The assessment of genetic diversity within and among the eight subpopulations of Japanese Black cattle using 52 microsatellite markers

Japanese Black cattle are at risk for genetic homogeneity due to intensive use of a few sires. Therefore, assessment of the actual genetic diversity of this breed is important for future breeding plans. In the present study, we investigated the genetic diversity within and among eight subpopulations of Japanese Black cattle using 52 microsatellite markers. The parameters for genetic diversity of Japanese Black cattle were comparable to those of other cattle breeds, suggesting that the relatively high genetic diversity of the breed. However, upon comparison among the eight subpopulations, the Hyogo subpopulation showed markedly low genetic diversity. The results of the pairwise F_ST values, phylogenetic network and structure analysis indicated that the Hyogo population has remarkably high level of genetic differentiation from other populations, while Yamagata, Niigata, Hiroshima and Kagawa populations have low levels of genetic differentiation. Furthermore, multidimensional scaling plots indicated that individuals in some subpopulations were separated from individuals in the other subpopulations. We conclude that while the overall genetic diversity of Japanese Black cattle is still maintained at a relatively high level, that of a particular subpopulation is significantly reduced, and therefore the effective population size of the breed needs to be controlled by correct mating strategies.     

Genetic characterization of the Burlina cattle breed using microsatellites markers.

The present study was a contribution on the genetic characterization of the Burlina local cattle breed, and an approach to understanding the relationships between Burlina, Holstein Friesian and Brown Swiss which represent the majority of the dairy cattle reared nowadays in North-East Italy. The obtained results helped to clarify the genetic diversity and distinctiveness of Burlina population. In particular, the low genetic distance between Burlina and Holstein Friesian and the assignment of a moderate percentage of Burlina animals to Holstein Friesian suggested that crosses between them took place in the past, while crosses with Brown Swiss seemed to be less frequent. However, analyses of marker genotypes, showed a cluster with only Burlina individuals, which demonstrates the genetic distinctness of this breed. The Burlina breed showed the highest variability among the analysed breeds and its inbreeding coefficient was low. The data contribute to the feasibility of a conservation and selection programme for this breed and the results are useful for the implementation of a conservation strategy that should aim to conserve animals where the contribution from foreign breeds is as small as possible.     

日本牛的遗传资源

本文扼要回顾了日本牛种资源的发展历史;介绍了日本牛的遗传资源状况和各主要牛种的特征特性;从日本牛的遗传可变性和遗传距离等方面分析了日本牛品种之间的遗传关系;并展望了日本黑毛和牛、日本褐牛、日本短角牛、日本无角牛、见岛牛、口子岛牛等日本牛种资源的发展前景。     

Prioritization based on neutral genetic diversity may fail to conserve important characteristics in cattle breeds

Conservation of the intraspecific genetic diversity of livestock species requires protocols that assess between-breed genetic variability and also take into account differences among individuals within breeds. Here, we focus on variation between breeds. Conservation of neutral genetic variation has been seen as promoting, through linkage processes, the retention of useful and potentially useful variation. Using public information on beef cattle breeds, with a total of 165 data sets each relating to a breed comparison of a performance variable, we have tested this paradigm by calculating the correlations between pairwise breed differences in performance and pairwise genetic distances deduced from biochemical and immunological polymorphisms, microsatellites and single-nucleotide polymorphisms. As already observed in floral and faunal biodiversity, significant positive correlations (n=54) were found, but many correlations were non-significant (n=100) or significantly negative (n=11). This implies that maximizing conserved neutral genetic variation with current techniques may conserve breed-level genetic variation in some traits but not in others and supports the view that genetic distance measurements based on neutral genetic variation are not sufficient as a determinant of conservation priority among breeds.     

Genetic diversity and differentiation of five Cuban cattle breeds using 30 microsatellite loci

Conservation and improvement strategies in farm animals should be based on a combination of genetic and phenotypic characteristics. Genotype data from 30 microsatellites were used to assess the genetic diversity and relationships among five Cuban cattle breeds (Siboney de Cuba, Criollo Cubano, Cebú Cubano, Mambí de Cuba and Taíno de Cuba). All microsatellite markers were highly polymorphic in all the breeds. The expected heterozygosity ranged from 0.67 ± 0.02 in the Taíno de Cuba breed to 0.75 ± 0.02 in the Mambí de Cuba breed, and the observed heterozygosity ranged from 0.66 ± 0.03 in the Cebú Cubano breed to 0.73 ± 0.02 in the Siboney de Cuba breed. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (F_ST). The exact test for Hardy‐Weinberg equilibrium within breeds showed a significant deviation in each breed (p < 0.0003) for one or more loci. The genetic distance and structure analysis showed that a significant amount of genetic variation is maintained in the local cattle population and that all breeds studied could be considered genetically distinct. The Siboney de Cuba and Mambí de Cuba breeds seem to be the most genetically related among the studied five breeds.     

