Genome-wide association study for semen traits of the bulls in Chinese Holstein

Qin, Chunhua; Yin, Hongwei; Zhang, Xu; Sun, Dongxiao; Zhang, Qin; Liu, Jianfeng; Ding, Xiangdong; Zhang, Yi; Zhang, Shengli

doi:10.1111/age.12433

Cited by 25 publications

(24 citation statements)

References 29 publications

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“…Heritability measures confirm this statement. Higher heritability values (0.40 to 0.51) have been observed in SC (Bourdon and Brinks, 1982;Smith et al, 1989;Pereira et al, 2001;Martínez-Velázquez et al, 2003;Corbet et al, 2009;Van Melis et al, 2010) in various breeds compared with spermatic traits (0.04 to 0.34) (Peddinti et al, 2008;Druet et al, 2009;Feugang et al, 2009;Gaviraghi et al, 2010;Silva et al, 2011;Suchocki and Szyda, 2015;Qin et al, 2017). Interestingly, heritability was reported in only 4 of 18 articles evaluated in this systematic review: 3 for spermatic traits (Blaschek et al, 2011;Suchocki and Szyda, 2015;Qin et al, 2017) and 1 for testicular traits (Soares et al, 2017).…”

Section: Genetic Heterogeneity and Heritability Of Spermatic And Testmentioning

confidence: 66%

“…To identify regions/genes regulating fertility traits in specific groups, genes were compared among groups created based on species (B. indicus or B. taurus) and selection purpose (Dairy or Beef): Crossbreed-Beef (Fortes et al, 2013a;Buzanskas et al, 2017), B. indicus-Beef (Irano et al, 2016;Soares et al, 2017), and B. Taurus-Dairy (Hering et al, 2014a, b;Hering et al, 2014c;Kamiński et al, 2016;Puglisi et al, 2016;Qin et al, 2017). The number of genes shared between each pair of these groups was estimated using 3 gene lists: all annotated genes within the determined genomic coordinate intervals, all genes with significant P value in the prioritization analysis, and the top 100 genes in the prioritization analysis.…”

Section: Identifying Genomic Regions With Taurine or Indicine Originmentioning

confidence: 99%

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Genetic mechanisms underlying spermatic and testicular traits within and among cattle breeds: systematic review and prioritization of GWAS results1

Fonseca

Santos

Lam

et al. 2018

Journal of Animal Science

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Reduced bull fertility imposes economic losses in bovine herds. Specifically, testicular and spermatic traits are important indicators of reproductive efficiency. Several genome-wide association studies (GWAS) have identified genomic regions associated with these fertility traits. The aims of this study were as follows: 1) to perform a systematic review of GWAS results for spermatic and testicular traits in cattle and 2) to identify key functional candidate genes for these traits. The identification of functional candidate genes was performed using a systems biology approach, where genes shared between traits and studies were evaluated by a guilt by association gene prioritization (GUILDify and ToppGene software) in order to identify the best functional candidates. These candidate genes were integrated and analyzed in order to identify overlapping patterns among traits and breeds. Results showed that GWAS for testicular-related traits have been developed for beef breeds only, whereas the majority of GWAS for spermatic-related traits were conducted using dairy breeds. When comparing traits measured within the same study, the highest number of

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Section: Genetic Heterogeneity and Heritability Of Spermatic And Testmentioning

confidence: 66%

Section: Identifying Genomic Regions With Taurine or Indicine Originmentioning

confidence: 99%

Genetic mechanisms underlying spermatic and testicular traits within and among cattle breeds: systematic review and prioritization of GWAS results1

Fonseca

Santos

Lam

et al. 2018

Journal of Animal Science

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show abstract

“…Genome-wide association studies using microarray-derived genotypes provided evidence that inherited differences in semen quality are amenable to genome-wide association testing (e.g., [19][20][21][22][23][24][25]). However, low marker density resulted in large QTL confidence intervals that contained many genes and candidate causal variants.…”

