Genetic diversity of Afrikaner cattle in southern Africa

The Afrikaner is an indigenous South African breed of “Sanga” type beef cattle along with breeds such as the Drakensberger and Nguni. Six composite breeds have been developed from crosses with the Afrikaner. Additionally, Afrikaner has been the base from which exotic breeds were established in South Africa through backcrossing. The study examined genetic diversity of Afrikaner cattle by genotyping 1257 animals from 27 herds in different geographic areas of South Africa and Namibia using 11 microsatellite markers. Multiple-locus assignment, performed using the Bayesian clustering algorithm of STRUCTURE, revealed three underlying genotypic groups. These groups were not geographically localized. Across herds and markers, the proportion of unbiased heterozygosity ranged from 0.49 to 0.72 averaging 0.57; mean number of alleles per locus ranged from 3.18 to 7.09, averaging 4.81; and allelic richness ranged from 2.35 to 3.38, averaging 2.67. It is concluded that a low inbreeding level of 2.7% and a moderate to high degree of variation still persists within the Afrikaner cattle breed, despite the recent decline in numbers of animals.     

Genetic diversity and population structure of South African smallholder farmer sheep breeds determined using the OvineSNP50 beadchip

Tropical Animal Health and Production - A population structure study was performed in South African ovine populations using the OvineSNP50 beadchip. Blood samples were obtained from 295 sheep of...     

Monitoring of genetic diversity in the endangered Martina Franca donkey population

The Martina Franca (MF) donkey, an ancient native breed of Apulia, was mostly famous for mule production. The breed was at serious risk of extinction in the 1980s following the decrease in demand for draft animals because they were increasingly replaced by agricultural machinery. Much has been done in the last few decades to safeguard the existing donkey breeds, but the situation remains critical. Successful implementation of conservation measures includes an evaluation of the present degree of breed endangerment, so the aim of this work was to analyze the demographic and genetic parameters of this breed to suggest effective conservation strategies. With a current breed register counting less than 500 recorded animals, the pedigree data set included 1,658 MF donkeys born between 1929 and 2006. Analyses were carried out on the whole data set as well as on a smaller one consisting of 422 living animals. Demographic and genetic variability parameters were evaluated using the ENDOG (v4.6) software. The pedigree completeness level was evaluated as well as the generation length, which was calculated for each of the 4 gametic pathways. This information was obtained from animal birth date records together with those of their fathers and mothers. The effective number of founders (f(e)), the effective number of ancestors (f(a)), the founder genome (f(g)), individual inbreeding (F), average relatedness (AR), and the rate of inbreeding per generation were analyzed to describe the genetic variability of the population. Because pedigree depth and completeness were appropriate, especially regarding the current population, the parameters defining genetic variability, namely, f(e), f(a), f(g), F, and AR, could be reliably estimated. Analysis of these parameters highlighted the endangerment status of the MF donkey. Our special concern was with the increased percentage of males and females exhibiting increased AR values. Moreover, the effective size of the current population, 48.08, is slightly less than the range of the minimum effective size, and the rates of inbreeding per generation found in the current MF population exceed the maximum recommended level of 1%. Such a scenario heightens concerns over the endangered status of the MF breed and calls for proper conservation measures and breeding strategies, such as selecting individuals for mating when relationships are below 12.5%.     

基于SRAP标记的海雀稗遗传多样性及群体结构分析

采用SRAP标记对来自不同国家的49份海雀稗(Paspalum vaginatum)种质资源遗传多样性进行分析,探讨其群体结构及种质间亲缘关系,为海雀稗种质的开发利用奠定基础.结果表明:从100对引物中共筛选出20对扩增稳定、多态性好的SRAP引物,对49份种质进行PCR扩增,共扩增出169条带,其中多态性条带为118条,多态性位点百分率为69.8％.49份海雀稗种质间遗传相似系数为0.52?0.88,平均值为0.67,表明供试海雀稗种质间存在较大遗传差异.采用UPGMA聚类分析、主成分分析、群体结构分析对49份海雀稗种质进行划分,基本都分为2类,且44份材料在3种方法下均表现为较一致的分类,5份材料表现出一定程度的变异,表明此研究结果反映的种质亲缘关系基本稳定,可用于育种应用.     

