CRAG (Centre for Research in Agricultural Genomics)

The CRAG is devoted to leading-edge research in the molecular basis of genetic characters of interest in plants and farm animals and in the applications of molecular approaches for breeding of species important for agriculture and food production. Research at CRAG spans from basic science to applied studies in close collaboration with industry.

 

Usage statistics Most popular
Latest additions:
2019-05-13
03:58
8 p, 1.0 MB pSBVB : A versatile simulation tool to evaluate genomic selection in polyploid species / Zingaretti, María L. (Centre de Recerca en Agrigenòmica) ; Monfort Vives, Amparo (Centre de Recerca en Agrigenòmica) ; Pérez-Enciso, Miguel (Centre de Recerca en Agrigenòmica)
Genomic Selection (GS) is the procedure whereby molecular information is used to predict complex phenotypes and it is standard in many animal and plant breeding schemes. However, only a small number of studies have been reported in horticultural crops, and in polyploid species in particular. [...]
2019 - 10.1534/g3.118.200942
G3: Genes, genomes, genetics, Vol. 9, Issue 2 (February 2019) , p. 327-334  
2019-04-11
15:13
15 p, 620.2 KB Endometrial gene expression profile of pregnant sows with extreme phenotypes for reproductive efficiency / Córdoba, Sarai (Centre de Recerca en Agrigenòmica) ; Balcells Ortega, Ingrid (Centre de Recerca en Agrigenòmica) ; Castelló, Anna (Centre de Recerca en Agrigenòmica) ; Ovilo, Cristina (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria) ; Noguera Jiménez, José Luis (Institut de Recerca i Tecnologia Agroalimentàries) ; Timoneda i Heredia, Oriol (Centre de Recerca en Agrigenòmica) ; Sánchez Bonastre, Armando (Centre de Recerca en Agrigenòmica) ; Universitat Autònoma de Barcelona. Departament de Genètica Animal
2015 0) and low (L, EBV 0) prolificacy phenotypes. For each sample, mRNA and small RNA libraries were RNA-sequenced, identifying 141 genes and 10 miRNAs differentially expressed between H and L groups. We selected four miRNAs based on their role in reproduction, and five genes displaying the highest differences and a positive mapping into known reproductive QTLs for RT-qPCR validation on the whole extreme population. Significant differences were validated for genes: PTGS2 (p = 0.03; H/L ratio = 3.50), PTHLH (p = 0.03; H/L ratio = 3.69), MMP8 (p = 0.01; H/L ratio = 4.41) and SCNN1G (p = 0.04; H/L ratio = 3.42). Although selected miRNAs showed similar expression levels between H and L groups, significant correlation was found between the expression level of ssc-miR-133a (p 0.01) and sscmiR-92a (p 0.01) and validated genes. These results provide a better understanding of the genetic architecture of prolificacy-related traits and embryo implantation failure in pigs. - 10.1038/srep14416
Scientific Reports, Vol. 5 (October 2015) , art. 14416  
2019-04-10
09:24
Chloroplasts modulate elongation responses to canopy shade by retrograde pathways involving HY5 and abscisic acid / Ortiz-Alcaide, Miriam (Centre de Recerca en Agrigenòmica) ; Llamas, Ernesto (Centre de Recerca en Agrigenòmica) ; Gómez-Cadenas, Aurelio (Universitat Jaume I) ; Nagatani, Akira (Kyoto University) ; Martínez-García, Jaime F. (Centre de Recerca en Agrigenòmica) ; Rodríguez-Concepción, Manuel (Centre de Recerca en Agrigenòmica)
Plants use light as energy for photosynthesis but also as a signal of competing vegetation. Using different concentrations of norflurazon and lincomycin, we found that the response to canopy shade in Arabidopsis (Arabidopsis thaliana) was repressed even when inhibitors only caused a modest reduction in the level of photosynthetic pigments. [...]
2019 - 10.1105/tpc.18.00617
The Plant Cell, Vol. 31, issue 2 (Feb. 2019)  
2019-04-08
16:30
7 p, 990.3 KB Rapid genome resequencing of an atoxigenic strain of Aspergillus carbonarius / Cabañes Sáenz, Francisco Javier (Universitat Autònoma de Barcelona. Departament de Sanitat i d'Anatomia Animals) ; Sanseverino, Walter (Sequentia Biotech SL) ; Castellà Gómez, Gemma (Universitat Autònoma de Barcelona. Departament de Sanitat i d'Anatomia Animals) ; Bragulat Arara, Mª Rosa (Universitat Autònoma de Barcelona. Departament de Sanitat i d'Anatomia Animals) ; Cigliano, Riccardo Aiese (Sequentia Biotech SL) ; Sánchez Bonastre, Armando (Centre de Recerca en Agrigenòmica)
In microorganisms, Ion Torrent sequencing technology has been proved to be useful in whole-genome sequencing of bacterial genomes (5 Mbp). In our study, for the first time we used this technology to perform a resequencing approach in a whole fungal genome (36 Mbp), a non-ochratoxin A producing strain of Aspergillus carbonarius. [...]
