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Additional file 2: Figure S1. Manhattan plots of lesion susceptibility for sole haemorrhage (SH), sole ulcers (SU), and white line disease (WL). The standardized SNP effects were calculated by the estimated SNP effects divided by their empirical standard deviation. The data provided represent the Manhattan plots of the standardized SNP effects for lesion susceptibility of sole haemorrhage (SH), sole ulcers (SU), and white line disease (WL) from the genome-wide association analysis.

Additional file 1: Table S1. The top ten markers associated with lesion severity for sole haemorrhage (SH), sole ulcer (SU), and white line disease (WL) from single-marker GWA analyses, including chromosome (BTA), position (Pos), minor allele frequency (MAF), and P-value. The data provided represent the position, allele frequency, and the P value of the top ten markers associated with lesion severity for sole haemorrhage (SH), sole ulcer (SU), and white line disease (WL) from the genome-wide association analysis. Table S2. The top ten markers with the largest standardized SNP effects (Std_SNP_effect) on lesion susceptibility for sole haemorrhage (SH), sole ulcer (SU), and white line disease (WL) from single-marker GWA analyses, including chromosome (BTA), position (Pos), and minor allele frequency. The data provided represent the position, allele frequency, and the effect size of the top ten markers associated with lesion susceptibility for sole haemorrhage (SH), sole ulcer (SU), and white line disease (WL) from the genome-wide association analysis.

Canine hip dysplasia, a debilitating orthopedic disorder that leads to osteoarthritis and cartilage degeneration, is common in several large-sized dog breeds and shows moderate heritability suggesting that selection can reduce prevalence. Estimating genomic breeding values require large reference populations, which are expensive to genotype for development of genomic prediction tools. Combining datasets from different countries could be an option to help build larger reference datasets without incurring extra genotyping costs. Our objective was to evaluate genomic prediction based on a combination of UK and US datasets of genotyped dogs with records of Norberg angle scores, related to canine hip dysplasia. Prediction accuracies using a single population were 0.179 and 0.290 for 1,179 and 242 UK and US Labrador Retrievers, respectively. Prediction accuracies changed to 0.189 and 0.260, with an increased bias of genomic breeding values when using a joint training set (biased upwards for the US population and downwards for the UK population). Our results show that in this study of canine hip dysplasia, little or no benefit was gained from using a joint training set as compared to using a single population as training set. We attribute this to differences in the genetic background of the two populations as well as the small sample size of the US dataset.

Background Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. This study applied genomic methods to investigate population structure and inbreeding in a common UK dog breed, the Labrador Retriever. Results We found substantial within-breed genetic differentiation, which was associated with the role of the dog (i.e. working, pet, show) and also with coat colour (i.e. black, yellow, brown). There was little evidence of geographical differentiation. Highly differentiated genomic regions contained genes and markers associated with skull shape, suggesting that at least some of the differentiation is related to human-imposed selection on this trait. We also found that the total length of homozygous segments (runs of homozygosity, ROHs) was highly correlated with inbreeding coefficient. Conclusions This study demonstrates that high-density genomic data can be used to quantify genetic diversity and to decipher demographic and selection processes. Analysis of genetically differentiated regions in the UK Labrador Retriever population suggests the possibility of human-imposed selection on craniofacial characteristics. The high correlation between estimates of inbreeding from genomic and pedigree data for this breed demonstrates that genomic approaches can be used to quantify inbreeding levels in dogs, which will be particularly useful where pedigree information is missing. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3933-x) contains supplementary material, which is available to authorized users.

Background The significant social and economic loss as a result of bovine tuberculosis (bTB) presents a continuous challenge to cattle industries in the UK and worldwide. However, host genetic variation in cattle susceptibility to bTB provides an opportunity to select for resistant animals and further understand the genetic mechanisms underlying disease dynamics. Methods The present study identified genomic regions associated with susceptibility to bTB using genome-wide association (GWA), regional heritability mapping (RHM) and chromosome association approaches. Phenotypes comprised de-regressed estimated breeding values of 804 Holstein-Friesian sires and pertained to three bTB indicator traits: i) positive reactors to the skin test with positive post-mortem examination results (phenotype 1); ii) positive reactors to the skin test regardless of post-mortem examination results (phenotype 2) and iii) as in (ii) plus non-reactors and inconclusive reactors to the skin tests with positive post-mortem examination results (phenotype 3). Genotypes based on the 50 K SNP DNA array were available and a total of 34,874 SNPs remained per animal after quality control. Results The estimated polygenic heritability for susceptibility to bTB was 0.26, 0.37 and 0.34 for phenotypes 1, 2 and 3, respectively. GWA analysis identified a putative SNP on Bos taurus autosomes (BTA) 2 associated with phenotype 1, and another on BTA 23 associated with phenotype 2. Genomic regions encompassing these SNPs were found to harbour potentially relevant annotated genes. RHM confirmed the effect of these genomic regions and identified new regions on BTA 18 for phenotype 1 and BTA 3 for phenotypes 2 and 3. Heritabilities of the genomic regions ranged between 0.05 and 0.08 across the three phenotypes. Chromosome association analysis indicated a major role of BTA 23 on susceptibility to bTB. Conclusion Genomic regions and candidate genes identified in the present study provide an opportunity to further understand pathways critical to cattle susceptibility to bTB and enhance genetic improvement programmes aiming at controlling and eradicating the disease. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0493-7) contains supplementary material, which is available to authorized users.