基于SRAP标记的海雀稗遗传多样性及群体结构分析

采用SRAP标记对来自不同国家的49份海雀稗(Paspalum vaginatum)种质资源遗传多样性进行分析,探讨其群体结构及种质间亲缘关系,为海雀稗种质的开发利用奠定基础.结果表明:从100对引物中共筛选出20对扩增稳定、多态性好的SRAP引物,对49份种质进行PCR扩增,共扩增出169条带,其中多态性条带为118...     

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.     

Genetic structure and diversity among sheep breeds in the United States: identification of the major gene pools

Understanding existing levels of genetic diversity of sheep breeds facilitates in situ and ex situ conservation activities. A comprehensive evaluation of US sheep breeds has not been previously performed; therefore, we evaluated the genetic diversity among and within 28 US sheep breeds. Both major and minor breeds were included in the analysis and consisted of 666 animals from 222 producers located in 38 states. The level of within-breed genetic diversity was variable and not dependent upon status of a breed as a major or minor breed. Bayesian cluster analysis indicated the breeds were grouped more by physiological differences (meat vs. wool production) rather than geographic origin. Results suggest several actionable items to improve in situ and ex situ conservation. The results clearly identify breeds in need of increased in situ and ex situ management (e.g., Hog Island and Karakul) and allow several suggestions for in situ management of flocks. Conversely, several of the breeds appear genetically similar and therefore require less emphasis on collecting germplasm samples for the gene bank. Commercially important breeds (e.g., Rambouillet and Suffolk) were found to have substantial variation, which should enable breeders to proceed, unencumbered by genetic diversity concerns, with selection strategies that maximize profit.     

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.     

Genetic diversity and structure of the West Balkan Pramenka sheep types as revealed by microsatellite and mitochondrial DNA analysis

Several different phenotypes of the native Pramenka sheep have been developed in the Balkan region for different environmental and socio‐cultural conditions. Animals from seven West Balkan Pramenka sheep types were analysed for 15 microsatellite markers and for mitochondrial DNA (mtDNA) and the results were used to assess genetic variation within and among the types and to infer the genetic population structure of the Pramenka sheep. Mean expected heterozygosity and allelic richness over the microsatellite loci and sheep types were 0.78 and 7.9, respectively. A Bayesian statistical method for estimating hidden genetic structure suggested that a core of the largest panmictic population was formed by Serbian, Kosovan, Bosnian, Montenegrin and Albanian types, while Croatian and Macedonian types comprised two other main populations, respectively. Mitochondrial DNA analysis revealed two mtDNA haplogroups in the Pramenka sheep, B and A, with a frequency of 93.7% and 6.3%, respectively. A total of 60 mtDNA haplotypes were found in 64 animals sequenced, and the mean nucleotide and haplotypic diversities over the types were 0.013 and 0.945, respectively. Molecular analysis suggests that the West Balkan Pramenka sheep types have their origins in two distinct maternal lineages of domestic sheep and different Pramenka phenotypes tend to form few panmictic populations. The Pramenka sheep represents a valuable resource of genetic diversity in sheep.     

Genetic diversity and matrilineal genetic origin of fat-rumped sheep in Ethiopia

Ethiopia is home to a diverse gene pool of indigenous sheep populations. Therefore, a better understanding of genetic variation holds the key to future utilization through conservation. Three of these breeds, Afar, Blackhead Somali, and Hararghe Highland, are found in eastern Ethiopia where they contribute significantly to the livelihood of most pastoralist, agro-pastoralist, and smallholder farmers. These indigenous sheep are recognized on the basis of morphotype and their genetic distinction remains unknown. Here, to assess genetic variation, and matrilineal genetic origin and relationship of fat-rumed sheep found in eastern Ethiopia, 300 individuals from the three breeds were genotyped for 22 microsatellite markers and sequenced for the mitochondrial DNA displacement loop (mtDNA d-loop) region. The overall H_O and H_E were 0.57 and 0.75, respectively. Differentiation statistics revealed that a high proportion (97%) of the total genetic variation was explained by differences between individuals within populations. Genotype assignment independent of the population of origin showed K?=?2 to be the optimum number of genetic backgrounds present in the dataset. This result was further confirmed by mtDNA D-loop sequences comparison in which the matrilineal genetic origin of eastern Ethiopia sheep is from two haplotype groups (types A and B) among the five haplotypes globally observed. Taken together, our findings suggest that the sheep populations from three breeds originated from two ancestral genetic backgrounds that may have diverged prior to their introduction to Ethiopia. However, to obtain a complete picture of the evolutionary dynamics of Ethiopian indigenous sheep, more samples and populations from within and outside of the country will need to be analyzed.

