JAK-STAT signaling maintains homeostasis in T cells and macrophages.

Immune cells need to sustain a state of constant alertness over a lifetime. Yet, little is known about the regulatory processes that control the fluent and fragile balance that is called homeostasis. Here we demonstrate that JAK-STAT signaling, beyond its role in immune responses, is a major regulator of immune cell homeostasis. We investigated JAK-STAT-mediated transcription and chromatin accessibility across 12 mouse models, including knockouts of all STAT transcription factors and of the TYK2 kinase. Baseline JAK-STAT signaling was detected in CD8+ T cells and macrophages of unperturbed mice-but abrogated in the knockouts and in unstimulated immune cells deprived of their normal tissue context. We observed diverse gene-regulatory programs, including effects of STAT2 and IRF9 that were independent of STAT1. In summary, our large-scale dataset and integrative analysis of JAK-STAT mutant and wild-type mice uncovered a crucial role of JAK-STAT signaling in unstimulated immune cells, where it contributes to a poised epigenetic and transcriptional state and helps prepare these cells for rapid response to immune stimuli.

The genomic distribution of transposable elements is driven by spatially variable purifying selection.

It is widely accepted that the genomic distribution of transposable elements (TEs) mainly reflects the outcome of purifying selection and insertion bias (1). Nevertheless, the relative importance of these two evolutionary forces could not be tested thoroughly. Here, we introduce an experimental system, which allows separating purifying selection from TE insertion bias. We used experimental evolution to study the TE insertion patterns in Drosophila simulans founder populations harboring 1040 insertions of an active P-element. After 10 generations at a large population size, we detected strong selection against P-element insertions. The exception were P-element insertions in genomic regions for which a strong insertion bias has been proposed (2-4). Because recurrent P-element insertions cannot explain this pattern, we conclude that purifying selection, with variable strength along the chromosomes, is the major determinant of the genomic distribution of P-elements. Genomic regions with relaxed purifying selection against P-element insertions exhibit normal levels of purifying selection against base substitutions. This suggests that different types of purifying selection operate on base substitutions and P-element insertions. Our results highlight the power of experimental evolution to understand basic evolutionary processes, which are difficult to infer from patterns of natural variation alone.

Reliability of fluoroscopic examination of nasopharyngeal dorsoventral dimension change in pugs and French bulldogs.

OBJECTIVE: To compare intra- and interobserver agreements in two-dimensional measurements of changes in nasopharyngeal dimensions during breathing in pugs and French bulldogs. STUDY DESIGN: Experimental randomized study. ANIMALS: A total of 20 French bulldogs and 16 pugs. METHODS: Four observers with different levels of experience measured the dorsoventral dimensions of the nasopharynx during inspiration and expiration on fluoroscopy videos. Measurements were performed at the maximal narrowing of the nasopharynx for the functional method and at the level of the tip of the epiglottis for the anatomically adjusted method. The intra- and interobserver agreements of the measurements, ratio of the dynamic nasopharyngeal change (ΔL), and grade of nasopharyngeal (NP) collapse (no, partial or complete) were evaluated. RESULTS: The functional method resulted in intraobserver correlation coefficients of 0.532 (p < .01) and 0.751 (p < .01) and interobserver correlation coefficients of 0.378 (p < .01) and 0.621 (p < .01) for NP collapse grade and ΔL, respectively. The anatomically adjusted method, 0.491 (p < .01) and 0.576 (p < .01) and 0.495 (p < .01) and 0.729 (p < .01) for NP collapse grade and ΔL, respectively, were being used. One observer (radiologist) achieved intraobserver correlation coefficients >0.9 for both methods. CONCLUSION: Fair interobserver agreement was found for NP collapse grade (functional method), moderate intra- and interobserver agreements were found for NP collapse grade and ΔL (both methods) while intraobserver agreement for ΔL was good (functional method). CLINICAL SIGNIFICANCE: Both methods seem repeatable and reproducible but only for experienced radiologists. The use of ΔL may offer higher repeatability and reproducibility than grade of NP collapse regardless of the method used.

Listeria monocytogenes infection rewires host metabolism with regulatory input from type I interferons.

