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.     

Genome‐wide linkage disequilibrium in the Blonde d'Aquitaine cattle breed

We present here the first genome‐wide characterization of linkage disequilibrium (LD) in the French Blonde d'Aquitaine (BLA) breed, a well‐muscled breed renowned for producing high‐yielding beef carcasses. To assess the pattern and extent of LD, we used a sample of 30 unrelated bulls and 36 923 single nucleotide polymorphisms (SNPs) covering all cattle autosomes. The squared correlation of the alleles at two loci (r²) was used as a measure of LD. The analysis of adjacent marker pairs revealed that the level of LD decreases rapidly with physical distance between SNPs. Overall mean r² was 0.205 (±0.262). Strong LD (r² > 0.8) and useful LD (measured as r² > 0.2) were observed within genomic regions of up to 720 and 724 kb, respectively. We analysed the genetic structure of the BLA population and found stratification. The observed genetic sub‐structuring is consistent with the known recent demographic history that occurred during BLA breed formation. Our results indicate that LD mapping of phenotypic traits in the BLA population is feasible; however, because of this sub‐structuring, special care is needed to reduce the likelihood of false‐positive associations between marker loci and traits of interest.     

Genetic characterization of Barbari goats using microsatellite markers

Genetic variation in Barbari goats, a highly prolific breed distributed widely in the northern part of India, known for better milk and meat quality, was studied as a part of genetic characterization and conservation. The genomic DNA from 50 unrelated Barbari goats were amplified via PCR with a panel of 21 microsatellite markers, and resolved through 6 per cent denaturing polyacrylamide gel electrophoresis followed by silver staining. The number of alleles ranged from 4 to 11, with allele sizes ranging from 88 to 220 bp. The distribution of allele frequencies was between 0.0104 and 0.5208. Polymorphism information content varied from 0.5563 to 0.8348. The population was not in Hardy-Weinberg equilibrium for all except two microsatellite loci (ILSTS044 and ILSTS060). The observed heterozygosity ranged from 0.8478 to 1.0000 while the expected heterozygosity ranged from 0.6208 to 0.8509. Based on the results of the present study, there is a good scope for exploiting the genetic variability in the Barbari goats for further improvement of performance.     

微卫星DNA标记在三个山羊品种中的遗传多态性研究

利用四个微卫星标记对波尔山羊、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、有效等位基因数和杂合度进行了遗传检测。结果表明：四个微卫星位点在波尔山羊、太行山羊和河北奶山羊三个品种中存在多态性。可以用于山羊遗传多样性的评估；位点OarFCB11变异最大，位点MCM38变异最小，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。     

Genetic diversity of Forest and Savannah chicken populations of Ghana as estimated by microsatellite markers

The characterization of indigenous animal genetic resources is a requisite step in providing needed information for the conservation of useful genotypes against future needs. Thus, in this study, 22 microsatellite markers were used to genotype 114 local chickens from the Forest (n = 59) and Savannah (n = 55) eco‐zones of Ghana and the results compared to those of the ancestral red junglefowl (n = 15) and two European commercial chicken populations – a broiler (n = 25) and white leghorn (n = 25). A total of 171 alleles were observed, with an average of 7.8 alleles per locus. The local Ghanaian chickens showed higher diversity in terms of the observed number of alleles per locus (6.6) and observed heterozygosity (0.568) compared with the combined control populations (6.0 and 0.458, respectively). However, Wright's F‐statistics revealed negligible genetic differentiation (F_ST) in local Ghanaian chicken populations. In addition, 65% of the Savannah chickens were inferred to be more likely from the Forest, suggesting a south‐north dispersal of chickens from their probable original location in the Forest zone to the Savannah areas. It is concluded that the Forest and Savannah chickens of Ghana are a single, randomly mating unselected population, characterized by high genetic diversity and constitute a valuable resource for conservation and improvement.     