     

Genetic diversity of Swiss sheep breeds in the focus of conservation research

There is constant pressure to improve evaluation of animal genetic resources in order to prevent their erosion. Maintaining the integrity of livestock species as well as their genetic diversity is of paramount interest for long-term agricultural policies. One major use of DNA techniques in conservation is to reveal genetic diversity within and between populations. Forty-one microsatellites were analysed to assess genetic diversity in nine Swiss sheep breeds and to measure the loss of the overall diversity when one breed would become extinct. The expected heterozygosities varied from 0.65 to 0.74 and 10.8% of the total genetic diversity can be explained by the variation among breeds. Based on the proportion of shared alleles, each of the nine breeds were clearly defined in their own cluster in the neighbour-joining tree describing the relationships among the breeds. Bayesian clustering methods assign individuals to groups based on their genetic similarity and infer the number of populations. In STRUCTURE, this approach pooled the Valais Blacknose and the Valais Red. With BAPS method the two Valais sheep breeds could be separated. Caballero & Toro approach (2002) was used to calculate the loss or gain of genetic diversity when each of the breeds would be removed from the set. The changes in diversity based on between-breed variation ranged from −12.2% (Valais Blacknose) to 0% (Swiss Black Brown Mountain and Mirror Sheep); based on within-breed diversity the removal of a breed could also produce an increase in diversity (−0.6% to + 0.6%). Allelic richness ranged from 4.9 (Valais Red) to 6.7 (Brown Headed Meat sheep and Red Engadine Sheep). Breed conservation decisions cannot be limited to genetic diversity alone. In Switzerland, conservation goals are embedded in the desire to carry the cultural legacy over to future generations.     

Genetic diversity in and conservation strategy considerations for Navajo Churro sheep

The objectives of this study were to 1) evaluate the genetic diversity of Navajo-Churro sheep using pedigree information; 2) examine the distribution of the Navajo-Churro population; and 3) evaluate the effect of breeder dynamics on genetic conservation of the breed. Pedigree data and breeder information (city and state) were obtained from the Navajo-Churro Sheep Breed Association. Inbreeding coefficients were calculated for each individual animal using pedigree information. A geographic information system program was used to divide the United States into four regions and overlay breeder locations, flock size, and flock inbreeding level. The small correlation between level of inbreeding and flock size (r = -0.07, P = 0.07) indicated that inbreeding levels are not different across flock sizes. The mean flock inbreeding levels ranged from 0 to 11% across regions. The level of inbreeding did not differ among regions (P = 0.15), except for Region 4 (Kansas and Missouri; P = 0.001). The number of breeders registering sheep averaged 34 per year. Most of the breeders were transient, with only eight breeders maintaining ownership for more than 7 yr. Average inbreeding level for 2000 was found to be 1.2%, with a linear increase in inbreeding of 0.1%/yr over the period studied, suggesting a minimal loss of genetic diversity for the Navajo-Churro. However, given the relatively small effective population size (92) and the transient nature of the breeders, development of an ex situ cryo-preserved germplasm bank may be the best long-term strategy for maintaining this breed's genetic diversity.     

