Linkage disequilibrium analysis for microsatellite loci in six cattle breeds

Autosomal microsatellites are valuable tools for investigating genetic diversity and population structure and making conservation decisions to preserve valuable breeds of domestic animals. We carried out a linkage disequilibrium analysis using 29 microsatellite markers in six cattle populations: Suksun, Istoben, Yaroslavl, Kholmogory, Grey Ukrainian and Pechora type of Khologory cattle. We discovered a significant linkage disequilibrium between microsatellites INRA037 and CSRM60 in Grey Ukrainian cattle.     

Microsatellite and Mitochondrial DNA Study of Native Eastern European Cattle Populations: The Case of the Romanian Grey

The Eastern European Grey cattle are regarded as the direct descendants of the aurochs (Bos taurus primigenius). Nowadays in Romania, less than 100 Grey animals are being reared and included in the national gene reserve. We examined the genetic diversity among Romanian Grey, Brown, Spotted and Black and White cattle breeds, with a particular focus on Romanian Grey through the use of (i) 11 bovine specific microsatellite markers on 83 animals and (ii) 638 bp length of mitochondrial DNA (mtDNA) D-loop region sequence data from a total of 81 animals. Both microsatellite and mtDNA analysis revealed a high level of genetic variation in the studied breeds. In Romanian Grey a total of 100 alleles were found, the mean number of observed alleles per locus was 9.091; the average observed heterozygosity was 0.940; the Wright’s fixation index (F_IS) was negative (-0.189) and indicates that there is no inbreeding and no selection pressure. MtDNA analysis revealed 52 haplotypes with 67 variable sites among the Romanian cattle breeds without any insertion or deletion. Haplotype diversity was 0.980 ± 0.007 and ranged from 0.883 ± 0.056 (Brown) to 0.990 ± 0.028 (Spotted and Black and White). The highest genetic variability of the mtDNA was recorded in the Grey breed, where 18 haplotypes were identified. The most frequent mtDNA D-loop region belonged to T3 haplogroup (80.247%), which was found across all studied breeds, while T2 haplotypes (16.049%) was only found in Grey, Spotted and Black and White genotypes. The T1 haplotypes (3.704%) were found in the Grey and Spotted. The current results contribute to the general knowledge on genetic diversity found in Eastern European cattle breeds and could prove a valuable tool for the conservation efforts of animal genetic resources (FAnGR).     

Molecular and genetic polymorphism in three cattle breeds

Determination of cattle breed and assignment of individual animals to that or another group based on distinctions of genotype is of great importance in genetics and selection. Using of PCR-analysis opened new possibilities for typing DNA. The procedure of PCR was optimized for animal DNA. Two methods of PCR, RAPD and SSRP, were applied for investigation of molecular-genetical polymorphism in three cattle breeds (Ukrainian red-motley lactescent, Golshtine and Simmental). A dendrogram reflecting genetical mutual relations between analyzed animals was drawn. The level of homo-heterozygosity and the distribution of microsatellite alleles were determined. System for investigation of molecular-genetical polymorphism in the cattle breeds and characterization of genotype of individual animals were developed and tested on a real population.     

Genetic structure of local Ukrainian cattle breeds

Analysis of 6 cattle breeds (5 local Ukrainian breeds and the Holstain breed) on the 9 polymorphous molecular-genetic markers (transferrin, ceruloplasmin, amylase-1, posttransferrin, receptor to vitamin D, haemoglobin, leptin, kapa-casein) was carried out. The rare allele of transferrin was revealed in two local breeds and the rare allele of leptin--in two another local breeds. Associations between syntenic loci (transferrin, ceruloplasmin, kappa-casein, receptor to vitamin D) were observed only in the local breeds but not in the Holstain one. Locus-specific conservation of the ancestor allelic variants in the local breeds and effect of selection on interloci associations are discussed.     

Population-genetic study of the polymorphism of structural genes and ISSR-PCR markers in some cattle breeds

The comparative analysis of genetic structures of five cattle breeds has been carried out using polymorphism of two different types of molecular-genetic markers--20 structural genes and 128 DNA loci (the DNA fragments flanked by inverted microsatellite loci repetitions--ISSR-PCR method). In spite of availability of breed-specific singularities of genotype distribution detected by the both methods the level of mean heterozygosity of structural genes was similar in all the investigated breeds. A part of polymorphic loci and the average value of the polymorphic information contents (PIC) of ISSR-PCR markers has appeared much higher in commercial breeds with high effective number in comparison with Ukrainian autochthonous breeds. The population-genetic processes detected by different methods are discussed.     

