A Novel Model to Explain Extreme Feather Pecking Behavior in Laying Hens.

Feather pecking (FP) is a serious economic and welfare problem in the domestic fowl. It has recently been shown that the distribution of FP bouts within groups is heterogeneous and contains a sub-population of extreme feather peckers (EFP). The present study proposed a novel model to detect EFP hens. A mixture of two negative binomial distributions was fitted to FP data of a F2 cross of about 960 hens, and, based on the results, a calculation of the posterior probability for each hen belonging to the EFP subgroup (pEFP) was done. The fit of the mixture distribution revealed that the EFP subgroup made up a proportion of one third of the F2 cross. The EFP birds came more frequently into pecking mood and showed higher pecking intensities compared to the remaining birds. Tonic immobility and emerge box tests were conducted at juvenile and adult age of the hens to relate fearfulness to EFP. After dichotomization, all traits were analyzed in a multivariate threshold model and a genomewide association study was performed. The new trait pEFP has a medium heritability of 0.35 and is positively correlated with the fear traits. Breeding for this new trait could be an interesting option to reduce the proportion of extreme feather peckers. An index of fear related traits might serve as a proxy to breed indirectly for pEFP. GWAS revealed that all traits are typical quantitative traits with many genes and small effects contributing to the genetic variance.

Comprehensive characterization of horse genome variation by whole-genome sequencing of 88 horses.

Whole-genome sequencing studies are vital to gain a thorough understanding of genomic variation. Here, we summarize the results of a whole-genome sequencing study comprising 88 horses and ponies from diverse breeds at 19.1× average coverage. The paired-end reads were mapped to the current EquCab3.0 horse reference genome assembly, and we identified approximately 23.5 million single nucleotide variants and 2.3 million short indel variants. Our dataset included at least 7 million variants that were not previously reported. On average, each individual horse genome carried ∼5.7 million single nucleotides and 0.8 million small indel variants with respect to the reference genome assembly. The variants were functionally annotated. We provide two examples for potentially deleterious recessive alleles that were identified in a heterozygous state in individual genome sequences. Appropriate management of such deleterious recessive alleles in horse breeding programs should help to improve fertility and reduce the prevalence of heritable diseases. This comprehensive dataset has been made publicly available, will represent a valuable resource for future horse genetic studies and supports the goal of accelerating the rates of genetic gain in domestic horse.

Analysis of the genetic architecture of energy balance and its major determinants dry matter intake and energy-corrected milk yield in primiparous Holstein cows.

The focus of modern dairy cow breeding programs has shifted from being mainly yield based toward balanced goals that increasingly consider functional traits such as fertility, metabolic stability, and longevity. To improve these traits, a less pronounced energy deficit postpartum is considered a key challenge. On the other hand, feed efficiency and methane emissions are gaining importance, possibly leading to conflicts in the design of breeding goals. Dry matter intake (DMI) is one of the major determinants of energy balance (EB), and recently some efforts were undertaken to include DMI in genomic breeding programs. However, there is not yet a consensus on how this should be achieved as there are different goals in the course of lactation (i.e., reducing energy deficit postpartum vs. subsequently improving feed efficiency). Thus, the aim of this study was to gain more insight into the genetic architecture of energy metabolism across lactation by genetically dissecting EB and its major determinants DMI and energy-corrected milk (ECM) yield at different lactation stages applying random regression methodology and univariate and multivariate genomic analyses to data from 1,174 primiparous Holstein cows. Daily heritability estimates ranged from 0.29 to 0.49, 0.26 to 0.37, and 0.58 to 0.68 for EB, DMI, and ECM, respectively, across the first 180 d in milk (DIM). Genetic correlations between ECM and DMI were positive, ranging from 0.09 (DIM 11) to 0.36 (DIM 180). However, ECM and EB were negatively correlated (rg = -0.26 to -0.59). The strongest relationship was found at the onset of lactation, indicating that selection for increased milk yield at this stage will result in a more severe energy deficit postpartum. The results also indicate that EB is more affected by DMI (rg = 0.71 to 0.81) than by its other major determinant, ECM. Thus, breeding for a higher DMI in early lactation seems to be a promising strategy to improve the energy status of dairy cows. We found evidence that genetic regulation of energy homeostasis is complex, with trait- and lactation stage-specific quantitative trait loci suggesting that the trajectories of the analyzed traits can be optimized as mentioned above. Especially from the multivariate genomic analyses, we were able to draw some conclusions on the mechanisms involved and identified the genes encoding fumarate hydratase and adiponectin as highly promising candidates for EB, which will be further analyzed.

