Replacement of microsatellite markers by imputed medium-density SNP arrays for parentage control in German warmblood horses.

In horses, parentage control is currently performed based on an internationally standardized panel of 17 microsatellite (MS) markers comprising 12 mandatory and five optional markers. Unlike MS, single nucleotide polymorphism (SNP) profiles support a wider portfolio of genomic applications, including parentage control. A transition to SNP-based parentage control is favorable, but requires additional efforts for ensuring generation-overlapping availability of marker genotypes of the same type. To avoid double genotyping of either parents or offspring for changing to SNP technology and enable efficient transition, we tested whether MS genotypes used for parentage control could be reliably imputed from a medium-density SNP panel in German warmblood horses. Imputation accuracy was tested in a tenfold cross-validation with two approaches: within breed (option A) and across breeds (option B). Average imputation accuracies of 97.98% (A) and 96.17% (B) were achieved, respectively. Due to interbreed differences in genotyping rates, five MS markers of low genotyping rate (GTR; < 90%) could be imputed with higher accuracy within breed (98.18%) than across breeds (90.73%). MS markers with high GTR performed homogeneously well in option B (98.44%) and showed slightly lower accuracy in option A (97.90%). Among these markers, AHT5 proved to be problematic for imputation regardless of the approach, revealing accuracies of 86.40% (A) and 88.70% (B). Better results for MS markers with high GTR and savings in computational processing justified the choice of option B for routine implementation. To date, more than 9500 horses have undergone the new parentage control based on imputed MS genotypes.

Mitochondrial DNA Variation Contributes to the Aptitude for Dressage and Show Jumping Ability in the Holstein Horse Breed.

Maternal lineages are considered an important factor in breeding. Mitochondrial DNA (mtDNA) is maternally inherited and plays an important role in energy metabolism. It has already been associated with energy consumption and performances, e.g., stamina in humans and racehorses. For now, corresponding studies are lacking for sport performance of warmblood breeds. MtDNA sequences were available for 271 Holstein mares from 75 maternal lineages. As all mares within a lineage showed identical haplotypes regarding the non-synonymous variants, we expanded our data set by also including non-sequenced mares and assigning them to the lineage-specific haplotype. This sample consisting of 6334 to 16,447 mares was used to perform mitochondrial association analyses using breeding values (EBVs) estimated on behalf of the Fédération Équestre Nationale (FN) and on behalf of the Holstein Breeding Association (HOL). The association analyses revealed 20 mitochondrial SNPs (mtSNPs) significantly associated with FN-EBVs and partly overlapping 20 mtSNPs associated with HOL-EBVs. The results indicated that mtDNA contributes to performance differences between maternal lineages. Certain mitochondrial haplogroups were associated with special talents for dressage or show jumping. The findings encourage to set up innovative genetic evaluation models that also consider information on maternal lineages.

Genetic and genomic characterization followed by single-step genomic evaluation of withers height in German Warmblood horses.

Reliability of genomic predictions is influenced by the size and genetic composition of the reference population. For German Warmblood horses, compilation of a reference population has been enabled through the cooperation of five German breeding associations. In this study, preliminary data from this joint reference population were used to genetically and genomically characterize withers height and to apply single-step methodology for estimating genomic breeding values for withers height. Using data on 2113 mares and their genomic information considering about 62,000 single nucleotide polymorphisms (SNPs), analysis of the genomic relationship revealed substructures reflecting breed origin and different breeding goals of the contributing breeding associations. A genome-wide association study confirmed a known quantitative trait locus (QTL) for withers height on equine chromosome (ECA) 3 close to LCORL and identified a further significant peak on ECA 1. Using a single-step approach with a combined relationship matrix, the estimated heritability for withers height was 0.31 (SE = 0.08) and the corresponding genomic breeding values ranged from - 2.94 to 2.96 cm. A mean reliability of 0.38 was realized for these breeding values. The analyses of withers height showed that compiling a reference population across breeds is a suitable strategy for German Warmblood horses. The single-step method is an appealing approach for practical genomic prediction in horses, because not many genotypes are available yet and animals without genotypes can by this way directly contribute to the estimation system.

Exploring the Origin and Relatedness of Maternal Lineages Through Analysis of Mitochondrial DNA in the Holstein Horse.

Maternal lineages are important for the breeding decision in the Holstein horse breed. To investigate the genetic diversity of the maternal lineages and the relationships between founder mares, the maternal inherited mitochondrial genome (except the repetitive part of the non-coding region) of 271 mares representing 75 lineages was sequenced. The sequencing predominantly revealed complete homology in the nucleotide sequences between mares from one lineage with exceptions in 13 lineages, where differences in one to three positions are probably caused by de novo mutations or alternate fixation of heteroplasmy. We found 78 distinct haplotypes that have not yet been described in other breeds. Six of these occurred in two or three different lineages indicating a common ancestry. Haplotypes can be divided into eight clusters with all mares from one lineage belonging to the same cluster. Within a cluster, the average number of pairwise differences ranged from zero to 16.49 suggesting close maternal relationships between these mares. The results showed that the current breeding population originated from at least eight ancestral founder mares.

