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1.
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12 p, 2.1 MB |
On the holobiont 'predictome' of immunocompetence in pigs
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Calle-García, Joan (Centre de Recerca en Agrigenòmica) ;
Ramayo-Caldas, Yuliaxis (Unitat mixta d'investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal) ;
Zingaretti, Laura M. (Centre de Recerca en Agrigenòmica) ;
Quintanilla, Raquel (Unitat mixta d'investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal) ;
Ballester Devis, Maria (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ;
Perez-Enciso, Miguel (Centre de Recerca en Agrigenòmica)
Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex traits, although methods to optimize this are still largely unexplored. [...]
2023 -  10.1186/s12711-023-00803-4
Genetics, selection, evolution, Vol. 55 (may 2023)
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2.
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14 p, 3.8 MB |
Disentangling the causal relationship between rabbit growth and cecal microbiota through structural equation models
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Mora Fenoll, Mònica (Institut de Recerca i Tecnologia Agroalimentàries) ;
Velasco-Galilea, María (Centre de Recerca en Agrigenòmica) ;
Sánchez, Juan Pablo (Institut de Recerca i Tecnologia Agroalimentàries) ;
Ramayo-Caldas, Yuliaxis (Institut de Recerca i Tecnologia Agroalimentàries) ;
Piles, Miriam (Institut de Recerca i Tecnologia Agroalimentàries)
Background: The effect of the cecal microbiome on growth of rabbits that were fed under different regimes has been studied previously. However, the term "effect" carries a causal meaning that can be confounded because of potential genetic associations between the microbiome and production traits. [...]
2022 - 10.1186/s12711-022-00770-2
Genetics, selection, evolution, Vol. 54 (December 2022) , art. 81
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3.
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20 p, 3.9 MB |
Opportunities and limits of combining microbiome and genome data for complex trait prediction
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Perez-Enciso, Miguel (Centre de Recerca en Agrigenòmica) ;
Zingaretti, Laura M. (Centre de Recerca en Agrigenòmica) ;
Ramayo-Caldas, Yuliaxis (Institut de Recerca i Tecnologia Agroalimentàries) ;
de los Campos, Gustavo (Michigan State University. Department of Epidemiology & Biostatistics)
Analysis and prediction of complex traits using microbiome data combined with host genomic information is a topic of utmost interest. However, numerous questions remain to be answered: how useful can the microbiome be for complex trait prediction? Are estimates of microbiability reliable? Can the underlying biological links between the host's genome, microbiome, and phenome be recovered? Here, we address these issues by (i) developing a novel simulation strategy that uses real microbiome and genotype data as inputs, and (ii) using variance-component approaches (Bayesian Reproducing Kernel Hilbert Space (RKHS) and Bayesian variable selection methods (Bayes C)) to quantify the proportion of phenotypic variance explained by the genome and the microbiome. [...]
2021 - 10.1186/s12711-021-00658-7
Genetics, selection, evolution, Vol. 53 (August 2021) , art. 65
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4.
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5.
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14 p, 2.9 MB |
VarGoats project : a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity
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Denoyelle, Laure (Université de Toulouse) ;
Talouarn, Estelle (Université de Toulouse) ;
Bardou, Philippe (Université de Toulouse) ;
Colli, Licia (Università Cattolica del Sacro Cuore. Dipartimento Di Scienze Animali, Della Nutrizione E Degli Alimenti) ;
Alberti, Adriana (Université Paris-Saclay) ;
Danchin Burge, Coralie (Institut de L'Elevage (Paris)) ;
Del Corvo, Marcello (Università Cattolica del Sacro Cuore. Dipartimento Di Scienze Animali, Della Nutrizione E Degli Alimenti) ;
Engelen, Stefan (Université Paris-Saclay) ;
Orvain, Céline (Université Paris-Saclay) ;
Palhière, Isabelle (Université de Toulouse) ;
Rupp, Rachel (Université de Toulouse) ;
Sarry, Julien (Université de Toulouse) ;
Salavati, Mazdak (University of Edinburgh) ;
Amills i Eras, Marcel (Centre de Recerca en Agrigenòmica) ;
Clark, Emily (University of Edinburgh) ;
Crepaldi, Paola (University of Milan. Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy) ;
Faraut, Thomas (Université de Toulouse) ;
Masiga, Clet Wandui (Tropical Institute of Development Innovations (TRIDI) (Uganda)) ;
Pompanon, François (Université Grenoble Alpes) ;
Rosen, Benjamin D. (USDA-ARS. Animal Genomics and Improvement Laboratory) ;
Stella, Alessandra (Istituto Di Biologia E Biotecnologia Agraria (Milan)) ;
Van Tassell, Curtis (USDA-ARS. Animal Genomics and Improvement Laboratory) ;
Tosser-Klopp, Gwenola (Université de Toulouse)
Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. [...]