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 analysis of Mexican Criollo cattle populations

The objective of this study was to evaluate the genetic structure of Mexican Criollo cattle populations using microsatellite genetic markers. DNA samples were collected from 168 animals from four Mexican Criollo cattle populations, geographically isolated in remote areas of Sierra Madre Occidental (West Highlands). Also were included samples from two breeds with Iberian origin: the fighting bull (n = 24) and the milking central American Criollo (n = 24) and one Asiatic breed: Guzerat (n = 32). Genetic analysis consisted of the estimation of the genetic diversity in each population by the allele number and the average expected heterozygosity found in nine microsatellite loci. Furthermore, genetic relationships among the populations were defined by their genetic distances. Our data shows that Mexican cattle populations have a relatively high level of genetic diversity based either on the mean number of alleles (10.2-13.6) and on the expected heterozygosity (0.71-0.85). The degree of observed homozygosity within the Criollo populations was remarkable and probably caused by inbreeding (reduced effective population size) possibly due to reproductive structure within populations. Our data shows that considerable genetic differentiation has been occurred among the Criollo cattle populations in different regions of Mexico.     

4个肉用绵羊品种微卫星标记的多态性与系统发育分析

利用10个微卫星座位对4个肉用绵羊品种进行遗传检测,计算出了各品种的平均杂合度、平均多态信息含量及品种间的遗传距离,并进行了系统发育分析。结果表明:10个微卫星座位上共检测到了107个等位基因,等位基因数在5~13个之间。各基因座位多态信息含量为0.498 5~0.890 4,均表现出了高度多态性。各基因座位杂合度较高,为0.563 0~0.899 5,说明肉用绵羊品种有着较丰富的遗传多样性。4个肉用绵羊品种间的遗传距离相对较远,萨福克羊和陶赛特羊先聚在一起,他们之间的遗传距离最近,为0.345 25,然后与夏洛来羊聚在一起,最后与中国美利奴羊聚在一起,中国美利奴羊与夏洛来羊之间的遗传距离最远,为0.516 39。研究结果对我国肉用绵羊资源的评估、保存和预测杂种优势具有一定的指导意义。     

利用微卫星标记分析乌骨大骨鸡的遗传多样性

利用微卫星标记分析了乌骨大骨鸡的遗传多样性和遗传结构,筛选了鸡基因组7条染色体上的7个微卫星标记位点,随机选取24羽乌骨大骨鸡个体,进行多态性检测,共检测到23个等位基因,每个座位等位基因数目从2个到5个不等,平均等位基因数为3.3个。该群体平均多态信息含量和平均杂合度分别为0.660 3和0.717 6。结果表明乌骨大骨鸡属多态性较丰富的群体。     

利用微卫星标记分析泸水中华蜜蜂遗传多样性

利用21对微卫星标记对云南泸水中华蜜蜂群体遗传多样性进行分析,共检测到121个等位基因,等位基因数目从2-12不等。平均等位基因数为5.76;所有位点的平均期望杂合度（He）和平均多态信息含量（PIC）值分别为0.6752和0.6192。表明泸水中华蜜蜂群体遗传多样性较为丰富。     

四川三个藏猪群体的微卫星遗传多样性分析

本研究利用已开发的18对微卫星引物,分析了四川境内阿坝、稻城和德格三个藏猪群体共143个个体18条常染色体上的微卫星遗传多样性。结果表明:阿坝藏猪群体多态信息含量和观测杂合度比其他两群低,群体遗传变异较小;三个群体Nei氏标准遗传距离均在0.6以上,平均基因流值大于1,表明三个群体各有特点,群内基因交流频繁。     

Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markers

The purpose of this study was to assess genetic diversity, phylogenetic relationship and population structure among nine Eurasian cattle populations using 58 single nucleotide polymorphism (SNP) markers. The calculated distribution of minor allele frequencies and heterozygosities suggested that the genetic diversity of Bos indicus populations was lower than that of Bos taurus populations. Phylogenetic analyses revealed the main divergence between the Bos taurus and Bos indicus populations, and subsequently between Asian and European populations. By principal components analysis, the Bos taurus and Bos indicus populations were clearly distinguished with PC1 (61.1%); however, six Bos taurus populations clustered loosely and the partial separation between European and Asian groups was observed by PC2 (12.5%). The structure analysis was performed using the STRUCTURE program. Distinct separation between Bos taurus and Bos indicus was shown at K = 2, and that between European and Asian populations at K = 3. At K = 4, 5 and 6, Mongolian population showed an admixture pattern with different ancestry of Asian and European cattle. At K = 7, all Bos taurus populations showed each cluster with little proportion of admixture. In conclusion, 58 SNP markers in this study could sufficiently estimate the genetic diversity, relationship and structure for nine Eurasian cattle populations, especially by analyses of principal components and STRUCTURE.     

