Determination of allele frequencies of growth hormone AluI polymorphism in Brown Swiss,Holstein, native East Anatolian Red and Turkish Grey breeds

A total of 177 cattle of four breeds were genotyped for the bovine growth hormone (BGH)‐AluI polymorphism by polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP). The genotype and gene frequencies for each breed were determined and tested to be in Hardy–Weinberg equilibrium. According to breeds, frequencies of allele L gene were 0.905 for Brown Swiss, 0.898 for Holstein, 0.976 for East Anatolian Red and 0.893 for Turkish Grey Breeds. The allele L was predominant and variant VV was not detected in the breeds studied. BGH‐AluI genotypes were found to be in equilibrium within and among breeds.     

Genetic variability in the kappa‐casein gene in Sahiwal,Cholistani and Red Sindhi cattle breeds

Polymorphism of kappa‐casein (κ‐CN) gene in three Bos indicus cattle breeds was investigated using a polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) technique. Only genotypes AA and AB were observed, and no BB, AE, BE, EE, AC or BC genotypes were detected in the three cattle breeds. In the Sahiwal, Cholistani and Red Sindhi breeds, the frequencies of the allele A were 0.69, 0.90 and 0.86, and the frequencies of the allele B were 0.31, 0.10 and 0.14, respectively. The Sahiwal breed was found to have a higher frequency of the AB genotype as compared to the Cholistani and Red Sindhi breeds. The frequency of the κ‐CN alleles noted in the three cattle breeds was similar to those observed in other cattle breeds of B. indicus origin.     

Identification of rare genetic variants of the αS-caseins in milk from native Norwegian dairy breeds and comparison of protein composition with milk from high-yielding Norwegian Red cows

Several factors influence the composition of milk. Among these, genetic variation within and between cattle breeds influences milk protein composition, protein heterogeneity, and their posttranslational modifications. Such variations may further influence technological properties, which are of importance for the utilization of milk into dairy products. Furthermore, these potential variations may also facilitate the production of differentiated products (e.g., related to specific breeds or specific genetic variants). The objective of this study was to investigate the genetic variation and relative protein composition of the major proteins in milk from 6 native Norwegian dairy breeds representing heterogeneity in geographical origin, using the modern Norwegian breed, Norwegian Red, as reference. In total, milk samples from 144 individual cows were collected and subjected to liquid chromatography-electrospray ionization/mass spectrometry–based proteomics for identification of genetic and posttranslational modification isoforms of the 4 caseins (α_S1-CN, α_S2-CN, β-CN, κ-CN) and the 2 most abundant whey proteins (α-lactalbumin and β-lactoglobulin). Relative quantification of these proteins and their major isoforms, including phosphorylations of α_S1-CN and glycosylation of κ-CN, were determined based on UV absorbance. The presence and frequency of genetic variants of the breeds were found to be very diverse and it was possible to identify rare variants of the CN, which, to our knowledge, have not been identified in these breeds before. Thus, α_S1-CN variant D was identified in low frequency in 3 of the 6 native Norwegian breeds. In general, α_S1-CN was found to be quite diverse between the native breeds, and the even less frequent A and C variants were furthermore detected in 1 and 5 of the native breeds, respectively. The α_S1-CN variant C was also identified in samples from the Norwegian Red cattle. The variant E of κ-CN was identified in 2 of the native Norwegian breeds. Another interesting finding was the identification of α_S2-CN variant D, which was found in relatively high frequencies in the native breeds. Diversity in more common protein genetic variants were furthermore observed in the protein profiles of the native breeds compared with milk from the high-yielding Norwegian Reds, probably reflecting the more diverse genetic background between the native breeds.     

Κ‐CN gene polymorphism in Nili‐ravi buffalo,Achai and Sahiwal cattle of Pakistan

Kappa‐casein (κ‐CN) is the subtype of casein protein, an important constituent of bovine milk protein. The current study was undertaken to investigate the genetic polymorphism in κ‐CN gene of Nili‐ravi buffalo, Achai and Sahiwal cattle of Pakistan using polymerase chain reaction–restriction fragment length polymorphism (PCR‐RFLP) technique. The Nili‐ravi buffalo was found to be monomorphic (genotype BB only) for κ‐CN gene. Achai cattle were polymorphic for κ‐CN (having three genotypes AA, AB and BB) with a frequency of 0.70, 0.18 and 0.12, respectively, while in Sahiwal cattle, both the genotypes AA and AB were found with genotypic frequencies of 0.92 and 0.08, respectively. The presence of genotype BB in Achai cattle is surprising as it is absent in most of the cattle breeds worldwide.     

