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| Pàgina inicial > Articles > Articles publicats > Identification of nonsense variants in the genomes of 15 Murciano-Granadina bucks and analysis of their segregation in parent-offspring trios |
(Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) (Centre de Recerca en Agrigenòmica) (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) (Departamento de Genética. Universidad de Córdoba) (Departamento de Genética. Universidad de Córdoba) (Centre de Recerca en Agrigenòmica) (Centre de Recerca en Agrigenòmica) (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
| Data: | 2024 |
| Resum: | Nonsense variants can inactivate gene function by causing the synthesis of truncated proteins or by inducing nonsense mediated decay of messenger RNAs. The occurrence of such variants in the genomes of livestock species is modulated by multiple demographic and selective factors. Even though nonsense variants can have causal effects on embryo lethality, abortions, and disease, their genomic distribution and segregation in domestic goats have not been characterized in depth yet. In this work, we have sequenced the genomes of 15 Murciano-Granadina bucks with an average coverage of 32. 92× ± 1. 45×. Bioinformatic analysis revealed 947 nonsense variants consistently detected with SnpEff and Ensembl-VEP. These variants were especially abundant in the 3' end of the protein-coding regions. Genes related to olfactory perception, ATPase activity coupled to transmembrane movement of substances, defense to virus, hormonal response, and sensory perception of taste were particularly enriched in nonsense variants. Seventeen nonsense variants expected to have harmful effects on fitness were genotyped in parent-offspring trios. We observed that several nonsense variants predicted to be lethal based on mouse knockout data did not have such effect, a finding that could be explained by the existence of multiple mechanisms counteracting lethality. These findings demonstrate that predicting the effects of putative nonsense variants on fitness is extremely challenging. As a matter of fact, such a goal could only be achieved by generating a high-quality telomere-to-telomere goat reference genome combined with carefully curated annotation and functional testing of promising candidate variants. |
| Ajuts: | Agencia Estatal de Investigación PID2019-105805RB-I00 Agencia Estatal de Investigación PID2022-136834OB-I00 Agencia Estatal de Investigación BES-2017-079709 Ministerio de Ciencia e Innovación CEX2019-000902-S |
| Nota: | Altres ajuts: acords transformatius de la UAB |
| Drets: | Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.  |
| Llengua: | Anglès |
| Document: | Article ; recerca ; Versió publicada |
| Matèria: | Knockout ; Stop gain variant ; Protein truncation ; Cost of domestication hypothesis |
| Publicat a: | Journal of dairy science, Vol. 107 Núm. 12 (december 2024) , p. 11224-11238, ISSN 1525-3198 |