Linkage disequilibrium pattern and genome-wide association mapping for meat traits in multiple porcine F2 crosses.

In the present study, data from four F2 crosses were analysed and used to study the linkage disequilibrium (LD) structure within and across the crosses. Genome-wide association analyses (GWASes) for conductivity and dressing out meat traits were conducted using single-marker and Bayesian multi-marker models using the pooled data from all F2 crosses. Porcine F2 crosses generated from the distantly related founder breeds Wild Boar, Piétrain and Meishan, as well as from a porcine F2 cross from the closely related founder breed Piétrain and an F1 Large White × Landrace cross were pooled. A total of 2572 F2 animals were genotyped using a 62K SNP chip. The positions of the SNPs were based on genome assembly Sscrofa11.1. After post-alignment and genotype filtering, approximately 50K SNPs were usable for LD studies and GWASes. The main findings of the present study are that the breakdown of LD was faster in crosses from closely related founder breeds compared to crosses from distantly related founders. The fastest breakdown of LD was observed by pooling the data. Based on the single-marker results and LD structure, clusters and windows were built for 1-Mb intervals. For conductivity and dressing out, 183 and 191 nominal significant associations respectively and six and five clusters respectively were found. Dominance was important for conductivity, and considering dominance in GWASes improved the mapping signals. Most clear signals were found for conductivity on SSC6, 8 and 15 and for dressing out on SSC2 and 7. Considering dominance might contribute to the accuracy of genomic selection and serve as a guide for choosing mating pairs with good combining abilities. However, further research is needed to investigate if dominance is also important in crossbreed pig breeding schemes.

A genome-wide significant association on chromosome 2 for footrot resistance/susceptibility in Swiss White Alpine sheep.

Footrot is one of the most important causes of lameness in global sheep populations and is characterized by a bacterial infection of the interdigital skin. As a multifactorial disease, its clinical representation depends not only on pathogen factors and environmental components but also on the individual resistance/susceptibility of the host. A genetic component has been shown in previous studies; however, so far no causative genetic variant influencing the risk of developing footrot has been identified. In this study, we genotyped 373 Swiss White Alpine sheep, using the ovine high-density 600k SNP chip, in order to run a DNA-based comparison of individuals with known clinical footrot status. We performed a case-control genome-wide association study, which revealed a genome-wide significant association for SNP rs418747104 on ovine chromosome 2 at 81.2 Mb. The three best associated SNP markers were located at the MPDZ gene, which codes for the multiple PDZ domain crumbs cell polarity complex component protein, also known as multi-PDZ domain protein 1 (MUPP1). This protein is possibly involved in maintaining the barrier function and integrity of tight junctions. Therefore, we speculate that individuals carrying MPDZ variants may differ in their footrot resistance/susceptibility due to modified horn and interdigital skin integrity. In conclusion, our study reveals that MPDZ might represent a functional candidate gene, and further research is needed to explore its role in footrot affected sheep.

Genome-wide mapping of 10 calving and fertility traits in Holstein dairy cattle with special regard to chromosome 18.

