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.     

Analysis of genetic diversity and conservation priorities for six north Ethiopian cattle breeds

Genetic diversity and conservation potential of six indigenous cattle breeds of north Ethiopia was analysed based on 20 microsatellite markers using core set methods. Expected future diversity (assuming assigned extinction probabilities are valid for the next 20-50 years) were 0.988+/-0.011 and 0.980+/-0.010 with expected loss of diversity estimated at 0.02% and 0.74% of current level for the Maximum Variance Total (MVT) and Maximum Variance Offspring (MVO) core sets, respectively. Even though all breeds have contributed to current diversity levels, the Afar and Abergelle breeds only contributed 51% and 62% to the MVT and MVO core sets, respectively, while the Raya breed contributed only 6% and 1.5% to the MVT and MVO core set diversities, respectively. Moreover, prioritizing the six north Ethiopian cattle breeds using the conservation potential obtained from the MVT core set method seems reasonable considering the origin and migration histories of the breeds. Our results suggest that the total current genetic diversity of these breeds can be sufficiently maintained by designing a conservation strategy based on conservation potential of each breed from the MVT core set so that priority is given to lowering the extinction probabilities of breeds with high conservation potential to zero.     

Genetic diversity and population structure analysis of eight local chicken breeds of Southern Xinjiang

ABSTRACT

1. The genetic diversity and population structure were studied for eight local chicken breeds, including Anjiyan (AN), Hetian Black (HH), Hetian Ma (HM), Aheqi (AH), Baicheng You (BC), Hejing (HJ), Tashkurghan (TS) and Ruoqiang (RQ), in the Southern Xinjiang region of China, using 20 microsatellite markers.

2. Total 336 alleles were obtained from all chicken breeds, with a mean of 16.8 alleles per locus. The polymorphism information content ranged from 0.444 to 0.911, with a mean of 0.729 and almost all of the loci showed significant deviation from Hardy-Weinberg standards. The observed and expected heterozygosity of the eight breeds ranged from 0.5 to 0.677 and from 0.656 to 0.774, with the lowest observed in the AN and the highest in BC breed. The average breed genetic diversity was 0.655 for AN and 0.766 for BC chickens.

3. According to the neighbour-joining (NJ) method, three main clusters were identified in the NJ phylogenetic tree with AN and RQ breeds in one clade, HH and HM breeds in the second clade and TS, HJ, AH and BC breeds in the third clade.

4. Based on STRUCTURE analysis, the most likely cluster number of all breeds was K = 4, whereby HH and HM breeds formed one cluster and AH, BC, HJ and TS formed another, and RQ, AN chicken formed their own distinct cluster. These results indicated that HH and HM breeds had similar genetic background, as did the breeds of AH, BC, HJ and TS. RQ, AN breed had unique genetic backgrounds, distinct from the other breeds. Genetic introgression was detected from AN to HH and HM.

5. The results of the current study can be used as baseline genetic information to implement effective conservation programs and to make better use of these local chicken breeds, especially for the AN, RQ and TS breeds.     

An evaluation of genetic diversity indices of the Red Bororo and White Fulani cattle breeds with different molecular markers and their implications for current and future improvement options

The genetic diversity of the Red Bororo and White Fulani cattle breeds of Cameroon and Nigeria was assessed with a panel of 32 markers. Estimates for the various indices of genetic diversity, total number of alleles (TNA), mean observed number of alleles (MNA), mean effective number of alleles (MNE), observed heterozygosity (H _ob) and expected heterozygosity (H _ex), were higher at microsatellite loci than at protein loci. Mean H _ex values were above 71% at microsatellite loci in all the breeds and ranged from 37% to 41.6% at milk protein loci and from 40.9% to 45.6% at blood protein loci. The highest TNA and MNA of microsatellites were recorded for the Nigerian White Fulani. MNE of milk protein loci was highest in the Cameroonian Red Bororo, while TNA of blood protein loci was highest in the Cameroonian White Fulani. The high genetic diversity levels indicate the presence of the necessary ingredients for improvement breeding and conservation. Multi-locus estimates of within-population inbreeding (f), total inbreeding (F) and population differentiation (θ) of the breeds were significantly different from zero, except for θ of blood proteins. A high level of gene flow was found between the breeds (5.829). The phylogenetic relationship existing among the four breeds is greatly influenced by location. The high gene flow between the breeds may lead to a loss of genetic diversity through genetic uniformity and a reduction in opportunities for future breed development. We propose an improvement scheme with aims to prevent loss of genetic diversity, improve productivity and reduce uncontrolled genetic exchanges between breeds.     

