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 variation analysis within and among Chinese indigenous swine populations using microsatellite markers

The genetic structure of five types of Taihu pig (Erhualian, Middle Meishan, Small Meishan, Mizhu and Shawutou), Jiangquhai and Dongchuan pigs in China were investigated, by means of 27 microsatellite markers proposed by the Food and Agriculture Organisation, International Society for Animal Genetics (FAO-ISAG). The Hardy-Weinberg equilibrium test indicated that genetic drift had occurred in these populations, which may be caused by founder effects, intensive selection and close breeding. Genetic heterozygosity and the effective number of alleles per population were calculated, and showed that the genetic variability of the Jiangquhai pig was the largest, while the Small Meishan had the lowest. Genetic differentiation was within each population as shown by the fixation index (F(ST)=0.18). Both a neighbour-joining (NJ) tree constructed from Nei's standard genetic distance and principal component analysis based on allele frequencies can distinguish types of Taihu pig from the other two breeds. Among Taihu pig populations, Erhualian and Mizhu grouped into one branch, while Middle Meishan, Small Meishan and Shawutou clustered as another branch. By including previously published data on European pigs reported, we confirmed that Chinese indigenous pigs and European pigs have diverged into two distinct groups.     

Evaluation of the genetic diversity of Laiwu pigs using twenty-seven microsatellite markers

The Laiwu pig, an indigenous pig breed known for extremely high intramuscular fat content, is a well-preserved ancient breed due to long-term natural and artificial selections. In this study, using 27 microsatellite markers jointly recommended by the International Society of Animal Genetics (ISAG) and the Food and Agriculture Organization (FAO), we investigated the genetic diversity of the Laiwu pig breed. The genetic diversity of Laiwu pigs is dramatically low, with the observed heterozygosity ranging from 0.067 to 0.767. Among the 27 microsatellite markers, 10 were high polymorphic loci, 10 were moderate polymorphic loci, six were low polymorphic loci, and no polymorphism was detected at one locus (IGFI). Further analyses with the 10 high polymorphic loci and five moderate polymorphic loci revealed that the Laiwu pig breed was inbred and heterozygous deficient to some extent, but not severely, and that the Laiwu pigs were relatively pure, with almost no hybridization with other breeds. Two subgroups of the current 13 Laiwu pig pedigrees were identified. These results suggest that the Laiwu pig breed has a low diversity and a conservation program must be developed to preserve the “Laiwu pig” gene pool.     

Evaluation of genetic variability in the collared peccary Pecari tajacu and the white-lipped peccary Tayassu pecari by microsatellite markers

In this study, the microsatellite technique was used to evaluate the genetic variability in populations of collared and white-lipped peccaries kept in captivity. Six primers developed for domestic pigs were used and amplified in both species. They revealed the presence of five polymorphic loci and one monomorphic locus. The polymorphic loci included 4 of the 16 alleles in collared peccaries, and 3 of the 10 alleles in the white-lipped peccaries. Polymorphic information content (PIC) in both species and all the loci was highly informative. The probability of paternity exclusion (PEC), if one of the parents is known, was almost as high in white-lipped peccaries (95.53%) as in the collared (99,48%). The Fst values for collared (0.042) and white-lipped (0.1387) peccaries showed that both populations are not structured. The Fis values for all loci, except ACTG2 in white-lipped peccaries (-0.0275) and in both species (0.1985 to 0.9284 in collared peccaries and 0.3621 to 0.4754 in the white-lipped), revealed a high level of homozygosis, probably caused by inbreeding. Data on heterologous amplification and genetic variability in collared and white-lipped peccaries are presented for the first time.     

