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.

 

Latest additions:
2018-03-13
13:57
25 p, 1.2 MB A generalized Watterson estimator for next-generation sequencing : from trios to autopolyploids / Ferretti, Luca (Université Pierre et Marie CURIE) ; Ramos Onsins, Sebastián E. (Centre de Recerca en Agrigenòmica)
Several variations of the Watterson estimator of variability for Next Generation Sequencing (NGS) data have been proposed in the literature. We present a unified framework for generalized Watterson estimators based on Maximum Composite Likelihood, which encompasses most of the existing estimators. [...]
2015 - 10.1016/j.tpb.2015.01.001
Theoretical population biology, Vol. 100 (March 2015) , p. 79-87  
2018-03-13
13:46
38 p, 1.7 MB Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genome / Sanseverino, Walter (Centre de Recerca en Agrigenòmica) ; Hénaff, Elizabeth (Centre de Recerca en Agrigenòmica) ; Vives, Cristina (Centre de Recerca en Agrigenòmica) ; Pinosio, Sara (Universita degli studi di Udine. Dipartimento di szience agrarie e ambientali) ; Burgos-Paz, William (Centre de Recerca en Agrigenòmica) ; Morgante, Michele (Universita degli studi di Udine. Dipartimento di szience agrarie e ambientali) ; Ramos Onsins, Sebastián E. (Centre de Recerca en Agrigenòmica) ; Garcia Mas, Jordi (Centre de Recerca en Agrigenòmica) ; Casacuberta, Josep Maria (Centre de Recerca en Agrigenòmica)
The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). [...]
2015 - 10.1093/molbev/msv152
Molecular biology and evolution, Vol. 32, issue 10 (Oct. 2015) , p. 2760-74  
2018-03-06
05:31
3 p, 146.0 KB ICTV virus taxonomy profile : potyviridae / Wylie, Stephen J (Murdoch University. State Agricultural Biotechnology Centre) ; Adams, Mike (Woodland Way (Regne Unit)) ; Chalam, Celia (National Bureau of Plant Genetic Resources (India). Division of Plant Quarantine) ; Kreuze, Jan (International Potato Center) ; López-Moya, Juan José (Centre de Recerca en Agrigenòmica) ; Ohshima, Kazusato (Saga University. Department of Applied Biological Sciences) ; Praveen, Shelly (Indian Agricultural Research Institute) ; Rabenstein, Frank (Julius Kühn-Institut. Institute for Epidemiological and Pathogen Diagnosis) ; Stenger, Drake (United States. Agricultural Research Service) ; Wang, Aiming (Canada. Agriculture and Agri-Food Canada) ; Zerbini, F. Murilo (Universidade Federal de Viçosa. Departamento de Fitopatologia)
The Potyviridae is the largest family of RNA plant viruses, members of which have single-stranded, positive-sense RNA genomes and flexuous filamentous particles 680–900 nm long and 11–20 nm wide. [...]
2017 - 10.1099/jgv.0.000740
The Journal of general virology, Vol. 98 (April 2017) , p. 352-354  
2018-02-08
08:22
14 p, 2.2 MB A pathway-centered analysis of pig domestication and breeding in Eurasia / Leno-Colorado, Jordi (Centre de Recerca en Agrigenòmica) ; Hudson, Nick J. (University of Queensland. School of Agriculture and Food Science) ; Reverter, Antonio (Commonwealth Scientific and Industrial Research Organisation) ; Pérez-Enciso, Miguel (Centre de Recerca en Agrigenòmica)
Ascertaining the molecular and physiological basis of domestication and breeding is an active area of research. Due to the current wide distribution of its wild ancestor, the wild boar, the pig (Sus scrofa) is an excellent model to study these processes, which occurred independently in East Asia and Europe ca. [...]
2017 - 10.1534/g3.117.042671
G3: genes, genomics, genetics, Vol. 7 (July 2017) , p. 2171-2184  
2018-02-08
08:22
12 p, 1.0 MB Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers / Zhang, Yu (Centre de Recerca en Agrigenòmica) ; Yan, Haidong (Sichuan Agricultural University. Grassland Science Department) ; Jiang, Xiaomei (Sichuan Agricultural University. Grassland Science Department) ; Wang, Xiaoli (Guizhou Institute of Prataculture) ; Huang, Linkai (Sichuan Agricultural University. Grassland Science Department) ; Xu, Bin (Nanjing Agricultural University. College of Grassland Science) ; Zhang, Xinquan (Sichuan Agricultural University. Grassland Science Department) ; Zhang, Lexin (Sichuan Agricultural University. Grassland Science Department)
To evaluate genetic variation, population structure, and the extent of linkage disequilibrium (LD), 134 switchgrass (Panicum virgatum L. ) samples were analyzed with 51 markers, including 16 ISSRs, 20 SCoTs, and 15 EST-SSRs. [...]
