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Animal genomics

Research of the Animal Genomics group is focused primarily on the elucidation of the genetic architecture of traits of economic interest (ETI) in pigs, such as growth, fatness, intramuscular fat and composition, prolificacy, meat pH and color, susceptibility to pathogens etc. With this aim, and in close collaboration with other leading Spanish scientific institutions as IRTA and INIA, we have analysed three resource populations including two intercrosses (Iberian x Landrace and Iberian x Meishan) and one Duroc commercial line.
We pioneered porcine QTL and microarray studies in Spain, generating a huge amount of information that has been unvaluable in order to map the genetic determinants of TEI and expression QTL. With more than 90 publications in international journals in the last 5 years, we have currently implemented state-of-the-art approaches, as genome-wide association analyses, RNAseq, miRNAseq and whole genome sequencing, allowing us to reach an unprecedented perspective about fundamental questions related with the biology of gene and phenotype expression in pigs. The main return of this research to society should be the identification of causal mutations that could be used in selection schemes to optimize production performance and, simultaneously, obtain a healthier and more nutritive food.
Other ongoing lines of research are related with the study of pig domestication and breed formation, the genetic analysis of milk composition in goats and the investigation of genetic susceptibility to hereditary and infectious diseases in dogs.

Selected Publications

Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, Bibe B, Bouix J, Caiment F, Elsen JM, Eychenne F, Larzul C, Laville E, Meish F, Milenkovic D, Tobin J, Charlier C, Georges M.

A mutation revealing a potential illegitimate miRNA target site in the myostatin gene affects muscularity in sheep

Nature Genetics, 2006, 38: 813-818

 

Francino O., Altet L., Sánchez-Robert E., Rodriguez A., Solano-Gallego L., Alberola J., Ferrer L., Sánchez A. ,X. Roura

Advantages of real-time PCR assay for diagnosis and monitoring of canine leishmaniosis

Veterinary Parasitology, 2006, 137:214-221

 

Amills M, O. Ramírez, A. Tomàs, G. Obexer-Ruff , O. Vidal

Positive selection on mammalian MHC-DQ genes revisited from a multispecies perspective

Genes and Immunity, 2008,  9: 651-658

 

Ramírez O, Ojeda A, Tomàs A, Gallardo D, Huang LS, Folch JM, Clop A, Sánchez A, Badaoui B, Hanotte O, Galman-Omitogun O, Makuza SM, Soto H, Cadillo J, Kelly L, Cho IC, Yeghoyan S, Pérez-Enciso M, Amills M.

Integrating Y-chromosome, mitochondrial, and autosomal data to analyze the origin of pig breeds

Molecular Biology and Evolution, 2009,  26: 2061-72

 

Ramayo-Caldas Y, Castelló A, Pena RN, Alves E, Mercadé A, Souza CA, Fernández AI, Perez-Enciso M, Folch JM.

Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip

BMC Genomics, 2010;11:593

 

Zidi A, Amills M, Tomás A, Vidal O, Ramírez O, Carrizosa J, Urrutia B, Serradilla JM, Clop A.

Genetic variability in the predicted microRNA target sites of caprine casein genes

Journal of Dairy Science,  2010, 93:1749-1753

 

Olsson M, Meadows JR, Truvé K, Rosengren Pielberg G, Puppo F, Mauceli E, Quilez J, Tonomura N, Zanna G, Docampo MJ, Bassols A, Avery AC, Karlsson EK, Thomas A, Kastner DL, Bongcam-Rudloff E, Webster MT, Sanchez A, Hedhammar A, Remmers EF, Andersson L, Ferrer L, Tintle L. and K. Lindblad-Toh

A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs

PLoS Genetics, 2011,  7(3):e1001332

 

Quilez J., Short A.D., Martínez V., Kennedy L.J, Ollier W., Sanchez A., Altet L., y O. Francino

A selective sweep of >8 Mb on chromosome 26 in the Boxer genome

BMC Genomics, 2011,  12(1):339

 

Quilez J., Martínez V., Sanchez A., Woolliams J.A., Pong-Wong R., Kennedy L.R., Quinnell R., Ollier W., Roura X., Ferrer Ll., Altet L., y Francino O.

Genetic Control of Canine Leishmaniasis: Genome-Wide Association Study and Genomic Selection Analysis

Plos One, 2012, 7(4):e35349

 

Timoneda O, Balcells I, Núñez JI, Egea R, Vera G, Castello A, Tomas A , A. Sánchez

miRNA Expression Profile Analysis in Kidney of Different Porcine Breeds

PLoS One, 2013,  8(1): e55402