Prolactin gene polymorphism in Nili‐Ravi buffaloes in relation to Sahiwal and Achai Cattle

In this study, prolactin gene polymorphism was investigated in Nili‐ Ravi buffaloes, Sahiwal and Achai cattle breeds, 100 per group, using polymerase chain reaction–restriction fragment length polymorphism (PCR‐RFLP) technique. Only genotype GG was observed in the case of Nili‐Ravi buffaloes. In Sahiwal and Achai cattle, three genotypes were found, AA, AG and GG: the frequency of these genotypes were 72%, 18% and 10% in Sahiwal cattle and 44%, 34% and 22% in Achai cattle, respectively. The frequency of genotype AA was found to be higher in both cattle breeds. Results of chi‐square test at P < 0.05 revealed that animals of Achai cattle were in Hardy–Weinberg equilibrium, whereas Sahiwal cattle were found to be deviating.     

Relatedness between numerically small Dutch Red dairy cattle populations and possibilities for multibreed genomic prediction

Red dairy breeds are a valuable cultural and historical asset, and often a source of unique genetic diversity. However, they have difficulties competing with other, more productive, dairy breeds. Improving competitiveness of Red dairy breeds, by accelerating their genetic improvement using genomic selection, may be a promising strategy to secure their long-term future. For many Red dairy breeds, establishing a sufficiently large breed-specific reference population for genomic prediction is often not possible, but may be overcome by adding individuals from another breed. Relatedness between breeds strongly decides the benefit of adding another breed to the reference population. To prioritize among available breeds, the effective number of chromosome segments (M_e) can be used as an indicator of relatedness between individuals from different breeds. The M_e is also an important parameter in determining the accuracy of genomic prediction. The M_e can be estimated both within a population and between 2 populations or breeds, as the reciprocal of the variance of genomic relationships. We investigated relatedness between 6 Dutch Red cattle breeds, Groningen White Headed (GWH), Dutch Friesian (DF), Meuse-Rhine-Yssel (MRY), Dutch Belted (DB), Deep Red (DR), and Improved Red (IR), focusing primarily on the M_e, to predict which of those breeds may benefit from including reference animals of the other breeds. All of these breeds, except MRY, are under high risk of extinction. Our results indicated high variability of M_e, especially between M_e ranging from ～3,500 to ～17,400, indicating different levels of relatedness between the breeds. Two clusters are especially important, one formed by MRY, DR, and IR, and the other comprising DF and DB. Although relatedness between breeds within each of these 2 clusters is high, across-breed genomic prediction is still limited by the current number of genotyped individuals, which for many breeds is low. However, adding MRY individuals would increase the reference population of DR substantially. We estimated that between 11 and 133 individuals from other breeds are needed to achieve accuracy of genomic prediction equivalent to using one additional individual from the same breed. Given the variation in size of the breeds in this study, the benefit of a multibreed reference population is expected to be lower for larger breeds than for the smaller ones.     

Fattening performance, carcass traits and meat quality characteristics of calves sired by Charolais, Simmental and Eastern Anatolian Red sires mated to Eastern Anatolian Red dams

Comparisons were made among calves sired by Charolais (C), Simmental (S) and Eastern Anatolian Red (EAR) breeds of bulls for fattening, carcass and meat quality traits when mated to EAR dams. C- and S-sired calves had 43.1% and 36.4% higher daily weight gain, 44.5% and 43.9% heavier final weight in fattening, respectively. Calves produced by C sires had best feed efficiency value (6.51 vs. 7.44 and 7.22) compared to the S and EAR sire breed groups. Carcasses of C- and S-sired calves had heavier weight, higher dressing percentage and greater Longissimus dorsi (LD) muscle area than those of EAR-sired calves. USDA yield grades were lower (P<0.01) for carcasses from C and S sires, and highest for carcasses from EAR calves. C-sired calves received higher (P<0.01) ratings for panel tenderness score, lower shear force value and number of chews before swallow than S- and EAR-sired progeny. Overall results of the study suggested that fattening performance, carcass and meat quality characteristics might be considerably improved by using C sires in the crossbreeding program as sire breed.     