Serum amylase isozyme in three Austrian cattle breeds

Serum amylase phenotypes were determined for 1227 animals from three Austrian cattle breeds, Tyrolean Grey, Carinthian Blondvieh and Waldviertler Blondvieh. The phenotypes were determined for 450 offspring from families where both sire and dam were typed. The distribution of the 450 progeny phenotypes in which 30 of the 36 possible mating combinations occur is compatible with the hypothesis of three autosomal co-dominant alleles.
All six possible phenotypes were found in all three breed groups. Gene frequencies of amylase alleles as well as the probability of excluding wrong parentage were estimated for all three breeds.     

Genetic diversity analysis of BMY cattle based on microsatellite DNA markers

BMY cattle (1/2 Brahman, 1/4 Murray Grey and 1/4 Yunnan Yellow cattle) has been inter se breeding since 1980s. Genetic diversity of BMY cattle was extensively investigated using 16 microsatellite markers. A total of 130 microsatellite alleles and high allele size variance were detected. All loci displayed high genetic diversity with overall mean of N(a) = 8.13, PIC = 0.7224 and H(e) = 0.7666, which were higher than those of many other beef breeds. The allele-sharing neighbour-joining tree clearly displayed the new genotypic combinations and the minglement from both BMY cattle and Brahman. The results provided the genetic information to match the standards of new beef breed in South China.     

Near East mtDNA haplotype variants in Roman cattle from Augusta Raurica, Switzerland, and in the Swiss Evolène breed

Typical Near East mitochondrial haplotypes of the T2 lineage were found in one cattle metacarpus sample from the Roman period and in two present-day Evolène cattle in Switzerland. Sequences from eight additional Evolène and four Raetian Grey aligned to the European haplotype T3. Analysis of nucleotide diversity within the mitochondrial D-loop of both studied Swiss cattle breeds revealed high haplotype diversity and similar diversity to a European cattle reference group. Mitochondrial T3 haplotypes radiated star-like from two similarly frequent haplotypes, possibly indicating two different expansion routes. The breed structure of Evolène cattle can be explained either by an introduction of diverse female lineages from the domestication centre or by later admixture. The introduction of the Near East lineage to Switzerland must have happened during the Roman time or earlier.     

Bos indicus introgression into (peri‐)alpine cattle breeds – evidence from the analysis of bovine whey protein variants

The major bovine whey proteins, α‐lactalbumin (α‐LA) and β‐lactoglobulin (β‐LG), exhibit breed‐specific genetic variation. The aim of this study was to identify possible new protein variants and determine the distribution of variants across a variety of 18 taurine and indicine cattle breeds applying a DNA‐based sequencing approach. To this end, the open reading frames of the respective genes (LALBA and LGB) were sequenced in 476 animals. Within the LALBA gene, a previously unknown synonymous and a previously undesignated non‐synonymous nucleotide exchange were identified. Furthermore, two known α‐LA variants (A and B) and four known β‐LG variants (A, B, C and W) were determined. The occurrence of typical indicine variants in some taurine cattle breeds, such as Suisse Eringer, German Hinterwälder and Hungarian Grey Steppe, further supports the hypothesis of ancient Bos indicus introgression into (peri‐)alpine cattle breeds.     

Traditional Cattle Grazing in a Mosaic Alkali Landscape: Effects on Grassland Biodiversity along a Moisture Gradient

Extensively managed pastures are of crucial importance in sustaining biodiversity both in local- and landscape-level. Thus, re-introduction of traditional grazing management is a crucial issue in grassland conservation actions worldwide. Traditional grazing with robust cattle breeds in low stocking rates is considered to be especially useful to mimic natural grazing regimes, but well documented case-studies are surprisingly rare on this topic. Our goal was to evaluate the effectiveness of traditional Hungarian Grey cattle grazing as a conservation action in a mosaic alkali landscape. We asked the following questions: (i) How does cattle grazing affect species composition and diversity of the grasslands? (ii) What are the effects of grazing on short-lived and perennial noxious species? (iii) Are there distinct effects of grazing in dry-, mesophilous- and wet grassland types? Vegetation of fenced and grazed plots in a 200-ha sized habitat complex (secondary dry grasslands and pristine mesophilous- and wet alkali grasslands) was sampled from 2006–2009 in East-Hungary. We found higher diversity scores in grazed plots compared to fenced ones in mesophilous- and wet grasslands. Higher cover of noxious species was typical in fenced plots compared to their grazed counterparts in the last year in every studied grassland type. We found an increasing effect of grazing from the dry- towards the wet grassland types. The year-to-year differences also followed similar pattern: the site-dependent effects were the lowest in the dry grassland and an increasing effect was detected along the moisture gradient. We found that extensive Hungarian Grey cattle grazing is an effective tool to suppress noxious species and to create a mosaic vegetation structure, which enables to maintain high species richness in the landscape. Hungarian Grey cattle can feed in open habitats along long moisture gradient, thus in highly mosaic landscapes this breed can be the most suitable livestock type.     

