Assessing genetic diversity of Vietnamese local chicken breeds using microsatellites

This study aimed to assess genetic diversity within and between nine Vietnamese local chicken breeds and two Chinese breeds included for comparison. Genotyping 29 microsatellites revealed high diversity of both Vietnamese and Chinese breeds. Cluster analysis using the structure software suggested six clusters as the most likely grouping of the 11 breeds studied. These groups encompassed four homogeneous clusters, one formed by the two Chinese breeds and the other three representing a single breed each: the Mekong Delta breed Ac, the South Central Coast breed Choi, and the Red River Delta breed Dong Tao. The six remaining breeds formed two additional admixed clusters.     

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.     

Prefreezing and post-thaw semen characteristics of five ram breeds collected by electroejaculation

Rams representing five breeds were electroejaculated twice weekly, during a three-week collection period. Ejaculates were evaluated for volume and concentration before freezing and for rate of motility and percentages of motile and abnormal cells both before and after freezing. Interactions between breed and collection period were evident (P<0.05) for semen volume and post-thaw values for rate of motility and percentage motile cells. Breeds differed (P<0.05) in these traits during some periods. In contrast, pre-freezing observations of rate of motility, percentage motile and abnormal cells and post-thaw percentage abnormal cells did not differ (P>0.15) among breeds. Sperm concentration per ejaculate tended to vary (P=0.11) among breeds. Semen characteristics frequently varied across collection periods. Rams within a breed differed (P<0.01) in all semen traits except post-thaw rate of motility and percentage motile cells. Semen was negatively affected by the freezing and thawing procedure. Ram within a breed and ejaculate within ram should be considered when selecting electroejaculated semen for freezing and subsequent use in artificial insemination.     

Assessing patterns of genetic admixture between sheep breeds: Case study in Algeria

In developing countries, cross‐breeding between local breeds and indigene or exotic breeds represents one of the main threats to the livestock diversity, leading to genetic dilution and loss of unique allelic combination underlying essential local adaptive traits. In this study, two Algerian sheep breeds, known to be highly admixed, were considered as a case study, to demonstrate how combination of different methodologies coupled with the use of specific softwares can be efficient to assess the spatial structuration of a hybrid zone, even in a case of extreme admixture. A fine sampling covering distribution areas of both breeds was implemented in order to study the admixture area and adjacent zones from a phenotypic (i.e., 19 quantitative traits were considered) and a genetic point of view (i.e., 21 microsatellites markers were used). Both approaches gave concordant patterns, highlighting areas with sheep most differentiated (or less admixed) for each breed. In detail, the region of Biskra appeared as the most preserved for the Ouled‐Djellal breed and the northwest of Laghouat was identified as the most preserved area for the Rembi breed. The approach proposed in the study offers a low‐cost solution to identify the most representative flocks of a breed, allowing the implementation of efficient conservation plans.     

Molecular structure in peripheral dog breeds: Portuguese native breeds as a case study

Genetic variability in purebred dogs is known to be highly structured, with differences among breeds accounting for ∼30% of the genetic variation. However, analysis of the genetic structure in non-cosmopolitan breeds and local populations is still limited. Nine Portuguese native dog breeds, and other peripheral dog populations (five) with regional affinities, were characterized using 16 microsatellites and 225 amplified fragment length polymorphism (AFLP) markers, and the pattern of genetic differentiation was investigated. Although the level of breed differentiation detected is below that of other dog breeds, there is in most cases a correlation between breed affiliation and molecular structure. AFLP markers and Bayesian clustering methods allowed an average of 73.1% of individuals to be correctly assigned to source populations, providing robust genotypic assessment of breed affiliation. A geographical genetic structure was also detected, which suggests a limited influence of African dogs on the Iberian breeds. The sampling effect on the estimation of population structure was evaluated and there was a 2.2% decrease in genetic differentiation among breeds when working animals were included. Genetic diversity of stray dogs was also assessed and there is no evidence that they pose a threat to the preservation of the gene pool of native dog breeds.     

Genetic relationships among Vietnamese local pigs investigated using genome‐wide SNP markers

Vietnam is one of the most important countries for pig domestication, and a total of 26 local breeds have been reported. In the present study, genetic relationships among the various pig breeds were investigated using 90 samples collected from local pigs (15 breeds) in 15 distantly separated, distinct areas of the country and six samples from Landrace pigs in Hanoi as an out‐group of a common Western breed. All samples were genotyped using the Illumina Porcine SNP60 v2 Genotyping BeadChip. We used 15 160–15 217 SNPs that showed a high degree of polymorphism in the Vietnamese breeds for identifying genetic relationships among the Vietnamese breeds. Principal components analysis showed that most pigs indigenous to Vietnam formed clusters correlated with their original geographic locations. Some Vietnamese breeds formed a cluster that was genetically related to the Western breed Landrace, suggesting the possibility of crossbreeding. These findings will be useful for the conservation and management of Vietnamese local pig breeds.     