Genetic diversity and population structure of Brachiaria brizantha (A.Rich.) Stapf accessions from Ethiopia

Brachiaria is a tropical, warm-season grass native to Africa. It is an extensively cultivated forage in the tropics with proven benefits on livestock productivity. Brachiaria is well-known for high biomass production, animal nutrition, carbon sequestration, biological nitrification inhibition, soil conservation, and adaptation to drought and low fertility soils. However, the use of Brachiaria grass for fodder production in Africa has been little explored largely due to lack of cultivars suitable to different production environments. The exploration and use of natural diversity is fundamental for an efficient Brachiaria breeding program. We analysed genetic diversity and population structure of 112 Ethiopian Brachiaria brizantha accessions using 23 microsatellite markers. A total of 459 alleles were detected with an average polymorphic information content of 0.75 suggesting high discriminating ability of these markers. The molecular variance analysis showed a high contribution (86%) of within-cluster differences to the total variation. Three allelic pools revealed by STRUCTURE analysis in 112 accessions were in agreement with the clustering patterns seen in neighbor-joining tree and principal coordinates analyses. A core collection of 39 B. brizantha accessions was constituted. This study concludes a high genetic diversity of Ethiopian B. brizantha accessions and their importance in Brachiaria breeding programs.     

河北小尾寒羊mtDNA变异及遗传多样性分析

旨在分析河北小尾寒羊线粒体基因组变异和遗传多样性,采用线粒体基因组测序方法获得线粒体基因组序列,进行编码区变异分析;利用群体遗传学方法对非编码区进行遗传多样性分析。结果表明:河北小尾寒羊线粒体基因组编码区共发现183个变异位点,其中多肽编码区156个,r RNA基因19个和t RNA基因8个;多肽编码区发现同义突变128个,错义突变28个。非编码区共发现81个变异位点,核苷酸多样性为(0.022 22±0.006 93),单倍型多样性为(0.996±0.015),83只个体构成的65种单倍型,聚为3个单倍型群:A单倍型群包括35只个体,其中9只河北小尾寒羊,26只山东小尾寒羊;B单倍型群包括38只个体,其中13只河北小尾寒羊,25只山东小尾寒羊;C单倍型群为10只山东小尾寒羊,该单倍型群为一个独立类群。3个单倍型群A、B和C的频率分别为0.42、0.46和0.12。由此说明河北小尾寒羊遗传多样性较为丰富,与山东小尾寒羊存在基因交流。     

AFLP标记检测大足黑山羊地方类群遗传多样性的研究

利用AFLP标记技术,从15对引物中选取11对扩增效果较好的引物,对17只大足黑山羊个体DNA进行扩增。结果共扩增出766个条带,其中59条为多态条带,平均每对引物扩增出69．6个条带,平均多态率为5．36％.     

唐古拉山牦牛群体的母系遗传多样性及遗传结构分析

[目的]从分子水平上探究青海省唐古拉山牦牛群体的母系遗传多样性、群体遗传结构及其遗传背景。[方法] 对52头唐古拉山牦牛个体mtDNA D-loop区序列进行测定后,使用生物信息学软件分析确定其核苷酸变异位点和单倍型数目,计算单倍型多样度和核苷酸多样度大小,并进行系统发育分析。[结果] 在619 bp唐古拉山牦牛D-loop区序列分析中,排除2处插入（缺失）后共检测到31处多态位点,包括单一多态位点5处和简约信息位点26处。根据序列间核苷酸变异共确定了13种单倍型,单倍型多样度和核苷酸多样度分别为0.821±0.043和0.007±0.004。与我国其他18个家牦牛品种和野牦牛相比,唐古拉山牦牛群体单倍型多样度和核苷酸多样度值均较低,表明该群体遗传变异较为贫乏,母系遗传多样性水平较低。以美洲野牛为外群,邻接法（即NJ法）构建的系统发育树结果显示：唐古拉山牦牛群体13种单倍型分布在A、B、C、D和E五种单倍型组中,且聚为2个大的母系分支（即I和II）,支系Ⅰ占比为77%,提示唐古拉山牦牛由2个母系支系组成,拥有2个母系起源且以支系Ⅰ为主。 [结论] 唐古拉山牦牛母系遗传多样性水平较低,由2个母系支系组成,以支系Ⅰ为主,推测其有2个母系起源。     

Genetic structure of Oestrus ovis populations in sheep and goats.