Listeria monocytogenes (L. monocytogenes) is a food-borne bacterial pathogen. Innate immunity to L. monocytogenes is profoundly affected by type I interferons (IFN-I). Here we investigated host metabolism in L. monocytogenes-infected mice and its potential control by IFN-I. Accordingly, we used animals lacking either the IFN-I receptor (IFNAR) or IRF9, a subunit of ISGF3, the master regulator of IFN-I-induced genes. Transcriptomes and metabolite profiles showed that L. monocytogenes infection induces metabolic rewiring of the liver. This affects various metabolic pathways including fatty acid (FA) metabolism and oxidative phosphorylation and is partially dependent on IFN-I signaling. Livers and macrophages from Ifnar1-/- mice employ increased glutaminolysis in an IRF9-independent manner, possibly to readjust TCA metabolite levels due to reduced FA oxidation. Moreover, FA oxidation inhibition provides protection from L. monocytogenes infection, explaining part of the protection of Irf9-/- and Ifnar1-/- mice. Our findings define a role of IFN-I in metabolic regulation during L. monocytogenes infection. Metabolic differences between Irf9-/- and Ifnar1-/- mice may underlie the different susceptibility of these mice against lethal infection with L. monocytogenes.

Genome-wide selection signatures reveal widespread synergistic effects of two different stressors in Drosophila melanogaster.

Experimental evolution combined with whole-genome sequencing (evolve and resequence (E&R)) is a powerful approach to study the adaptive architecture of selected traits. Nevertheless, so far the focus has been on the selective response triggered by a single stressor. Building on the highly parallel selection response of founder populations with reduced variation, we evaluated how the presence of a second stressor affects the genomic selection response. After 20 generations of adaptation to laboratory conditions at either 18°C or 29°C, strong genome-wide selection signatures were observed. Only 38% of the selection signatures can be attributed to laboratory adaptation (no difference between temperature regimes). The remaining selection responses are either caused by temperature-specific effects, or reflect the joint effects of temperature and laboratory adaptation (same direction, but the magnitude differs between temperatures). The allele frequency changes resulting from the combined effects of temperature and laboratory adaptation were more extreme in the hot environment for 83% of the affected genomic regions-indicating widespread synergistic effects of the two stressors. We conclude that E&R with reduced genetic variation is a powerful approach to study genome-wide fitness consequences driven by the combined effects of multiple environmental factors.

Genetic redundancy fuels polygenic adaptation in Drosophila.

The genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic-i.e., result from selection on a large number of genetic loci-but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the difficulty in detecting small allele frequency changes (AFCs) across many contributing loci. To resolve this, we use laboratory natural selection to detect signatures for selective sweeps and polygenic adaptation. We exposed 10 replicates of a Drosophila simulans population to a new temperature regime and uncovered a polygenic architecture of an adaptive trait with high genetic redundancy among beneficial alleles. We observed convergent responses for several phenotypes-e.g., fitness, metabolic rate, and fat content-and a strong polygenic response (99 selected alleles; mean s = 0.059). However, each of these selected alleles increased in frequency only in a subset of the evolving replicates. We discerned different evolutionary paradigms based on the heterogeneous genomic patterns among replicates. Redundancy and quantitative trait (QT) paradigms fitted the experimental data better than simulations assuming independent selective sweeps. Our results show that natural D. simulans populations harbor a vast reservoir of adaptive variation facilitating rapid evolutionary responses using multiple alternative genetic pathways converging at a new phenotypic optimum. This key property of beneficial alleles requires the modification of testing strategies in natural populations beyond the search for convergence on the molecular level.

Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature.

BACKGROUND: Insect pest control programs often use periods of insecticide treatment with intermittent breaks, to prevent fixing of mutations conferring insecticide resistance. Such mutations are typically costly in an insecticide-free environment, and their frequency is determined by the balance between insecticide treatment and cost of resistance. Ace, a key gene in neuronal signaling, is a prominent target of many insecticides and across several species, three amino acid replacements (I161V, G265A, and F330Y) provide resistance against several insecticides. Because temperature disturbs neuronal signaling homeostasis, we reasoned that the cost of insecticide resistance could be modulated by ambient temperature. RESULTS: Experimental evolution of a natural Drosophila simulans population at hot and cold temperature regimes uncovered a surprisingly strong effect of ambient temperature. In the cold temperature regime, the resistance mutations were strongly counter selected (s = - 0.055), but in a hot environment, the fitness costs of resistance mutations were reduced by almost 50% (s = - 0.031). We attribute this unexpected observation to the advantage of the reduced enzymatic activity of resistance mutations in hot environments. CONCLUSION: We show that fitness costs of insecticide resistance genes are temperature-dependent and suggest that the duration of insecticide-free periods need to be adjusted for different climatic regions to reflect these costs. We suggest that such environment-dependent fitness effects may be more common than previously assumed and pose a major challenge for modeling climate change.

