Analysis of genetic relationships between 10 cattle breeds with 17 microsatellites

To guide genetic conservation programmes with objective criteria, general genetic variability has to be taken into account. This study was conducted to determine the genetic variation between 10 cattle breeds by using 17 microsatellite loci and 13 biochemical markers (11 blood groups, the transferrin and β-casein loci). Microsatellite loci were amplified in 31–50 unrelated individuals from 10 cattle breeds: Charolais, Limousin, Breton Black Pied, Parthenais, Montbéliard, Vosgien, Maine-Anjou, Normande, Jersey and Holstein. Neighbor-joining trees were calculated from genetic distance estimates. The robustness of tree topology was obtained by bootstrap resampling of loci. A total of 210 alleles of the 17 microsatellites were detected in this study and average heterozygosities ranged from 0·53 in the Jersey breed to 0·66 in the Parthenais breed. In general, low bootstrap values were obtained: with the 17 microsatellites, the highest bootstrap values concerned the Holstein/Maine-Anjou grouping with an occurrence of 74%; with the biochemical markers, this node had an occurrence of 79% and the Charolais/Limousin grouping appeared with an occurrence of 74%; when microsatellites and biochemical polymorphism were analysed together, the occurrence of the Holstein/Maine-Anjou grouping was 90% and that of the Charolais/Limousin grouping was 42%. These results suggest that 30 microsatellites, a number currently considered as sufficient to distinguish closely related breeds is, in fact, probably insufficient.     

Use of breed-specific single nucleotide polymorphisms to discriminate between Holstein and Jersey dairy cattle breeds

Emphasis on livestock genetic improvement in the past decades has led to commercialization of different breeds of livestock species. Breed validation has become increasingly important to assess the safety and authenticity of livestock products in global and domestic markets. The objective of this study was to evaluate the use of breed-specific single nucleotide polymorphisms (SNPs) in discriminating between Holstein and Jersey dairy cattle breeds. Two separate resource populations were used, including a reference population consisting of 498 Holstein and 83 Jersey bull DNA samples, and a validation population consisting of 260 Holstein and 34 Jersey cow DNA samples. Five Jersey-specific and four Holstein-specific SNPs were identified and genotyped on the reference and validation resource populations. The reference population was used to validate the breed-specific SNPs used in this study and to predict the allocation efficiencies and misclassification probabilities of different combinations of SNPs. Individual animals in the validation population were allocated to either breed based on the presence of breed-specific alleles. It was found that any combination of three breed-specific SNPs had, on average, high breed allocation efficiency of >95% and low misclassification probability of <5%. In conclusion, this study demonstrates a simple, yet effective, method of using breed-specific SNPs to discriminate between Jersey and Holstein cattle breeds.     

Genetic diversity and differentiation in Portuguese cattle breeds using microsatellites

Genotype data from 30 microsatellites were used to assess genetic diversity and relationships among 10 native Portuguese cattle breeds, American Charolais and the Brazilian Caracú. Hardy–Weinberg equilibrium was observed for all loci/population combinations except for five loci in Brava de Lide and one locus in Alentejana that exhibited heterozygote deficiency. Estimates of average observed and expected heterozygosities, total number of alleles (TNA) per breed and mean number of alleles (MNA) per locus/population were obtained. A total of 390 alleles were detected. TNA among Iberian cattle ranged from 170 to 237 and MNA ranged from 5.67 to 8.07. The highest observed heterozygosities were found in the Caracú, Maronesa, Garvonesa and Arouquesa and the lowest in Brava de Lide and Mirandesa. Estimation of population subdivision using Wright's F_ST index showed that the average proportion of genetic variation explained by breed differences was 9%. Neighbour‐joining phylogenetic trees based on D_A distances showed that the genetic relationships of present‐day Portuguese native breeds are consistent with historical origins in the Brown Concave (Arouquesa, Mirandesa, Marinhoa) and Red Convex (Mertolenga, Alentejana, Garvonesa, Minhota) evolutionary groups. The Iberian Black Orthoide group, represented by Brava de Lide and Maronesa, and the Barrosã breed appeared to be more closely related to the Brown Concave group but may represent a separate lineage. The Caracú breed was not found to be closely associated with any of the native Portuguese breeds.     

Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers

Genotype data from 20 microsatellites typed in 253 animals is used here to assess the genetic structure of seven European pedigree cattle breeds. Estimation of genetic subdivision using classical drift-based measures shows that the average proportion of genetic variation among breeds varies between 10 and 11% of the total, depending on the estimator used. We demonstrate that a simple allele-sharing genetic distance parameter can be used to construct a dendrogram of relationships among animals. This phylogenetic tree displays a remarkable degree of breed clustering and reflects an extensive underlying kinship structure, particularly for the Swiss Simmental breed and four breeds originating from the British Isles. Condensation of allele frequencies and individual genotypic compositions using principal component analysis is also used to investigate genetic structure among breeds and individual animals. In addition, the underlying genetic demarcation of European cattle breeds is emphasized in simulations of breed assignment using allele frequency distributions from samples of microsatellite loci. Correct breed designation can be inferred with accuracies approaching 100% using data from a panel of 10 microsatellite loci.     

Evaluation of genetic diversity and population structure of west‐central Indian cattle breeds

Evaluations of genetic diversity in domestic livestock populations are necessary to implement region‐specific conservation measures. We determined the genetic diversity and evolutionary relationships among eight geographically and phenotypically diverse cattle breeds indigenous to west‐central India by genotyping these animals for 22 microsatellite loci. A total of 326 alleles were detected, and the expected heterozygosity ranged from 0.614 (Kenkatha) to 0.701 (Dangi). The mean number of alleles among the cattle breeds ranged from 7.182 (Khillar) to 9.409 (Gaolao). There were abundant genetic variations displayed within breeds, and the genetic differentiation was also high between the Indian cattle breeds, which displayed 15.9% of the total genetic differentiation among the different breeds. The genetic differentiation (pairwise F_ST) among the eight Indian breeds varied from 0.0126 for the Kankrej–Malvi pair to 0.2667 for Khillar–Kenkatha pair. The phylogeny, principal components analysis, and structure analysis further supported close grouping of Kankrej, Malvi, Nimari and Gir; Gaolao and Kenkatha, whereas Dangi and Khillar remained at distance from other breeds.     

Polymorphic forms of the epithelial mucin, PAS-I (MUC1), in milk of Holstein cows (Bos taurus)

The polymorphic epithelial mucin, PAS-I (also known as MUC1), in individual milk samples from 119 Holstein cows was resolved into bands on SDS-gels. Mobility indices established for these bands provided evidence of four and possibly five polymorphic forms. Sialic acid, a major component of the oligosaccharide portion of PAS-I, was removed from the mucin by treatment of milk samples with neurominidase. This reduced the mobility of the mucin bands but did not alter their mobility relationships within a sample or among samples. Consideration of evidence from this and other studies indicates that the four or five polymorphic forms correspond to alleles, which are inherited, one each from sire and dam, and co-dominantly expressed. It appears that the Holstein population may carry several more alleles for PAS-I than do Ayrshire, Jersey or Brown Swiss cattle. In addition to these breed differences, some remarkable molecular differences have been noted between MUC1 (PAS-I) of human and mouse suggesting that research regarding molecular evolution of this mucin could provide another approach to understanding relationships among species.     

Expressed 2-5A synthetase genes and pseudogenes in the marine sponge Geodia barretti

In cattle, bovine leukocyte antigens (BoLAs) have been extensively used as markers for bovine diseases and immunological traits. In this study, we sequenced alleles of the BoLA class II loci, BoLA-DRB3 and BoLA-DQA1, from 650 Japanese cattle from six herds [three herds (507 animals) of Japanese Black cattle and three herds (143 animals) of Holstein cattle] using polymerase chain reaction-sequence-based typing (PCR-SBT) methods. We identified 26 previously reported distinct DRB3 alleles in the two populations: 22 in Japanese Black and 17 in Holstein. The number of DRB3 alleles detected in each herd ranged from 9 to 20. Next, we identified 15 previously reported distinct DQA1 alleles: 13 in Japanese Black and 10 in Holstein. The number of alleles in each herd ranged from 6 to 10. Thus, allelic divergence is significantly greater for DRB3 than for DQA1. A population tree on the basis of the frequencies of the DRB3 and DQA1 alleles showed that, although the genetic distance differed significantly between the two cattle breeds, it was closely related within the three herds of each breed. In addition, Wu-Kabat variability analysis indicated that the DRB3 gene was more polymorphic than the DQA1 gene in both breeds and in all herds, and that the majority of the hypervariable positions within both loci corresponded to pocket-forming residues. The DRB3 and DQA1 heterozygosity for both breeds within each herd were calculated based on the Hardy-Weinberg equilibrium. Only one Japanese Black herd showed a significant difference between the expected and observed heterozygosity at both loci. This is the first report presenting a detailed study of the allelic distribution of BoLA-DRB3 and -DQA1 genes in Japanese Black and Holstein cattle from different farms in Japan. These results may help to develop improved livestock breeding strategies in the future.     