Population structure in Indian sheep ascertained using microsatellite information

This study attempts to provide a comprehensive insight into the prevailing genetic status of Indian sheep breeds using microsatellite markers. Seventeen Indian sheep breeds from 3 agroecological zones were analysed using a panel of 25 microsatellite markers. All of the sheep breeds investigated were genetically diverse, as evident from the high allele (>6) and gene (>0.6) diversity values. The gene diversity values for all breeds ranged from 0.621 to 0.780. The within-population heterozygote deficit (F(IS)) varied from -0.098 to 0.234, reflecting significant levels for 12 of the 17 breeds investigated. The average genetic differentiation between all breeds (F(ST)) was 11.1%, revealing moderate discrimination between the indigenous sheep breeds. The genetic distance and principal component analysis revealed a separation of sheep breeds based on geographical propinquity. The Bayesian clustering approach suggested poor breed differentiation in the north-western arid and semi-arid region when compared to the breeds from the eastern and southern peninsular regions. The observed results mirror the divergent management strategies in the different agroecological regions, lack of specific selection policies, and intermixing of breeds in close proximity. Immediate steps to curb the intermixing and erosion of breed purity for some of these breeds need to be implemented, for example, by introducing measures like making proven rams available and ensuring their frequent exchange between flocks. The data generated here provides valuable information about the genetic structure of the 17 Indian sheep breeds and this can be used for designating priorities for their conservation.     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F _ST) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such as Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei’s genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken resources.     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is regarded as one of the domestication cen-ters for chickens and archaeological studies provided evidence of chicken domestication in northern Chinaas early as 6000 BC[1]. At present, China has the larg-est chicken population in the world, represen…     

采用微卫星标记分析13个中外牛品种的遗传变异和品种间的遗传关系

本研究应用联合国粮农组织(FAO)和国际动物遗传学会(ISAG)推荐的10对微卫星引物,结合荧光–多重PCR技术,检测了10个中国地方黄牛品种和3个外来牛品种的基因型。通过计算基因频率、多态信息含量和遗传杂合度,以Nei’s遗传距离和Nei’s标准遗传距离为基础,采用非加权组对算术平均聚类法构建了聚类图,分析了13个牛品种的群体内遗传变异和群体间遗传关系。并以聚类分析和群体结构分析为基础,将13个中外黄牛品种分为三类:Ⅰ类属于普通黄牛品种,包括延边牛、沿江牛、长白地方牛、蒙古牛、阿勒泰白头牛、哈萨克牛、复州牛和西藏牛;Ⅱ类属于含有瘤牛血统的黄牛品种,包括日喀则驼峰牛和阿沛甲咂牛;Ⅲ类属于外来牛品种,包括德国黄牛、西门塔尔牛和夏洛来牛。研究结果为加强我国地方黄牛品种种质特性研究以及地方牛品种资源的保护与利用提供了科学的依据。     

Genetic variation in eight Chinese cattle breeds based on the analysis of microsatellite markers

Genetic variability and genetic relationships were investigated among eight Chinese cattle breeds using 12 microsatellite markers. Three hundred and fifty-two alleles were detected and the average number of alleles per locus ranged from 8.33 ± 1.67 in the Jiaxian breed to 21.33 ± 5.60 in the Qinchuan breed with a mean value of 13.91. The total number of alleles per microsatellite ranged from 21 (INRA005, HEL1) to 40 (HEL13), with a mean of 29.33 per locus. The fixation indices at the 12 loci in the eight breeds were very low with a mean of 0.006. A principal components analysis and the construction of a neighborjoining tree showed that these eight Chinese cattle breeds cluster into three groups i.e. the Yanbian andChineseHolstein, theNanyang and Jiaxian, and the four remaining breeds.This clustering agrees with the origin and geographical distributions of these Chinese breeds.     

Genetic relationships of five Indian horse breeds using microsatellite markers

The genetic relationships of five Indian horse breeds, namely Marwari, Spiti, Bhutia, Manipuri and Zanskari were studied using microsatellite markers. The DNA samples of 189 horses of these breeds were amplified by polymerase chain reaction using 25 microsatellite loci. The total number of alleles varied from five to 10 with a mean heterozygosity of 0.58 ± 0.05. Spiti and Zansakari were the most closely related breeds, whereas, Marwari and Manipuri were most distant apart with Nei's D_A genetic distance of 0.071 and 0.186, respectively. In a Nei's D_A genetic distances based neighbour joining dendrogram of these breeds and a Thoroughbred horse outgroup, the four pony breeds of Spiti, Bhutia, Manipuri and Zanskari clustered together and then with the Marwari breed. All the Indian breeds clustered independently from Thoroughbreds. The genetic relationships of Indian horse breeds to each other correspond to their geographical/environmental distribution.     