A missense mutation in TUBD1 is associated with high juvenile mortality in Braunvieh and Fleckvieh cattle.

BACKGROUND: Haplotypes with reduced or missing homozygosity may harbor deleterious alleles that compromise juvenile survival. A scan for homozygous haplotype deficiency revealed a short segment on bovine chromosome 19 (Braunvieh haplotype 2, BH2) that was associated with high juvenile mortality in Braunvieh cattle. However, the molecular genetic underpinnings and the pathophysiology of BH2 remain to be elucidated. RESULTS: The frequency of BH2 was 6.5 % in 8,446 Braunvieh animals from the national bovine genome databases. Both perinatal and juvenile mortality of BH2 homozygous calves were higher than the average in Braunvieh cattle resulting in a depletion of BH2 homozygous adult animals (P = 9.3x10(-12)). The analysis of whole-genome sequence data from 54 Braunvieh animals uncovered a missense mutation in TUBD1 (rs383232842, p.H210R) that was compatible with recessive inheritance of BH2. The availability of sequence data of 236 animals from diverse bovine populations revealed that the missense mutation also segregated at a low frequency (1.7 %) in the Fleckvieh breed. A validation study in 37,314 Fleckvieh animals confirmed high juvenile mortality of homozygous calves (P = 2.2x10(-15)). Our findings show that the putative disease allele is located on an ancestral haplotype that segregates in Braunvieh and Fleckvieh cattle. To unravel the pathophysiology of BH2, six homozygous animals were examined at the animal clinic. Clinical and pathological findings revealed that homozygous calves suffered from chronic airway disease possibly resulting from defective cilia in the respiratory tract. CONCLUSIONS: A missense mutation in TUBD1 is associated with high perinatal and juvenile mortality in Braunvieh and Fleckvieh cattle. The mutation is located on a common haplotype likely originating from an ancient ancestor of Braunvieh and Fleckvieh cattle. Our findings demonstrate for the first time that deleterious alleles may segregate across closed cattle breeds without recent admixture. Homozygous calves suffer from chronic airway disease resulting in poor growth performance and high juvenile mortality. The respiratory manifestations resemble key features of diseases resulting from impaired function of airway cilia.

Evaluation of variant identification methods for whole genome sequencing data in dairy cattle.

BACKGROUND: Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. The challenges of variant identification in organisms with lower quality reference genomes are less well documented. We explored the consequences of commonly recommended preparatory steps and the effects of single and multi sample variant identification methods using four publicly available software applications (Platypus, HaplotypeCaller, Samtools and UnifiedGenotyper) on whole genome sequence data of 65 key ancestors of Swiss dairy cattle populations. Accuracy of calling next-generation sequence variants was assessed by comparison to the same loci from medium and high-density single nucleotide variant (SNV) arrays. RESULTS: The total number of SNVs identified varied by software and method, with single (multi) sample results ranging from 17.7 to 22.0 (16.9 to 22.0) million variants. Computing time varied considerably between software. Preparatory realignment of insertions and deletions and subsequent base quality score recalibration had only minor effects on the number and quality of SNVs identified by different software, but increased computing time considerably. Average concordance for single (multi) sample results with high-density chip data was 58.3% (87.0%) and average genotype concordance in correctly identified SNVs was 99.2% (99.2%) across software. The average quality of SNVs identified, measured as the ratio of transitions to transversions, was higher using single sample methods than multi sample methods. A consensus approach using results of different software generally provided the highest variant quality in terms of transition/transversion ratio. CONCLUSIONS: Our findings serve as a reference for variant identification pipeline development in non-human organisms and help assess the implication of preparatory steps in next-generation sequencing pipelines for organisms with incomplete reference genomes (pipeline code is included). Benchmarking this information should prove particularly useful in processing next-generation sequencing data for use in genome-wide association studies and genomic selection.