A genetic analysis using RAPD markers was performed on 12 natural populations of Oestrus ovis (Linné, 1761). Three-hundred and six O. ovis larvae (first, second and third instars) were randomly recovered in nasal cavities of sheep and goats naturally infected in Algeria, Ethiopia, France, Mauritania, Rumania and Tunisia and were analysed by 56 RAPD fragments. The results showed a high diversity within all samples. A significant genetic divergence was showed by discriminant analyses among the 12 populations sampled (p<0.0001). Moreover, discriminant analyses showed significant differentiation (p<0.0001) between O. ovis larva populations of sheep and goats and also among samples collected in the same region.     

亚丁牦牛和拉日马牦牛遗传多样性及遗传结构分析

亚丁牦牛和拉日马牦牛均为肉乳兼用型优良地方牦牛资源,本研究旨在探究亚丁牦牛和拉日马牦牛的遗传多样性及各牦牛群体间的亲缘关系,对亚丁牦牛、拉日马牦牛以及其他7个地方牦牛群体(九龙牦牛、麦洼牦牛、金川牦牛、昌台牦牛、中甸牦牛、玉树牦牛、类乌齐牦牛)进行RAD简化基因组测序,基于检测到的SNP信息计算遗传统计量.结果表明,亚...     

Genetic diversity of the Mexican Lidia bovine breed and its divergence from the Spanish population

Lidia bovine breed exists since the XIV century in the Iberian Peninsula. These animals were initially produced for meat but some, showing an aggressive behaviour which difficulted their management, were used to participate in popular traditional and social events. A specialization of the breed giving rise to the original Lidia population is documented in Spain since mid-XVIII century. Following the same tradition than in the Spanish population, Mexico used aggressive animals at the beginning of the XX century until two families of breeders started importing Lidia breed bovines from Spain with the aim of specializing their production. Each family (Llaguno and González) followed different breeding managements, and currently, most of the Lidia Mexican population derives from the Llaguno line. Although genetic structure and diversity of the Spanish population have been studied (using autosomal microsatellite markers, Y chromosome DNA markers and mitochondrial DNA sequences), the Mexican population is not analysed. The aim of the study was to assess both the genetic structure and diversity of the Mexican Lidia breed and its relationship with the original Spanish population using the same molecular tools. A total of 306 animals belonging to 20 breeders issued from both existing Mexican families were genotyped, and the genetic information was compared to the previously existing Spanish information. Slightly higher levels of genetic diversity in Mexican population were found when comparing to the Spanish population, and the variability among populations accounted for differences within them showing mean values of 0.18 and 0.12, respectively. Animals from the Mexican breeders, belonging to each of the two families, clustered together, and there was little evidence of admixture with the Spanish population. The analysis of Y chromosome diversity showed a high frequency of the H6 haplotype in the Mexican population, whereas this haplotype is rare in the Spanish, which is only found in the Miura (100%) and Casta Navarra (38%) lineages. Mitochondrial DNA revealed similar haplotypic pattern in both Spanish and Mexican populations, which is in accordance with most of the Mediterranean bovine breeds. In conclusion, as the Mexican Lidia population had initially a small number of founders and its current population has been reared isolated from their Spanish ancestors since a long time, these bottleneck effects and a combination of mixed cattle origin are the factors that might erase any trace of the Spanish origin of this population.     

Genetic diversity,population structure,and correlations between locally adapted zebu and taurine breeds in Brazil using SNP markers

Genetic diversity is one of the most important issues in studies on conservation of cattle breeds and endangered species. The objective of this study was to estimate the levels of genetic differentiation between locally adapted taurine (Bos taurus taurus) and zebu (Bos taurus indicus) breeds in Brazil, which were genotyped for more than 777,000 SNPs. The fixation index (F _ST), principal component analysis (PCA), and Bayesian clustering were estimated. The F _ST highlighted genetic differentiation between taurine and zebu breeds. The taurine lines, Caracu and Caracu Caldeano, had significant genetic differentiation (F _ST close to 5%) despite their recent selection for different uses (meat and milk). This genetic variability can be used for conservation of locally adapted animals, as well as for breeding programs on zebu breeds. Introgression of zebu in locally adapted breeds was identified, especially in Curraleiro Pé-Duro breed. The Gyr breed, however, had low breed purity at genomic level due to its very heterogeneous mixing pattern.