Molecular characterization of bovine CSN1S2*B and extensive distribution of zebu-specific milk protein alleles in European cattle

The B allele of the bovine α_S2-casein gene (CSN1S2) was characterized at the molecular level and the distribution of zebu-specific milk protein alleles was determined in 26 cattle breeds originating from 3 continents. The CSN1S2 *B allele is characterized by a C → T transition affecting nucleotide 17 of exon 3, which leads to a change in the eighth amino acid of the mature protein, from Ser to Phe (i.e., TCC →TCC). DNA-based methods were developed to identify carriers of CSN1S2*B and the other alleles (CSN1S2 *A, C, and D) at the same locus. CSN1S2*B and other zebu-specific milk protein alleles and casein haplotypes are widely distributed in European cattle breeds, particularly those of southeastern origin. Alleles CSN1S2 *B and CSN3*H are important in searching for zebu imprints in European cattle breeds. Diversity estimates at the milk protein loci were highest in the zebus followed by southeastern European taurines. Anatolian Black had the highest number of zebu alleles among European taurines. Common, group, and intergroup haplotypes occurred in the breeds and demonstrated relationships that concurred with developmental histories, genetic makeup, and, in particular, exposed the extent of zebu influence on southeastern European cattle.     

Genome-wide association study using high-density single nucleotide polymorphism arrays and whole-genome sequences for clinical mastitis traits in dairy cattle

Mastitis is a mammary disease that frequently affects dairy cattle. Despite considerable research on the development of effective prevention and treatment strategies, mastitis continues to be a significant issue in bovine veterinary medicine. To identify major genes that affect mastitis in dairy cattle, 6 chromosomal regions on Bos taurus autosome (BTA) 6, 13, 16, 19, and 20 were selected from a genome scan for 9 mastitis phenotypes using imputed high-density single nucleotide polymorphism arrays. Association analyses using sequence-level variants for the 6 targeted regions were carried out to map causal variants using whole-genome sequence data from 3 breeds. The quantitative trait loci (QTL) discovery population comprised 4,992 progeny-tested Holstein bulls, and QTL were confirmed in 4,442 Nordic Red and 1,126 Jersey cattle. The targeted regions were imputed to the sequence level. The highest association signal for clinical mastitis was observed on BTA 6 at 88.97 Mb in Holstein cattle and was confirmed in Nordic Red cattle. The peak association region on BTA 6 contained 2 genes: vitamin D-binding protein precursor (GC) and neuropeptide FF receptor 2 (NPFFR2), which, based on known biological functions, are good candidates for affecting mastitis. However, strong linkage disequilibrium in this region prevented conclusive determination of the causal gene. A different QTL on BTA 6 located at 88.32 Mb in Holstein cattle affected mastitis. In addition, QTL on BTA 13 and 19 were confirmed to segregate in Nordic Red cattle and QTL on BTA 16 and 20 were confirmed in Jersey cattle. Although several candidate genes were identified in these targeted regions, it was not possible to identify a gene or polymorphism as the causal factor for any of these regions.     

Comparison of milk protein composition and rennet coagulation properties in native Swedish dairy cow breeds and high-yielding Swedish Red cows

Recent studies have reported a very high frequency of noncoagulating milk in Swedish Red cows. The underlying factors are not fully understood. In this study, we explored rennet-induced coagulation properties and relative protein profiles in milk from native Swedish Mountain and Swedish Red Polled cows and compared them with a subset of noncoagulating (NC) and well-coagulating (WC) milk samples from modern Swedish Red cows. The native breeds displayed a very low prevalence of NC milk and superior milk coagulation properties compared with Swedish Red cows. The predominant variants in both native breeds were α_S1-casein (α_S1-CN) B, β-CN A² and β-lactoglobulin (β-LG) B. For κ-CN, the B variant was predominant in the Swedish Mountain cows, whereas the A variant was the most frequent in the Swedish Red Polled. The native breeds displayed similar protein composition, but varied in content of α_S1-CN with 9 phosphorylated serines (9P) form. Within the Swedish Mountain cows, we observed a strong inverse correlation between the relative concentration of κ-CN and micelle size and a positive correlation between ionic calcium and gel firmness. For comparison, we investigated a subset of 29 NC and 28 WC milk samples, representing the extremes with regard to coagulation properties based on an initial screening of 395 Swedish Red cows. In Swedish Red, NC milk properties were found to be related to higher frequencies of β-CN A², κ-CN E and A variants, as well as β-LG B, and the predominant composite genotype of β- and κ-CN in the NC group was A²A²/AA. Generally, the A²A²/AA composite genotype was related to lower relative concentrations of κ-CN isoforms and higher relative concentrations of α_S1-, α_S2-, and β-CN. Compared with the group of WC milk samples, NC milk contained a higher fraction of α_S2-CN and α-lactalbumin (α-LA) but a lower fraction of α_S1-CN 9P. In conclusion, milk from native Swedish breeds has good characteristics for cheese milk, which could be exploited in niche dairy products. In milk from Swedish Mountain cows, levels of ionic calcium seemed to be more important for rennet-induced gel firmness than variation in the relative protein profile. In Swedish Red, lower protein content as well as higher fraction of α_S2-CN and lower fraction of α_S1-CN 9P were related to NC milk. Further, a decrease in the frequency of the composite β-κ-CN genotype A²A²/AA through selective breeding could have a positive effect on milk coagulation properties.     