Genomic prediction based on runs of homozygosity.

BACKGROUND: Genomic prediction is based on the accurate estimation of the genomic relationships among and between training animals and selection candidates in order to obtain accurate estimates of the genomic estimated breeding values (GEBV). Various methods have been used to predict GEBV based on population-wide linkage disequilibrium relationships (G IBS ) or sometimes on linkage analysis relationships (G LA ). Here, we propose a novel method to predict GEBV based on a genomic relationship matrix using runs of homozygosity (G ROH ). Runs of homozygosity were used to derive probabilities of multi-locus identity by descent chromosome segments. The accuracy and bias of the prediction of GEBV using G ROH were compared to those using G IBS and G LA . Comparisons were performed using simulated datasets derived from a random pedigree and a real pedigree of Italian Brown Swiss bulls. The comparison of accuracies of GEBV was also performed on data from 1086 Italian Brown Swiss dairy cattle. RESULTS: Simulations with various thresholds of minor allele frequency for markers and quantitative trait loci showed that G ROH achieved consistently more accurate GEBV (0 to 4% points higher) than G IBS and G LA . The bias of GEBV prediction for simulated data was higher based on the real pedigree than based on a random pedigree. In the analyses with real data, G ROH and G LA had similar accuracies. However, G LA achieved a higher accuracy when the prediction was done on the youngest animals. The G IBS matrices calculated with and without standardized marker genotypes resulted in similar accuracies. CONCLUSIONS: The present study proposes G ROH as a novel method to estimate genomic relationship matrices and predict GEBV based on runs of homozygosity and shows that it can result in higher or similar accuracies of GEBV prediction than G LA , except for the real data analysis with validation of young animals. Compared to G IBS , G ROH resulted in more accurate GEBV predictions.

Estimates of missing heritability for complex traits in Brown Swiss cattle.

BACKGROUND: Genomic selection estimates genetic merit based on dense SNP (single nucleotide polymorphism) genotypes and phenotypes. This requires that SNPs explain a large fraction of the genetic variance. The objectives of this work were: (1) to estimate the fraction of genetic variance explained by dense genome-wide markers using 54 K SNP chip genotyping, and (2) to evaluate the effect of alternative marker-based relationship matrices and corrections for the base population on the fraction of the genetic variance explained by markers. METHODS: Two alternative marker-based relationship matrices were estimated using 35 706 SNPs on 1086 dairy bulls. Both pedigree- and marker-based relationship matrices were fitted simultaneously or separately in an animal model to estimate the fraction of variance not explained by the markers, i.e. the fraction explained by the pedigree. The phenotypes considered in the analysis were the deregressed estimated breeding values (dEBV) for milk, fat and protein yield and for somatic cell score (SCS). RESULTS: When dEBV were not sufficiently accurate (50 or 70%), the estimated fraction of the genetic variance explained by the markers was around 65% for yield traits and 45% for SCS. Scaling marker genotypes with locus-specific frequencies of heterozygotes slightly increased the variance explained by markers, compared with scaling with the average frequency of heterozygotes across loci. The estimated fraction of the genetic variance explained by the markers using separately both relationships matrices followed the same trends but the results were underestimated. With less accurate dEBV estimates, the fraction of the genetic variance explained by markers was underestimated, which is probably an artifact due to the dEBV being estimated by a pedigree-based animal model. CONCLUSIONS: When using only highly accurate dEBV, the proportion of the genetic variance explained by the Illumina 54 K SNP chip was approximately 80% for Brown Swiss cattle. These results depend on the SNP chip used and the family structure of the population, i.e. more dense SNPs and closer family relationships are expected to result in a higher fraction of the variance explained by the SNPs.

The genomic signature of splicing-coupled selection differs between long and short introns.