Over the last decades, a dramatic decrease in reproductive performance has been observed in Holstein cattle and fertility problems have become the most common reason for a cow to leave the herd. The premature removal of animals with high breeding values results in both economic and breeding losses. For efficient future Holstein breeding, the identification of loci associated with low fertility is of major interest and thus constitutes the aim of this study. To reach this aim, a genome-wide combined linkage disequilibrium and linkage analysis (cLDLA) was conducted using data on the following 10 calving and fertility traits in the form of estimated breeding values: days from first service to conception of heifers and cows, nonreturn rate on d 56 of heifers and cows, days from calving to first insemination, days open, paternal and maternal calving ease, paternal and maternal stillbirth. The animal data set contained 2,527 daughter-proven Holstein bulls from Germany that were genotyped with Illumina's BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). For the cLDLA, 41,635 sliding windows of 40 adjacent single nucleotide polymorphisms (SNP) were used. At each window midpoint, a variance component analysis was executed using ASReml. The underlying mixed linear model included random quantitative trait locus (QTL) and polygenic effects. We identified 50 genome-wide significant QTL. The most significant peak was detected for direct calving ease at 59,179,424 bp on chromosome 18 (BTA18). Next, a mixed-linear model association (MLMA) analysis was conducted. A comparison of the cLDLA and MLMA results with special regard to BTA18 showed that the genome-wide most significant SNP from the MLMA was associated with the same trait and located on the same chromosome at 57,589,121 bp (i.e., about 1.5 Mb apart from the cLDLA peak). The results of 5 different cLDLA and 2 MLMA models, which included the fixed effects of either SNP or haplotypes, suggested that the cLDLA method outperformed the MLMA in accuracy and precision. The haplotype-based cLDLA method allowed for a more precise mapping and the definition of ancestral and derived QTL alleles, both of which are essential for the detection of underlying quantitative trait nucleotides.

Genetic variability of the equine casein genes.

The casein genes are known to be highly variable in typical dairy species, such as cattle and goat, but the knowledge about equine casein genes is limited. Nevertheless, mare milk production and consumption is gaining importance because of its high nutritive value, use in naturopathy, and hypoallergenic properties with respect to cow milk protein allergies. In the current study, the open reading frames of the 4 casein genes CSN1S1 (αS1-casein), CSN2 (ß-casein), CSN1S2 (αS2-casein), and CSN3 (κ-casein) were resequenced in 253 horses of 14 breeds. The analysis revealed 21 nonsynonymous nucleotide exchanges, as well as 11 synonymous nucleotide exchanges, leading to a total of 31 putative protein isoforms predicted at the DNA level, 26 of which considered novel. Although the majority of the alleles need to be confirmed at the transcript and protein level, a preliminary nomenclature was established for the equine casein alleles.

Identification of a haplotype associated with cholesterol deficiency and increased juvenile mortality in Holstein cattle.

Over the last decades, several genetic disorders have been discovered in cattle. However, the genetic background of disorders in calves is less reported. Recently, German cattle farmers reported on calves from specific matings with chronic diarrhea and retarded growth of unknown etiology. Affected calves did not respond to any medical treatment and died within the first months of life. These calves were underdeveloped in weight and showed progressive and severe emaciation despite of normal feed intake. Hallmark findings of the blood biochemical analysis were pronounced hypocholesterolemia and deficiency of fat-soluble vitamins. Results of the clinical and blood biochemical examination had striking similarities with findings reported in human hypobetalipoproteinemia. Postmortem examination revealed near-complete atrophy of the body fat reserves including the spinal canal and bone marrow. To identify the causal region, we performed a genome-wide association study with 9 affected and 21,077 control animals genotyped with the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA), revealing a strong association signal on BTA 11. Subsequent autozygosity mapping identified a disease-associated haplotype encompassing 1.01 Mb. The segment of extended homozygosity contains 6 transcripts, among them the gene APOB, which is causal for cholesterol disorders in humans. However, results from multi-sample variant calling of 1 affected and 47 unaffected animals did not detect any putative causal mutation. The disease-associated haplotype has an important adverse effect on calf mortality in the homozygous state when comparing survival rates of risk matings vs. non-risk matings. Blood cholesterol values of animals are significantly associated with the carrier status indicating a codominant inheritance. The frequency of the haplotype in the current Holstein population was estimated to be 4.2%. This study describes the identification and phenotypic manifestation of a new Holstein haplotype characterized by pronounced hypocholesterolemia, chronic emaciation, growth retardation, and increased mortality in young cattle, denominated as cholesterol deficiency haplotype. Our genomic investigations and phenotypic examinations provide additional evidence for a mutation within the APOB gene causing cholesterol deficiency in Holstein cattle.