Evaluation of genetic richness among Vietnamese native pig breeds using microsatellite markers

We have elucidated genetic relationships of Vietnamese native pigs (VNP) using preliminarily collected samples by a single‐nucleotide polymorphism (SNP) array. In order to confirm our previous results and compare with the results of a previous study using microsatellite (MS) markers, we aimed to characterize genetic diversity and population structure in wider varieties (24 breeds from 21 Provinces) of VNP across the country using 20 polymorphic MS markers recommended by ISAG/FAO (International Society for Animal Genetics/Food and Agriculture Organization) for diversity study. In this study, we collected 1,136 DNA samples of the VNPs and three exotic breeds. Our results revealed that the average number of alleles and allelic richness across the loci in VNPs were 10.0 and 7.6, which were higher than those of exotic breeds. Genomic components among VNPs were subjected to the sampling locations. Interestingly, Co Binh Thuan showed remarkable genetic feature compared to the other VNPs, because the habitation of Co Binh Thuan was relatively far from the other breeds. The results of this study provided useful information for exploitation, conservation, and development trends of the VNP breeds. More recently, African swine fever caused significant damage to most of the VNP populations. Therefore, our findings will help a reconstruction scheme of the VNP genetic resources.     

Genetic closeness of Zanskari and Spiti ponies of India inferred through microsatellite markers

The Zanskari and Spiti ponies were characterized for genetic variation using a set of 25 equine microsatellite markers. The DNA was isolated from the 42 blood samples of Zanskari and 32 blood samples of Spiti ponies collected from their respective breeding tracts. The DNA was amplified by polymerase chain reaction at the studied microsatellite loci and amplified product was resolved for alleles by denaturing urea-polyacrylamide gel electrophoresis. The allelic frequency data so obtained was statistically analyzed using POPGENE computer program. The PCR product size-range varied from 84 to 102 at locus HTG6 to 238 to 244 at locus UCDEQ425. The observed number of alleles ranged from four to nine with a mean (± standard deviation) of 5.80 ± 1.32 alleles per locus in Zanskari and 5.40 ± 1.04 alleles per locus in Spiti ponies. The mean observed heterozygosity was found to be 0.61 ± 0.06 and 0.56 ± 0.09 for Zanskari and Spiti ponies, respectively. The Nei's standard and unbiased genetic distance were found to be 0.11 and 0.09, respectively, indicating close genetic relatedness of Zanskari and Spiti ponies.     

Characteristics of PCR fragments amplified using five microsatellite markers for identifying the Nagoya breed

The Nagoya breed is a native chicken of Aichi Prefecture, Japan, a dual‐purpose breed for eggs and meat. A method for distinguishing the Nagoya breed from Aichi Prefecture from other chickens using five microsatellite markers (ABR0015, ABR0257, ABR0417, ABR0495 and ADL0262) has already been utilized in order to check the authenticity of Nagoya breed‐labeled chicken on the market. The present study was conducted to investigate nucleotide sequences and sizes of PCR fragments containing the five microsatellite regions for the Nagoya breed and to confirm that the genomic identification could continue to be applied in the future. The DNA sequencing of fragments containing the five markers showed that ABR0015, ABR0417 and ABR0495 had a single haplotype, ABR0257 had three haplotypes, and ADL0262 had two haplotypes, although all the markers exhibited one fixed fragment size each upon sequencing of the fragments and fragment analysis. The results of the fragment analysis of each marker using DNA samples of 28 Nagoya breed males (G0 generation) reared in 2000–2001 and 20 of their offspring males (G8) reared in 2008–2009 showed one fixed fragment size in both populations. Therefore, we confirmed that the five microsatellite markers are useful tools for accurately distinguishing the Nagoya breed from other chickens.     

Analysis of genetic variability in the Czech Dachshund population using microsatellite markers

The primary goal of this study was to analyse genetic variation within and among six Dachshund varieties in the Czech Republic using 10 microsatellites from StockMarks^® Paternity Polymerase Chain Reaction (PCR) Typing kit. A total of 632 Dachshunds were sampled – 99 Standard Smooth-haired, 72 Standard Long-haired, 272 Standard Wire-haired, 42 Miniature Smooth-haired, 73 Miniature Long-haired and 74 Miniature Wire-haired. Average observed heterozygosity and polymorphic information content ranged in particular Dachshund varieties between 0.58–0.70 and 0.57–0.64, respectively. Subsequent analysis of the population structure ( F -statistics; Nei's genetic identity) showed that Standard Dachshunds shared allele frequencies most closely with their miniature equivalents, and smooth coat type is closer to Wire-haired coat type than to the Long-haired one. Analysis of molecular variance revealed that 11.81% of the total variance occured among varieties. The value of combined exclusion probability (0.9955) validated usefulness of this panel of microsatellites for parentage verification in all analysed populations. We carried out 234 parentage verifications with 1.28% cases where parentage did not match.     