Genetic diversity analysis of BMY cattle based on microsatellite DNA markers

cattle (1/2 Brahman, 1/4 Murray Grey and 1/4 Yunnan Yellow cattle) has been inter se breeding since 1980s. Genetic diversity of BMY cattle was extensively investigated using 16 microsatellite markers. A total of 130 microsatellite alleles and high allele size variance were detected. All loci displayed high genetic diversity with overall mean of N _a = 8.13, PIC = 0.7224 and H _e = 0.7666, which were higher than those of many other beef breeds. The allele-sharing neighbour-joining tree clearly displayed the new genotypic combinations and the minglement from both BMY cattle and Brahman. The results provided the genetic information to match the standards of new beef breed in South China.     

Genetic diversity between Piedmontese, Maremmana, and Podolica cattle breeds

One hundred twenty animals of three native Italian cattle breeds, Piedmontese, Maremmana, and Podolica, were genetically characterized at 21 microsatellite loci located on 13 chromosomes. Allele numbers ranged from 3 to 19; average gene diversity ranged from 0.206 to 0.878 (average 0.738). The breed that preserved the highest genetic variability was the Podolica, where the chosen markers show the highest gene diversity (0.741) and the highest heterozygosity (0.155). The lowest inbreeding rate (0.102) was registered by the Piedmontese. Genetic distances were 0.069 (Piedmontese versus Maremmana), 0.050 (Piedmontese versus Podolica), and 0.041 (Maremmana versus Podolica) and reflect the different phylogenetic origins of the breeds: Maremmana and Podolica originated from the Grey Steppe cattle group, while Piedmontese belongs to the Northern Italy Lowland cattle group. Observed heterozygosity was not significantly different from expected in any of the breeds, which is an indication that they maintain a random mating structure. The probabilistic assignment of all sampled individuals to three theoretical populations, on the basis of allele frequencies, indicated that 82% of Piedmontese, 66% of Maremmana, and 33% of Podolica can be assigned to the appropriate breed with a probability higher than 90%. This result very well reflects the impact of the selection activity on the breed genetic structure. The chosen microsatellites proved to be a good tool for describing the correct reality of the analyzed populations, but they are not sufficient to discriminate between breeds.     

Gray Ukrainian cattle and their closely related forms

Data of previous investigations on the origin of Gray Ukrainian cattle and their relatives in European countries are duscussed. Literature data on the biodiversity of the exterior, phenotypic, and productive indices of ecotypes and breed groups of Gray Ukrainian cattle under various environmental and geographical conditions are reported, which are supplemented with our own experimental data on the differentiation of a number of genetic-biochemical systems of different groups of Gray Ukrainian cattle raised under various environmental and geographic conditions.     

Characterization of the <Emphasis Type="Italic">GHR</Emphasis> gene genetic variation in Chinese indigenous goat breeds

The aim of the present work was to investigate single nucleotide polymorphism (SNP) of growth hormone receptor (GHR) gene exon 10, characterize the genetic variation in three Chinese indigenous goat breeds, and search for its potential association with cashmere traits. In this study, a polymerase chain reaction-single strand conformation polymorphism (PCR–SSCP) protocol has been developed for rapid genotyping of the GHR gene in goats. One hundred seventy-eight goats from Liaoning Cashmere (96), Inner Mongolia White Cashmere (40), and Chengdu Grey (42) breeds in China were genotyped at GHR locus using the protocol developed. In all goat breeds investigated, a SNP in exon 10 of GHR gene has been identified by analyzing genomic DNA. The polymorphism consists of a single nucleotide substitution A → G, resulting in two alleles named, respectively, A and G based on the nucleotide at the position. The allele A was found to be more common in the animals investigated, and seems to be more consistent with cattle and zebu at this polymorphic site found in goats. The Hardy–Weinberg equilibrium of genotype distributions of GHR locus was verified in Liaoning Cashmere, and Inner Mongolia White Cashmere breeds. According to the classification of polymorphism information content (PIC), Chengdu Grey was less polymorphic than Liaoning Cashmere and Inner Mongolia White Cashmere breeds at this locus. The phylogenetic tree of different species based on the nucleotide sequences of GHR gene exon 10 is generally in agreement with the known species relationship. No significant association was found between the polymorphism revealed and the cashmere traits analyzed in present work.     

