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Animal genomics
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Overview
Research of the Animal Genomics Group is focused primarily on the elucidation of the genomic architecture of traits of agronomic interest (TAI) in pigs (fat deposition, intramuscular fat content and composition, prolificacy, immunity, sperm quality etc.) and goats (milk yield and quality and body and udder conformation traits, resistance to infectious diseases, etc). With this aim, and in close collaboration with other leading scientific institutions and industrial partners, we have mapped the genetic determinants of TAI by using high throughput genotyping and next generation sequencing techniques in porcine experimental crosses and commercial populations as well as in dairy goats. We have also used RNA-Seq to investigate the regulation of gene expression in organs with key biological functions on the physiology of traits under study (e.g. liver, muscle and mammary gland) as well as of sperm cells. We are currently working in the integration of data obtained from genome-wide association studies, RNA-Seq, whole genome sequencing and single-cell multi-omic analysis, to reach new insights into fundamental questions related with the (i) the characterization of the genetic variation existing in the pig and goat genomes and the prediction of its functional impact; (ii) the genetic and epigenetic regulation of gene expression; and (iii) the molecular basis of phenotypic traits. One of the most important goals of our research is to identify causal mutations that could be used in selection schemes to optimize production performance and, simultaneously, obtain healthier and more nutritive food. An additional goal of the Animal Genomics Group is to investigate the genetic diversity of domestic animals and to understand the impact of selection and domestication on their genetic and phenotypic variation.
Selected Publications
González-Prendes R, Quintanilla R, Mármol-Sánchez E, Pena RN, Ballester M, Cardoso TF, Manunza A, Casellas J, Cánovas Á, Díaz I, Noguera JL, Castelló A, Mercadé A, Amills M.
Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles.
(2019) BMC Genomics 20:170.
Gòdia M, Mayer FQ, Nafissi J, Castelló A, Rodríguez-Gil JE, Sánchez A, Clop A.
A technical assessment of the porcine ejaculated spermatozoa for a sperm-specific RNA-seq analysis.
(2018) Systems Biology in Reproductive Medicine 64:291-303
Crespo-Piazuelo D, Estellé J, Revilla M, Criado-Mesas L, Ramayo-Caldas Y, Óvilo C, Fernández AI, Ballester M, Folch JM.
Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions.
(2018) Scientific Reports 8:12727
Cardoso TF, Quintanilla R, Castelló A, Mármol-Sánchez E, Ballester M, Jordana J, Amills M.
Analysing the expression of eight clock genes in five tissues from fasting and fed sows.
(2018) Frontiers in Genetics 9:475.
Revilla M, Puig-Oliveras A, Crespo-Piazuelo D, Criado-Mesas L, Castelló A, Fernández AI, Ballester M, Folch JM.
Expression analysis of candidate genes for fatty acid composition in adipose tissue and identification of regulatory regions.
(2018) Scientific Reports 8:2045
Cardoso TF, Quintanilla R, Castelló A, González-Prendes R, Amills M, Cánovas Á.
Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles.
(2018) BMC Genomics 19:145.
Revilla M, Puig-Oliveras A, Castelló A, Crespo-Piazuelo D, Paludo E, Fernández AI, Ballester M, Folch JM.
A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits.
(2017) PLoS One 12:e0177014.
Núñez-Hernández F, Pérez LJ, Muñoz M, Vera G, Accensi F, Sánchez A, Rodríguez F, Núñez JI.
Differential expression of porcine microRNAs in African swine fever virus infected pigs: a proof-of-concept study.
(2017) Virology Journal 14:198
Ballester M, Ramayo-Caldas Y, Revilla M, Corominas J, Castelló A, Estellé J, Fernández AI, Folch JM.
Integration of liver gene co-expression networks and eGWAs analyses highlighted candidate regulators implicated in lipid metabolism in pigs.
(2017) Scientific Reports 7:46539
Cardoso TF, Quintanilla R, Tibau J, Gil M, Mármol-Sánchez E, González-Rodríguez O, González-Prendes R, Amills M.
Nutrient supply affects the mRNA expression profile of the porcine skeletal muscle.
(2017) BMC Genomics 18: 603
Clop A, Sharaf A, Castelló A, Ramos-Onsins S, Cirera S, Mercadé A, Derdak S, Beltran S, Huisman A, Fredholm M, van As P, Sánchez A.
Identification of protein-damaging mutations in 10 swine taste receptors and 191 appetite-reward genes.
(2016) BMC Genomics 17:685
Clop A, Huisman A, van As P, Sharaf A, Derdak S, Sanchez A.
Identification of genetic variation in the swine toll-like receptors and development of a porcine TLR genotyping array.
(2016) Genetics Selection and Evolution 48:28.