Breed differences in the distribution of BoLA-A locus antigens in American cattle

A total of 627 cattle representing seven breeds from south central Nebraska, USA were tested for 37 BoLA antigens which behave as products of 37 distinct alleles of the class I BoLA-A locus. Four antigens were absent from all breeds tested. The other antigens showed marked and statistically significant differences in breed distribution. There was no evidence for blank (null) alleles. The number of alleles in each breed ranged from 10 to 20. The Hereford and Simmental populations tested were less polymorphic than the Angus, Brown Swiss, Charolais, Gelbvieh and Limousin populations.     

A whole genome scan for differences in recombination rates among three Bos taurus breeds

Twenty paternal half-sib families of a granddaughter design were genotyped for 265 genetic markers, most of them microsatellites. These were 16 Holstein families, 3 Simmental families, and 1 Brown Swiss family. The number of sires per breed was 872, 170, and 32, respectively. Two-point recombination rates were estimated both jointly for all breeds and each single breed separately. Of 1168 marker intervals, 865 provided estimates for at least two breeds. Differences between breeds were tested by likelihood ratio tests. Four marker intervals, representing three genomic regions on BTA19, BTA24, and BTA27, show a significant impact of the breed at a false discovery rate of 0.23 and indicate a genetic component of observed heterogeneity of recombination. The variability of recombination rates between cattle breeds might not be a common feature of the whole genome, but rather might be restricted to certain chromosomal segments. Thus, attention should be paid to heterogeneities when pooling data of such regions from different breeds. Received: 14 March 2001 / Accepted: 8 May 2001     

Genome‐wide variability and selection signatures in Italian island cattle breeds

In the present study, a sample of 88 animals belonging to four local (Modicana, Sarda, Sardo‐Bruna and Sardo‐Modicana) and one cosmopolitan (Italian Brown Swiss) cattle breeds were genotyped with a medium density SNP beadchip and compared to investigate their genetic diversity and the existence of selection signatures. A total of 43 012 SNPs distributed across all 29 autosomal chromosomes were retained after data quality control. Basic population statistics, Wright fixation index and runs of homozygosity (ROH) analyses confirmed that the Italian Brown Swiss genome was shaped mainly by selection, as underlined by the low values of heterozygosity and minor allele frequency. As expected, local cattle exhibited a large within‐breed genetic heterogeneity. The F_ST comparison revealing the largest number of significant SNPs was Sardo‐Bruna vs. Sardo‐Modicana, whereas the smallest was observed for Italian Brown Swiss vs. Sardo‐Modicana. Modicana exhibited the largest number of detected ROHs, whereas the smallest was observed for Sardo‐Modicana. Signatures of selection were detected in genomic regions that harbor genes involved in milk production traits for Italian Brown Swiss and fitness traits for local breeds. According to the results of multi‐dimensional scaling and the admixture analysis the Sardo‐Bruna is more similar to the Sarda than to the Italian Brown Swiss breed. Moreover, the Sardo‐Modicana is genetically closer to the Modicana than to the Sarda breed. Results of the present work confirm the usefulness of single nucleotide polymorphisms in deciphering the genetic architecture of livestock breeds.     

Genetic diversity and population structure of 20 North European cattle breeds

Blood samples were collected from 743 animals from 15 indigenous, 2 old imported, and 3 commercial North European cattle breeds. The samples were analyzed for 11 erythrocyte antigen systems, 8 proteins, and 10 microsatellites, and used to assess inter- and intrabreed genetic variation and genetic population structures. The microsatellites BoLA-DRBP1 and CSSM66 were nonneutral markers according to the Ewens-Watterson test, suggesting some kind of selection imposed on these loci. North European cattle breeds displayed generally similar levels of multilocus heterozygosity and allelic diversity. However, allelic diversity has been reduced in several breeds, which was explained by limited effective population sizes over the course of man-directed breed development and demographic bottlenecks of indigenous breeds. A tree showing genetic relationships between breeds was constructed from a matrix of random drift-based genetic distance estimates. The breeds were classified on the basis of the tree topology into four major breed groups, defined as Northern indigenous breeds, Southern breeds, Ayrshire and Friesian breeds, and Jersey. Grouping of Nordic breeds was supported by documented breed history and geographical divisions of native breeding regions of indigenous cattle. Divergence estimates between Icelandic cattle and indigenous breeds suggested a separation time of more than 1,000 years between Icelandic cattle and Norwegian native breeds, a finding consistent with historical evidence.     

