Hemotypes in Spanish sheep breeds

The structure and the genetic diversity of the Churra, Lacha and Manchega sheep breeds have been analysed using hemotypes observed in eight loci. The three breeds are different in their hemotypes in terms both of quantity and quality. The proportions of unique hemotypes in Churra (60%), Lacha (61%) and Manchega (67%) revealed a high level of individual diversity within each breed. Racial genetic diversity follows the descending order of: Manchega-Lacha-Churra. The value of N:H (number of animals: total hemotypes) in the multi-racial population was 3.05.     

Genetic relationships among Spanish sheep using microsatellites

Five indigenous Spanish breeds of sheep, Churra, Latxa, Manchega, Rasa–Aragonesa and Merino, with Awassi sheep as a reference breed were genotyped for 19 DNA microsatellites. Allele frequencies and mean heterozygosities revealed the greatest genetic variation in Merino sheep and the lowest in Awassis. Differences in variability were not great in the other breeds studied. The dendrograms obtained based on genetic distances showed a large differentiation between Awassi sheep and the Spanish breeds, as was to be expected from their distinct genetic origin. Merinos appeared separated from the other four breeds, of which, according to a classification based on the fleece characteristics, Churra and Latxa belong to the churro type and Manchega and Rasa–Aragonesa to the so called entrefino type, though no clear separation was evident between the two types. These results suggest that morphological data alone are insufficient for determining relationships between breeds and that studies involving genetic markers may be of great assistance.     

Genetic relationships between Spanish Assaf (Assaf.E) and Spanish native dairy sheep breeds

At present, the Assaf is the main dairy sheep in Spain. The Spanish Assaf (Assaf.E) was formed by male-mediated absorption of native Spanish sheep. Here we assess the genetic relationships among the Assaf.E and major native Spanish dairy breeds using microsatellites to contribute to the knowledge of the formation and within-population genetic variability of the breed. Blood samples from 44 unrelated Assaf.E individuals from 23 different Assaf.E flocks spread throughout 6 different Spanish provinces were obtained and genotyped using 14 microsatellites. Up to 312 additional samples belonging to the Awassi and Milchschaf sheep breeds and to six native Spanish dairy sheep breeds (Castellana, Churra, Latxa, Manchega, and Rubia de El Molar) as well as samples from Merino individuals to be used as the outgroup were also analysed observed (H_o) and expected (H_e) heterozygosity, rarefacted number of alleles per locus and distances based on molecular coancestry information were computed. Probabilities of assignment of the Assaf.E individuals to native Spanish dairy sheep breeds and cryptic genetic structure in the whole dataset were also assessed. It can be concluded that the Assaf.E breed has low genetic variability and high genetic distance with respect native Spanish dairy sheep breeds. From our results, the formation of the Assaf.E breed basically occurred via the absorption of individuals belonging to the Entrefino type, particularly to the Castellana and Manchega populations. Furthermore, Churra individuals may have participated in the formation of the Assaf.E breed at an early moment of the introduction of the breed into Spain.     

Genetic relationships between Spanish Assaf (Assaf.E) and Spanish native dairy sheep breeds

At present, the Assaf is the main dairy sheep in Spain. The Spanish Assaf (Assaf.E) was formed by male-mediated absorption of native Spanish sheep. Here we assess the genetic relationships among the Assaf.E and major native Spanish dairy breeds using microsatellites to contribute to the knowledge of the formation and within-population genetic variability of the breed. Blood samples from 44 unrelated Assaf.E individuals from 23 different Assaf.E flocks spread throughout 6 different Spanish provinces were obtained and genotyped using 14 microsatellites. Up to 312 additional samples belonging to the Awassi and Milchschaf sheep breeds and to six native Spanish dairy sheep breeds (Castellana, Churra, Latxa, Manchega, and Rubia de El Molar) as well as samples from Merino individuals to be used as the outgroup were also analysed observed (H_o) and expected (H_e) heterozygosity, rarefacted number of alleles per locus and distances based on molecular coancestry information were computed. Probabilities of assignment of the Assaf.E individuals to native Spanish dairy sheep breeds and cryptic genetic structure in the whole dataset were also assessed. It can be concluded that the Assaf.E breed has low genetic variability and high genetic distance with respect native Spanish dairy sheep breeds. From our results, the formation of the Assaf.E breed basically occurred via the absorption of individuals belonging to the Entrefino type, particularly to the Castellana and Manchega populations. Furthermore, Churra individuals may have participated in the formation of the Assaf.E breed at an early moment of the introduction of the breed into Spain.     

