- All other QTL are not associated with any of the semen quality traits investigated. - Full list of author information is available at the end of the article. - Our association studies revealed five recessive QTL for bull fertility. - Genomic restricted maximum likeli- hood estimation indicated that the autosomal markers explained of the phenotypic variance in bull fertility.. - Due to its large effect on male fertility, we subsequently fixed the top haplotype of the BTA6 QTL as a covariate in the association model.. - When the top haplotype of the BTA6 QTL was fixed as a covariate in the model, the association signal at BTA6 disappeared (Fig. - In the conditional analysis, the P value of the top-associated haplotype at the BTA1 QTL did not meet the Bonferroni-corrected significance threshold by a small margin (Fig. - The associ- ation with bull fertility was more pronounced (i.e., the P values of the top haplotypes were lower) at the QTL on chromosomes 1, 6 and 26 (Table 1, Fig. - Frequency of the fertility-. - Effect of the top haplotypes at BTA1 (e), BTA18 (f), BTA25 (g) and BTA26 (h) on bull fertility (0-non-carrier, 1-heterozygous, 2-homozygous). - The values above the boxplots indicate the number of bulls carrying 0, 1 and 2 copies of the top haplotype. - In order to quantify the impact of the five recessive QTL on insemination success in the BSW population, we investigated the 56-day non-return rate (NRR56. - A recessive QTL for bull fertility is located on BTA1.. - The association pattern of the BTA1 top haplotype was puzzling. - However, the vast majority of the spermatozoa (85 and 84.6%) were nor- mal. - First, we used whole-genome se- quence data of 125 BSW bulls to identify variants that are compatible with the inheritance of the top haplotype.. - The average fold coverage of the sequenced bulls was fold. - Second, we imputed whole-genome sequence variant genotypes for the 3736 BSW bulls of the mapping cohort using 368 reference animals to perform an association study between im- puted sequence variant genotypes and bull fertility.. - 2 Effect of the BTA1 top haplotype on sperm morphology. - Of the 764 compatible variants, 505 were also signifi- cantly associated with bull fertility at the genome-wide Bonferroni-corrected significance threshold of Fig. - Two of the significantly associated variants compatible with recessive inheritance were in coding regions: a missense variant in SPATA16 (rs440830663 at BTA A >. - Imputed sequence variants that exceeded the Bonferroni-corrected significance threshold and were compatible with recessive inheritance of the top haplotype are displayed in red. - The isoleucine at pos- ition 193 is on the surface of the protein (Fig. - The P values of the most significantly associated variant (BTA1:. - 93,972,058 bp) and of the top haplotype from the condi- tional analysis were and . - When the association analysis was conditioned on the BTA bp variant, i.e., the most significantly associated variant from the sequence-based association study, the QTL signal was absent in both association studies (Supplementary Fig- ure 4c). - standard deviations) on bull fertility, the top haplotype was neither associated with routinely examined semen quality nor with sperm morphology features that were assessed as part of the andrological examination.. - We detected 48,121 sequence variants within ±3 Mb of the top haplotype, of which 778 were compatible with the recessive inheritance of the top. - Of the compatible variants, six reside in protein-coding sequences: four synonymous variants in ZP2 (rs110876106, BTA C >. - The frequency of the top haplotype in the BSW population is 0.26. - 4 Detailed view of a QTL for bull fertility on BTA25. - However, both variants were not compatible with the in- heritance of the top haplotype.. - rs720936782 variant was still associated with bull fertility (P and . - In our set of the imputed sequence variant genotypes, rs378141069 and rs720936782 were in moderate linkage disequilib- rium (r . - a Zoom on the Manhattan plot on chromosome 26, 49.5 to 51.5 Mb, of the whole-genome GWAS on bull fertility with recessive model. - 434 were homozygous and 1690 heterozygous carriers of the top haplotype.. - Sequence variant genotyping revealed 30,018 polymorphic sites between and bp, of which 212 were compatible with the recessive inheritance of the top haplotype. - These variants were as well com- patible with the recessive inheritance of the top haplo- type. - In a mapping cohort of 3736 BSW bulls from which semen was collected at semen collection centers under standardized conditions, only 10% of the phenotypic variation of bull fertility was explained by autosomal var- iants. - Candidate causal variants for recessive traits are fre- quently prioritized if they are compatible with the segrega- tion of the top haplotype . - 6 Detailed view of a QTL for bull fertility at BTA18. - inheritance of the top haplotype takes genotyping errors into account. - Bulls that are homozygous for the top haplotype encompassing SPATA16 are less fertile likely because their ejaculates contain an increased num- ber of sperm with morphological abnormalities of the sperm head. - Thus, the actual effect of the BTA1 QTL on bull fertility is likely more pronounced than observed in our study that was based on insemination success from ejac- ulates meeting minimum quality requirements.. - We found no clues from the analysis of semen quality data why fertility is reduced in bulls that are homozy- gous carriers of the top haplotypes at the BTA18, BTA25, and BTA26 QTL. - Of the five fertility-associated QTL, only two QTL on BTA1 and BTA6 are also associated with reduced semen quality. - Bull fertility in Swiss BSW sires. - or cow), PR k is the cost of the semen dose, (BS x BK) lm. - Bull fertility in German and Austrian BSW sires. - For the association study, we considered three trait categories of the sperm morphology examination:. - PC j þ bHT þ ck þ e, where y is a vector of phenotypes (see above), μ is the intercept, PC j are the top 10 princi- pal components of the genomic relationship matrix, a, b and c are effects of the principal components, the haplo- type (HT) tested and a covariable k (e.g., the recessive. - 0.40) and were compatible with the inherit- ance of the top haplotype were considered as candidate causal variants. - To identify variants compatible with the inheritance of the top haplotype, we considered se- quence variant genotypes from 125 BSW cattle with bull. - We considered sequence variants within ±3 Mb of the top haplotype as positional candidate causal variants. - Fresh semen samples were provided by Swissgenetics for two bulls that were homozygous carriers of the fertility- associated haplotype on BTA1. - The haplotype status of the bulls was derived using microarray-derived geno- types. - FSH estimated bull fertility for the Swiss BSW bulls. - All authors reviewed and approved the final version of the manuscript.. - HP is a member of the editorial board of BMC Genomics. - https://doi.org/10.1016/S . - https://doi.org/1 0.3168/jds.S . - https://doi.. - https://doi.org/10.1016/j.a nireprosci . - doi.org/10.1016/j.theriogenology . - https://doi.org/10.1016/j.. - https://doi.org/10.1111/j x.. - 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