2021 - 10.1186/s12711-021-00659-6
Genetics, selection, evolution, Vol. 53 (November 2021) , art. 86
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6.
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15 p, 1.6 MB |
Use of Bayes factors to evaluate the effects of host genetics, litter and cage on the rabbit cecal microbiota
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Velasco-Galilea, María (Centre de Recerca en Agrigenòmica) ;
Piles, Miriam (Institut de Recerca i Tecnologia Agroalimentàries) ;
Ramayo-Caldas, Yuliaxis (Institut de Recerca i Tecnologia Agroalimentàries) ;
Varona, Luis (Universidad de Zaragoza) ;
Sánchez, Juan Pablo (Institut de Recerca i Tecnologia Agroalimentàries)
The rabbit cecum hosts and interacts with a complex microbial ecosystem that contributes to the variation of traits of economic interest. Although the influence of host genetics on microbial diversity and specific microbial taxa has been studied in several species (e. [...]
2022 - 10.1186/s12711-022-00738-2
Genetics, selection, evolution, Vol. 54 (June 2022) , art. 46
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7.
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21 p, 2.2 MB |
Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes
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Mármol-Sánchez, Emilio (Centre de Recerca en Agrigenòmica) ;
Luigi Sierra, Maria Gracia (Centre de Recerca en Agrigenòmica) ;
Castelló Farré, Anna (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ;
Guan, Dailu (Centre de Recerca en Agrigenòmica) ;
Quintanilla, Raquel (Institute for Research and Technology in Food and Agriculture. Animal Breeding and Genetics Program) ;
Tonda, Raul (Centre de Regulació Genòmica) ;
Amills i Eras, Marcel (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Mature microRNAs (miRNAs) play an important role in repressing the expression of a wide range of mRNAs. The presence of polymorphic sites in miRNA genes and their corresponding 3'UTR binding sites can disrupt canonical conserved miRNA-mRNA pairings, and thus modify gene expression patterns. [...]
2021 - 10.1186/s12711-021-00632-3
Genetics, selection, evolution, Vol. 53 (May 2021) , art. 43
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8.
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10 p, 1.2 MB |
Phenomes : the current frontier in animal breeding
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Perez-Enciso, Miguel (Centre de Recerca en Agrigenòmica) ;
Steibel, Juan P. (Michigan State University. Department of Fisheries and Wildlife)
Improvements in genomic technologies have outpaced the most optimistic predictions, allowing industry-scale application of genomic selection. However, only marginal gains in genetic prediction accuracy can now be expected by increasing marker density up to sequence, unless causative mutations are identified. [...]
2021 - 10.1186/s12711-021-00618-1
Genetics, selection, evolution, Vol. 53 (March 2021) , art. 22
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10.
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12 p, 2.5 MB |
On the performance of tests for the detection of signatures of selection : a case study with the Spanish autochthonous beef cattle populations
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González-Rodríguez, Aldemar (Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal) ;
Munilla, Sebastián (Universidad de Buenos Aires. Departamento de Producción Animal) ;
Mouresan, Elena F. (Universidad de Zaragoza. Departamento de Anatomía, Embriología y Genética Animal) ;
Cañas Álvarez, Jhon Jacobo (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ;
Díaz, Clara (INIA Departamento de Mejora Genética Animal) ;
Piedrafita Arilla, Jesús (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ;
Altarriba, Juan (Instituto Agroalimentario de Aragón) ;
Baro, Jesús Á. (Universidad de Valladolid. Departamento de Ciencias Agroforestales) ;
Molina, Antonio (Universidad de Córdoba. MERAGEM) ;
Varona, Luis (Instituto Agroalimentario de Aragón)
Procedures for the detection of signatures of selection can be classified according to the source of information they use to reject the null hypothesis of absence of selection. Three main groups of tests can be identified that are based on: (1) the analysis of the site frequency spectrum, (2) the study of the extension of the linkage disequilibrium across the length of the haplotypes that surround the polymorphism, and (3) the differentiation among populations. [...]
2016 - 10.1186/s12711-016-0258-1
Genetics, selection, evolution, Vol. 48 (october 2016)
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