中曾掺有白耳黄鸡血缘的选育历史相吻合。 Abstract:Random amphfied polymorphic DNAs (RAPD) analysis was explored to investigate genetic polymorphisms of pooled genomic DNA from 8 native and 1 cultivated chicken breeds in Jiangxi province as well as 1 exotic chicken breed,which include Guangfeng baier huang,Jingde huang,Yugan wuhei,Nancheng hei,Congren ma,Taihe Silky Fowl,Ningdu san huang,Dongxiang green-shell,Wanzai kangle huang and Israel Recessive White Feather Fowl.of 100 OPERON random primers screened,14 primers produced 34 polymorphic RAPD markers.The genetic distance index and UPGMA dendrogram indicated that Nancheng hei and Yugan wuhei chickens had very closely genetic relationship,the genetic distance between the two populations was closer than any other pair of breeds.Therefore,the two chicken populations were suggested to be classified into one breed.In addition,Guangfeng baier huang and Jingde huang shown intimately relationship,it was consistent with the cultivation history of Jingde huang chicken breed,in which Guangfeng baier huang was introduced as one of parental breed.     

Genome‐wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium‐density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (H_O) and expected (H_E) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub‐structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f₄ statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within‐breed diversity and heterozygote advantage in crossbreeding schemes.     

Marker-derived phylogeny of European cattle supports demic expansion of agriculture

Using frequencies of 86 genes from 23 loci of blood group systems, blood and milk proteins, the genetic relationships among 14 cattle breeds including four native Balkan and four synthetic Balkan-Alp breeds were studied. The dendrogram and nonlinear map construction shows a consensus ‘Balkan breed cluster’, an ‘Alp breed cluster’, an unstable position of synthetic breeds and well-separated American breeds. Positive partial correlations between genetic distance and time elapsed since introduction of farming while keeping geographical distances constant, and regular patterns over thousands of kilometres indicate that large-scale cattle population movements together with human migration (in the Neolithic age) from the Near East into Europe across the Balkans are the most likely explanation for the genetic distances observed in our data. More recent breed differentiation and selection do not yet blur this initial pattern of European cattle populations.     

利用微卫星标记分析我国13个地方灰羽鹅品种的遗传多样性

我国地方鹅品种具有很多优良性状,但长期以来由于没有形成科学的选育制度和培育方法,品种的遗传多样性没有得到完整保存。为了深入了解我国地方鹅品种的遗传结构,使之得到更好的保护和利用,作者选用31个多态性较高的微卫星标记(其中19个是首次用磁珠富集法从AFLP片段中分离),检测了我国13个地方灰羽鹅(An-sercygnnoides)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)和群体间的遗传距离(DA)。结果表明:13个地方灰羽鹅品种中,平均多态信息含量为0.323–0.398,平均杂合度为0.4985–0.6727,各品种的杂合度都较高,最高的是狮头鹅(0.6727),最低的是雁鹅(0.4985)。用UPGMA法进行聚类分析的结果显示,13个品种被聚为4类:丰城灰鹅、武冈铜鹅、兴国灰鹅、狮头鹅、乌棕鹅、阳江鹅、马冈鹅、钢鹅、雁鹅聚为第1类;伊犁鹅自聚为第2类;长乐鹅、右江鹅聚为第3类;永康灰鹅自聚为第4类。本研究为鹅遗传育种提供了参考资料。     

Genetic characterization and breed assignment in five Italian sheep breeds using microsatellite markers

The knowledge of the genetic relationship and admixture among neighbouring populations is crucial for conservation efforts. The aim of this study was to analyse the genetic diversity of five Italian sheep breeds (Appenninica, Garfagnina Bianca, Massese, Pomarancina and Zerasca) using a panel of 24 microsatellite markers. Blood samples from 226 individuals belonging to the aforementioned populations were obtained and genotyped. All the investigated breeds showed a significant heterozygote deficiency caused by the high level of inbreeding indicated also by the high level of F_IS (0.146). Genetic differentiation between breeds was moderate (F_ST = 0.05) but significant and the individuals could be assigned to their breeds with an high success rate even if the inter-individual distances showed that few animals clustered separately from the other individuals of the same breed, especially for Pomarancina breed. The genetic distances reflect the historical knowledge of these breeds and some patterns of ancestral and recent gene flow between neighbour populations arise. The clustering analysis detects the presence of six clusters. Massese and Zerasca breeds were grouped together as well as Appenninica and Pomarancina with the latter forming two distinct clusters equally represented. The formation of this last breed is occurred with the absorption of individuals of the Appenninica breed and the gene flow probably continued in these recent years allowing the presence of a population substructure for Pomarancina breed. Such substructure supports the high level of heterozygote deficiency found for this breed despite the relatively high population size. The five populations analysed presented some genetic similarities but a clear uniqueness of the populations has been showed for almost all of them. Special attention to monitor genetic variability and to organize mating plans should be given especially for the three endangered breeds.     

