Genomic evaluation of Brown Swiss dairy cattle with limited national genotype data and integrated external information.

This study demonstrated the feasibility of a genomic evaluation for the dairy cattle population for which the small national training population can be complemented with foreign information from international evaluations. National test-day milk yield data records for the Slovenian Brown Swiss cattle population were analyzed. Genomic evaluation was carried out using the single-step genomic best linear unbiased prediction method (ssGBLUP), resulting in genomic estimated breeding values (GEBV). The predominantly female group of genotyped animals, representing the national training population in the single-step genomic evaluation, was further augmented with 7,024 genotypes of foreign progeny-tested sires from an international Brown Swiss InterGenomics genomic evaluation (https://interbull.org/ib/whole_cop). Additionally, the estimated breeding values for the altogether 7,246 genotyped domestic and foreign sires from the 2019 sire multiple across-country evaluation (MACE), were added to the ssGBLUP as external pseudophenotypic information. The ssGBLUP method, with integration of MACE information by avoiding double counting, was then performed, resulting in MACE-enhanced GEBV (GEBVM). The methods were empirically validated with forward prediction. The validation group consisted of 315 domestic males and 1,041 domestic females born after 2012. Increase, inflation, and bias of the GEBV(M) reliability (REL) were assessed for the validation group with a focus on females. All individuals in the validation benefited from genomic evaluations using both methods, but the GEBV(M) REL increased most for the youngest selection candidates. Up to 35 points of GEBV REL could be assigned to national genomic information, and up to 17 points of GEBVM REL could additionally be attributed to the integration of foreign sire genomic and MACE information. Results indicated that the combined foreign progeny-tested sire genomic and external MACE information can be used in the single-step genomic evaluation as an equivalent replacement for domestic phenotypic information. Thus, an equal or slightly higher genomic breeding value REL was obtained sooner than the pedigree-based breeding value REL for the female selection candidates. When the abundant foreign progeny-tested sire genomic and MACE information was used to complement available national genomic and phenotypic information in single-step genomic evaluation, the genomic breeding value REL for young-female selection candidates increased approximately 10 points. Use of international information provides the possibility to upgrade small national training populations and obtain satisfying reliability of genomic breeding values even for the youngest female selection candidates, which will help to increase selection efficiency in the future.

Changes in fatty acid profile of Bovec sheep milk due to different pasture altitude.

Sheep rearing on mountain pastures is an ancestral tradition in northwestern Slovenia. The indigenous Bovec sheep are widespread there and are well adapted to the rough Alpine rearing conditions. Every year, after weaning, the sheep start grazing in the lowlands (L) and then gradually move to mountain pastures, and finally, to the highland (H) pastures of the Alps. Grazing positively affects the fatty acid (FA) composition in sheep milk fat with increased availability of polyunsaturated FA (PUFA) in grass, and subsequently, in milk. Consequently, the objective of this work was to study the FA profile in sheep milk during grazing in four geographical areas in the Alps. A total of 15 ewes of the Bovec sheep breed were randomly selected and milk samples from these ewes were taken at four different pasture locations that differed with regard to altitude: the L pasture location at an altitude of 480 m, the mountain pastures (M1 and M2) at altitudes of 1100 to 1300 m and 1600 to 1900 m, respectively, and the H pastures at altitudes of 2100 to 2200 m. Milk samples from the ewes were taken during the grazing season from April to September. The chemical and FA composition of the milk samples from each pasture location were determined. There were significant differences in the concentrations of FA among the L, M1, M2 and H milk samples. We observed decreases of the concentrations of saturated FA (SFA) in milk from L to H pastures. The concentration of α-linolenic FA, monounsaturated FA (MUFA), PUFA and n-3 PUFA in milk were increased significantly with pasture altitude. The n-6/n-3 PUFA ratio was reduced by the change of pasture altitude with the lowest value at the M1 pasture (1.5). The concentrations of total SFA decreased significantly and was lowest at the L pasture. Our results underline the importance of the effect of grazing in the Alpine region associated with pasture altitude on the FA profile of sheep milk. The first variation in FA concentration in sheep milk occurred between L and M1, although it was more evident on H pastures in the Alpine mountains. Changes of the FA profile in sheep milk due to pasture altitude were related to variation in FA concentration in the pasture and the botanical composition of the pasture location.

National single-step genomic method that integrates multi-national genomic information.

The aim of this paper was to develop a national single-step genomic BLUP that integrates multi-national genomic estimated breeding values (EBV) and associated reliabilities without double counting dependent data contributions from the different evaluations. Simultaneous use of all data, including phenotypes, pedigree, and genotypes, is a condition to obtain unbiased EBV. However, this condition is not always fully met, mainly due to unavailability of foreign raw data for imported animals. In dairy cattle genetic evaluations, this issue is traditionally tackled through the multiple across-country evaluation (MACE) of sires, performed by Interbull Centre (Uppsala, Sweden). Multiple across-country evaluation regresses all the available national information onto a joint pedigree to obtain country-specific rankings of all sires without sharing the raw data. In the context of genomic selection, the issue is handled by exchanging sire genotypes and by using MACE information (i.e., MACE EBV and reliabilities), as a valuable source of "phenotypic" data. Although all the available data are considered, these "multi-national" genomic evaluations use multi-step methods assuming independence of various sources of information, which is not met in all situations. We developed a method that handles this by single-step genomic evaluation that jointly (1) uses national phenotypic, genomic, and pedigree data; (2) uses multi-national genomic information; and (3) avoids double counting dependent data contributions from an animal's own records and relatives' records. The method was demonstrated by integrating multi-national genomic EBV and reliabilities of Brown Swiss sires, included in the InterGenomics consortium at Interbull Centre, into the national evaluation in Slovenia. The results showed that the method could (1) increase reliability of a national (genomic) evaluation; (2) provide consistent ranking of all animals: bulls, cows, and young animals; and (3) increase the size of a genomic training population. These features provide more efficient and transparent selection throughout a breeding program.

FTO gene variants are associated with growth and carcass traits in cattle.

An important aim in animal breeding is the improvement of growth and meat quality traits. Previous studies have demonstrated that genetic variants in the fat mass and obesity associated (FTO) gene have a relatively large effect on human obesity as well as on body composition in rodents and, more recently, in livestock. Here, we examined the effects of the FTO gene variants on growth and carcass traits in the Slovenian population of Simmental (SS) and Brown (SB) cattle. To validate and identify new polymorphisms, we used sequencing, PCR-RFLP analysis and TaqMan assays in the SS breed and FTO gene variants data from the Illumina BovineSNP50 v1 array for the SB breed. Sequencing of the eight samples of progeny-tested SS sires detected 108 single nucleotide polymorphisms (SNPs) in the bovine FTO gene. Statistical analyses between growth and carcass traits and 34 FTO polymorphisms revealed significant association of FTO variants with lean meat percentage in both breeds. Additionally, FTO SNPs analyzed in SS cattle were associated with fat percentage, bone weight and live weight at slaughter. The FTO gene can thus be regarded as a candidate gene for the marker-assisted selection programs in our and possibly other populations of cattle. Future studies in cattle might reveal novel roles for the FTO gene in shaping carcass traits in livestock species as well as body composition control in other mammals.