Evaluation of genetic architecture and mutation drift equilibrium of Marathwada buffalo population in Central India

In the present study, microsatellite data on 24 loci were generated and utilized to evaluate the genetic architecture and mutation drift equilibrium of Marathwada buffaloes, a Central Indian population maintained under low input system. Sufficient allelic diversity was observed with a total of 109 alleles across different loci. The genetic diversity analysis of Marathwada buffaloes displayed moderate level of within breed variability in terms of mean number of alleles per locus (4.48) and heterozygosity values (Ho = 0.532, He = 0.624). The studied Indian buffalo population showed considerable heterozygote deficiency (F_IS = 0.138) and deviation from HWE at many investigated loci. Three quantitative tests viz. sign test, standardized difference test and Wilcoxon sign rank test and a qualitative test for mode shift distortion of allelic frequencies were employed to evaluate mutation drift equilibrium under three different models of microsatellite evolution. The population was found to deviate significantly under IAM and TPM, while it was reverse under SMM. The qualitative test for mode shift supported the results under SMM indicating the absence of genetic bottleneck in the recent past in Marathwada buffaloes.     

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.     

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.     

Sheep genetic diversity in Bhutan using microsatellite markers

Genotype data from eight microsatellite markers were used to assess genetic diversity and relationships among five indigenous Bhutanese sheep populations, Sakten, Jakar, Sarpang, Sipsu and Tsirang. Estimates of mean observed and expected heterozygosities, mean number of alleles per locus/population were obtained. The highest observed heterozygosities were found in Jakar (0.657) and Sakten (0.647), while the lowest one was found in Tsirang (0.539). Genetic distances, pairwise proportion of different alleles, UPGMA tree, and principal component analysis indicate close relationship among Tsirang, Sipsu and Sarpang populations, while Jakar and Sakten populations are located in one cluster. These two clusters are separated geographically, and show distinct phenotypic as well as molecular characters. We therefore recommend that the Bhutanese native sheep populations be classified into at least two distinct breeds, Jakar‐Sakten sheep and Sipsu sheep. Since Jakar and Sakten sheep have different morphological phenotypes, further analyses will be required to understand the genetic differences between these two sheep populations.     

Genetic diversity analysis of two buffalo populations of northern India using microsatellite markers

The genetic diversity in two buffalo populations of northern India, the Bhadawari and the Tarai was assessed using a set of 22 heterologous (bovine) microsatellite markers. The average number of alleles across all loci in both populations was found to be 4.7, indicating that this set of 22 bovine microsatellite markers could be used to study genetic variation in buffalo species also. The overall polymorphic information content (PIC) value for these markers was 0.54. The average observed and expected heterozygosities for both populations were 0.59 and 0.64, respectively. Common alleles with varying allele frequencies in both populations also represented the genetic variability existing between Bhadawari and Tarai buffaloes. However the θ estimates for population differentiation indicated low levels of differentiation between the two populations. This was further supported by the low genetic distance (0.155) between Bhadawari and Tarai, which was calculated using Nei's standard genetic distance method. The present study on Bhadawari and Tarai populations represents a much‐needed preliminary effort that could be extended to other local buffalo populations of India as well.     

Genetic variability and relationships in nine South African cattle breeds using microsatellite markers

Tropical Animal Health and Production - Genetic variability within and between breeds allows adaptation to a changing environment and consequently prepares producers for the future. Eleven...     

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 variability of six indigenous goat breeds using major histocompatibility complex-associated microsatellite markers

The present study aimed at analyzing the genetic variability of indigenous goat breeds (Capra hircus) using the MHC-associated microsatellite markers BF1, BM1818, BM1258, DYMS1, and SMHCC1. The following breeds were included: Chinese Xuhuai, Indian Changthangi and Pashmina, Kenyan Small East African (SEA) and Galla, and Albanian Vendi. To examine genetic variability, the levels of heterozigosity, degrees of inbreeding, and genetic differences among the breeds were analyzed. The mean number of alleles ranged from nine in the Galla to 14.5 in the Vendi breed. The mean observed heterozygosity and mean expected heterozygosity varied from 0.483 in the Vendi to 0.577 in the Galla breed, and from 0.767 in the SEA to 0.879 in the Vendi breed, respectively. Significant loss of heterozygosity (p < 0.01) indicated that these loci were not in Hardy-Weinberg equilibrium. The mean F_IS values ranged from 0.3299 in the SEA to 0.4605 in the Vendi breed with a mean value of 0.3623 in all breeds (p < 0.001). Analysis of molecular variance indicated that 7.14% and 4.74% genetic variation existed among the different breeds and geographic groups, whereas 92.86% and 95.26% existed in the breeds and the geographic groups, respectively (p < 0.001). The microsatellite marker analysis disclosed a high degree of genetic polymorphism. Loss of heterozygosity could be due to genetic drift and endogamy. The genetic variation among populations and geographic groups does not indicate a correlation of genetic differences with geographic distance.     