Genetic diversity and historic introgression in German Angler and Red Dual Purpose cattle and possibilities to reverse introgression

Recovering native uniqueness has major importance for breeds with historic introgression. The aim of the study was to estimate population genetic parameters for two local red cattle breeds from Northern Germany and to study possibilities to reverse introgression. Genealogical information consisted of 90,783 individuals for German Angler and 187,255 individuals for Red Dual-Purpose cattle breed, with additional information on sex, born, breed, status, and conventional breeding values. It is concluded that the native genetic contribution could be included as an additional trait in the total merit index in order to recover a part of the native genetic background. Native contributions should be estimated in the long term from marker data in order to account for Mendelian sampling. The maintenance of a sufficient genetic diversity of native alleles can be achieved by an advanced OCS with appropriate constraints.     

Relationships between Podolic cattle breeds assessed by single nucleotide polymorphisms (SNPs) genotyping

Italian Maremmana, Turkish Grey and Hungarian Grey breeds belong to the same Podolic group of cattle, have a similar conformation and recently experienced a similar demographic reduction. The aim of this study was to assess the relationship among the analysed Podolic breeds and to verify whether their genetic state reflects their history. To do so, approximately 100 single nucleotide polymorphisms (SNPs) were genotyped on individuals belonging to these breeds and compared to genotypes of individuals of two Italian beef breeds, Marchigiana and Piemontese, which underwent different selection and migration histories. Population genetic parameters such as allelic frequencies and heterozygosity values were assessed, genetic distances calculated and assignment test performed to evaluate the possibility of recent admixture between the populations. The data show that the physical similarity among the Podolic breeds examined, and particularly between Hungarian Grey and Maremmana cattle that experienced admixture in the recent past, is mainly morphological. The assignment of individuals from genotype data was achieved using Bayesian inference, confirming that the set of chosen SNPs is able to distinguish among the breeds and that the breeds are genetically distinct. Individuals of Turkish Grey breed were clearly assigned to their breed of origin for all clustering alternatives, showing that this breed can be differentiated from the others on the basis of the allelic frequencies. Remarkably, in the Turkish Grey there were differences observed between the population of Enez district, where in situ conservation studies are practised, and that of Bandirma district of Balikesir, where ex situ conservation studies are practised out of the original raising area. In conclusion, this study demonstrates that molecular data could be used to reveal an unbiased view of past events and provide the basis for a rational exploitation of livestock, suggesting appropriate cross-breeding plans based on genetic distance or breeding strategies that include the population structure.     

The Agersoe cattle: the last remnants of the Danish island cattle (Bos taurus)?

A phenotypically interesting strain of cattle existed on the small island of Agersoe, on the west coast of Zealand, Denmark, in the beginning of the last decade. The cattle share a great resemblance to the extinct Danish breed, the Island cattle. The objective of this study was to genetically characterize the Agersoe cattle, using microsatellites, amplified fragment length polymorphism (AFLP) and mtDNA markers, and analyse the genetic variability within the breed and the genetic relationship to 14 European breeds with focus on the Red Danish and Jutland breed. The results show diversity in nuclear markers comparable to that of modern breeds and that the Agersoe cattle are separable from the two native breeds. The absence of inbreeding and the degree of genetic diversity are taken as a sign of recent admixture. The Agersoe cattle did not exhibit a consistent association with any of the European breeds. Several arguments based on this survey have been put forward in favour of characterizing the Agersoe cattle as being the last remnants of the Danish Island Cattle.     

利用微卫星标记对4个肉牛品种进行遗传多样性分析

本研究利用10个微卫星标记分析了鲁西黄牛、布莱凯特肉牛、渤海黑牛和日本和牛4个品种185个个体的品种内遗传变异情况及各品种间的亲缘关系,共检测到58个等位基因,每个位点平均观察等位基因数为5.8个,从4(BM1818)到8个(ETH225和TGLA53)不等;有效等位基因数为2.5417～3.5849个;观察杂合度、期望杂合度和多态信息含量变异范围分别为0.2270～0.5459、0.6082～0.7230和0.5482～0.6791,均属高度多态性位点。群体间遗传分化明显,有34.49%的遗传分化来自群体间的变异。以Nei氏遗传距离(D_A)构建UPGMA系统进化树,聚类结果表明,渤海黑牛与鲁西黄牛首先聚为一类,布莱凯特肉牛和日本和牛聚为一类。布莱凯特肉牛的3个微卫星座位10个克隆的PCR扩增片段测序获得的序列已提交GenBank,登录号分别为：GQ368896、GQ368897、GQ368898、GQ368899、GQ368900、GQ368901、GQ368902、GQ368903、GQ368904、GQ368905。10对微卫星座位可作为有效的遗传标记用于4个肉牛品种的遗传多样性和系统发生关系分析。     

