Animals; Cattle/genetics; Female; Fertility; Haplotypes; Male; Pedigree; Quantitative Trait Loci; X Chromosome/genetics; Cattle; X Chromosome; Biotechnology; Genetics
Abstract :
[en] BACKGROUND: Meiotic recombination plays an important role in reproduction and evolution. The individual global recombination rate (GRR), measured as the number of crossovers (CO) per gametes, is a complex trait that has been shown to be heritable. The sex chromosomes play an important role in reproduction and fertility related traits. Therefore, variants present on the X-chromosome might have a high contribution to the genetic variation of GRR that is related to meiosis and to reproduction.
RESULTS: We herein used genotyping data from 58,474 New Zealand dairy cattle to estimate the contribution of the X-chromosome to male and female GRR levels. Based on the pedigree-based relationships, we first estimated that the X-chromosome accounted for 30% of the total additive genetic variance for male GRR. This percentage was equal to 19.9% when the estimation relied on a SNP-BLUP approach assuming each SNP has a small contribution. We then carried out a haplotype-based association study to map X-linked QTL, and subsequently fine-mapped the identified QTL with imputed sequence variants. With this approach we identified three QTL with large effect accounting for 7.7% of the additive genetic variance of male GRR. The associated effects were equal to + 0.79, - 1.16 and + 1.18 CO for the alternate alleles. In females, the estimated contribution of the X-chromosome to GRR was null and no significant association with X-linked loci was found. Interestingly, two of the male GRR QTL were associated with candidate genes preferentially expressed in testis, in agreement with a male-specific effect. Finally, the most significant QTL was associated with PPP4R3C, further supporting the important role of protein phosphatase in double-strand break repair by homologous recombination.
CONCLUSIONS: Our study illustrates the important role the X-chromosome can have on traits such as individual recombination rate, associated with testis in males. We also show that contribution of the X-chromosome to such a trait might be sex dependent.
Disciplines :
Genetics & genetic processes
Author, co-author :
Kadri, N K; Unit of Animal Genomics, GIGA-R, 11 Avenue de l'Hôpital (B34), University of Liège, 4000, Liège, Belgium ; Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
Zhang, J; Unit of Animal Genomics, GIGA-R, 11 Avenue de l'Hôpital (B34), University of Liège, 4000, Liège, Belgium
Oget-Ebrad, C; Unit of Animal Genomics, GIGA-R, 11 Avenue de l'Hôpital (B34), University of Liège, 4000, Liège, Belgium
Wang, Y; Livestock Improvement Corporation Ltd, Private Bag 3016, 3240, Hamilton, New Zealand
Couldrey, C; Livestock Improvement Corporation Ltd, Private Bag 3016, 3240, Hamilton, New Zealand
Spelman, R; Livestock Improvement Corporation Ltd, Private Bag 3016, 3240, Hamilton, New Zealand
Charlier, Carole ; Université de Liège - ULiège > GIGA > GIGA Medical Genomics - Unit of Animal Genomics
Georges, Michel ; Université de Liège - ULiège > GIGA > GIGA Medical Genomics - Unit of Animal Genomics
Druet, Tom ; Université de Liège - ULiège > GIGA > GIGA Medical Genomics - Unit of Animal Genomics
Language :
English
Title :
High male specific contribution of the X-chromosome to individual global recombination rate in dairy cattle.
Carole Charlier and Tom Druet are Senior Research Associates from the F.R.S.-FNRS. We used the supercomputing facilities of the ?Consortium d?Equipements en Calcul Intensif en F?d?ration Wallonie-Bruxelles? (CECI), funded by the F.R.S.-FNRS.This work was supported by the F.R.S.-FNRS under grant T.0080.20 (“LoCO motifs” research project) and supported by the Damona European Research Council grant ERC AdG-GA323030 to Michel Georges.
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