Understanding the function of noncoding regions in the genome, such as introns, is of central importance to evolutionary biology. One approach is to assay for the targets of natural selection. On one hand, the sequence of introns, especially short introns, appears to evolve in an almost neutral manner. Whereas on the other hand, a large proportion of intronic sequence is under selective constraint. This discrepancy is largely dependent on intron length and differences in the methods used to infer selection. We have used a method based on DNA strand asymmetery that does not require comparison with any putatively neutrally evolving sequence, nor sequence conservation between species, to detect selection within introns. The strongest signal we identify is associated with short introns. This signal comes from a family of motifs that could act as cryptic 5' splice sites during mRNA processing, suggesting a mechanistic justification underlying this signal of selection. Together with an analysis of intron length and splice site strength, we observe that the genomic signature of splicing-coupled selection differs between long and short introns.

Extensive paternal mtDNA leakage in natural populations of Drosophila melanogaster.

Strict maternal inheritance is considered a hallmark of animal mtDNA. Although recent reports suggest that paternal leakage occurs in a broad range of species, it is still considered an exceptionally rare event. To evaluate the impact of paternal leakage on the evolution of mtDNA, it is essential to reliably estimate the frequency of paternal leakage in natural populations. Using allele-specific real-time quantitative PCR (RT-qPCR), we show that heteroplasmy is common in natural populations with at least 14% of the individuals carrying multiple mitochondrial haplotypes. However, the average frequency of the minor mtDNA haplotype is low (0.8%), which suggests that this pervasive heteroplasmy has not been noticed before due to a lack of power in sequencing surveys. Based on the distribution of mtDNA haplotypes in the offspring of heteroplasmic mothers, we found no evidence for strong selection against one of the haplotypes. We estimated that the rate of paternal leakage is 6% and that at least 100 generations are required for complete sorting of mtDNA haplotypes. Despite the high proportion of heteroplasmic individuals in natural populations, we found no evidence for recombination between mtDNA molecules, suggesting that either recombination is rare or recombinant haplotypes are counter-selected. Our results indicate that evolutionary studies using mtDNA as a marker might be biased by paternal leakage in this species.

Nonsense-mediated decay enables intron gain in Drosophila.

Intron number varies considerably among genomes, but despite their fundamental importance, the mutational mechanisms and evolutionary processes underlying the expansion of intron number remain unknown. Here we show that Drosophila, in contrast to most eukaryotic lineages, is still undergoing a dramatic rate of intron gain. These novel introns carry significantly weaker splice sites that may impede their identification by the spliceosome. Novel introns are more likely to encode a premature termination codon (PTC), indicating that nonsense-mediated decay (NMD) functions as a backup for weak splicing of new introns. Our data suggest that new introns originate when genomic insertions with weak splice sites are hidden from selection by NMD. This mechanism reduces the sequence requirement imposed on novel introns and implies that the capacity of the spliceosome to recognize weak splice sites was a prerequisite for intron gain during eukaryotic evolution.

Comparing effects of food mechanical properties on oral processing behaviors in two sympatric lemur species.

OBJECTIVES: The link between diet and the masticatory apparatus in primates is complex. We investigated how food mechanical properties (FMPs) and food geometry affect feeding behaviors and subsequent jaw loading. We compared oral processing in two sympatric lemur species with distinct diets and mandibular morphologies. MATERIALS AND METHODS: All-day focal follows of Lemur catta (Lc) and Propithecus verreauxi (Pv) were conducted in both the dry and wet seasons at Beza Mahafaly Special Reserve. We collected activity budget data, filmed feeding bouts, and collected food items to measure their mechanical properties with an FLS-1 portable tester. Feeding videos for the top food items they spent the most time consuming were analyzed frame-by-frame to assess bite and chew numbers and rates. RESULTS: Lc bite more and at a slower rate on tougher (maximum) foods, chew more for tougher (average) foods, and chew less for stiffer leaves. Pv initially increase chew number for tougher (average) foods, but their behavior is less affected as food toughness increases. Pv chew less and more slowly but spend more of the day feeding than Lc. Additionally, they have a tougher (maximum) diet than Lc. DISCUSSION: Lc adjust their feeding behaviors depending on the FMPs of their top food items, while Pv feed more consistently. The more robust masticatory apparatus of Pv may not require them to adjust their feeding behaviors for more mechanically challenging foods. Furthermore, the two species show distinct differences in chewing. Exploring chewing on a daily scale could aid in understanding its impact on the loading of the masticatory apparatus.