Blood groups and protein polymorphisms in five goat breeds (Capra hircus)

Data on allele frequencies at six red cell blood group systems and three blood protein polymorphic loci in five goat breeds are reported. Two blood proteins, albumin and carbonic anhy-drase, were not found to be polymorphic. The B blood group system of goats, like its homologue in cattle and sheep, is highly complex. At least 44 B phenogroups (haplotypes) have been distinguished in this study. Based on the variation in allele frequencies between breeds, genetic distances were calculated. The distances estimated by four different methods were in close agreement with data from the history and geographic origins of the breeds examined.     

3个山羊群体中4个微卫星DNA多态性及其与杂种优势的关系

利用4个微卫星标记（OarFCB11,OarAE101,McM218,McM38）对波尔山羊、太行山羊和河北奶山羊的等位基因频率、群体多态信息含量、有效等位基因数、杂合度和遗传距离进行了遗传检测,并测定了波尔山羊与河北奶山羊及太行山羊的杂交效果。结果表明：4个微卫星标记在波尔山羊、太行山羊和河北奶山羊3个品种中存在多态性,可以用于山羊遗传多样性的评估;从不同品种来看,太行山羊的遗传变异程度最大,而波尔山羊的遗传变异程度相对较小;波尔山羊与河北奶山羊的遗传距离大于与太行山羊,波尔山羊与河北奶山羊的杂种优势高于与太行山羊,与实际杂种优势测定结果相符。 Abstract: Gene frequency, polymorphism information contents, number of effective alleles, heterozygosity and genetic distances were studied in Boer goat, Taihang goat and Hebei dairy goat using four microsatellite markers（OarFCB11,OarAE101,McM218,McM38）. The crossing effects on Hebei dairy goat and Taihang goat with Boer goat were tested. The results indicated that there are genetic polymorphisms at four microsatellite markers in three goat breeds. Four microsatellite markers can be used for genetic diversity evaluation in goat breeds. The genetic variability of Taihang goat is the highest, and Boer goat is the lowest in three goat breeds. Genetic distances between Boer goat and Hebei dairy goat is bigger than that between Boer goat and Taihang goat. The heterosis between Boer goat and Hebei dairy goat is higher than that between Boer goat and Taihang goat. It accords with testing results on actual heterosis.     

中国蒙系绵羊品种间的基因流动

利用结构基因座和微卫星标记分析了中国蒙系绵羊4个品种间的基因流动情况。结果显示, 由结构基因座得出的遗传分化系数在0.0164 ~ 0.0455之间, 由微卫星位点得出的遗传分化系数在0.0107 ~ 0.0239之间, 说明遗传变异绝大部分存在于品种内, 蒙系绵羊品种间的遗传分化水平很低。结构基因座(N_m = 7.971)和微卫星位点(N_m = 15.732)都反映出品种间的基因流通畅。品种间的遗传差异与地理距离之间无直接相关关系。初步推断我国蒙系绵羊品种间的遗传分化主要是自然选择(生境异质性)作用的结果。     

Assessing genetic diversity in indigenous Veneto chicken breeds using AFLP markers

Genetic variation in four indigenous chicken breeds from the Veneto region of Italy was assessed using amplified fragment length polymorphism (AFLP) markers. A total of 99 individuals were analysed using three AFLP primer combinations that produced 70 polymorphisms. Four indigenous Veneto chicken breeds (Ermellinata, Padovana, Pépoi and Robusta) and a reference broiler line were included in the analysis. Breed-specific markers were identified in each breed. The expected heterozygosity did not differ significantly among the indigenous Veneto chicken breeds and the broiler line. The coefficient of gene variation (Gst) value across loci indicated that almost half of the total variability was observed among breeds. Nei's standard genetic distance between pairs of breeds showed that the distance between the broiler line and the Pépoi breed was greater than the distances between the broiler line and the other three chicken breeds. Cluster analysis based on standard genetic distances between breeds indicated that the Padovana and Pépoi breeds were closely related. Factorial analysis based on a binary matrix of the AFLP data showed a clear distinction of all breeds.     

