Showing results for: [ Reverter-Gomez, Toni ]
X chromosome variants were associated to heritable fertility traits, in two bovine populations.
Fortes, Porto-Neto et al. 2019.
Background: Targeting phenotypes related to bull fertility, such as spe... morerm morphology and sperm DNA fragmentation can help identify mutations that limit reproduction capacity. Twenty-five fertility-related phenotypes were measured as indicators of bull fertility (1,099 Brahman bulls and 1,719 Tropical Composite bulls). Measurements included standard bull breeding soundness measures (e.g. sperm motility), scrotal circumference, sperm DNA fragmentation and sperm protamine deficiency. These phenotypes were used in a genome-wide association studies that aimed to detect quantitative trait loci (QTL).
Results: Genomic analyses confirmed some QTL in both breeds (Brahman and Tropical Composites) while others were breed specific. For example, only in Brahman cattle, we identified polymorphisms associated (P < 10-16) with sperm midpiece morphological abnormalities. The QTL identified and mutations occurring only in Bos indicus suggest that the gene A-kinase anchoring protein (AKAP)14 might be related to midpiece abnormalities in Brahman. Associated mutations described herein corroborate with known genes affecting spermatogenesis, including those in the AKAP and testis-expressed gene (TEX) families. Polymorphism associations suggest that AKAP14 and TEX11 are positional and functional candidate genes in chromosome X affecting bull fertility. Most significant variants and QTLs mapped to chromosome X. These results add evidence to a mammalian specialization of X that evolved to harbor genes linked to spermatogenesis, as similarly observed in mice and humans. Some variants in X may affect more than one genetically correlated trait (r2 ~ 0.33–0.51), such as sperm morphology and sperm DNA fragmentation. Correlations and shared QTL support the hypothesis that these phenotypes have the same underlying cause: faulty spermatogenesis. In addition, heritabilities for sperm DNA fragmentation and sperm protamine deficiency were moderate (h2 ~ 0.21–0.47), being the first reported estimates.
Conclusions: Genetic improvement for bull fertility is possible through selective breeding. Genomic selection for bull fertility might be more accurate if the X chromosome mutations that underlie the discovered QTL are included in the analyses. Variants associated with bull fertility accumulate in the X chromosome, as they do in humans and mice, thus, suggesting specialization of this chromosome.
MLA: L.GEN.1818 Bull fertility update: historical data, new cohort and advanced genomics - Livestock genetics and genomics - Published 11 Sep 2019
Data related to Naval-Sanchez et al. 2019 "Selection Signatures in heat-resistant cattle reveal missense mutations in damage response gene HELB".
Whole genome sequences from the 1000 Bull Gen... moreomes Project (Run6, Bos taurus, and Bos indicus) for breeds chosen as a reference for imputation were retrieved (Daetwyler et al. 2014; Hayes and Daetwyler 2018). This results in 440 whole-genome sequences across 18 cattle breeds.
Breeds were grouped in accordance to their phenotypes and reported genomic crosses as taurine (humpless), indicine (with hump), admixed or African sanga, the two latter being stabilized composite breeds (Rege J 1999; Hanotte et al. 2002; Rege J et al. 2007; Mwai et al. 2015; Felius, Marleen et al. 2016).
The dataset contains 186 European Taurine, 102 Asiatic indicine and 80 cross-bred genomes as well as a set of African samples composed of 12 taurine, 41 sanga and 19 indicine.
Genomic Analytics in the Realm of Big Data (OCE Post-Doc) - - Published 17 Jun 2019
In the absence of detailed functional annotation for any livestock genome, we used comparative genomics to predict ovine regulatory elements using human data. Reciprocal liftOver was used to predict t... morehe ovine genome location of ENCODE promoters and enhancers, along with 12 chromatin states built using 127 diverse epigenome.
Here we make available the following files:
a) Sheep_epigenome_predicted_features.tar.gz: contains the final reciprocal best alignment from ENCODE proximal as well as chromHMM ROADMAP features. The result of reciprocal liftOver.
b) liftOver_sheep_temporary_files.tar.gz: We have
added a new tar file with liftOver temporary files
i) LiftOver temporary files mapping human to sheep,
ii) LiftOver temporary files mapping sheep back to human and
iii) Dictionary files containing the link between human to sheep coordinates for exact best-reciprocal files.
OCE Post Doc - Conseq Animal Domesticati - - Published 09 Nov 2017