2016 - 10.1186/s41065-016-0007-z
Hereditas, Vol. 153. art. 4 (April 2016)  
2018-02-07
13:21
21 p, 16.5 MB Paracrine brassinosteroid signaling at the stem cell niche controls cellular regeneration / Lozano Elena, Fidel (Centre de Recerca en Agrigenòmica) ; Planas Riverola, Ainoa (Centre de Recerca en Agrigenòmica) ; Vilarrasa Blasi, Josep (Centre de Recerca en Agrigenòmica) ; Schwab, Rebecca (Cold Spring Harbor Laboratory) ; Caño Delgado, Ana I. (Centre de Recerca en Agrigenòmica)
Stem cell regeneration is crucial for both cell turnover and tissue healing in multicellular organisms. In Arabidopsis roots, a reduced group of cells known as the quiescent center (QC) act as a cell reservoir for surrounding stem cells during both normal growth and in response to external damage. [...]
2018 - 10.1242/jcs.204065
Journal of cell science, Vol. 131, Issue 2 (January 2018) , p. 1-11  
2018-02-07
13:10
11 p, 2.5 MB A deletion affecting an LRR-RLK gene co-segregates with the fruit flat shape trait in peach / Lopez Girona, Elena (Institut de Recerca i Tecnologia Agroalimentàries) ; Zhang, Yu (Centre de Recerca en Agrigenòmica) ; Eduardo Muñoz, Iban (Institut de Recerca i Tecnologia Agroalimentàries) ; Hernández Mora, José R. (Institut de Recerca i Tecnologia Agroalimentàries) ; Alexiou, Konstantinos G. (Institut de Recerca i Tecnologia Agroalimentàries) ; Arús i Gorina, Pere (Institut de Recerca i Tecnologia Agroalimentàries) ; Aranzana Civit, Mª José (Institut de Recerca i Tecnologia Agroalimentàries)
In peach, the flat phenotype is caused by a partially dominant allele in heterozygosis (Ss), fruits from homozygous trees (SS) abort a few weeks after fruit setting. Previous research has identified a SSR marker (UDP98–412) highly associated with the trait, found suitable for marker assisted selection (MAS). [...]
2017 - 10.1038/s41598-017-07022-0
Scientific reports, Vol. 7, (July 2017) , art. 6714  
2018-02-07
12:47
11 p, 1.1 MB Optimized next-generation sequencing genotype-haplotype calling for genome variability analysis / Navarro Fernández, Javier (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius) ; Nevado, Bruno (University of Oxford. Department of Plant Sciences) ; Hernández Budé, Porfidio (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius) ; Vera Rodríguez, Gonzalo (Centre de Recerca en Agrigenòmica) ; Ramos Onsins, Sebastián E. (Centre de Recerca en Agrigenòmica)
The accurate estimation of nucleotide variability using next-generation sequencing data is challenged by the high number of sequencing errors produced by new sequencing technologies, especially for nonmodel species, where reference sequences may not be available and the read depth may be low due to limited budgets. [...]
2017 - 10.1177/1176934317723884
Evolutionary bioinformatics, Vol. 13, (August 2017) , p. 1-11  
2018-02-07
12:38
DnaSP 6 : DNA sequence polymorphism analysis of large data sets / Rozas, Julio (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística) ; Ferrer-Mata, Albert (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística) ; Sánchez-DelBarrio, Juan Carlos (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística) ; Guirao-Rico, Sara (Centre de Recerca en Agrigenòmica) ; Librado, Pablo (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística) ; Ramos-Onsins, Sebastián E. (Centre de Recerca en Agrigenòmica) ; Sánchez-Gracia, Alejandro (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística)
We present version 6 of the DnaSP (DNA Sequence Polymorphism) software, a new version of the popular tool for performing exhaustive population genetic analyses on multiple sequence alignments. This major upgrade incorporates novel functionalities to analyse large datasets, such as those generated by high-throughput sequencing (HTS) technologies. [...]
2017 - 10.1093/molbev/msx248
Molecular biology and evolution, Vol. 34, issue 12 (Dec. 2017) p. 3299-3302  
2018-02-07
12:24
Porcine Y-chromosome variation is consistent with the occurrence of paternal gene flow from non-Asian to Asian populations / Guirao-Rico, Sara (Centre de Recerca en Agrigenòmica) ; Ramírez Bellido, Óscar (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ; Ojeda García, Ana (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ; Amills i Eras, Marcel (Centre de Recerca en Agrigenòmica) ; Ramos Onsins, Sebastián E. (Centre de Recerca en Agrigenòmic)
Pigs (Sus scrofa) originated in Southeast Asia and expanded to Europe and North Africa approximately 1 MYA. Analyses of porcine Y-chromosome variation have shown the existence of two main haplogroups that are highly divergent, a result that is consistent with previous mitochondrial and autosomal data showing that the Asian and non-Asian pig populations remained geographically isolated until recently. [...]
2018 - 10.1038/s41437-017-0002-9
Heredity, Vol. 120 (2018) , p. 63–76