Comparison of protein markers and microsatellites in differentiation of cattle populations

Five cattle populations, representing four breeds, were analysed for 14 protein markers and five microsatellite loci. The breeds studied were Brown Swiss and three autochthonous Spanish cattle: Avileña-Negra Ibérica (A-NI), two populations (A-NI 1 and A-NI 2) from different, reproductively isolated, locations; Sayaguesa; and Morucha. A total of 752 animals were examined for biochemical polymorphisms, of which 488 were also DNA typed. Genetic parameters and phylogenetic trees were obtained separately for each group of markers and results were compared. Estimates of heterozygosity and genetic distances from microsatellites were greater than those obtained using protein markers. The overall topology of the two dendrograms was similar. A-NI 1 and A-NI 2 populations were grouped together, related to Morucha, and the three of them related to Sayaguesa. Brown Swiss appeared in a separate branch from Spanish cattle. These results support the usefulness of microsatellites in the study of genetic relationships among closely related populations and breeds.     

Genetic distances within and across cattle breeds as indicated by biallelic AFLP markers

We tested the use of biallelic Amplified fragment length polymorphism (AFLP) polymorphisms for the estimation of relative genetic distances of cattle individuals within or across breeds. An allele permutation procedure was developed to estimate the stochastic variation of the genetic distance that is inherent to a given dataset. In a panel of 47 Holstein-Friesian cattle analysed with 248 polymorphic markers, the average genetic distance of bulls selected for breeding was slightly lower than the distance of the cows. The observed standard deviation (SD) of the distance indicated genetic subdivision, which for the bulls was explained by variation in the additive relationship derived from herdbook data. Animals from three different breeds, the highly selected Holstein-Friesian, the Italian Brown and the historic Maremmana, were compared on the basis of 106 polymorphic markers. No breed-specific fragments were observed. The mean pair-wise genetic distance within breeds was 85% of the value across breeds, but principal coordinates analysis clustered the animals according to their breed of origin. Calculation of distances between the breeds indicated a relatively divergent position of the Maremmana, relative to the two other breeds. However, biallelic markers indicate that the process of breed formation had only a limited effect on the diversity at marker loci.     

Genetic Diversity Among Turkish Native Chickens, Denizli and Gerze, Estimated by Microsatellite Markers

The genetic diversity of the Turkish native chicken breeds Denizli and Gerze was evaluated with 10 microsatellite markers. We genotyped a total of 125 individuals from five subpopulations. Among loci, the mean number of alleles was 7.5, expected heterozygosity (H (e)) was 0.665, PIC value was 0.610, and Wright's fixation index was 0.301. H (e) was higher in the Denizli breed (0.656) than in the Gerze breed (0.475). The PIC values were 0.599 and 0.426 for Denizli and Gerze, respectively. A phylogenetic tree was constructed using genetic distance and the neighbor-joining method. Its topology reflects the general pattern of genetic differentiation among the Denizli and Gerze breeds. The present study suggests that Denizli and Gerze subpopulations have a rich genetic diversity. The information about Denizli and Gerze breeds estimated by microsatellite analysis may also be useful as an initial guide in defining objectives for designing future investigations of genetic variation and developing conservation strategies.     

Genome-wide linkage disequilibrium in two Japanese beef cattle breeds

There is little knowledge about the degree of linkage disequilibrium (LD) in beef cattle. This study aims to perform a genome-wide search for LD in Japanese Black and Japanese Brown beef cattle and to compare the level of LD between these two breeds. Parameter D' (the LD coefficient) was used as a measure of LD, and LD was tested for significance of allelic associations between syntenic and between non-syntenic marker pairs. Effects of breed, chromosome, genetic map distance and their interactions with D' were tested based on least squares analyses. Both breeds showed high levels of LD, which ranged over several tens of cM and declined as the marker distance increased for syntenic marker pairs. A rapid decline of the D' value was observed between markers that were spaced 5 and 20 cM apart. LD was significant in most cases for marker pairs <40 cM apart but was not significant between non-syntenic loci. The pattern of LD found in these two breeds was similar to that previously published for dairy cattle. The D' value between breeds was not significantly different (P > 0.05), but the interaction between breed and chromosome was highly significant (P < 0.001). Genetic selection seems to have caused the heterogeneity of the D' values among chromosomes within breed. These results indicate that LD mapping is a useful tool for fine-mapping quantitative trait loci of economically important traits in Japanese beef cattle.     