Assessment of genetic diversity and conservation priority of Omani local chickens using microsatellite markers

Designing strategies for conservation and improvement livestock should be based on assessment of genetic characteristics of populations under consideration. In Oman, conservation programs for local livestock breeds have been started. The current study assessed the genetic diversity and conservation potential of local chickens from Oman. Twenty-nine microsatellite markers were analyzed in 158 birds from six agroecological zones: Batinah, Dhofar, North Hajar, East Hajar, Musandam, and East Coast. Overall, a total of 217 alleles were observed. Across populations, the average number of alleles per locus was 7.48 and ranged from 2 (MCW98 and MCW103) to 20 (LEI094). The mean expected heterozygosity (H _E) was 0.62. Average fixation index among populations (F _ST) was 0.034, indicating low population differentiation, while the mean global deficit of heterozygotes across populations (F _IT) was 0.159. Based on Nei’s genetic distance, a neighbor-joining tree was constructed for the populations, which clearly identified the Dhofar population as the most distant one of the Omani chicken populations. The analysis of conservation priorities identified Dhofar and Musandam populations as the ones that largely contribute to the maximal genetic diversity of the Omani chicken gene pool.     

利用微卫星标记技术分析太湖鹅保种效果

本研究利用微卫星标记对太湖鹅两个世代群体10个微卫星位点进行遗传多样性鉴定,通过分析世代间遗传差异来检测小群保种效果。结果表明:太湖鹅2个世代的10个位点共检测到52个等位基因,0世代和1世代分别检测到49和51个等位基因;两个世代的10个微卫星位点的多态信息含量为0.157 2~1.000 0,两个世代平均多态信息含量分别为0.511 7,0.504 0;两个世代的期望杂合度和表观杂合度分别在0.172 8~0.800 7和0.190 0~1.000 0之间,平均值分别为0.584 4,0.569 6和0.650 0,0.627 0,这两个世代在等位基因、多态信息含量、杂合度上差异均不显著(P0.05)。2个世代相似性系数为0.990 7,遗传距离0.009 3,世代间的相似性系数极高,遗传距离极低。在10个微卫星位点中,0世代和1世代分别存在6个位点不平衡,哈代-温伯格平衡趋于下降趋势。近交增量为0.078%,近交系数达到2%需要的世代数为25。结果提示该保种场保种效果可行。     

Dissection of additive genetic variability for quantitative traits in chickens using SNP markers

The aim of this study was to separate marked additive genetic variability for three quantitative traits in chickens into components associated with classes of minor allele frequency (MAF), individual chromosomes and marker density using the genomewide complex trait analysis (GCTA) approach. Data were from 1351 chickens measured for body weight (BW), ultrasound of breast muscle (BM) and hen house egg production (HHP), each bird with 354 364 SNP genotypes. Estimates of variance components show that SNPs on commercially available genotyping chips marked a large amount of genetic variability for all three traits. The estimated proportion of total variation tagged by all autosomal SNPs was 0.30 (SE 0.04) for BW, 0.33 (SE 0.04) for BM, and 0.19 (SE 0.05) for HHP. We found that a substantial proportion of this variation was explained by low frequency variants (MAF <0.20) for BW and BM, and variants with MAF 0.10–0.30 for HHP. The marked genetic variance explained by each chromosome was linearly related to its length (R² = 0.60) for BW and BM. However, for HHP, there was no linear relationship between estimates of variance and length of the chromosome (R² = 0.01). Our results suggest that the contribution of SNPs to marked additive genetic variability is dependent on the allele frequency spectrum. For the sample of birds analysed, it was found that increasing marker density beyond 100K SNPs did not capture additional additive genetic variance.     

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。     

Analysis of genetic diversity and the determination of relationships among western Mediterranean horse breeds using microsatellite markers

The distribution of genetic diversity and the genetic relationships among western Mediterranean horse breeds were investigated using microsatellite markers. The examined sample included seven Spanish and three Italian local horse breeds and populations, plus a Spanish Thoroughbred outgroup. The total number of animals examined was 682 (on average 62 animals per breed; range 20–122). The microsatellite marker set analysed provided 128 alleles (10.7 alleles per locus). Within‐breed genetic diversity was always high (>0.70), with breeds contributing about 8% of the total genetic variability. The mean molecular coancestry of the entire population examined was 0.205, Losino being the breed that contributed most. In addition to Nei's standard and Reynolds’ genetic distances, pair‐wise kinship distance and molecular coancestry were estimated. Remarkably similar breed rankings were obtained with all methods. Clustering analysis provided an accurate representation of the current genetic relationships among the breeds. Determining coancestry is useful for analysing genetic diversity distribution between and within breeds and provides a good framework for jointly analysing molecular markers and pedigree information. An integrated analysis was undertaken to obtain information on the population dynamics in western Mediterranean native horse populations, and to better determine conservation priorities.     

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.     

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.     

利用微卫星标记分析4个食蟹猴群体的遗传多样性

利用7个恒河猴源微卫星标记和4个人源微卫星标记共11个标记,分析了来源于束埔寨(Pop1)、老挝(Pop2)、越南1(Pop3)和越南2(Pop4)共4个群体食蟹猴的遗传多样性.研究结果显示,所选择的11个微卫星位点表现出很高的多态性,群体内的多态性较低,存在较严重的近亲交配.Hardy-Weinberg平衡检测说明4个群体在这11个位点上均处于不平衡状态,可能存在较严重的人工选择繁育.亚群体内的固定指数平均为0.526 2,说明群体内存在近亲交配;亚种群间的固定指数均值为0.016 6,说明各群体间的遗传分化很小;各位点上的基因流均值为14.814 2,说明其交流很活跃,可有效地防止因遗传漂移而产生的遗传分化.从基于Nei氏标准遗传距离的UPGMS聚类图看出,先是Pop3和Pop4聚为一类,再和Pop1聚在一起,最后和Pop2聚在一起,其结果和其地理分布所表现的遗传差异一致.