Unravelling the sexual developmental biology of Cystoisospora suis, a model for comparative coccidian parasite studies.

Introduction: The apicomplexan parasite Cystoisospora suis has global significance as an enteropathogen of suckling piglets. Its intricate life cycle entails a transition from an asexual phase to sexual development, ultimately leading to the formation of transmissible oocysts. Methods: To advance our understanding of the parasite's cellular development, we complemented previous transcriptome studies by delving into the proteome profiles at five distinct time points of in vitro cultivation through LC/MS-MS analysis. Results: A total of 1,324 proteins were identified in the in vitro developmental stages of C. suis, and 1,082 proteins were identified as significantly differentially expressed. Data are available via ProteomeXchange with identifier PXD045050. We performed BLAST, GO enrichment, and KEGG pathway analyses on the up- and downregulated proteins to elucidate correlated events in the C. suis life cycle. Our analyses revealed intriguing metabolic patterns in macromolecule metabolism, DNA- and RNA-related processes, proteins associated with sexual stages, and those involved in cell invasion, reflecting the adaptation of sexual stages to a nutrient-poor and potentially stressful extracellular environment, with a focus on enzymes involved in metabolism and energy production. Discussion: These findings have important implications for understanding the developmental biology of C. suis as well as other, related coccidian parasites, such as Eimeria spp. and Toxoplasma gondii. They also support the role of C. suis as a new model for the comparative biology of coccidian tissue cyst stages.

Species comparison: human and minipig PBMC reactivity under the influence of immunomodulating compounds in vitro.

Considering the similarities between swine and humans, it is a logical consequence to use swine as a translational model in research and drug development, including non-clinical safety. Here, we compared the reactivity of peripheral blood mononuclear cells (PBMCs) from humans and minipigs under the influence of different compounds in vitro. We conducted a flow cytometry-based proliferation assay that focused on the T-cell response to three different stimuli: concanavalin A (ConA), phytohemagglutinin-L (PHA-L), and staphylococcal Enterotoxin B (SEB). Furthermore, four approved immunosuppressive drugs-abatacept, belatacept, rapamycin, and tofacitinib-which are used for the treatment of rheumatoid arthritis or rejection in transplant recipients, were combined with the different stimuli. This allowed us to study the effect of suppressive drugs in comparison with the different stimuli in both species. We examined proliferating T cells (CD3+) and investigated the presence of TCR-αß+ and TCR-γδ+ T cells. Differences in the response of T cells of the two species under these various conditions were evident. CD4+ T cells were more activated within humans, whereas CD8+ T cells were generally more abundant in swine. The effectiveness of the used humanized antibodies is most likely related to the conserved structure of CTLA-4 as abatacept induced a much stronger reduction in swine compared with belatacept. The reduction of proliferation of rapamycin and tofacitinib was highly dependent on the used stimuli. We further investigated the effect of the immunosuppressive compounds on antigen-specific restimulation of pigs immunized against porcine circovirus 2 (PCV2). Treatment with all four compounds resulted in a clear reduction of the proliferative response, with rapamycin showing the strongest effect. In conclusion, our findings indicate that the effectiveness of suppressive compounds is highly dependent on the stimuli used and must be carefully selected to ensure accurate results. The results highlight the importance of considering the response of T cells in different species when evaluating the potential of an immunomodulatory drug.

Combining evidence of selection with association analysis increases power to detect regions influencing complex traits in dairy cattle.

BACKGROUND: Hitchhiking mapping and association studies are two popular approaches to map genotypes to phenotypes. In this study we combine both approaches to complement their specific strengths and weaknesses, resulting in a method with higher statistical power and fewer false positive signals. We applied our approach to dairy cattle as they underwent extremely successful selection for milk production traits and since an excellent phenotypic record is available. We performed whole genome association tests with a new mixed model approach to account for stratification, which we validated via Monte Carlo simulations. Selection signatures were inferred with the integrated haplotype score and a locus specific permutation based integrated haplotype score that works with a folded frequency spectrum and provides a formal test of signifance to identify selection signatures. RESULTS: About 1,600 out of 34,851 SNPs showed signatures of selection and the locus specific permutation based integrated haplotype score showed overall good accordance with the whole genome association study. Each approach provides distinct information about the genomic regions that influence complex traits. Combining whole genome association with hitchhiking mapping yielded two significant loci for the trait protein yield. These regions agree well with previous results from other selection signature scans and whole genome association studies in cattle. CONCLUSION: We show that the combination of whole genome association and selection signature mapping based on the same SNPs increases the power to detect loci influencing complex traits. The locus specific permutation based integrated haplotype score provides a formal test of significance in selection signature mapping. Importantly it does not rely on knowledge of ancestral and derived allele states.