Short communication: Use of genomic and metabolic information as well as milk performance records for prediction of subclinical ketosis risk via artificial neural networks.

Subclinical ketosis is one of the most prevalent metabolic disorders in high-producing dairy cows during early lactation. This renders its early detection and prevention important for both economical and animal-welfare reasons. Construction of reliable predictive models is challenging, because traits like ketosis are commonly affected by multiple factors. In this context, machine learning methods offer great advantages because of their universal learning ability and flexibility in integrating various sorts of data. Here, an artificial-neural-network approach was applied to investigate the utility of metabolic, genetic, and milk performance data for the prediction of milk levels of ß-hydroxybutyrate within and across consecutive weeks postpartum. Data were collected from 218 dairy cows during their first 5wk in milk. All animals were genotyped with a 50,000 SNP panel, and weekly information on the concentrations of the milk metabolites glycerophosphocholine and phosphocholine as well as milk composition data (milk yield, fat and protein percentage) was available. The concentration of ß-hydroxybutyric acid in milk was used as target variable in all prediction models. Average correlations between observed and predicted target values up to 0.643 could be obtained, if milk metabolite and routine milk recording data were combined for prediction at the same day within weeks. Predictive performance of metabolic as well as milk performance-based models was higher than that of models based on genetic information.

Bos indicus introgression into (peri-)alpine cattle breeds - evidence from the analysis of bovine whey protein variants.

The major bovine whey proteins, α-lactalbumin (α-LA) and ß-lactoglobulin (ß-LG), exhibit breed-specific genetic variation. The aim of this study was to identify possible new protein variants and determine the distribution of variants across a variety of 18 taurine and indicine cattle breeds applying a DNA-based sequencing approach. To this end, the open reading frames of the respective genes (LALBA and LGB) were sequenced in 476 animals. Within the LALBA gene, a previously unknown synonymous and a previously undesignated non-synonymous nucleotide exchange were identified. Furthermore, two known α-LA variants (A and B) and four known ß-LG variants (A, B, C and W) were determined. The occurrence of typical indicine variants in some taurine cattle breeds, such as Suisse Eringer, German Hinterwälder and Hungarian Grey Steppe, further supports the hypothesis of ancient Bos indicus introgression into (peri-)alpine cattle breeds.

Genetic and genomic dissection of dry matter intake at different lactation stages in primiparous Holstein cows.

Dry matter intake (DMI) and feed efficiency are economically relevant traits. Simultaneous selection for low DMI and high milk yield might improve feed efficiency, but bears the risk of aggravating the negative energy balance and related health problems in early lactation. Lactation stage-specific selection might provide a possibility to optimize the trajectory of DMI across days in milk (DIM), but requires in-depth knowledge about genetic parameters within and across lactation stages. Within the current study, daily heritabilities and genetic correlations between DMI records from different lactation stages were estimated using random regression models based on 910 primiparous Holstein cows. The heritability estimates from DIM 11 to 180 follow a slightly parabolic curve varying from 0.26 (DIM 121) to 0.37 (DIM 11 and 180). Genetic correlations estimated between DIM 11, 30, 80, 130, and 180 were all positive, ranging from 0.29 (DIM 11 and 180) to 0.97 (DIM 11 and 30; i.e., the correlations are inversely related to the length of the interval between compared DIM). Deregressed estimated breeding values for the same lactation days were used as phenotypes in sequential genome-wide association studies using 681 cows drawn from the study population and genotyped for the Illumina SNP50 BeadChip (Illumina Inc., San Diego, CA). A total of 21 SNP on 10 chromosomes exceeded the chromosome-wise significance threshold for at least 1 analyzed DIM, pointing to some interesting candidate genes directly involved in the regulation of feed intake. Association signals were restricted to certain lactation stages, thus supporting the genetic correlations. Partitioning the explained variance onto chromosomes revealed a large contribution of Bos taurus autosome 7 not harboring any associated marker in the current study. The results contribute to the knowledge about the genetic architecture of the complex phenotype DMI and might provide valuable information for future selection efforts.

