Genomic relatedness and diversity of Swedish native cattle breeds.

BACKGROUND: Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150 K single nucleotide polymorphisms (SNPs) to investigate the level of genetic diversity and relatedness between these breeds. RESULTS: We used various SNP-based approaches on this dataset to connect the demographic history with the genetic diversity and population structure of these Swedish cattle breeds. Our results suggest that the Väne and Ringamåla breeds originating from southern Sweden have experienced population isolation and have a low genetic diversity, whereas the Fjäll breed has a large founder population and a relatively high genetic diversity. Based on the shared ancestry and the constructed phylogenetic trees, we identified two major clusters in Swedish native cattle. In the first cluster, which includes Swedish mountain cattle breeds, there was little differentiation among the Fjäll, Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red. Interestingly, we also identified sub-structuring in the Fjällnära breed, which indicates different breeding practices on the farms that maintain this breed. CONCLUSIONS: This study represents the first comprehensive genome-wide analysis of the genetic relatedness and diversity in Swedish native cattle breeds. Our results show that different demographic patterns such as genetic isolation and cross-breeding have shaped the genomic diversity of Swedish native cattle breeds and that the Swedish mountain breeds have retained their authentic distinct gene pool without significant contribution from any of the other European cattle breeds that were included in this study.

Serial translocation by means of circular intermediates underlies colour sidedness in cattle.

Colour sidedness is a dominantly inherited phenotype of cattle characterized by the polarization of pigmented sectors on the flanks, snout and ear tips. It is also referred to as 'lineback' or 'witrik' (which means white back), as colour-sided animals typically display a white band along their spine. Colour sidedness is documented at least since the Middle Ages and is presently segregating in several cattle breeds around the globe, including in Belgian blue and brown Swiss. Here we report that colour sidedness is determined by a first allele on chromosome 29 (Cs(29)), which results from the translocation of a 492-kilobase chromosome 6 segment encompassing KIT to chromosome 29, and a second allele on chromosome 6 (Cs(6)), derived from the first by repatriation of fused 575-kilobase chromosome 6 and 29 sequences to the KIT locus. We provide evidence that both translocation events involved circular intermediates. This is the first example, to our knowledge, of a phenotype determined by homologous yet non-syntenic alleles that result from a novel copy-number-variant-generating mechanism.

Quality of bull spermatozoa after preparation by single-layer centrifugation.

The present study aimed to evaluate the effect of single-layer centrifugation (SLC) through a species-specific colloid (Androcoll-B; patent pending, J. M. Morrell) on bull sperm quality. Computer-assisted sperm analysis of motility and flow cytometric analysis of sperm viability (SYBR-14/propidium iodide staining), chromatin integrity (acridine orange staining), reactive oxygen species production [Hoechst 33258-hydroethidine-2',7'-dichlorodihydrofluorescein diacetate (HO-HE-DCFDA) staining], mitochondrial membrane potential (staining with JC-1 probe), and protein tyrosine phosphorylation (specific antibody staining) were performed on unselected and SLC-selected sperm samples. Single-layer centrifugation of bull spermatozoa resulted in the selection of a sperm population that had high mitochondrial membrane potential, a higher content of phosphorylated protein, and more reactive oxygen species than control samples. Sperm chromatin damage was lower in the SLC samples although sperm viability and motility did not differ between SLC samples and controls. These observations suggest that SLC of bull semen in a soybean-containing extender improved some, but not all, parameters of sperm quality.

Genomic selection in relation to bovine milk composition and processability.

Genomic selection is a new technology in which selection decisions are based on direct genomic values (DGVs) or genomic enhanced breeding values (GEBVs). The objective of this study was to evaluate the relations between DGVs and several milk traits important for both the nutritional value and processability of milk. This is a new approach and can be used to increase the knowledge on how genomic selection can be used in practice. Morning milk samples from Swedish Holstein cows were analyzed for milk composition and technological properties. DGVs were received for each cow for milk, protein and fat yield, milk index, udder health, Nordic total merit and a quota was calculated between fat and milk yield as well as protein and milk yield. The results show that linear correlations exist (P<0·10) between the studied DGVs and contents and yields of parameters in the protein (P=0·002-0·097), fat (P=0·024-0·055) and mineral profiles (P=0·001-0·099) as well as for cheese characteristics (P=0·004-0·065), thus making it possible to obtain detailed information on milk traits that are not registered in the milk recording scheme. Hence, genomic selection will be an efficient tool for breeding and dairy industry to select cows early in life for targeted milk production.

Effect of polymorphisms in the leptin, leptin receptor and acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) genes and genetic polymorphism of milk proteins on bovine milk composition.