Development and characterization of nine polymorphic microsatellite markers in the Chilean kelp Lessonia nigrescens

A total of nine microsatellite loci were isolated and characterized in the Chilean kelp Lessonia nigrescens Bory. Using two different enriched libraries, we observed 1-14 alleles per locus in two samples of 21 kelp individuals each. The observed heterozygosities ranged from 0.05 to 0.80 and all loci are in Hardy-Weinberg equilibrium for one or both samples. Seventeen samples collected from different sites showed high allele diversity along the species distribution. The variation detected at these markers is currently being used for the study of populations of Lessonia nigrescens at different geographical scales.     

Evaluation of the genetic diversity and population structure of Chinese indigenous horse breeds using 27 microsatellite markers

We determined the genetic diversity and evolutionary relationships among 26 Chinese indigenous horse breeds and two introduced horse breeds by genotyping these animals for 27 microsatellite loci. The 26 Chinese horse breeds come from 12 different provinces. Two introduced horse breeds were the Mongolia B Horse from Mongolia and the Thoroughbred Horse from the UK. A total of 330 alleles were detected, and the expected heterozygosity ranged from 0.719 (Elenchuns) to 0.780 (Dali). The mean number of alleles among the horse breeds ranged from 6.74 (Hequ) to 8.81 (Debao). Although there were abundant genetic variations found, the genetic differentiation was low between the Chinese horses, which displayed only 2.4% of the total genetic variance among the different breeds. However, genetic differentiation (pairwise FST) among Chinese horses, although moderate, was still apparent and varied from 0.001 for the Guizou–Luoping pair to 0.064 for the Jingjiang–Elenchuns pair. The genetic differentiation patterns and genetic relationships among Chinese horse breeds were also consistent with their geographical distribution. The Thoroughbred and Mongolia B breeds could be discerned as two distinct breeds, but the Mongolia B horse in particular suffered genetic admixture with Chinese horses. The Chinese breeds could be divided into five major groups, i.e. the south or along the Yangtze river group (Bose, Debao, Wenshan, Lichuan, Jianchang, Guizhou, Luoping, Jinjiang and Dali), the Qinghai‐Tibet Plateau group (Chaidamu, Hequ, Datong, Yushu, Tibet Grassland and Tibet Valley), the Northeast of China group (Elenchuns, Jilin and Heihe), the Northwest of China group (Kazakh, Yili and Yanqi) and the Inner Mongolia group (Mongolia A, Sanhe, Xinihe,Wuzhumuqin and Sengeng). This grouping pattern was further supported by principal component analysis and structure analysis.     

Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (H_E) over all the populations varied between 0.637 and 0.684 in this study. The low G_ST value showed that only 3.6% of the diversity was between breeds (P < 0.01). Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, except HMS5 that showed agreement in all analysed populations. The cumulative exclusion probability (PE) was 0.999 in each breed, suggesting that the loci would be suitable for donkey parentage testing. The constructed dendrogram from the D_A distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans.     

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.     

采用微卫星标记分析10个双峰驼群体的遗传变异和群体间的遗传关系

为从分子水平上对我国双峰驼(Camelus bactrianus)群体的遗传多样性、群体间遗传关系、群体遗传分化及近交情况进行全面、系统地研究,为双峰驼种质资源保护和新品种培育提供基础数据,本文利用18对微卫星引物,分析了我国9个双峰驼群体和1个蒙古双峰驼群体的遗传多样性和遗传关系。结果显示:10个群体均具有较高的遗传多样性,共检测到242个等位基因,平均等位基因数为13.44,平均有效等位基因数为4.18,平均观察杂合度(Ho)为0.5528。10个群体间存在显著的遗传分化,有9.6%的遗传变异来自群体间,90.4%的遗传变异来自群体内部的个体间。聚类分析、主成分分析和群体遗传结构分析结果都表明10个群体被分成2个明显的分支,新疆4个群体单独聚为一类,剩下的6个群体聚为一类。这一结果可能与它们的地理分布和群体间的地理屏障有关。     

Genetic variability at the pig SLA complex in U.S. breeds of pigs1

Lymphocytes from 90 mature pigs and 548 growing pigs from 6.5 litters were screened with cytotoxic antibodies against swine lymphocyte antigens. Pigs included in the survey were from the Chester White, Duroc, Hampshire, Landrace and Yorkshire breeds. Significant differences between breeds were found in the frequency of the three haplotypes tested. Such differences may provide the genetic variability needed to determine associations between disease susceptibility and the pig's major histocompatibility gene complex.     