Effect of genetic merit for energy balance on luteal activity and subsequent reproductive performance in primiparous Holstein-Friesian cows.

Postpartum energy status is critically important to fertility. However, studies dealing with the relationship between both traits are rare and most refer only to the phenotypic level. In this study, random regression models were used to generate cow-specific lactation curves for daily breeding values (BV) of energy balance (EB) to assess the effect of genetic merit for energy status on different traits derived from progesterone profiles and on subsequent reproductive performance of high-producing dairy cows. Individual feed intake, milk yield, and live weight were recorded for lactation d 11 to 180, and EB was estimated on a daily basis. The results provided the basis for the estimation of BV for 824 primiparous Holstein-Friesian cows. For a subset of these cows (n = 334), progesterone profiles for the resumption of ovarian activity were available. Four different traits describing the genetic merit for EB were defined to evaluate their relationship with fertility. Two EB traits referred to the period in which the average daily EB across all cows was negative (d 11 to 55 postpartum), and 2 parameters were designed considering only daily BV for d 11 to 180 in lactation that were negative. We found that cows with a high genetic merit for EB had a significantly earlier resumption of ovarian activity postpartum. Thus, an EB (indicator) trait should be included in future breeding programs to reduce the currently prolonged anovulatory intervals after parturition.

Whole-genome association study for energy balance and fat/protein ratio in German Holstein bull dams.

The metabolic status of cows is important to health and fertility, especially in early lactation, and energy balance (EB) and fat/protein ratio (FPR) are considered as appropriate indicators for metabolic disorders. The aim of this study was to detect SNPs (single nucleotide polymorphisms) associated with EB and FPR in German Holstein bull dams belonging to the research herd Karkendamm. Bull dams were genotyped using the Illumina Bovine SNP 50K Bead chip(®) comprising 54 001 SNPs. A total of 43 593 SNPs and 586 (EB) and 668 (FPR) bull dams passed the quality control criteria. Phenotypes were deregressed breeding values estimated via random regression animal models for lactation days 11, 20, 30, and 42 for EB and FPR. Whole-genome association analyses were carried out fitting principal components as covariates to adjust for genetic substructure. Permutation tests were applied to estimate genome-wise significance. Across all observed lactation days, 19 SNPs located in four different intervals on chromosomes 1, 14, 16, and 27 were detected. For EB, seven markers across four chromosomes were identified. There was no overlap between markers associated with FPR and EB. SNPs associated with FPR were mostly located in QTL regions for milk production traits, especially in the region of DGAT1, whereas SNPs associated with EB mainly showed positional relationships to previously described QTL regions affecting functional traits, especially fertility.

A genome-wide association study indicates LCORL/NCAPG as a candidate locus for withers height in German Warmblood horses.

A genome-wide association scan for loci affecting withers height was conducted in 782 German Warmblood stallions, which were genotyped using the Illumina EquineSNP50 Bead Chip. A principal components approach was applied to correct for population structure. The analysis revealed a single major QTL on ECA3 explaining ~18 per cent of the phenotypic variance, which is in concordance with recent reports from other horse populations. The LCORL/NCAPG locus represents a strong candidate gene for this QTL. This locus is among a small number that have consistently been identified to influence human height in several large meta-analyses. Furthermore, a mutation within the NCAPG gene was found to affect growth and body frame size in cattle. Together with the results of this study in German Warmbloods, these findings strongly indicate LCORL/NCAPG as a candidate locus for withers height in horses. Further studies are, however, needed to confirm this.

