BackgroundUse of whole-genome sequence data (WGS) is expected to improve identification of quantitative trait loci (QTL). However, this requires imputation to WGS, often with a limited number of sequenced animals for the target population. The objective of this study was to investigate imputation to WGS in two pig lines using a multi-line reference population and, subsequently, to investigate the effect of using these imputed WGS (iWGS) for GWAS.MethodsPhenotypes and genotypes were available on 12,184 Large White pigs (LW-line) and 4943 Dutch Landrace pigs (DL-line). Imputed 660 K and 80 K genotypes for the LW-line and DL-line, respectively, were imputed to iWGS using Beagle v.4.1. Since only 32 LW-line and 12 DL-line boars were sequenced, 142 animals from eight commercial lines were added. GWAS were performed for each line using the 80 K and 660 K SNPs, the genotype scores of iWGS SNPs that had an imputation accuracy (Beagle R2) higher than 0.6, and the dosage scores of all iWGS SNPs.ResultsFor the DL-line (LW-line), imputation of 80 K genotypes to iWGS resulted in an average Beagle R2 of 0.39 (0.49). After quality control, 2.5 × 106 (3.5 × 106) SNPs had a Beagle R2 higher than 0.6, resulting in an average Beagle R2 of 0.83 (0.93). Compared to the 80 K and 660 K genotypes, using iWGS led to the identification of 48.9 and 64.4% more QTL regions, for the DL-line and LW-line, respectively, and the most significant SNPs in the QTL regions explained a higher proportion of phenotypic variance. Using dosage instead of genotype scores improved the identification of QTL, because the model accounted for uncertainty of imputation, and all SNPs were used in the analysis.ConclusionsImputation to WGS using the multi-line reference population resulted in relatively poor imputation, especially when imputing from 80 K (DL-line). In spite of the poor imputation accuracies, using iWGS instead of a lower density SNP chip increased the number of detected QTL and the estimated proportion of phenotypic variance explained by these QTL, especially when dosage scores were used instead of genotype scores. Thus, iWGS, even with poor imputation accuracy, can be used to identify possible interesting regions for fine mapping.Electronic supplementary materialThe online version of this article (10.1186/s12711-019-0445-y) contains supplementary material, which is available to authorized users.

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Peripheral muscle strength predicted 6-minute walking distance; this finding suggests that quadriceps strength training should be included in physical training to increase functional exercise capacity. Attention should be paid to further increasing 6-minute walking distance between 6 and 12 months after transplantation.

Significance testing for genome‐wide association study (GWAS) with increasing SNP density up to whole‐genome sequence data (WGS) is not straightforward, because of strong LD between SNP and population stratification. Therefore, the objective of this study was to investigate genomic control and different significance testing procedures using data from a commercial pig breeding scheme. A GWAS was performed in GCTA with data of 4,964 Large White pigs using medium density, high density or imputed whole‐genome sequence data, fitting a genomic relationship matrix based on a leave‐one–chromosome‐out approach to account for population structure. Subsequently, genomic inflation factors were assessed on whole‐genome level and the chromosome level. To establish a significance threshold, permutation testing, Bonferroni corrections using either the total number of SNPs or the number of independent chromosome fragments, and false discovery rates (FDR) using either the Benjamini–Hochberg procedure or the Benjamini and Yekutieli procedure were evaluated. We found that genomic inflation factors did not differ between different density genotypes but do differ between chromosomes. Also, the leave‐one‐chromosome‐out approach for GWAS or using the pedigree relationships did not account appropriately for population stratification and gave strong genomic inflation. Regarding different procedures for significance testing, when the aim is to find QTL regions that are associated with a trait of interest, we recommend applying the FDR following the Benjamini and Yekutieli approach to establish a significance threshold that is adjusted for multiple testing. When the aim is to pinpoint a specific mutation, the more conservative Bonferroni correction based on the total number of SNPs is more appropriate, till an appropriate method is established to adjust for the number of independent tests.

Currently, there is no animal model known that mimics natural nasal colonization by Staphylococcus aureus in humans. We investigated whether rhesus macaques are natural nasal carriers of S. aureus. Nasal swabs were taken from 731 macaques. S. aureus isolates were typed by pulsed-field gel electrophoresis (PFGE), spa repeat sequencing and multi-locus sequence typing (MLST), and compared with human strains. Furthermore, the isolates were characterized by several PCRs. Thirty-nine percent of 731 macaques were positive for S. aureus. In general, the macaque S. aureus isolates differed from human strains as they formed separate PFGE clusters, 50% of the isolates were untypeable by agr genotyping, 17 new spa types were identified, which all belonged to new sequence types (STs). Furthermore, 66% of macaque isolates were negative for all superantigen genes. To determine S. aureus nasal colonization, three nasal swabs from 48 duo-housed macaques were taken during a 5 month period. In addition, sera were analyzed for immunoglobulin G and A levels directed against 40 staphylococcal proteins using a bead-based flow cytometry technique. Nineteen percent of the animals were negative for S. aureus, and 17% were three times positive. S. aureus strains were easily exchanged between macaques. The antibody response was less pronounced in macaques compared to humans, and nasal carrier status was not associated with differences in serum anti-staphylococcal antibody levels. In conclusion, rhesus macaques are natural hosts of S. aureus, carrying host-specific lineages. Our data indicate that rhesus macaques are useful as an autologous model for studying S. aureus nasal colonization and infection prevention.