10个牛品种线粒体12S rRNA基因多态性分析

以鲁西牛、渤海黑牛、大别山牛、南阳牛、晋南牛、秦川牛、中国西门塔尔牛、日本和牛、海福特牛和安格斯牛10个牛品种共计353头牛为研究对象,利用单链构象多态性（SSCP）分子标记方法对其线粒体DNA 12S rRNA基因进行了多态性分析,结果发现该基因出现分布频率不同的3种单倍型（Ⅰ、Ⅱ、Ⅲ）,其中单倍型Ⅰ出现的频率最低,仅在晋南牛1个个体中发现;单倍型Ⅱ在中国本地黄牛中都存在,在中国西门塔尔牛中的分布频率很低,但在3个国外品种海福特牛、安格斯牛和日本和牛中不存在;单倍型Ⅲ在这10个牛品种中均有分布,但以国外品种最丰富。计算平均多态信息含量,发现我国地方品种在0.232～0.423之间,基本属于中度多态,说明我国地方黄牛品种在12S rRNA上多态性比较丰富,国外品种较为贫乏;但是单倍型Ⅰ频率很低有丢失的趋势,需要对其进行保护。     

The use of SWOT analysis to explore and prioritize conservation and development strategies for local cattle breeds

SWOT (Strengths, Weaknesses, Opportunities and Threats) analysis is a tool widely used to help in decision making in complex systems. It suits to exploring the issues and measures related to the conservation and development of local breeds, as it allows the integration of many driving factors influencing breed dynamics. We developed a quantified SWOT method as a decision-making tool for identification and ranking of conservation and development strategies of local breeds, and applied it to a set of 13 cattle breeds of six European countries. The method has four steps: definition of the system, identification and grouping of the driving factors, quantification of the importance of driving factors and identification and prioritization of the strategies. The factors were determined following a multi-stakeholder approach and grouped with a three-level structure. Animal genetic resources expert groups ranked the factors, and a quantification process was implemented to identify and prioritize strategies. The proposed SWOT methodology allows analyzing the dynamics of local cattle breeds in a structured and systematic way. It is a flexible tool developed to assist different stakeholders in defining the strategies and actions. The quantification process allows the comparison of the driving factors and the prioritization of the strategies for the conservation and development of local cattle breeds. We identified 99 factors across the breeds. Although the situation is very heterogeneous, the future of these breeds may be promising. The most important strengths and weaknesses were related to production systems and farmers. The most important opportunities were found in marketing new products, whereas the most relevant threats were found in selling the current products. The across-breed strategies utility decreased as they gained specificity. Therefore, the strategies at European level should focus on general aspects and be flexible enough to be adapted to the country and breed specificities.     

Genetic diversity and relationship among southern Indian goat breeds based on microsatellite markers

Genetic diversity and relationship among goat breeds of southern India were investigated based on microsatellite markers. All five breeds of south India, namely Attappady, Osmanabadi, Sangamneri, Malabari and Kanniadu, along with Ganjam of eastern India were considered for the investigation. In total, 190 alleles were observed from 288 DNA samples analysed with 25 microsatellite loci across six breeds. The most diverse breed was Kanniadu and the least was Osmanabadi. Gene diversity for each breed ranged from 0.73 in Kanniadu to 0.61 in Osmanabadi. The genetic distance tended to be least (0.22) between Ganjam and Malabari and the widest (0.83) between Kanniadu and Malabari. The genetic differentiation between different pairs of the breeds was significantly different from zero. Majority of the loci in almost all the breeds were heterozygote deficit. The overall F_is value (0.20) was moderate and significantly different from zero. Principal-component analysis showed the clustering of the goat breeds according to their geographical origin. Therefore, the geographical origin of the breeds should be taken into consideration while deciding conservation and improvement options for these breeds.     

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.     

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).     

Iberian origin of Brazilian local pig breeds based on Cytochrome b (MT-CYB) sequence

The aim of this work was to investigate the possible origin of local Brazilian pig breeds through Cytochrome b ( MT-CYB ) mitochondrial analyses. The results indicated that the main local pig breeds descended from two different European maternal lineages, both Iberian varieties. The haplotype relationship analysis showed that Monteiro, Nilo, Piau and Tatu breeds share haplotypes only with Iberian varieties, while the Moura breed presented a different maternal lineage. The Moura appears to share a high frequency of haplotypes with the Black Hairy Iberian variety and Hungarian Mangalica breed.     