Angiopoietin-2 (ANGPT2) as a candidate gene for somatic cell score in German Holstein cattle.

This study evaluated the bovine angiopoietin-2 (ANGPT2) gene as a functional and positional candidate gene underlying a previously fine mapped quantitative trait locus (QTL) for somatic cell score on bovine chromosome 27. The gene product angiopoietin-2 is directly involved in the extravasation of neutrophils, making it a promising candidate to control the amount of somatic cells in milk. A total of 11 polymorphisms were identified within the gene by comparatively resequencing the entire open reading frame of the gene as well as adjacent intronic regions. Four selected variants were genotyped in the same granddaughter design used for QTL mapping and an association study was carried out applying 2 complementary approaches. A variable number of tandem repeats in intron 7 of the gene was found to be significantly associated with cell score in all approaches and explains approximately half of the QTL variance. Analysis of ANGPT2 mRNA expression in different localizations of the udder in animals putatively carrying divergent QTL alleles revealed differential expression in the udder lymph node. Together with the physiological role of angiopoietin-2, these results support a role of ANGPT2 in the genetic control of somatic cell score. Further studies are, however, needed to further underpin this hypothesis.

DNA-based identification of novel bovine casein gene variants.

In cattle, at least 39 variants of the 4 casein proteins (α(S1)-, ß-, α(S2)- and κ-casein) have been described to date. Many of these variants are known to affect milk-production traits, cheese-processing properties, and the nutritive value of milk. They also provide valuable information for phylogenetic studies. So far, the majority of studies exploring the genetic variability of bovine caseins considered European taurine cattle breeds and were carried out at the protein level by electrophoretic techniques. This only allows the identification of variants that, due to amino acid exchanges, differ in their electric charge, molecular weight, or isoelectric point. In this study, the open reading frames of the casein genes CSN1S1, CSN2, CSN1S2, and CSN3 of 356 animals belonging to 14 taurine and 3 indicine cattle breeds were sequenced. With this approach, we identified 23 alleles, including 5 new DNA sequence variants, with a predicted effect on the protein sequence. The new variants were only found in indicine breeds and in one local Iranian breed, which has been phenotypically classified as a taurine breed. A multidimensional scaling approach based on available SNP chip data, however, revealed an admixture of taurine and indicine populations in this breed as well as in the local Iranian breed Golpayegani. Specific indicine casein alleles were also identified in a few European taurine breeds, indicating the introgression of indicine breeds into these populations. This study shows the existence of substantial undiscovered genetic variability of bovine casein loci, especially in indicine cattle breeds. The identification of new variants is a valuable tool for phylogenetic studies and investigations into the evolution of the milk protein genes.

Development of a new grading system to assess the foster performance of lactating sows.