The role of agro-ecological factors and transboundary transhumance in shaping the genetic diversity in four indigenous cattle populations of Benin

The indigenous cattle population of Benin is a diverse mix of taurine and hybrid breeds shaped by diverse ecological and climatic conditions with eight agro-ecological zones (AEZ). Presumably, the taurine breeds face current endangerment due to ongoing indicine introgression following climate change and transboundary transhumance. The aim of the study was to investigate the genetic diversity and population structure of the indigenous breeds Lagune, Somba, Pabli and Borgou considering spatial agro-ecological and socio-economic factors (transhumance) based on 50k SNP and microsatellite data. Among the four sampled breeds, six genetic clusters were identified using model-free (discriminant analysis of principal components) and model-based (TESS and ADMIXTURE) methods separating taurine from hybrid breeds. Results based on an extension with publicly available historic SNP data sets from taurine and indicine West African cattle and additional outgroups provided additional insight into changes of genetic structure in the sampled breeds over time. Both taurine breeds, Somba and Lagune, showed a stable foundation but also spatially limited partial indicine introgression associated with transhumance leading to high genetic diversity. In addition, we found evidence for spatial diversity and changes in genetic structure over time in the Borgou breed in comparison of our samples with the historic samples which could be explained by potential continuous indicine introgression into the Borgou breed in two sample regions. Results for the Pabli breed do not conclusively point to full absorbance by the Borgou in comparison with all available Borgou samples. Further research is needed in this regard.     

Relationship of Icelandic cattle with Northern and Western European cattle breeds,admixture and population structure

ABSTRACT

Icelandic cattle is believed to have been brought from Norway during the settlement of Iceland around AD 870-930. Previous research on genetic relationships has indicated that Icelandic cattle is most related to northern Nordic indigenous breeds. Using single nucleotide polymorphism genotype data from Icelandic cattle and 29 Northern and Western European cattle breeds, we studied relationships and admixture among these breeds, and assessed population structure in Icelandic cattle. Population structure analysis through principal component analysis, estimation of ancestry, and analysis of patterns of population splitting and mixing revealed that Icelandic cattle are most related to three Finncattle breeds (Eastern, Northern and Western Finncattle), and Swedish Mountain cattle. Icelandic cattle has very low levels of admixture. We observed very limited population structure in Icelandic cattle. The observed structure was due to variable sire contributions. Over 1000 years of almost complete isolation has made Icelandic cattle highly genetically distinct from other cattle breeds.     

利用基因组重测序技术鉴定黑安格斯牛的纯度

【目的】基于10头黑安格斯牛和60头对照组牛的全基因组重测序数据,分析黑安格斯牛的纯度、遗传多样性及群体结构。【方法】全基因组重测序技术和生物信息学方法。【结果】通过对10头黑安格斯牛全基因组数据进行分析,共检测到15,064,459个SNP位点,其核苷酸多样性（pi）为0.0015,观测杂合度（Ho）为0.2381,期望杂合度（He）为0.2430,表明黑安格斯牛的遗传多样性较低;主成分分析和群体遗传结构分析发现,黑安格斯牛与欧洲普通牛聚为一类,其中有4头黑安格斯牛存在偏离情况,表明这4头牛主要与中国瘤牛与东亚普通牛韩牛之间存在杂交。【结论】10头黑安格斯牛中,6头为纯种黑安格斯牛,4头为杂种牛。     

Conservation priorities for the different lines of Dutch Red and White Friesian cattle change when relationships with other breeds are taken into account