2015 - 10.1038/srep09086
Scientific Reports, Vol. 5 (2015) , art. 9086  
2019-04-03
15:25
10 p, 860.4 KB Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK / Manunza, Arianna (Centre de Recerca en Agrigenòmica) ; Cardoso, Tainã Figueiredo (Centre de Recerca en Agrigenòmica) ; Noce, Antonia (Centre de Recerca en Agrigenòmica) ; Martínez Martínez, Amparo (Universidad de Córdoba. Departamento de Genética) ; Pons Barro, Agueda (Servei de Millora Agrària i Pesquera (SEMILLA)) ; Bermejo Asensio, Luis Alberto (Universidad de la Laguna) ; Landi, Vincenzo (Universidad de Córdoba. Departamento de Genética) ; Sánchez Bonastre, Armando (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ; Jordana i Vidal, Jordi (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ; Delgado, Juan Vicente (Universidad de Córdoba. Departamento de Genética) ; Adán Belmonte, Silvia (Federación de Razas Autóctonas de Galicia (BOAGA)) ; Capote Álvarez, Juan (Instituto Canario de Investigaciones Agrarias) ; Vidal i Fàbrega, Oriol (Universitat de Girona. Departament de Biologia) ; Ugarte Sagastizabal, Eva (Neiker-Tecnalia) ; Arranz Santos, Juan José (Universidad de León. Departamento de Producción Animal) ; Calvo Lacosta, Jorge Hugo (Centro de Investigación y Tecnología Agroalimentaria de Aragón) ; Casellas Vidal, Joaquim (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ; Amills i Eras, Marcel (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). [...]
2016 - 10.1038/srep27296
Scientific Reports, Vol. 6 (June 2016) , art. 27296  
2019-04-03
14:43
9 p, 905.1 KB Romanian wild boars and Mangalitza pigs have a European ancestry and harbour genetic signatures compatible with past population bottlenecks / Manunza, Arianna (Centre de Recerca en Agrigenòmica) ; Amills i Eras, Marcel (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ; Noce, Antonia (Centre de Recerca en Agrigenòmica) ; Cabrera Pane, Betlem (Centre de Recerca en Agrigenòmica) ; Zidi, Ali (Centre de Recerca en Agrigenòmica) ; Eghbalsaied, Shahin (Islamic Azad University (Isfahan, Iran). Department of Animal Science) ; Carrillo de Albornoz, Eva (Centre de Recerca en Agrigenòmica) ; Portell, M. (Centre de Recerca en Agrigenòmica) ; Mercadé Carceller, Anna (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ; Sánchez Bonastre, Armando (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ; Balteanu, Valentin Adrian (University of Agricultural Sciences and Veterinary Medicine)
We aimed to analyse the genetic diversity of Romanian wild boars and to compare it with that from other wild boar and pig populations from Europe and Asia. Partial sequencing of the mitochondrial encoded cytochrome b (MT-CYB) gene from 36 Romanian wild boars and 36 domestic pigs (Mangalitza, Bazna and Vietnamese breeds) showed that the diversity of Romanian wild boars and Mangalitza pigs is fairly reduced, and that most of the members of these two populations share a common MT-CYB haplotype. [...]
2016 - 10.1038/srep29913
Scientific Reports, Vol. 6 (July 2016) , art. 29913  
2018-12-21
12:05
9 p, 1.8 MB An improved assembly and annotation of the melon (Cucumis melo L.) reference genome / Ruggieri, Valentino (Centre de Recerca en Agrigenòmica) ; Alexiou, Konstantinos G. (Institut de Recerca i Tecnologia Agroalimentàries) ; Morata, Jordi (Centre de Recerca en Agrigenòmica) ; Argyris, Jason (Centre de Recerca en Agrigenòmica) ; Pujol, Maria (Institut de Recerca i Tecnologia Agroalimentàries) ; Yano, Ryoichi (University of Tsukuba. Faculty of Life and Environmental Sciences) ; Nonaka, Satoko (University of Tsukuba. Faculty of Life and Environmental Sciences) ; Ezura, Hiroshi (University of Tsukuba. Faculty of Life and Environmental Sciences) ; Latrasse, David (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ; Boualem, Adnane (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ; Benhamed, Moussa (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ; Bendahmane, Abdelhafid (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ; Cigliano, Riccardo Aiese (Sequentia Biotech SL) ; Sanseverino, Walter (Sequentia Biotech SL) ; Puigdomènech, Pere, 1948- (Centre de Recerca en Agrigenòmica) ; Casacuberta i Suñer, Josep M. (Centre de Recerca en Agrigenòmica) ; Garcia Mas, Jordi (Centre de Recerca en Agrigenòmica)
We report an improved assembly (v3. 6. 1) of the melon (Cucumis melo L. ) genome and a new genome annotation (v4. 0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. [...]