东方白鹳微卫星遗传标记的筛选及其在种群遗传分析中的应用

东方白鹳(Ciconia boyciana)是分布于东亚的大型濒危涉禽,亟待深入开展其种群的保护遗传学研究.本研究采用微卫星标记技术筛选东方白鹤的微卫星位点,并进行种群的遗传多样性分析.所用的36对微卫星引物7对来自白鹳(Ciconia ciconia),12对来自朱鹮(Nipponia nippon),17对来自大蓝...     

Genetic diversity and population structure of Polish Arabian horses assessed through breeding and microsatellite data

Polish Arabian horses are one of the most important populations of this breed in the world. Their post‐war history can be divided into two periods, with the dominant role of state studs until 1989, and the increasing significance of private breeding in the next years. The goal of the study was to evaluate genetic diversity and structure of the population under a new breeding policy. The analyses of breeding and microsatellite data from 1996 to 2012 provide a coherent picture of the population with constant flow of horses only in one direction from state to private studs. An increase in the number of broodmares was observed, from 396 mares in 1996 to 1021 mares in 2012. The proportion of foreign sires used in Polish studs also increased, from 7.1% to 37.0%. An increasing number of alleles and progressive differentiation in mares were observed. STRUCTURE analysis indicated that the Polish horses were clearly separated from foreign horses used in Polish breeding, although only one of the 75 alleles found can be considered as typically Polish. The high heterozygosity is an important feature of the Polish population; however, the decrease of heterozygosity in state broodmares was noted. This issue needs to be studied further.     

基于微卫星标记的中国斑翅山鹑遗传多样性及遗传结构分析

斑翅山鹑(Perdix dauuricae)是具有很高经济价值的猎用禽.为了获得其群体遗传多样性及遗传变异信息,为我国斑翅山鹑进一步有效保护和合理利用提供科学依据,本研究共采用了8个微卫星标记位点对分布于我国北方的斑翅山鹑23个地理种群285个个体进行了群体遗传多样性及遗传结构分析.结果表明,我国斑翅山鹑为遗传多样性较丰富的群体,且每一群体均表现出较高的遗传多样性,其中柴达木盆地地区的种群拥有最高的遗传多样性.遗传分化分析显示组间及组内种群间均表现为遗传分化显著,遗传分化系数(FST)值表明大部分种群间表现出显著的遗传分化.系统树构建和贝叶斯聚类分析结果均显示斑翅山鹑23个地理种群被分化为明显的两个组群.另外,通过BOTTLENECK对各地理种群的分析显示斑翅山鹁种群曾经历过近期瓶颈效应.本研究结果表明,柴达木盆地地区种群、华北平原地区种群、静宁种群、张家川种群以及六盘山地区种群应予以相应关注,以保证有足够的种群大小来保持这些种群的遗传多样性.     

Genetic and morphometric characterization of a local Vietnamese Swamp Buffalo population

The water buffalo plays a key role in the socio-economy of South-East Asia as it is the main draught power for paddy rice cultivation. While in the Indian subcontinent the water buffalo is the riverine type, in South-East Asia the majority of buffaloes are of the swamp type. In the poor remote northern province of Ha Giang in Vietnam, improvement of the swamp buffalo breed may be one of the best ways to increase sustainability of farming systems. Therefore, analysis of the genetic structure of the province buffalo population is a prerequisite to any conservation or improvement project. A total of 1122 animals were described for 11 body and horn measurements for morphometric characterization. From this sample set, 744 animals were genotyped for 17 microsatellite markers. Also 17 animals from southern provinces of Vietnam were genotyped as a comparative sample. The results showed that genetic diversity as well as inbreeding value in the Ha Giang was high. The F _ST values within the province and across Vietnam were low indicating that most of the population variation is explained by individual variability. Bayesian clustering analysis did not highlight the presence of subdivided populations. These results are useful for the implementation of a conservation and improvement strategy of the swamp buffalo in order to guarantee the householders' needs for sustainability of the farming system in the Ha Giang province.