利用17个微卫星标记分析鳙鱼的遗传多样性

选用本实验室克隆的17个鳙鱼微卫星分子标记分析四川泸州和江西鄱阳湖的两个种群鳙鱼的遗传多样性及种质特性,计算和统计了杂合度、多态信息含量（PIC）、有效等位基因数、等位基因频率、遗传距离、遗传相似系数、Hardy-Weinberg平衡偏离指数等方面内容。结果表明：选择使用17个微卫星标记,其中有4个为单态标记,13个为多态标记。江西和四川鳙鱼群体每个微卫星位点的平均等位基因数分别为3.325及3.882,平均有效等位基因数分别为3.531及2.676,多态位点百分率分别为82.4及70.5, 17个微卫星标记共有等位基因71个,多态微卫星位点的PIC在0.114~0.960之间变动,平均为0.417 ,两群体位点平均观测杂合度为0.385和0.452,平均期望杂合度为0.360和0.422,两个群体间的遗传相似系数为0.897,群体间的遗传距离为0.109。     

Development and mapping of ten porcine microsatellite markers

Thirty (TG)_n microsatellite clones were isolated from a pig genomic library, sequenced, and tested for their suitability to detect polymorphism on a panel of animals by means of the polymerase chain reaction. Ten of these clones were developed into suitable markers and subsequently segregation of these markers was determined in the five PiGMaP reference pedigrees. A linkage analysis was performed on these 10 microsatellites together with 365 other loci that have been typed on these reference families. Eight of the microsatellites have been mapped to eight different linkage groups that have been previously assigned to different chromosomes (chromosomes 1, 6, 7, 9, 14, 15, 17 and 18). Of the remaining two markers, one is X-linked and the other shows no linkage. The number of alleles detected by these microsatellites, in the reference pedigrees, varied from six to sixteen and the heterozygosity varied from 42 to 85% in the 26 unrelated founder animals of these reference pedigrees.     

Characterization of porcine polymorphic microsatellite loci

Twenty-seven (CA)_n and two (GA)_n microsatellite clones were isolated out of a size-selected genomic pig library. These were sequenced and the number of uninterrupted dinucleotides was found to range from 12 to 26. Flanking primers were chosen for 11 dinucleotide repeats and optimal conditions for polymerase chain reaction (PCR) amplifications were established. Different microsatellite loci were amplified simultaneously by combining primer sets. Related and unrelated pigs were screened for length polymorphisms of the different microsatellite loci. The polymorphic information content (PIC) of these loci ranged between 0.62 and 0.83. Segregation studies in pig reference families established Mendelian inheritance. Locus S0022 was found to be X-linked.     

Analysis of 22 heterologous microsatellite markers for genetic variability in Indian goats

The genetic variability of 22 heterologous microsatellite markers was analyzed in two Indian goat breeds, namely Bengal and Chegu. The heterozygosity, polymorphism information content (PIC), and probability of identity of two individuals were calculated for all microsatellite loci in both the breeds. The observed number of alleles varied between 4 and 13 at the studied microsatellite loci. The evaluated microsatellite loci exhibited high mean heterozygosity of 0.69 +/- 0.11 and 0.66 +/- 0.07 in Bengal and Chegu goats, respectively. The mean PIC values of the studied loci in these breeds were 0.79 +/- 0.08 and 0.78 +/- 0.05, respectively. The probability of identity of two random individuals from different breeds, taking into account, all the 22 microsatellite loci was as low as 5.523 x 10(-40). On the basis of these results, we propose that these microsatellite markers may be used with reliability for studying genetic diversity and for identification of individuals in Indian goat breeds.