Linkage disequilibrium (r2) map of a QTL region on BTA 23 affecting bTB (phenotype 2). The region ranges from SNP ARS-BFGL-NGS-88425 (bp = 38206814) to SNP BTA-01409-rs29012374 (bp = 39411428); white for r2 = 0, shades of grey for 0

Background The effects of different evolutionary forces are expected to lead to the conservation, over many generations, of particular genomic regions (haplotypes) due to the development of linkage disequilibrium (LD). The detection and identification of early (ancestral) haplotypes can be used to clarify the evolutionary dynamics of different populations as well as identify selection signatures and genomic regions of interest to be used both in conservation and breeding programs. The aims of this study were to develop a simple procedure to identify ancestral haplotypes segregating across several generations both within and between populations with genetic links based on whole-genome scanning. This procedure was tested with simulated and then applied to real data from different genotyped populations of Spanish, Fleckvieh, Simmental and Brown-Swiss cattle. Results The identification of ancestral haplotypes has shown coincident patterns of selection across different breeds, allowing the detection of common regions of interest on different bovine chromosomes and mirroring the evolutionary dynamics of the studied populations. These regions, mainly located on chromosomes BTA5, BTA6, BTA7 and BTA21 are related with certain animal traits such as coat colour and milk protein and fat content. Conclusion In agreement with previous studies, the detection of ancestral haplotypes provides useful information for the development and comparison of breeding and conservation programs both through the identification of selection signatures and other regions of interest, and as indicator of the general genetic status of the populations. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0405-2) contains supplementary material, which is available to authorized users.

BACKGROUND: Canine hip dysplasia (CHD) is characterised by a malformation of the hip joint, leading to osteoarthritis and lameness. Current breeding schemes against CHD have resulted in measurable but moderate responses. The application of marker-assisted selection, incorporating specific markers associated with the disease, or genomic selection, incorporating genome-wide markers, has the potential to dramatically improve results of breeding schemes. Our aims were to identify regions associated with hip dysplasia or its related traits using genome and chromosome-wide analysis, study the linkage disequilibrium (LD) in these regions and provide plausible gene candidates. This study is focused on the UK Labrador Retriever population, which has a high prevalence of the disease and participates in a recording program led by the British Veterinary Association (BVA) and The Kennel Club (KC).RESULTS: Two genome-wide and several chromosome-wide QTLs affecting CHD and its related traits were identified, indicating regions related to hip dysplasia.CONCLUSION: Consistent with previous studies, the genetic architecture of CHD appears to be based on many genes with small or moderate effect, suggesting that genomic selection rather than marker-assisted selection may be an appropriate strategy for reducing this disease.

En poblaciones en riesgo de extinción, puede ser necesario establecer un programa de conservación ex situ que, desde el punto de vista genético, permita controlar su estructura reproductiva para minimizar los efectos de la consanguinidad y la deriva. En tales programas, a menudo se recomienda igualar las contribuciones familiares al grupo reproductor (estrategia CI) para maximizar el censo efectivo. Este procedimiento causa una relajación parcial de la selección natural, impidiendo su acción sobre fecundidad y limitando su acción sobre viabilidad. El resultado conjunto de estas circunstancias se ha estudiado mediante simulación, cálculo numérico y experimentación en laboratorio, y se han desarrollado predicciones teóricas. Sin embargo, la relajación parcial de la selección no sólo afecta a la variabilidad genética debida a la segregación de alelos deletéreos incondicionales, sino también a la selección responsable de cualquier adaptación a la cautividad. El presente trabajo aborda empíricamente, en un experimento de laboratorio con Drosophila melanogaster, la importancia relativa de las consecuencias de la relajación parcial de la selección sobre fertilidad y sobre viabilidad, tanto en lo que refiere a la selección purificadora como a la adaptación a cautividad. En dicho experimento, partiendo de una población recién capturada, se han mantenido durante 34 generaciones poblaciones replicadas bajo CI o sin manejo de las contribuciones familiares (estrategia CA), utilizando dos censos diferentes (10 y 50 individuos). Los resultados confirman las predicciones teóricas respecto de viabilidad y eficacia, y muestran que la selección natural es capaz de purgar una parte importante de la depresión consanguínea. También ponen de manifiesto un proceso paralelo de adaptación a la cautividad, revelando que bajo CI se produce una selección intensa sobre fecundidad, por selección en contra de parejas estériles, que puede llegar a ser más eficiente que bajo CA. Estos resultados ilustran aspectos importantes en el diseño de programas de conservación.