The relations between cow genetics and milk composition have gained a lot of attention during the past years, however, generally only a few compositional traits have been examined. The aim of this study was to determine if polymorphisms in the leptin (LEP), leptin receptor (LEPR) and acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) genes as well as genetic polymorphism of ß-casein (ß-CN), κ-CN and ß-lactoglobulin (ß-LG) impact several bovine milk composition traits. Individual milk samples from the Swedish Red and Swedish Holstein breeds were analyzed for components in the protein, lipid, carbohydrate and mineral profiles. Cow alleles were determined on the following SNP: A1457G, A252T, A59V and C963T on the LEP gene, T945M on the LEPR gene and Nt984+8(A-G) on the DGAT1 gene. Additionally, genetic variants of ß-CN, κ-CN and ß-LG were determined. For both the breeds, the same tendency of minor allele frequency was found for all SNPs and protein genes, except on LEPA1457G and LEPC963T. This study indicated significant (P<0·05) associations between the studied SNPs and several compositional parameters. Protein content was influenced by LEPA1457G (G>A) and LEPC963T (T>C), whereas total Ca, ionic Ca concentration and milk pH were affected by LEPA1457G, LEPA59V, LEPC963T and LEPRT945M. However, yields of milk, protein, CN, lactose, total Ca and P were mainly affected by ß-CN (A2>A1) and κ-CN (A>B>E). ß-LG was mainly associated with whey protein yield and ionic Ca concentration (A>B). Thus, this study shows possibilities of using these polymorphisms as markers within genetic selection programs to improve and adjust several compositional parameters.

Sperm Quality in Young Bull Semen Can Be Improved by Single Layer Centrifugation.

Interest in using semen from young bulls is increasing due to identifying promising animals by genomic selection. However, sperm quality in these ejaculates may not reach currently accepted standards for the cattle breeding industry. The purpose of this study was to determine if centrifugation of semen from young bulls through the Bovicoll colloid could improve sperm quality sufficiently for the frozen semen to be acceptable for artificial insemination. Ejaculates from 19 young bulls were split and either processed by Single-Layer Centrifugation (SLC) or not (CON) before freezing. After thawing, sperm quality was evaluated by determination of membrane integrity, mitochondrial membrane potential, DNA integrity, production of reactive oxygen species, sperm morphology and motility. Approximately half of the CON samples reached acceptable post-thaw quality (membrane integrity ≥ 40%) despite being below the breeding company´s desired sperm concentration threshold pre-freezing. In the remaining samples, sperm quality was improved by SLC such that 45% of them reached acceptable quality post-thaw. Almost 75% of the young bull sperm samples could have produced usable frozen semen doses by adjusting the breeding company´s current processing protocols. Since lowering the generation interval has a direct effect on the genetic gain per year, SLC could aid genetic progress in cattle breeding.

Post-thaw semen quality in young bull ejaculates before being accepted for commercial semen doses.

BACKGROUND: Genomic selection enables bulls with desirable characteristics to be identified at a young age, but sperm quality can be poor in the ejaculates of young bulls. Few studies have been done on post-thaw sperm quality in bulls less than 10 months old. The objective of this study was to determine the age at which post-thaw sperm quality was acceptable for artificial insemination. METHODS: Semen was collected by artificial vagina; samples containing 100-500 million spermatozoa/ml were frozen for this study. Post-thaw analyses of membrane integrity (MI), mitochondrial membrane potential (MMP), chromatin integrity, morphology, production of reactive oxygen species and sperm kinematics were made. RESULTS: The age at which ejaculates exceeded the breeding company's thresholds of acceptance varied considerably among individuals, with 285 days being the earliest. Morphology (p < 0.003), MI (p = 0.0096), high MMP (p = 0.043) and superoxide production (p = 0.0084) increased between the first and last ejaculates but reached acceptable levels at different ages for individual bulls. CONCLUSIONS: It was possible to obtain acceptable post-thaw sperm quality from samples even though sperm concentration was lower than the breeding company's threshold. Therefore, it might be feasible to use ejaculates earlier than is currently considered possible, by modifying semen handling protocols.

Effects of complex vertebral malformation on fertility in Swedish holstein cattle.

Complex vertebral malformation (CVM) is an autosomal recessive inherited defect in the Holstein breed. It causes intra-uterine mortality through the entire gestation period leading to repeat breeding and involuntary culling of cows and thereby economic losses. The defect was first reported in Denmark in 1999 and a direct DNA test for the defect has been available since February 2001. The aim of this study was to investigate if Holstein bulls heterozygous for the CVM gene had reduced reproductive performance, measured as non-return rate (NRR) and in a daughter fertility index. All genotyped Swedish Holstein bulls born between 1995 and 1999 were included. Altogether 228 bulls were analysed, of which 53 bulls, i.e. 23%, were confirmed CVM carriers. A statistically significant difference between carriers and non-carriers in the relative breeding value for NRR was observed for 168 days NRR (101.1+/-0.9 vs. 103.1+/-0.6, p<0.05). There was no difference for 28 days NRR whereas the difference approached significance for 56 days NRR. No significant effect of the paternal CVM genotype on the daughter fertility index was shown probably due to the complexity of traits this index is composed of. In conclusion, the study showed that carriers of the CVM defect have an inferior NRR compared with non-carriers.