Section: Introductionmentioning

confidence: 99%

Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility

et al. 2020

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Cattle are ideally suited to investigate the genetics of male reproduction, because semen quality and fertility are recorded for all ejaculates of artificial insemination bulls. We analysed 26,090 ejaculates of 794 Brown Swiss bulls to assess ejaculate volume, sperm concentration, sperm motility, sperm head and tail anomalies and insemination success. The heritability of the six semen traits was between 0 and 0.26. Genome-wide association testing on 607,511 SNPs revealed a QTL on bovine chromosome 6 that was associated with sperm motility (P = 2.5 x 10 −27), head (P = 2.0 x 10 −44) and tail anomalies (P = 7.2 x 10 −49) and insemination success (P = 9.9 x 10 −13). The QTL harbors a recessive allele that compromises semen quality and male fertility. We replicated the effect of the QTL on fertility (P = 7.1 x 10 −32) in an independent cohort of 2481 Brown Swiss bulls. The analysis of wholegenome sequencing data revealed that a synonymous variant (BTA6:58373887C>T, rs474302732) in WDR19 encoding WD repeat-containing protein 19 was in linkage disequilibrium with the fertility-associated haplotype. WD repeat-containing protein 19 is a constituent of the intraflagellar transport complex that is essential for the physiological function of motile cilia and flagella. Bioinformatic and transcription analyses revealed that the BTA6:58373887 T-allele activates a cryptic exonic splice site that eliminates three evolutionarily conserved amino acids from WDR19. Western blot analysis demonstrated that the BTA6:58373887 T-allele decreases protein expression. We make the remarkable observation that, in spite of negative effects on semen quality and bull fertility, the BTA6:58373887 T-allele has a frequency of 24% in the Brown Swiss population. Our findings are the first to uncover a variant that is associated with quantitative variation in semen quality and male fertility in cattle.

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“…Genome-wide association testing between microarray-derived genotypes and semen characteristics uncovered quantitative trait loci (QTL) that are associated with male reproduction in cattle (e.g., [27][28][29][30][31][32][33]). These studies provided evidence that inherited differences in semen quality are amenable to genome-wide association testing.…”

Section: Introductionmentioning

confidence: 99%

Activation of cryptic splicing in bovineWDR19is associated with reduced semen quality and male fertility

Hiltpold

Niu²,

Kadri

et al. 2020

Preprint

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Cattle are uniquely suited to investigate the genetics of male reproduction disorders, as semen quality and fertility are recorded for all ejaculates of artificial insemination bulls. Using 26,090 ejaculates of 794 Brown Swiss bulls, we analysed ejaculate volume, sperm concentration, sperm motility, sperm head and tail anomalies, and bull fertility. The heritability of the six semen traits was between 0 and 0.26. Genome-wide association testing between semen quality and 607,511 SNPs reveaed a QTL on bovine chromosome 6 that was associated with sperm motility (P = 2.5 x 10 -27 ), head (P = 2.0 x 10 -44 ) and tail anomalies (P = 7.2 x 10 -49 ) and insemination success (P = 9.9 x 10 -13 ). The QTL harbors a recessive allele that compromises semen quality and male fertility. We replicated the effect of the QTL on fertility (P = 7.1 x 10 -32 ) in 2481 bulls from an independent cohort of Brown Swiss bulls. The analysis of whole-genome sequencing data revealed that a synonymous variant (BTA6:58373887C>T, rs474302732) in WDR19 encoding WD repeat-containing protein 19 was in linkage disequilibrium with the fertility-associated haplotype. WD repeat-containing protein 19 is a constituent of the intraflagellar transport complex that is essential for the physiological function of motile cilia and flagella. Bioinformatic and transcription analyses showed that the BTA6:58373887 T-allele activates a cryptic splice site that eliminates three evolutionarily conserved amino acids from the WD-repeat domain, thus reducing semen quality and fertility. Western blot analysis demonstrated that the BTA6:58373887 T-allele decreases the WDR19 protein expression. We make the remarkable observation that, in spite of negative effects on semen quality and bull fertility, the deleterious allele has a frequency of 24 % in the Brown Swiss population. Our findings are the first to uncover a variant that controls quantitative variation in semen quality and male fertility in cattle. Author summaryMale reproductive disorders occur in many species. In cattle farming, artificial insemination is widely used. To ensure high fertilization rates, the quality of each ejaculate is recorded and the insemination success is monitored for every artificial insemination bull. We analyse semen quality and microarray-called genotypes at more than 600,000 genome-wide SNP markers in 794 bulls to identify a recessive allele that compromises semen quality and fertility. We take advantage of whole-genome sequencing to pinpoint a variant in the coding sequence of WDR19 encoding WD repeat-containing protein 19 that activates a novel exonic splice site. Our results indicate that cryptic splicing in WDR19 is associated with reduced male reproductive performance in cattle. This is the first report to reveal a variant associated with quantitative variation in bovine semen quality.

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Genome-wide association study for semen traits of the bulls in Chinese Holstein

Cited by 25 publications

References 29 publications

Genetic mechanisms underlying spermatic and testicular traits within and among cattle breeds: systematic review and prioritization of GWAS results1

Genetic mechanisms underlying spermatic and testicular traits within and among cattle breeds: systematic review and prioritization of GWAS results1

Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility

Activation of cryptic splicing in bovineWDR19is associated with reduced semen quality and male fertility

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