From a genetic point of view, the selection of breeds and animals within breeds for conservation in a national gene pool can be based on a maximum diversity strategy. This implies that priority is given to conservation of breeds and animals that diverge most and overlap of conserved diversity is minimized. This study investigated the genetic diversity in the Dutch Red and White Friesian (DFR) cattle breed and its contribution to the total genetic diversity in the pool of the Dutch dairy breeds. All Dutch cattle breeds are clearly distinct, except for Dutch Friesian breed (DF) and DFR and have their own specific genetic identity. DFR has a small but unique contribution to the total genetic diversity of Dutch cattle breeds and is closely related to the Dutch Friesian breed. Seven different lines are distinguished within the DFR breed and all contribute to the diversity of the DFR breed. Two lines show the largest contributions to the genetic diversity in DFR. One of these lines comprises unique diversity both within the breed and across all cattle breeds. The other line comprises unique diversity for the DFR but overlaps with the Holstein Friesian breed. There seems to be no necessity to conserve the other five lines separately, because their level of differentiation is very low. This study illustrates that, when taking conservation decisions for a breed, it is worthwhile to take into account the population structure of the breed itself and the relationships with other breeds.     

对平陆山地牛保种与开发的思考

作者从平陆山地牛的发展历史出发,从品种特性上分析了平陆山地牛保种的必要性和重要性,介绍了产区资源概况与养牛业的发展潜力,同时详细论述了平陆山地牛的3种保种技术,最后提出了保护与开发利用该品种应采取的几项措施,为今后开展此项工作提供了参考资料.     

阿拉善蒙古牛的种质资源保护与产业发展建议

阿拉善牛是蒙古牛的一个重要群体,作为我国北方地区的优良肉牛品种之一,具有乳肉役兼备的特点,适应干旱寒冷的气候,适合荒漠化草原和沙漠放牧等优异特性,主要分布在腾格里沙漠、巴丹吉林沙漠和乌兰布和沙漠湖泊湿地及其周边地区,现存栏约3.3万余头,是我国宝贵的肉牛遗传资源。但是阿拉善蒙古牛存在长期近亲繁殖,群体内的遗传变异越来越窄的趋势,加之本身生长速度缓慢、体型小等不足,未来可使阿拉善蒙古牛品种资源不断枯竭。为了保护阿拉善蒙古牛等蒙古牛群体的优异特性和种质资源,本文综述了阿拉善蒙古牛的体貌特征、数量分布以及对阿拉善蒙古牛种质资源的保护措施和产业发展建议。     

Analysis of genetic and cultural conservation value of three indigenous Croatian cattle breeds in a local and global context

It is widely accepted that autochthonous cattle breeds can be important genetic resources for unforeseeable environmental conditions in the future. Apart from that, they often represent local culture and tradition and thus assist in the awareness of ethnic identity of a country. In Croatia, there are only three indigenous cattle breeds, Croatian Bu?a, Slavonian Syrmian Podolian and Istrian Cattle. All of them are threatened but specialized in a particular habitat and production system. We analysed 93 microsatellites in 51 animals of each breed to get thorough information about genetic diversity and population structure. We further set them within an existing frame of additional 16 breeds that have been genotyped for the same marker set and cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the north‐west of Europe. The cultural value was evaluated regarding the role in landscape, gastronomy, folklore and handicraft. The overall results recognize Croatian Bu?a being partly admixed but harbouring an enormous genetic diversity comparable with other traditional unselected Bu?a breeds in the Anatolian and Balkan areas. The Podolian cattle showed the lowest genetic diversity at the highest genetic distance to all remaining breeds but are playing an important role as part of the cultural landscape and thus contribute to the tourist industry. The genetic diversity of the Istrian cattle was found in the middle range of this study. It is already included in the tourist industry as a local food speciality. Current and future conservation strategies are discussed.     

不同肉牛品种杂交组合肥育效果对比试验

[目的]为了观察不同品种杂交肉用牛的育肥效果.[方法]试验选择20月龄左右(体重300±20.5 kg)的西杂牛(西门塔尔♂×本地黄牛♀)、利杂牛(利木赞♂×本地黄牛♀)和本地黄牛各20头,以青贮玉米和苜蓿干草为基础粗饲料,经过90d的短期肥育,研究肉牛肥育效果与品种之间的关系,进而分析各项屠宰指标.[结果]表明:西杂...     