Using 2-DE for the differentiation of local chicken breeds

The aim of this study was to apply a proteomic approach for the characterisation of local chicken breeds. The experiment involved a total of 29 males of three local Italian chicken breeds: Pépoi, Padovana and Ermellinata di Rovigo. Sarcoplasmic protein fractions of breast muscle were analysed by 2-DE. Image analysis followed by statistical analysis enabled to differentiate groups of individuals based on the similarities of protein expression. Individuals were distinguished into clusters and groups, corresponding to the breed of origin. Distances among individuals, calculated using data on spot volumes, were used to draw a neighbour-joining tree, showing clear individual and breed grouping. The most relevant spots regarding breed differentiation were detected; 11 were identified by MS revealing preliminary evidences on the mechanisms of the breed differentiation process. The results evidenced the ability of proteomic analyses for the characterisation of chicken breeds.     

Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples: differences in microsatellite variation between two areas of domestication

Microsatellite diversity in European and Chinese pigs was assessed using a pooled sampling method on 52 European and 46 Chinese pig populations. A Neighbor Joining analysis on genetic distances revealed that European breeds were grouped together and showed little evidence for geographic structure, although a southern European and English group could tentatively be assigned. Populations from international breeds formed breed specific clusters. The Chinese breeds formed a second major group, with the Sino-European synthetic Tia Meslan in-between the two large clusters. Within Chinese breeds, in contrast to the European pigs, a large degree of geographic structure was noted, in line with previous classification schemes for Chinese pigs that were based on morphology and geography. The Northern Chinese breeds were most similar to the European breeds. Although some overlap exists, Chinese breeds showed a higher average degree of heterozygosity and genetic distance compared to European ones. Between breed diversity was even more pronounced and was the highest in the Central Chinese pigs, reflecting the geographically central position in China. Comparing correlations between genetic distance and heterozygosity revealed that China and Europe represent different domestication or breed formation processes. A likely cause is a more diverse wild boar population in Asia, but various other possible contributing factors are discussed.     

On the bovine F blood group system

The F system of three Danish cattle breeds as determined by four specific anti-sera is described. In the Jersey breed three alleles are recognised. In the Danish cattle breeds there was no indication of a null allele. However, the phenotypes observed in zebu cattle by means of four reagents suggest the presence of at least six alleles in the bovine F system. Furthermore, the data show that the factors V₁ and V₂ do not form a linear subtype system in all cattle breeds.     

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.     

Maternal and paternal genetic variation in Estonian local horse breeds in the context of geographically adjacent and distant Eurasian breeds

The maternal and paternal genetic variation of horse breeds from the Baltic Sea region, including three local Estonian breeds, was assessed and compared with that of Altai and Yakutian horses. In the mtDNA D‐loop region, 72 haplotypes assigned to 20 haplogroups in the nine breeds were detected. In Estonian local breeds, 38 mtDNA haplotypes were found, and five of them were shared by the three breeds. More than 60% of all identified haplotypes were rare. Compared with the Estonian Native and Estonian Heavy Draught breeds, a higher haplotypic diversity was found in the Tori breed (h = 0.969). Moreover, four haplotypes shared among Finnish and Estonian local horse breeds indicated ancient ancestry, and of these, H30 (haplogroup D3) showed global sharing and genetic links between modern Baltic Sea region and Siberian horses, specifically. The studied breed set showed high variability in maternal inheritance and mixed patterns of the international and native breeds of the Siberian and Baltic regions. No variation was found in paternally inherited markers among horse breeds in the Baltic Sea region.     

Genetic diversity of dog breeds: between-breed diversity, breed assignation and conservation approaches

Genetic relationships between 61 dog breeds were investigated, using a sampling of 1514 animals and a panel of 21 microsatellite markers. Based on the results from distance-based and Bayesian methods, breed constituted the main genetic structure, while groups including genetically close breeds showed a very weak structure. Depending on the method used, between 85.7% and 98.3% of dogs could be assigned to their breed, with large variations according to the breed. However, breed heterozygosity influenced assignment results differently according to the method used. Within-breed and between-breed diversity variations when breeds were removed were highly negatively correlated ( r  = −0.963, P  <   0.0001), because of the genetic structure of the breed set.     

Determination of genetic relationships among five indigenous Chinese goat breeds with six microsatellite markers

Microsatellite variation was analyzed in five Chinese indigenous goat breeds, which include four Cashmere breeds (Tibetan, Neimonggol, Liaoning, Taihang) and one Hubei local breed (Matou) used for meat production. Five ovine and one bovine microsatellites, selected from eight ovine microsatellites and five bovine microsatellites were suitable for use in this study. With these six microsatellites, allele frequencies, heterozygosity, polymorphism information content (PIC) and effective allele number were calculated. A neighbor-joining tree was constructed using Nei's standard genetic distance (1978). In the tree, Neimonggol and Liaoning were grouped together, then with Taihang; while Tibetan and Matou individually had their own branch. The genetic relationship of five breeds corresponds to their history and geographic origins.     

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.