The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers

A genetic study of 32 local Chinese, three foreign pig breeds [Duroc (DU), Landrace and Yorkshire], and two types of wild boar (Hainan and Dongbei wild boar) based on 34 microsatellite loci was carried out to clarify the phylogeny of Chinese indigenous pig breeds. The allele frequencies, effective numbers of alleles, and the average heterozygosity within populations were calculated. The results showed that the genetic variability of the Lingao pig was the largest, while the Jiaxing pig was the lowest. The greatest distance between domestic pigs was found between Shanggao and DU pig and the shortest was found between Wuzhishan and Lingao pig, respectively. A neighbour-joining tree constructed from Modified Cavalli-Sforza genetic distances divided Chinese pigs into two clusters; four subclusters were also identified. Our results only partly agree with the traditional types of classification and also provide a new relationship among Chinese local pig breeds. Our data also confirmed that Chinese pig breeds have a different origin from European/American breeds and can be utilized in programmes that aim to maintain Chinese indigenous pig breeds.     

Genetic diversity in the Churra tensina and Churra lebrijana endangered Spanish sheep breeds and relationship with other Churra group breeds and Spanish mouflon

The aim of the present study was to estimate the genetic intra-breed variability of Churra tensina and Churra lebrijana endangered breeds and to establish genetic relationships with Churra, Latxa and Merino breeds, as well as Spanish mouflon, by using 28 microsatellite markers, to provide useful information for their conservation. Allele frequencies and heterozygosity revealed high genetic variation in the two endangered breeds despite their small population size. Estimates of inbreeding coefficient (F_IS) were significant for all breeds studied, except for Churra lebrijana breed. The highest inbreeding coefficient (F_IS = 0.143) was found in the Spanish mouflon. Genetic differentiation tests (F_ST = 0.121) and assignment of individuals to populations indicated the existence of defined breed populations, and low genetic flow between these breeds. The highest pairwise Reynolds distance (D_R) values were observed between Mouflon and the domestic sheep breeds. Considering only domestic sheep breeds, the Churra lebrijana breed showed the highest pairwise D_R values_. The lowest values were found between Latxa and the other domestic sheep, except for Churra lebrijana. Results of pairwise D_R values, as well as phylogenetic tree and bottleneck analysis showed an important genetic isolation of the Churra lebrijana breed from the other Churra types, and genetic signatures of a demographic bottleneck. Finally, structure analysis of populations detected a population subdivision in the Latxa sheep breed. In conclusion, this study presents valuable insight into the existing genetic variability of two Spanish endangered breeds, as well as the first study in Spanish mouflon based on microsatellite analysis. The high degree of variability demonstrated in Churra tensina and Churra lebrijana implies that these populations are rich reservoirs of genetic diversity.     

福建家鸭品种的分子遗传多样性

通过筛选的28个多态性较好的微卫星标记检测了福建省金定鸭、莆田黑鸭、连城白鸭、山麻鸭4个家鸭品种的遗传多样性.利用等位基因频率计算了各群体的遗传参数、群体间的Nei氏标准遗传距离D_S和D_A遗传距离,并采用邻近法（NJ）和类平均法（UPGMA）进行聚类分析和比较.结果表明,福建省4个家鸭品种全部群体的平均杂合度为0.5353,遗传一致性较好,应加强各保种场（区）多样性的保护;各品种间的遗传距离远近顺序在两种遗传距离D_S和D_A的结果中完全一致,以D_A和D_S为基础分别得到的UPGMA和NJ的聚类结果完全相同,表明在应用微卫星标记分析品种的遗传多样性时,使用更多的微卫星位点,才可以获得更准确更具普遍性的结论.4个家鸭品种的聚类与各品种的经济类型、生态地域分布关系密切.     