Genetic diversity analysis of an indigenous Chinese buffalo breed and hybrids based on microsatellite data

Chinese native buffaloes have faced the threat of extinction, along with an increase in crossbreeding with domesticated river buffaloes; consequently, conservation of local buffalo genetic resources has become a priority. A Chinese native breed, Jianghan, is often crossed intentionally and unintentionally with imported breeds from India and Pakistan, Murrah, and Nili-Ravi. A total of 128 buffaloes of the breeds Jianghan, Murrah, and Nili-Ravi and their presumed hybrid offspring were genotyped for 10 microsatellite markers. Heterozygosity and Wright's F-statistics were calculated to determine the genetic variation in those populations. The observed average heterozygosities ranged from 0.836 (Murrah) to 0.986 (Jianghan), higher than the expected heterozygosities and all the inbreeding values within the populations were negative. The genetic distances between the presumed hybrid buffaloes and the two imported river type dairy buffalo breeds (Murrah and Nili-Ravi) were lower than with the native Jianghan, indicating strong contributions of the imported breeds to this presumed hybrid buffalo population. This information will be useful for the development of rational breeding for the dairy buffalo industry and for conservation strategies for the Jianghan buffalo.     

Genetic diversity among chicken breeds estimated through randomly amplified polymorphic DNA.

The randomly amplified polymorphic DNA (RAPD) markers were used to detect polymorphism among five breeds of chicken i.e. White Leghorn and Rhodes Island Red (selected for part period egg production and egg mass respectively), Red Cornish and White Plymouth Rock (selected for early body weights) and Kadaknath (native breed). Twelve of the fifty random primers screened yielded distinct polymorphic RAPD profiles. Of the total 96 fragments amplified, about 25% showed polymorphism. Using the RAPD data matrix, the within population and between population genetic similarity was estimated. The selected improved breeds showed higher within population genetic similarity in comparison to the native breed. The two meat type breeds showed a high level of genetic similarity between themselves. The White Leghorn breed showed a low genetic similarity with other breeds. The native breed showed highest similarity with Rhodes Island Red. The dendogram was constructed to show phylogenetic relationship among these breeds. As expected, the genetic distances were lowest within similar type breeds and were highest between dissimilar type breeds. The results indicated the effectiveness of RAPD in detecting polymorphism between chicken populations and their applicability in population studies and establishing genetic relationships among the chicken populations.     

Characterization of the Russian beef cattle breed gene pools using inter simple sequence repeat DNA analysis (ISSR analysis)

The gene pools of beef cattle breeds bred in Russia were characterized on the basis of inter simple sequence repeat DNA analysis (ISSR analysis). Samples of Aberdeen Angus, Kalmyk, and Kazakh Whitehead breeds from Russia, as well as of Hereford breed, hybrids of Kazakh Whitehead and Hereford breeds, and Kazakh Whitehead breed from the Republic of Kazakhstan, were examined. In the examined breeds, 27 AG-ISSR fragments were identified, 25 of which were polymorphic. The examined breeds were different both in the fragment profiles (the presence/absence of individual ISSR fragments) and in their frequencies. It was demonstrated that the hybrid animals lacked some ISSR fragments that were present with high frequencies in parental forms, suggesting considerable genome rearrangement in the hybrid animals (at the regions of microsatellite localization) in crossings of the individuals from different breeds. The level of genetic diversity in Russian beef breeds was consistent with the values typical of farmed populations (breeds). The genetic diversity parameters assessed by applying Nei’s gene diversity index and the Shannon index varied from 0.0218 to 0.0605 and from 0.0225 to 0.0819, respectively. The highest Shannon index value was detected in the Kalmyk breed (0.0837) and Kazakh Whitehead breed from Russia (0.0819), and the highest level of Nei’s gene diversity index was found in the Kalmyk breed (0.0562) and in both populations of the Kazakh Whitehead breed (0.0509 and 0.0605). The high level of genetic similarity (according to Nei) was revealed between Russian beef cattle breeds and Hereford cattle: 0.839 (for the Kazakh Whitehead breed from Russia) and 0.769 (for the Kalmyk breed).     

Genetic diversity present within the near-complete mtDNA genome of 17 breeds of indigenous Chinese pigs

The genetic diversity present within the near-complete mitochondrial genome (15,982 bp) was determined from 17 indigenous Chinese pig breeds and 3 European breeds. Animals were selected from 17 Chinese breeds that reflect the large phenotypic diversity of Chinese pigs and represent each of the six breed types, which are grouped based on morphological characteristics. Analysis of nucleotide diversity confirmed a high level of divergence between animals of European versus Asian origin; however, much more limited variation was observed between the 17 indigenous Chinese breeds. Each had a unique haplotype, but the lowest pairwise sequence divergence was only 0.01 +/- 0.01%, observed between the Tongcheng and Yushan Black. Comparison of control region sequence diversity revealed the 17 Chinese breeds contain a lower average pairwise distance (0.61 +/- 0.19%) than a group of European commercial breeds (0.91 +/- 0.21%). The dendrogram constructed from the near-complete mtDNA sequences showed the Chinese sequences loosely clustering into two groups. Although some correspondence with geographic origin was present, notable differences between the dendrogram and the traditional pig breed grouping system were observed.