Comparison of DNA variants in the PRNP and NF1 regions between bovine spongiform encephalopathy and control cattle

DNA from 252 bovine spongiform encephalopathy (BSE) cattle and 376 non-diseased control cattle were genotyped for nine loci in the prion protein (PRNP) gene region, three loci in the neurofibromin 1 (NF1) region and four control loci on different chromosomes. The allele and genotype frequencies of the control loci were similar in BSE and control cattle. In the analysed 7.4 Mb PRNP region, the largest differences between BSE and control cattle were found for the loci REG2, R16 and R18, which are located between +300 and +5600 bp, spanning PRNP introns 1 to 2. Carriers of the REG2 genotype 128/128 were younger at BSE diagnosis than those with the other genotypes (128/140 or 140/140). The predominant haplotype REG2 128 bp-R18 173 bp occurred more frequently (P < 0.001), and the second-most frequent haplotype (REG2 140 bp-R18 175 bp) occurred less frequently (P < 0.05) in BSE than in control cattle. The largest frequency differences between BSE and control groups were observed in the Brown Swiss breed. Across all breeds, most of the same alleles and haplotypes of the PRNP region were associated with BSE. In the 23-cM NF1 region, associations with BSE incidence were found for the RM222 allele and for the DIK4009 genotype frequencies. Cattle carrying RM222 genotypes with the 127- or 129-bp alleles were about half a year older at BSE incidence than those with other genotypes. Across the breeds, different alleles and genotypes of the NF1 region were associated with BSE. The informative DNA markers were used to localize the genetic disposition to BSE and may be useful for the identification of the causative DNA variants.     

中国地方黄牛的遗传多样性*

中国黄牛起源复杂,我国地方黄牛群体不同品种在毛色、形态外貌、细胞遗传学、血液蛋白座位分析均表现出多样性。计算我国黄牛群体6个毛色座位平均杂合度和6个血液蛋白座位平均杂合度分别为0.3144和0.4873,表明我国地方黄牛群体的遗传多样性非常丰富。计算我国黄牛群体的6个毛色座位和6个血液蛋白座位的基因分化系数分别为0.3404和0.095,表明我国黄牛群体毛色差异中有34.04％是由品种间的差异造成的。血液蛋白的多态性有9.5％是由品种间的差异造成的。我国黄牛群体的遗传多样性主要来自品种内的遗传多样性。保存我国黄牛品种资源多样性不仅要从整个中国黄牛群体上考虑,而且要针对每个品种（或类群）进行保种。     

Restriction Fragment Length Polymorphism (RFLP) in Exon 2 of the BoLA-DRB3 Gene in South American Cattle

The Bola-DRB3 gene participates in the development of the immune response and is highly polymorphic. For these reasons, it has been a candidate gene in studies of the genetic basis of disease resistance and in population genetic analysis. South American native cattle breeds have been widely replaced by improved exotic breeds leading to a loss of genetic resources. In particular, South American native breeds have high levels of fertility and disease resistance. This work describes genetic variability in the BoLA-DRB3 gene in native (Caracu, Pantaneiro, Argentinean Creole) and exotic (Holstein, Jersey, Nelore, Gir) cattle breeds in Brazil and Argentina. PCR-RFLP alleles were identified by combining the restriction patterns for the BoLA-DRB3.2 locus obtained with RsaI, BstY and HaeIII restriction enzymes. Allelic frequencies and deviations from the Hardy-Weinberg equilibrium were also calculated. Analysis of the 24 BoLA-DRB3 PCR-RFLP alleles identified showed differences in the allele distributions among breeds.     

Bayesian segregation analysis of milk flow in Swiss dairy cattle using Gibbs sampling

Segregation analyses with Gibbs sampling were applied to investigate the mode of inheritance and to estimate the genetic parameters of milk flow of Swiss dairy cattle. The data consisted of 204 397, 655 989 and 40 242 lactation records of milk flow in Brown Swiss, Simmental and Holstein cattle, respectively (4 to 22 years). Separate genetic analyses of first and multiple lactations were carried out for each breed. The results show that genetic parameters especially polygenic variance and heritability of milk flow in the first lactation were very similar under both mixed inheritance (polygenes + major gene) and polygenic models. Segregation analyses yielded very low major gene variances which favour the polygenic determinism of milk flow. Heritabilities and repeatabilities of milk flow in both Brown Swiss and Simmental were high (0.44 to 0.48 and 0.54 to 0.59, respectively). The heritability of milk flow based on scores of milking ability in Holstein was intermediate (0.25). Variance components and heritabilities in the first lactation were slightly larger than those estimates for multiple lactations. The results suggest that milk flow (the quantity of milk per minute of milking) is a relevant measurement to characterise the cows milking ability which is a good candidate trait to be evaluated for a possible inclusion in the selection objectives in dairy cattle.