β-Lactoglobulin genetic variants in Brown Swiss breed and its association with compositional properties and rennet clotting time of milk

β-Lactoglobulin (β-Lg) polymorphism of Holstein Friesian and Brown Swiss breeds were studied by applying native polyacrylamide gel electrophoresis. In addition, total solids, protein, fat ash, lactose and solid non-fat contents, rennet clotting time and major minerals (potassium, calcium, phosphorus and magnesium) of milk from Brown Swiss breed were examined. Phenotype and allele frequencies of β-Lg in both breeds were estimated and the association of the β-Lg genetic variants with the examined properties of Brown Swiss milk was studied. As a result of the study, β-Lg AA, AB and BB phenotypes were found in both Holstein Friesian and Brown Swiss breeds. The gene frequencies of β-Lg A and B were 0.27 and 0.73 in Holstein Friesian and 0.44 and 0.56 in Brown Swiss breeds, respectively. Therefore, β-Lg B allele gene was found more common in both breeds. In addition, significant differences were observed in β-Lg genotypes between two breeds. Also, significant relationships were found between β-Lg genetic variants and total solids (p<0.05), fat (p<0.01), calcium (p<0.05) and phosphorus (p<0.05), while no relationship was obtained for the other parameters studied in the milk of Brown Swiss breed.     

Evaluation of ISSR markers for genetic diversity analysis in Anatolian water buffaloes

BACKGROUND: The utilisation of molecular markers has increased in molecular research recently. Inter‐simple sequence repeat (ISSR) markers allow the analysis of genomes without preliminary sequence information, since random primers are used. The purpose of the present study was to evaluate ISSR markers for assessing the genetic diversity of indigenous Anatolian Water Buffaloes reared in Afyon, Konya and Sivas provinces of Turkey, with a view to conservation of the gene resources. RESULTS: The 11 ISSR primers chosen for the analysis revealed a total of 110 bands, of which 76 (69.09%) were polymorphic. Also, genetic similarity, polymorphic information content (PIC), resolving power (R_p) and mean resolving power (R_p ), heterozygosity (H) and Shannon index (I) were calculated as 0.9479–0.9562, 0.35 ± 0.20, 2.73, 0.27, 0.18 ± 0.07 and 0.28 ± 0.11, respectively. CONCLUSION: The ISSR markers were found to be promising for assessing the genetic diversity in buffalo populations. Potential genetic parameters such as PIC, R_p, R_p , H and I were effectively used in this study. Copyright © 2011 Society of Chemical Industry     

Short communication: a polymorphism in ABCG2 in Bos indicus and Bos taurus cattle breeds

A single nucleotide change (A/C) in exon 14 is capable of encoding a substitution of tyrosine-581 to serine (Y581S) in the ABCG2 (ATP binding cassette, subfamily G, member 2) gene and affects milk production traits. The ABCG2^A allele decreases milk yield and increases protein and fat concentration. The allele frequencies were determined in 32 Bos taurus and 3 Bos indicus breeds; ABCG2^A was predominant in all populations. This allele approached fixation in 23 out of 35 breeds, including all 3 Bos indicus breeds. The ABCG2^C allele was found in the Belgian Blue (beef), Belgian Blue Mix, British Friesian, Bohemian Red, East Anatolian Red, German Angus, German Black Pied, German Brown, German Simmental, Israeli Holstein, Menorquina, and US Holstein breeds. Thus, the genetic gain expected from selection for ABCG2^A may be limited. The detection of ABCG2^C only in Bos taurus breeds may indicate that ABCG2^A is the ancestral allele, and that the Y581S substitution occurred after the separation of the Bos indicus and Bos taurus lineages.     