Increasing litter size has created the need for more sophisticated, accurate, and welfare-oriented systems for assessing the foster performance of lactating sows. The estimation of milk yield alone is not sufficient for meeting these requirements. Therefore, the aim of the current study was to develop a grading system for assessing the foster performance of lactating sows that can be easily applied in commercial farm practice. Data were collected in two German conventional farrow-to-feeder farms with a total sample size of 639 sows (4.05 ± 2.86 parities) and 1 728 litters. Besides general performance data, the piglets were weighed individually within the first 24 hours after birth and at the peak of lactation (day 18.22 ± 2.48). Based on these data, we proposed a new score referring to the milk score (MS). This score was compared with the commonly used formula for estimating milk yield (est. MY), which solely involves litter weight gain and litter size. The improvement of the developed MS allowed us to distinguish between the birth and foster performances of the lactating sows through considering cross-fostering, litter size, individual piglet weights, and piglet mortality during lactation. Both scores showed a similar progression across parities. It was found that litter size had a significant impact on the performance of lactating sows. A high est. MY was found to be associated with a significantly higher number of piglets per litter (15.79 ± 2.20), lower weight gain per piglet, and increased piglet mortality during lactation compared with sows with high MS, which showed a smaller litter size (13.51 ± 2.18) (P < 0.05). The focus on smaller litter size indicates a performance limitation, which seems to be related to the average teat number of 13-15 teats per sow. We recommend the consideration of the number of functional teats, because a litter size above it will not result in a sow having higher foster performance. In conclusion, as an extension of the common est. MY calculation, the MS considers cross-fostering as current farm-management practice when dealing with larger litters. Our recommendations emphasise the importance of an MS which indicates smaller litter size, higher piglet weight gain, and lower piglet mortality during lactation; these factors are related to an improvement in animal welfare for sows and piglets. Moreover, the presented MS could be used to develop a management tool for farmers to assess the foster performance of lactating sows, considering individual farm-management practices.

The placental growth factor (PGF)--a positional and functional candidate gene influencing calving ease and stillbirth in German dairy cattle.

The bovine placental growth factor-encoding gene (PGF) was analysed as a positional and functional candidate gene for the maternal effect on stillbirth and calving ease in first parity. Prominent levels of PGF expression have been reported for the whole human placenta and umbilical vein endothelial cells. Modulation of angiogenesis, vessel remodelling and vascular permeability during implantation and placentation suggest an influence on trophoblast function during pregnancy. Changes of expression or protein function may therefore be crucial to pregnancy and parturition. By comparative sequencing of bulls with extreme approximate daughter yield deviations for calving traits, we identified 37 SNPs and two insertions/deletions within the PGF gene. Seventeen of the identified polymorphisms were genotyped in 368 selected bulls and tested for association with approximate daughter yield deviations for calving traits. In a single marker analysis, all SNPs were significantly associated with maternal stillbirth and calving ease first parity. The allele substitutions of the significant SNPs explain 8% to 14% and 8% to 15% of the additive genetic variance for maternal stillbirth and maternal calving ease first parity, respectively. There is no evidence that any of the polymorphisms identified within this study could be the causal mutation underlying the QTL, which is likely to be a regulatory mutation. In summary, we report polymorphisms in the bovine PGF gene significantly associated with the maternal effect on stillbirth and calving ease in animals under selection. These results should be confirmed and extended in further studies to identify the causal mutation underlying the QTL analysed.

Exploration of relationships between production and fertility traits in dairy cattle via association studies of SNPs within candidate genes derived by expression profiling.

The objective of this work was to integrate findings from functional genomics studies with genome-wide association studies for fertility and production traits in dairy cattle. Association analyses of production and fertility traits with SNPs located within or close to 170 candidate genes derived from two gene expression studies and from the literature were performed. Data from 2294 Holstein bulls genotyped for 39557 SNPs were used. A total of 111 SNPs were located on chromosomal segments covered by a candidate gene. Allele substitution effects for each SNP were estimated using a mixed model with a fixed effect of marker and a random polygenic effect. Assumed covariance was derived either from marker or from pedigree information. Results from the analysis with the kinship matrix built from marker genotypes were more conservative than from the analysis with the pedigree-derived relationship matrix. From sixteen SNPs with significant effects on both classes of traits, ten provided evidence of an antagonistic relationship between productivity and fertility. However, we found four SNPs with favourable effects on fertility and on yield traits, one SNP with favourable effects on fertility and percentage traits, and one SNP with antagonistic effects on two fertility traits. While most quantitative genetic studies have proven genetic antagonisms between yield and functional traits, improvements in both production and functionality may be possible when focusing on a few relevant SNPs. Investigations combining input from quantitative genetics and functional genomics with association analysis may be applied for the identification of such SNPs.