按运铁蛋白多态性分析青海黄牛与其它黄牛的遗传关系

按血清运铁蛋白等位基因频率分析了柴达木黄牛和青海东部黄牛与我国其它地方品种黄牛间的遗传关系，如果发现，黄牛与蒙古牛、延中、复 州牛、蒙山牛和安西牛等北方品种黄牛的遗传距离最短（0．00305－0．06131），且与这些品种牛聚成一个树系。由此将青海黄牛归属于诺－蒙古利亚系统的第一大类无峰牛内。     

基因芯片技术在晋南牛种公牛选育中的应用

为了更好的保护开发利用晋南牛,确保晋南牛的遗传多样性,本研究应用基因芯片技术,对晋南牛进行群体遗传特性的检测及后备种公牛的遗传评估,为晋南牛的分子辅助选育与保种提供理论与技术支持。采集18月龄健康、体重相近（（350±20）kg）的荷斯坦牛、和顺肉牛、西门塔尔牛、延边牛及利木赞牛血样各10份,及晋南牛后备公牛血样25份,根据不同牛品种分为6组,其中前5组每组10个重复,晋南牛后备公牛25个重复。应用Illumina SNP 50K高密度牛SNP芯片进行基因型检测,分析比较晋南牛的群体遗传特征,运用亲缘矩阵计算晋南牛后备公牛的亲缘系数,同时用BLUP进行遗传评估。结果表明,晋南牛在遗传结构上与荷斯坦牛、和顺肉牛、西门塔尔牛及利木赞牛关系较远,与延边牛较近,为中国地方品种群体;对晋南牛后备公牛进行遗传评估,得出了牛的基因组胴体重方差育种值排名,JN23的胴体重倍数性状标准差最大,从基因组水平可选作肉用种公牛;应用亲缘分析对晋南牛后备公牛家系进行分类,避免群体间的近交。本研究对晋南牛后备公牛进行了遗传评估、近交家系分析、传统表型选择及遗传疾病检测,最终选留的种公牛为JN07、JN23、JN05、JN08、JN02、JN13、JN19、JN14,通过多种选育方法结合提高了公牛的选择准确性,为晋南牛的群体选育提高奠定了基础。     

Animal genetic resource trade flows: The utilization of newly imported breeds and the gene flow of imported animals in the United States of America

Animal germplasm exchange has recently received attention as a product of the FAO's State of the World's Animal Genetic Resources effort. Some have advocated a need to explore policies and regulations on the exchange of germplasm (e.g., Hiemstra, S.J., Drucker, A., Tvedt, M., Louwaars, N., Oldenbroek, J., Awgichew, K., Kebede, S., Bhat, P., da Silva Mariante, A. 2006. Exchange, use and conservation of animal genetic resources: policies and regulatory options. Centre for Genetic Resources. Wageningen Univ., the Netherlands, pp. 1­43). However, there has been little comprehensive assessment of either the economic or genetic impact of introduced germplasm into national populations. As a result, much of the discussion of gene flows has been based on assumptions and generalizations. The objective of this paper is to evaluate the genetic impact of germplasm imported into the United States during the last 25 to 50 years. The paper considers both new breeds (Meishan pigs, Tuli cattle, and Boer goats) and new animals within existing breeds (Limousin and Jersey cattle). Of the new breeds recently imported only one had an impact on US animal agriculture. Neither the Tuli nor the Meishan has impacted the US livestock industry. It appears that these breeds were initially viewed as attractive because of single traits, but producers did not find it attractive to adopt the new breeds based on these specific traits. In the end, these breeds did not prove competitive in the US under the current set of market conditions. This result would indicate that importation of new genetic resources due to a single trait of interest is not a viable importation strategy. By contrast, the Boer goat exhibited a number of production characteristics which made it desirable to US producers and thereby allowed the breed to become well established. A second portion of the study evaluated the importation and parentage pattern of Limousin cattle as they became established in the U. S. and the gene flow of imported Jersey cattle since the 1950′s. In both cases, the study relied on pedigree analysis. Over the past fifty years, Jersey cattle have been sporadically imported from various countries, but no imported animal has had an overpowering effect on the population. It appears that by the great-grand progeny level, the genes from imported animals are diminishing rather than increasing in the population. In evaluating the predicted transmitting abilities for imported cattle relative to high and moderately ranked domestically bred cattle, there were significant differences between these groups for milk production. This would be sufficient to explain why the impact of the imported cattle diminished. The results of our analysis at both the breed and individual level underscore the speculative nature of germplasm importation — even within breeds where there is a great deal of information available about production characteristics. From this analysis, we conclude that successful importation of new breeds into the US must be based on a large number of production characteristics; importation for a single characteristic (e.g., high prolificacy) while the breed is deficient in other areas does not lead to the breed's adoption. While not fully explored in this work, it appears that initial interest and acceptance from the private sector is crucial for breed acceptance, as the Boer goat demonstrates. Within an existing breed, importation of individual animals still appears to have a relatively high degree of risk and is dependent upon the importer's ability to pick viable candidates. However, once animals are imported their progeny must effectively compete with the domestic population, or else their genetic contribution will rapidly diminish.