Table 1.
Semen quality and fertility of 794 BSW bulls.
Fig 1.
Detection of QTL for semen quality and fertility in BSW bulls.
Manhattan plots representing the association (–log10(P)) of haplotypes with (A) ejaculate volume (genomic inflation factor lambda = 1.25), (B) sperm concentration (lambda = 1.12), (C) sperm motility (lambda = 1.05), (D) sperm head anomalies (lambda = 1.10), (E) sperm tail anomalies (lambda = 1.12), (F) sperm per straw (lambda = 1.16), and (G) bull fertility (lambda = 1.06) assuming a recessive mode of inheritance. Red color indicates significantly associated haplotypes (P < Bonferroni-corrected significance threshold).
Fig 2.
A recessive haplotype compromises semen quality and bull fertility.
Boxplots representing the effect of the top haplotype on semen quality and fertility in non-carrier, heterozygous and homozygous bulls (haplotype status 0, 1, and 2, respectively). (A) Sperm motility of homozygous bulls is reduced by 1.6 phenotypic standard deviations (σp) (82.77 ± 2.59% vs. 86.37 ± 2.14%). Scores for sperm head (B) and tail (C) anomalies are increased by 2 and 2.1 σp in homozygous bulls. (D) The reduced semen quality of homozygous bulls is compensated with an increased number of sperm per dose (19.15 ± 2.83 vs. 16.29 ± 1.7 million). (E) Fertility of homozygous bulls is reduced by 1.2 σp (90.1 ± 12.3 vs. 101.27 ± 8.74).
Fig 3.
Detailed view of the associated region on chromosome 6.
(A) Association (-log10(P)) of haplotypes located between 48 and 72 Mb on BTA6 with head and tail anomalies (ANOHEAD, ANOTAIL), motility (MOTIL), number of sperm per straw (NTARGET) and bull fertility (FERT) assuming recessive inheritance. The red line represents the Bonferroni-corrected significance threshold. The grey shaded area contains haplotypes that were associated with at least two traits. (B) A segment of extended autozygosity was detected in 46 bulls that were homozygous for the top-haplotype. Blue and pale blue represent homozygous genotypes (AA and BB), heterozygous genotypes are displayed in grey. The solid red bar indicates the common 2.38 Mb segment of extended autozygosity (from 57,465,157 to 59,846,532 bp). (C) The segment of extended autozygosity encompasses 23 protein-coding genes. Vertical bars at the bottom represent variants that are compatible with recessive inheritance, including 126 that are located within the segment of extended autozygosity. Dark grey, light grey, green and orange bars represent intronic, intergenic, synonymous and missense variants, respectively.
Fig 4.
Effect of the BTA6:58373887 C/T variant on WDR19 mRNA and protein expression.
(A) Two WDR19 isoforms with 1342 (ENSBTAT00000019294.6) and 1242 (ENSBTAT00000069073.1) amino acids are annotated in cattle. The BTA6:58373887C>T variant is located at the 3’ end of exon 12 (ENSBTAT00000019294.6), 8 basepairs from the splice donor site of intron 12. The red triangle indicates the 58373887C>T variant, and green arrows indicate RT-PCR primers. (B) Genomic sequence surrounding the 58373887C>T-variant. Grey background indicates exons of the wild type (wt) and mutant (mt) transcripts, respectively. Underlined nucleotides indicate splice donor and splice acceptor sites. Upper and lower case letters indicate exonic and intronic nucleotides, respectively. (C) RT-PCR analysis on testis tissue samples from wild type, mutant and heterozygous bulls. Resequencing of the transcripts confirmed that the BTA6:58373887 T-allele activates a novel exonic splice site that is predicted to eliminate 3 amino acids from the resulting protein. (D) The mutation is located in the WD repeat domain of WDR19. The long (ENSBTAT00000019294.6, upper figure) and short (ENSBTAT00000069073.1, lower figure) WDR19 isoform contains 13 and 10 WD repeats, respectively. Residues at predicted amino acid hotspot positions differ between the wild-type and mutated protein for both WDR19 isoforms. (E) Western Blot analysis in wild type, mutant and heterozygous bulls. GAPDH was used as the control. (F) Multi-species alignment of the WDR19 protein sequence. Bold type indicates residues that are missing in the mutated (mt) WDR19 protein. Protein sequences were obtained from Ensembl for Bos taurus (ENSBTAT00000019294.6), Rattus norvegicus (ENSRNOT00000003991.6), Homo sapiens (ENST00000399820.8), Macaca mulatta (ENSMMUT00000003922.4), Equus caballus (ENSECAT00000026479.2), Felis catus (ENSFCAT00000060823.2) and Canis lupus familiaris (ENSCAFT00000025574.4).
Fig 5.
Detection of QTL for male fertility in 2481 Austrian and German BSW bulls.
(A) Manhattan plot representing the association (-log10(P)) of 112,667 haplotypes with male fertility assuming a recessive mode of inheritance. Red color indicates significantly associated haplotypes (P < Bonferroni-corrected significance threshold). (B) The fertility of homozygous haplotype carriers is reduced by 1.01 phenotypic standard deviations.
Table 2.
Quality control on the raw semen quality data.