10个牛品种线粒体12S rRNA基因多态性分析

以鲁西牛、渤海黑牛、大别山牛、南阳牛、晋南牛、秦川牛、中国西门塔尔牛、日本和牛、海福特牛和安格斯牛10个牛品种共计353头牛为研究对象,利用单链构象多态性（SSCP）分子标记方法对其线粒体DNA 12S rRNA基因进行了多态性分析,结果发现该基因出现分布频率不同的3种单倍型（Ⅰ、Ⅱ、Ⅲ）,其中单倍型Ⅰ出现的频率最低,仅在晋南牛1个个体中发现;单倍型Ⅱ在中国本地黄牛中都存在,在中国西门塔尔牛中的分布频率很低,但在3个国外品种海福特牛、安格斯牛和日本和牛中不存在;单倍型Ⅲ在这10个牛品种中均有分布,但以国外品种最丰富。计算平均多态信息含量,发现我国地方品种在0.232～0.423之间,基本属于中度多态,说明我国地方黄牛品种在12S rRNA上多态性比较丰富,国外品种较为贫乏;但是单倍型Ⅰ频率很低有丢失的趋势,需要对其进行保护。     

Genetic characterization of the Indian cattle breeds,Ongole and Deoni (<Emphasis Type="Italic">Bos indicus</Emphasis>), using microsatellite markers – a preliminary study

Background  

Molecular characterization of cattle breeds is important for the prevention of germplasm erosion by cross breeding. The Indian zebu cattle have their significant role in evolution of present day cattle breeds and development of some of the exotic breeds. Microsatellites are the best available molecular tools for characterization of cattle breeds. The present study was carried out to characterize two Indian cattle breeds, Ongole and Deoni, using microsatellite markers.     

Accuracies of genomically estimated breeding values from pure-breed and across-breed predictions in Australian beef cattle

Background

The major obstacles for the implementation of genomic selection in Australian beef cattle are the variety of breeds and in general, small numbers of genotyped and phenotyped individuals per breed. The Australian Beef Cooperative Research Center (Beef CRC) investigated these issues by deriving genomic prediction equations (PE) from a training set of animals that covers a range of breeds and crosses including Angus, Murray Grey, Shorthorn, Hereford, Brahman, Belmont Red, Santa Gertrudis and Tropical Composite. This paper presents accuracies of genomically estimated breeding values (GEBV) that were calculated from these PE in the commercial pure-breed beef cattle seed stock sector.

Methods

PE derived by the Beef CRC from multi-breed and pure-breed training populations were applied to genotyped Angus, Limousin and Brahman sires and young animals, but with no pure-breed Limousin in the training population. The accuracy of the resulting GEBV was assessed by their genetic correlation to their phenotypic target trait in a bi-variate REML approach that models GEBV as trait observations.

Results

Accuracies of most GEBV for Angus and Brahman were between 0.1 and 0.4, with accuracies for abattoir carcass traits generally greater than for live animal body composition traits and reproduction traits. Estimated accuracies greater than 0.5 were only observed for Brahman abattoir carcass traits and for Angus carcass rib fat. Averaged across traits within breeds, accuracies of GEBV were highest when PE from the pooled across-breed training population were used. However, for the Angus and Brahman breeds the difference in accuracy from using pure-breed PE was small. For the Limousin breed no reasonable results could be achieved for any trait.

Conclusion

Although accuracies were generally low compared to published accuracies estimated within breeds, they are in line with those derived in other multi-breed populations. Thus PE developed by the Beef CRC can contribute to the implementation of genomic selection in Australian beef cattle breeding.     

利用RAPD标记分析鸵鸟种群的遗传变异

为探讨分子遗传标记在鸵鸟（Struthio camelus)育种中的应用,利用RAPD技术分析了我国养殖的三个主要要鸵鸟品种内和品种间的遗传变异。蓝颈鸵鸟、澳洲灰和非洲黑三个品种在品种内和品种间显示出低水平的变异。品种间的遗传距离好地说胆了三个品种的育种改良过程。同时预示出用澳洲灰与其他品种鸵鸟进行杂交育种的可行性。选择的20条在鸡中能稳定扩增的RAPD引物其75％能在鸵鸟基因组中扩增出产物。显示出两种禽类DNA具有同源性、为今后利用鸡的微卫星引物对鸵鸟进行基因扫描（genome scan）分析奠定基础。