Economic weights of fertility, prolificacy, milk yield and longevity in dairy sheep

Economic weights have been estimated in two breeds (Latxa and Manchega) using economic and technical data collected in 41 Latxa and 12 Manchega dairy sheep flocks. The traits considered were fertility (lambing per year), prolificacy (number of lambs), milk yield (litres) and longevity (as productive life, in years). A linear function was used, relating these traits to the different costs in the flock. The variable costs involved in the profit function were feed and labour. From this function, economic weights were obtained. Labour is considered in the Latxa breed to be a constraint. Moreover, farm profits are unusually high, which probably means that some costs were not included according to the economic theory. For that reason, a rescaling procedure was applied constraining total labour time at the farm. Genetic gains were estimated with the resulting economic weights to test if they give any practical difference. Milk yield only as selection criterion was also considered. The medians of the estimated economic weights for fertility, prolificacy, milk yield and longevity were 138.60 € per lambing, 40.00 € per lamb, 1.18 € per l, 1.66 € per year, and 137.66 € per lambing, 34.17 € per lamb, 0.73 € per l, 2.16 € per year under the linear approach in the Latxa and Manchega breeds respectively. Most differences between breeds can be related to differences in production systems. As for the genetic gains, they were very similar for all economic weights, except when only milk yield was considered, where a correlated decrease in fertility led to a strong decrease in profit. It is concluded that the estimates are robust for practical purposes and that breeding programmes should consider inclusion of fertility. More research is needed to include other traits such as somatic cell score, milk composition and udder traits.     

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 polymorphism in sheep plasma detected using antibodies to human plasminogen

Protein variation was identified in sheep when Western blots of polyacrylamide gels (routinely used to resolve transferrin polymorphism) were stained using antibodies to human plasminogen. The affinity of the antibodies to ovine plasma was less than 7% that of a human standard but they bound specifically to a single polymorphic protein. In 146 lambs and their parents the inheritance of the ovine plasminogen antigen polymorphism was consistent with four autosomal alleles segregating codominantly. However, an additional two lambs had types which were incompatible with their putative parents. The pedigrees of these lambs were tested by DNA fingerprinting and shown to have been incorrectly recorded. The genetic polymorphism detected by human plasminogen antiserum provided a probability of sire exclusion (PE) ranging from 0.04 to 0.32 and a polymorphic information content (PIC) of 0.08 to 0.50 in flocks of five sheep breeds: Perendale, Romney, Merino, Texel and Coopworth (in order of increasing genetic variation in this locus). Significant differences in allele frequency were observed between breeds but sampling did not assess the variation among flocks within a breed.     

Genetic relationships between seven Spanish native breeds of cattle

Summary. Ten genetic markers were studied in seven Spanish native cattle breeds, using a total of 725 animals. Of the ten, two were found to be monomorphic in all seven breeds. The genetic relationships of the seven breeds are estimated by three different genetic-statistical methods (genetic distances, main coordinate analysis and cluster analysis), which indicate three clearly distinct groups of populations: one where the Cárdena Andaluza and Alistana Sanabresa are very closely related, one comprising Sayaguesa, Morucha, Asturiana de los Valles and Asturiana de la Montaña cattle, and a third, genetically distant from the other two, comprising only Blanca Cacereña. The dendrogram drawn from the genetic distances matrix would seem to imply that the seven breeds are descended from different ancestors.     