2018 - 10.1038/s41598-018-26416-2
Scientific Reports, Vol. 8 (May 2018) , art. 8088  
2018-12-21
12:05
14 p, 1.3 MB The tomato subtilase family includes several cell death-related proteinases with caspase specificity / Reichardt, Sven (University of Hohenheim. Institute of Plant Physiology and Biotechnology) ; Repper, Dagmar (University of Hohenheim. Institute of Plant Physiology and Biotechnology) ; Tuzhikov, Alexander I. (Moscow State University. Belozersky Institute of Physico-Chemical Biology.) ; Galiullina, Raisa A. (Moscow State University. Belozersky Institute of Physico-Chemical Biology) ; Planas Marquès, Marc (Centre de Recerca en Agrigenòmica) ; Chichkova, Nina V. (Moscow State University. Belozersky Institute of Physico-Chemical Biology) ; Vartapetian, Andrey B. (Moscow State University. Belozersky Institute of Physico-Chemical Biology) ; Stintzi, Annick (University of Hohenheim. Institute of Plant Physiology and Biotechnology) ; Schaller, Andres (University of Hohenheim. Institute of Plant Physiology and Biotechnology)
Phytaspases are Asp-specific subtilisin-like plant proteases that have been likened to animal caspases with respect to their regulatory function in programmed cell death (PCD). We identified twelve putative phytaspase genes in tomato that differed widely in expression level and tissue-specific expression patterns. [...]
2018 - 10.1038/s41598-018-28769-0
Scientific Reports, Vol. 8 (July 2018) , art. 10531  
2018-12-21
12:05
13 p, 1.8 MB Expression analysis of candidate genes for fatty acid composition in adipose tissue and identification of regulatory regions / Revilla, Manuel (Centre de Recerca en Agrigenòmica) ; Puig-Oliveras, Anna (Centre de Recerca en Agrigenòmica) ; Crespo-Piazuelo, Daniel (Centre de Recerca en Agrigenòmica) ; Criado-Mesas, Lourdes (Centre de Recerca en Agrigenòmica) ; Castelló, Anna (Centre de Recerca en Agrigenòmica) ; Fernández Ávila, Ana Isabel (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria) ; Ballester Devis, Maria (Institut de Recerca i Tecnologia Agroalimentàries) ; Folch Albareda, Josep Maria (Centre de Recerca en Agrigenòmica)
The aim of this work was to study the genetic basis of the backfat expression of lipid-related genes associated with meat quality traits in pigs. We performed a genome-wide association study with the backfat gene expression measured in 44 genes by qPCR and the PorcineSNP60 BeadChip genotypes in 115 Iberian x Landrace backcross animals. [...]
2018 - 10.1038/s41598-018-20473-3
Scientific Reports, Vol. 8 (February 2018) , art. 2045  
2018-12-21
12:05
5 p, 572.2 KB Revised nomenclature and functional overview of the ULP gene family of plant deSUMOylating proteases / Humberto Castro, Pedro (Universidade do Porto. Research Network in Biodiversity and Evolutionary Biology) ; Bachmair, Andreas (University of Vienna. Departament of Biochemistry and Cell Biologyç) ; Bejarano, Eduardo R. (Universidad de Málaga-Consejo Superior de Investigaciones Científicas. Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora') ; Coupland, George (Max Planck Institute for Plant Breeding Research) ; Lois, L. Maria (Centre de Recerca en Agrigenòmica) ; Sadanandom, Ari (Durham University. Department of BioSciences) ; Van Den Burg, Harrold A. (University of Amsterdam. Molecular Plant Pathology. Swammerdam Institute for Life Sciences) ; Vierstra, Richard D. (Washington University in St Louis. Department of Biology) ; Azevedo, H. (Universidade do Porto. Departamento de Biologia. Faculdade de Ciências.)
Functional insight on the post-translational modifier SUMO and its biochemical pathway in plants has steadily increased over the past decade. In contrast to the low number of core components that catalytically control SUMO attachment to targets, the enzymes that control deconjugation and SUMO maturation seem to have diversified in terms of both gene number and biological function. [...]
2018 - 10.1093/jxb/ery301
Journal of Experimental Botany, Vol. 69, Núm. 19 (August 2018) , p. 4505-4509