Isolation and identification of Treponema pedis and Treponema phagedenis-like organisms from bovine digital dermatitis lesions found in dairy cattle in Turkey

The isolation and identification of microorganisms associated with digital dermatitis (DD) in Turkish dairy cattle was investigated using punch skin biopsy samples from typical clinical lesions; they were collected from dairy farms and abattoirs in 5 different geographical locations in Turkey. Morphological characteristics and flagellation types were examined using a transmission electron microscope, and their enzyme profiles by enzyme activation kits; their catalase reaction characteristics were evaluated by the addition of 3% H₂O₂. Their phylogenies were identified using 16S rRNA and the results compared with known gene bank data. Bacterial cells were 5.0 to 18.2 µm long, 0.2 to 0.5 µm wide, and their minimum number of periplasmic flagellum was 4 (4:8:4) with a maximum of 8 (8:16:8). All isolates were catalase negative. Of the spirochetes isolated and identified, group I organisms showed close similarity with Treponema pedis (99% genetic homology), whereas those in group II were similar to Treponema phagedenis (98% homology). This is the first report of specific sub-groups of Treponema spp., isolated from Turkish dairy cattle presenting with DD lesions, being associated with this disease; these morphotypes were similar to those found globally in housed dairy cattle units and are probably significant microorganisms associated with the aetiopathogensis of this infectious disease causing acute bovine lameness. These results suggest that the distribution of DD-associated treponemes is not specific to particular geographic regions of Turkey.     

Suitability of the milk of native breeds of cows from low‐input farms for cheese production,including rennet curd texture

The cheesemaking suitability of the milk of native cow breeds [Polish Red (RP) and White‐Backed (BG)] raised on low‐input farms was assessed. The milk of Polish Holstein‐Friesian cows raised in an intensive system constituted the reference group. Chemical composition, pH, rennet coagulation time, fat dispersion and curd texture were determined. The cows on the low‐input farms produced over 40% less milk, but with higher (P ≤ 0.01) fat content, shorter coagulation time by over 2 min and lower (P ≤ 0.05) fat dispersion. The curds from this milk were significantly springier, more cohesive and harder. The best milk indices were obtained for the RP cows.     

Development of discrimination SNP markers for Hanwoo (Korean native cattle)

In the Korean meat market, the native cattle, Hanwoo beef, are preferred over imported beef and domestic Holstein beef despite its relatively high price. In order to hold the beef industry accountable and support consumers' right to know, correct beef-origin labeling is required. For this purpose, we developed 90 single-nucleotide polymorphism markers to discriminate between Hanwoo and other breeds including Holstein using 1602 cattle DNAs. The probability of discrimination was found to be 100% in a subsequent validation set consisting of 632 DNAs. Our study suggests that improved beef-origin discrimination can be achieved by using a combined genetic model that takes into account small genetic differences among a large number of markers. These markers could be useful for discriminating between Hanwoo and imported breeds including domestic Holsteins, and would contribute to the prevention of falsified beef origin.     

Variation and genetic control of individual recombination rates in Norwegian Red dairy cattle

Meiotic recombination is an important evolutionary mechanism that breaks up linkages between loci and creates novel haplotypes for selection to act upon. Understanding the genetic control of variation in recombination rates is therefore of great interest in both natural and domestic breeding populations. In this study, we used pedigree information and medium-density (～50K) genotyped data in a large cattle (Bos taurus) breeding population in Norway (Norwegian Red cattle) to investigate recombination rate variation between sexes and individual animals. Sex-specific linkage mapping showed higher rates in males than in females (total genetic length of autosomes = 2,492.9 cM in males and 2,308.9 cM in females). However, distribution of recombination along the genome showed little variation between males and females compared with that in other species. The heritability of autosomal crossover count was low but significant in both sexes (h² = 0.04 and 0.09 in males and females, respectively). We identified 2 loci associated with variation in individual crossover counts in female, one close to the candidate gene CEP55 and one close to both MLH3 and NEK9. All 3 genes have been associated with recombination rates in other cattle breeds. Our study contributes to the understanding of how recombination rates are controlled and how they may vary between closely related breeds as well as between species.     

The effects of breed and other factors on the composition and freezing point of cow’s milk in Poland

The milk obtained from six cow breeds (Polish Holstein‐Friesian Black‐White and Red‐White, Simmental, Jersey, Polish Red and Polish Black‐White) managed in the Lubelskie region and the Bieszczady Mountains was analysed. A total of 3618 milk samples collected between 2005 and 2008 were evaluated for the total solids content, percentage concentrations of fat, protein and lactose, and the freezing point: the mean milk freezing point was ?0.538°C. The freezing point of milk was influenced by breed, successive lactations, lactation stage and the geographic region. In milk with a high urea concentration (over 300 mg/L), the increased apparent protein level caused a decrease in the milk freezing point values. The combined influence of geographic region and production season showed significant interactions for daily milk yield and total solids content (P < 0.01) and the milk freezing point (P < 0.05).