The importance of identity-by-state information for the accuracy of genomic selection.

BACKGROUND: It is commonly assumed that prediction of genome-wide breeding values in genomic selection is achieved by capitalizing on linkage disequilibrium between markers and QTL but also on genetic relationships. Here, we investigated the reliability of predicting genome-wide breeding values based on population-wide linkage disequilibrium information, based on identity-by-descent relationships within the known pedigree, and to what extent linkage disequilibrium information improves predictions based on identity-by-descent genomic relationship information. METHODS: The study was performed on milk, fat, and protein yield, using genotype data on 35 706 SNP and deregressed proofs of 1086 Italian Brown Swiss bulls. Genome-wide breeding values were predicted using a genomic identity-by-state relationship matrix and a genomic identity-by-descent relationship matrix (averaged over all marker loci). The identity-by-descent matrix was calculated by linkage analysis using one to five generations of pedigree data. RESULTS: We showed that genome-wide breeding values prediction based only on identity-by-descent genomic relationships within the known pedigree was as or more reliable than that based on identity-by-state, which implicitly also accounts for genomic relationships that occurred before the known pedigree. Furthermore, combining the two matrices did not improve the prediction compared to using identity-by-descent alone. Including different numbers of generations in the pedigree showed that most of the information in genome-wide breeding values prediction comes from animals with known common ancestors less than four generations back in the pedigree. CONCLUSIONS: Our results show that, in pedigreed breeding populations, the accuracy of genome-wide breeding values obtained by identity-by-descent relationships was not improved by identity-by-state information. Although, in principle, genomic selection based on identity-by-state does not require pedigree data, it does use the available pedigree structure. Our findings may explain why the prediction equations derived for one breed may not predict accurate genome-wide breeding values when applied to other breeds, since family structures differ among breeds.

Estimates of marker effects for measures of milk flow in the Italian brown Swiss dairy cattle population.

BACKGROUND: Milkability is a complex trait that is characterized by milk flow traits including average milk flow rate, maximum milk flow rate and total milking time. Milkability has long been recognized as an economically important trait that can be improved through selection. By improving milkability, management costs of milking decrease through reduced labor and improved efficiency of the automatic milking system, which has been identified as an important factor affecting net profit. The objective of this study was to identify markers associated with electronically measured milk flow traits, in the Italian Brown Swiss population that could potentially improve selection based on genomic predictions. RESULTS: Sires (n = 1351) of cows with milk flow information were genotyped for 33,074 single nucleotide polymorphism (SNP) markers distributed across 29 Bos taurus autosomes (BTA). Among the six milk flow traits collected, ascending time, time of plateau, descending time, total milking time, maximum milk flow and average milk flow, there were 6,929 (time of plateau) to 14,585 (maximum milk flow) significant SNP markers identified for each trait across all BTA. Unique regions were found for each of the 6 traits providing evidence that each individual milk flow trait offers distinct genetic information about milk flow. This study was also successful in identifying functional processes and genes associated with SNPs that influences milk flow. CONCLUSIONS: In addition to verifying the presence of previously identified milking speed quantitative trait loci (QTL) within the Italian Brown Swiss population, this study revealed a number of genomic regions associated with milk flow traits that have never been reported as milking speed QTL. While several of these regions were not associated with a known gene or QTL, a number of regions were associated with QTL that have been formerly reported as regions associated with somatic cell count, somatic cell score and udder morphometrics. This provides further evidence of the complexity of milk flow traits and the underlying relationship it has with other economically important traits for dairy cattle. Improved understanding of the overall milking pattern will aid in identification of cows with lower management costs and improved udder health.