Genetic distances within and across cattle breeds as indicated by biallelic AFLP markers

We tested the use of biallelic Amplified fragment length polymorphism (AFLP) polymorphisms for the estimation of relative genetic distances of cattle individuals within or across breeds. An allele permutation procedure was developed to estimate the stochastic variation of the genetic distance that is inherent to a given dataset. In a panel of 47 Holstein-Friesian cattle analysed with 248 polymorphic markers, the average genetic distance of bulls selected for breeding was slightly lower than the distance of the cows. The observed standard deviation (SD) of the distance indicated genetic subdivision, which for the bulls was explained by variation in the additive relationship derived from herdbook data. Animals from three different breeds, the highly selected Holstein-Friesian, the Italian Brown and the historic Maremmana, were compared on the basis of 106 polymorphic markers. No breed-specific fragments were observed. The mean pair-wise genetic distance within breeds was 85% of the value across breeds, but principal coordinates analysis clustered the animals according to their breed of origin. Calculation of distances between the breeds indicated a relatively divergent position of the Maremmana, relative to the two other breeds. However, biallelic markers indicate that the process of breed formation had only a limited effect on the diversity at marker loci.     

利用微卫星标记分析七品种（类群）小型猪的遗传多样性

采用世界粮农组织（FAO）和国际动物遗传学会（ISAG）推荐的27个微卫星,对久仰香猪、剑白香猪、从江香猪、环江香猪、黑香猪（贵州省种猪场）、五指山猪和滇南小耳猪等我国7小型猪种（类群）及杜洛克、长白和大白等3个外来猪种的群内遗传变异性和群间遗传差异进行了分析。结果表明,7个小型猪品种（类群）均有较高的群内遗传变异,但久仰、剑白、从江和环江4个香猪类群的群内遗传变异（平均多态信息含量（PIC）为0.61～0.64）显著低于其他3个小型猪种（平均PIC为0.80～0.84）。久仰、剑白、从江和环江4个香猪类群彼此间的遗传差异较小（奈氏标准遗传距离为0.12~0.22）,但它们与其他3个小型猪种有较大的遗传差异（奈氏标准遗传距离为1.61～1.96）,与3个外来猪种的遗传差异更大（奈氏标准遗传距离为1.99～3.30）。通过聚类分析,可将这些猪种清晰地分为3大类,久仰、剑白、从江和环江4个香猪类群紧密地聚为一类,其他3个小型猪种聚为一类,3个外来猪种聚为另一类。这一结果基本符合这些猪种的地理分布和品种来源。
     

Evaluation of the genetic variability of 23 bovine microsatellite markers in four Belgian cattle breeds

The polymorphism of 23 microsatellites in the four main cattle breeds in Belgium (Holstein Friesian, Belgian Blue, Belgian Red Pied and East Flemish) was analysed. Heterozygosity, polymorphism information content, the effective number of alleles, exclusion probability and the probability of genotypic identity for two random individuals were calculated for all microsatellites and all breeds. The Belgian Blue breed is generally a little less polymorphic in comparison with the other three breeds. Estimates of the genetic distances between these breeds confirmed the widely accepted proposition that the Belgian Blue is the most genetically distinct of these breeds. The three other breeds are likely to become one population, given current breeding strategies. Exclusion probabilities in parentage control cases are >0·9999 in all four breeds when all 23 microsatellites are used and >0·98 with only the two most polymorphic multiplexes.     

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.     

Marker-assisted conservation of European cattle breeds: An evaluation

Two methods have been developed for the assessment of conservation priorities on the basis of molecular markers. According to the Weitzman approach, contributions to genetic diversity are derived from genetic distances between populations. Alternatively, diversity within and across populations is optimized by minimizing marker-estimated kinships. We have applied, for the first time, both methods to a comprehensive data set of 69 European cattle breeds, including all cosmopolitan breeds and several local breeds, for which genotypes of 30 microsatellite markers in 25–50 animals per breed have been obtained. Both methods were used to calculate the gain in diversity if a breed was added to a set of nine non-endangered breeds. Weitzman-derived diversities were confounded by genetic drift in isolated populations, which dominates the genetic distances but does not necessarily increase the conservation value of a breed. Marker-estimated kinships across populations were less disturbed by genetic drift than the Weitzman diversities and assigned high conservation values to Mediterranean breeds, which indeed have genetic histories that differ from the non-endangered breeds. Prospects and limitations of marker-assisted decisions on conservation priorities are discussed.