Genetic characterization of the Blonde d'Aquitaine cattle breed using microsatellite markers and relationship with three other French cattle populations

This study was conducted to evaluate the genetic diversity of Blonde d'Aquitaine, a well-muscled native French beef breed, and to understand the relationships between Blonde d'Aquitaine, Limousin and Salers. We also compared these three beef breeds to the Holstein dairy breed. For this purpose, a set of 16 microsatellite markers were investigated. The obtained results show that Blonde d'Aquitaine has a high level of genetic diversity. Our study shows also that the French beef breeds have genetic differentiation among them, with approximately 9% of the total variation owing to breed differences. Our results show also that Blonde d'Aquitaine and Salers populations are genetically more similar to each other than to the Limousin.     

太湖流域地方猪种遗传结构评估和体重体尺性状差异相关选择位点鉴定

旨在解析太湖流域地方猪品种内部遗传结构,鉴定梅山猪亚群间、二花脸群体间和米猪群体间体重体尺性状差异的候选基因。试验采集440头猪样本(代表太湖流域地方猪最全面血统)进行基因芯片分型,并使用该基因分型数据集进行多种群体遗传学分析,明确太湖流域地方猪品种内部的遗传结构,并鉴定梅山猪亚群间、以及二花脸和米猪群体间体重体尺性状差异的候选SNP位点和候选基因。结果显示:在太湖流域地方猪种内部,二花脸猪与米猪间的亲缘关系最接近,其遗传距离小于梅山猪两个亚群间的遗传距离,并且拥有最为一致的进化路线。太湖流域地方猪各品种及梅山猪品种内两个亚群间都达到高度分化水平,Fst值均大于0.25,ADMIXTURE分析表明,包括梅山猪两个亚群在内的8个群体的群体结构不完全一致,在K=8时,各自展现出完全不同的祖先血统组成。通过梅山猪亚群间Fst分析、以及米猪和二花脸猪间Fst分析,在猪1、3和6号等染色体上,共鉴定到24个位点在两个分析中都表现出受选择状态,并在这些位点上下游50 kb范围注释到20个基因,其中有8个基因被报道与体重体尺性状相关。此外,受选择位点形成的选择区域与多个猪体重体尺相关QTLs重叠。试...     

A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls

The objectives of this study were to characterize the genetic variability of village chickens from three agro‐ecological regions of western Algeria: coastal (CT), inland plains (IP) and highlands (HL), to reveal any underlying population structure, and to evaluate potential genetic introgression from commercial lines into local populations. A set of 233 chickens was genotyped with a panel of 23 microsatellite markers. Geographical coordinates were individually recorded. Eight reference populations were included in the study to investigate potential gene flow: four highly selected commercial pure lines and four lines of French slow‐growing chickens. Two populations of wild red jungle fowls were also genotyped to compare the range of diversity between domestic and wild fowls. A genetic diversity analysis was conducted both within and between populations. Multivariate redundancy analyses were performed to assess the relative influence of geographical location among Algerian ecotypes. The results showed a high genetic variability within the Algerian population, with 184 alleles and a mean number of 8.09 alleles per locus. The values of heterozygosity (He and Ho) ranged from 0.55 to 0.62 in Algerian ecotypes and were smaller than values found in Jungle fowl populations and higher than values found in commercial populations. Although the structuring analysis of genotypes did not reveal clear subpopulations within Algerian ecotypes, the supervised approach using geographical data showed a significant (p < 0.01) differentiation between the three ecotypes which was mainly due to altitude. Thus, the genetic diversity of Algerian ecotypes may be under the influence of two factors with contradictory effects: the geographical location and climatic conditions may induce some differentiation, whereas the high level of exchanges and gene flow may suppress it. Evidence of gene flow between commercial and Algerian local populations was observed, which may be due to unrecorded crossing with commercial chickens. Chicken ecotypes from western Algeria are characterized by a high genetic diversity and must be safeguarded as an important reservoir of genetic diversity.