The relationship between methane emission and daytime-dependent fecal archaeol concentration in lactating dairy cows fed two different diets.

Archaeol is a cell membrane lipid of methanogenic archaea excreted in feces and is therefore a potential biomarker for individual methane emission (MEM). The aims of this study were to examine the potential of the fecal archaeol concentration (fArch) to be a proxy for MEM prediction in cows fed different diets and determine if the time of fecal collection affected the archaeol concentration. Thus, we investigated (i) the variation of the fArch concentration in spot samples of feces taken thrice within 8 h during respiration chamber measurements and (ii) the effect of two diets differing in nutrient composition and net energy content on the relationship between fArch and MEM in lactating cows. Two consecutive respiration trials with four primiparous and six multiparous lactating Holstein cows were performed. In the first trial (T1) at 100 ± 3  d in milk (IM), a diet moderate in starch and fat content was fed for ad libitum intake, whereas in the second trial (T2) at 135 ± 3  d IM, cows received a diet lower in starch and fat. Individual MEM (g d - 1 ) was measured for 24 h. Fecal samples were taken at 06:30, 10:00, and 14:30 LT and analyzed for fArch using Soxhlet lipid extraction and GC-MS. Cows produced less methane (364 g  CH 4  d - 1 ) during T1 and had significantly lower fArch concentrations (37.1  µ g g - 1 dry matter; DM) compared to T2 (392 g  CH 4  d - 1 and 47.6  µ g g - 1  DM). A significant positive relationship between fArch ( µ g g - 1 fecal DM) and MEM, expressed on a dry matter intake (DMI) basis (g kg - 1  DMI), was found ( R 2 = 0.53 , n = 20 ). Among samples collected over the day, those collected at 10:00 LT provided the best coefficient of determination for MEM ( R 2 = 0.23 ). In conclusion, fArch offers some potential in serving as a proxy for innovative breeding schemes to lower enteric methane when fecal samples are taken at a certain time of the day, but more data on the sources of variation of the MEM  :  fArch ratios are required.

Estimation of genetic parameters for growth and carcass traits in turbot (Scophthalmus maximus).

Information on phenotypic and genetic (co)variance for production traits in turbot is required to improve breeding programs. So far, information on morphometric growth traits is sparse and completely lacking on quality carcass traits like fillet weight or fillet yield for turbot. As part of a long-term study we explored the phenotypic and genetic (co)variance of 16 biometrical and carcass traits of three different European turbot strains. Fish were reared under commercial grow-out conditions, including size grading. We used molecular relatedness (MR) methods based on genotyping with 96 microsatellite markers and animal models. We included an adapted condition factor for Pleuronectiformes (FCI PLN ) and average daily weight gain (ADG) between the ages of 300 and 500 d post-hatch (dph) for their potential correlation with body weight at harvest. Heritability estimates for all traits were low to medium (0.04-0.29) when strains were jointly analyzed. Separate analysis of strains yielded higher heritability estimates (0.12-0.43). Genetic correlations between weight-related traits were highly positive (0.70-0.99), while runs with yield and ratio traits often resulted in unreliable estimates of genetic correlation due to high standard errors. Body weight ( h 2 = 0.19 ), fillet yield ( h 2 = 0.1 5), and dressing percentage ( h 2 = 0.17 ) are particularly promising selection traits for turbot breeding.

Polymorphisms within the APOBR gene are highly associated with milk levels of prognostic ketosis biomarkers in dairy cows.

Essentially all high-yielding dairy cows experience a negative energy balance during early lactation leading to increased lipomobilization, which is a normal physiological response. However, a severe energy deficit may lead to high levels of ketone bodies and, subsequently, to subclinical or clinical ketosis. It has previously been reported that the ratio of glycerophosphocholine to phosphocholine in milk is a prognostic biomarker for the risk of ketosis in dairy cattle. It was hypothesized that this ratio reflects the ability to break down blood phosphatidylcholine as a fatty acid resource. In the current study, 248 animals from a previous study were genotyped with Illumina BovineSNP50 BeadChip, and genome-wide association studies were carried out for the milk levels of phosphocholine, glycerophosphocholine, and the ratio of both metabolites. It was demonstrated that the latter two traits are heritable with h2 = 0.43 and h2 = 0.34, respectively. A major quantitative trait locus was identified on cattle chromosome 25. The APOBR gene, coding for the apolipoprotein B receptor, is located within this region and was analyzed as a candidate gene. The analysis revealed highly significant associations of polymorphisms within the gene with glycerophosphocholine as well as the metabolite ratio. These findings support the hypothesis that differences in the ability to take up blood phosphatidylcholine from low-density lipoproteins play an important role in early lactation metabolic stability of dairy cows and indicate APOBR to contain a causative variant.