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.

  • Research Articles
  • Dissemination Articles
  • Doctoral theses
  • Books and Book chapters

    Usage statistics Most popular
    Latest additions:
    16 p, 2.7 MB An efficient CRISPR-Cas9 enrichment sequencing strategy for characterizing complex and highly duplicated genomic regions : A case study in the Prunus salicina LG3-MYB10 genes cluster / Fiol, Arnau (Centre de Recerca en Agrigenòmica) ; Jurado-Ruiz, Federico (Centre de Recerca en Agrigenòmica) ; López-Girona, Elena (The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research)) ; Aranzana, Maria José (Institut de Recerca i Tecnologia Agroalimentàries)
    Background: Genome complexity is largely linked to diversification and crop innovation. Examples of regions with duplicated genes with relevant roles in agricultural traits are found in many crops. In both duplicated and non-duplicated genes, much of the variability in agronomic traits is caused by large as well as small and middle scale structural variants (SVs), which highlights the relevance of the identification and characterization of complex variability between genomes for plant breeding. [...]
    2022 - 10.1186/s13007-022-00937-4
    Plant methods, Vol. 18 (August 2022) , art. 105  
    19 p, 1.3 MB A mini-TGA protein modulates gene expression through heterogeneous association with transcription factors / Tomaž, Špela (Jožef Stefan International Postgraduate School) ; Petek, Marko (National Institute of Biology. Department of Biotechnology and Systems Biology) ; Lukan, Tjaša (National Institute of Biology. Department of Biotechnology and Systems Biology) ; Pogačar, Karmen (National Institute of Biology. Department of Biotechnology and Systems Biology) ; Stare, Katja (National Institute of Biology. Department of Biotechnology and Systems Biology) ; Prates, Erica Teixeira (Oak Ridge National Laboratory. Biosciences Division) ; Jacobson, Daniel (Oak Ridge National Laboratory. Biosciences Division) ; Zrimec, Jan (National Institute of Biology. Department of Biotechnology and Systems Biology) ; Bajc, Gregor (University of Ljubljana. Department of Biology) ; Butala, Matej (University of Ljubljana. Department of Biology) ; Novak, Maruša Pompe (University of Nova Gorica. School for Viticulture and Enology) ; Dudley, Quentin (Earlham Institute) ; Patron, Nicola J. (Earlham Institute) ; Taler-Verčič, Ajda (University of Ljubljana. Institute of Biochemistry and Molecular Genetics) ; Usenik, Aleksandra (Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins) ; Turk, Dusan (Jožef Stefan Institute. Department of Biochemistry and Molecular and Structural Biology) ; Prat, Salomé (Centre de Recerca en Agrigenòmica) ; Coll, Anna (National Institute of Biology. Department of Biotechnology and Systems Biology) ; Gruden, Kristina (National Institute of Biology. Department of Biotechnology and Systems Biology)
    TGA (TGACG-binding) transcription factors, which bind their target DNA through a conserved basic region leucine zipper (bZIP) domain, are vital regulators of gene expression in salicylic acid (SA)-mediated plant immunity. [...]
    2023 - 10.1093/plphys/kiac579
    Plant physiology, Vol. 191 Issue 3 (March 2023) , p. 1934-1952  
    8 p, 3.4 MB Comparative QTL analysis in peach 'Earlygold' F2 and backcross progenies / Kalluri, Naveen (Centre de Recerca en Agrigenòmica) ; Eduardo, Iban (Centre de Recerca en Agrigenòmica) ; Arús i Gorina, Pere (Centre de Recerca en Agrigenòmica)
    Based on detailed maps, DNA sequences and phenotypic data, there is a great deal of information on the genetics and genomics of 'Earlygold', a historical peach cultivar from the US. The F between 'Texas' almond and 'Earlygold' peach (T × E) was used to construct the first saturated peach linkage map that later became the reference map for the Prunus genus. [...]
    2022 - 10.1016/j.scienta.2021.110726
    Scientia Horticulturae, Vol. 293 (February 2022) , art. 110726  
    7 p, 1.6 MB Crop archaeogenomics : A powerful resource in need of a well-defined regulation framework / Iob, Alice (Centre de Recerca en Agrigenòmica) ; Botigué, Laura (Centre de Recerca en Agrigenòmica)
    Societal Impact Statement: Crop archaeogenomics has rapidly flourished in recent years, leading to a new way of understanding the past and bringing answers to important questions about human history in relation to plant management and food production. [...]
    2022 - 10.1002/ppp3.10233
    Plants People Planet, Vol. 4, Issue 1 (January 2022) , p. 44-50  
    16 p, 1.5 MB Development and carotenoid synthesis in dark-grown carrot taproots require PHYTOCHROME RAPIDLY REGULATED1 / Arias, Daniela (Universidad de Chile. Centro de Biología Molecular Vegetal) ; Ortega, Angélica (Universidad de Chile. Centro de Biología Molecular Vegetal) ; González-Calquin, Christian (Universidad de Chile. Centro de Biología Molecular Vegetal) ; Quiroz Iturra, Luis Felipe (Universidad de Chile. Centro de Biología Molecular Vegetal) ; Moreno Romero, Jordi (Centre de Recerca en Agrigenòmica) ; Martínez García, Jaime F. (Centre de Recerca en Agrigenòmica) ; Stange, Claudia (Universidad de Chile. Centro de Biología Molecular Vegetal)
    Light stimulates carotenoid synthesis in plants during photomorphogenesis through the expression of PHYTOENE SYNTHASE (PSY), a key gene in carotenoid biosynthesis. The orange carrot (Daucus carota) synthesizes and accumulates high amounts of carotenoids in the taproot that grows underground. [...]
    2022 - 10.1093/plphys/kiac097
    Plant physiology, Vol. 189, Issue 3 (July 2022) , p. 1450-1465  
    20 p, 3.0 MB Protein and antibody purification followed by immunoprecipitation of MYB and GATA zinc finger-type maize proteins with magnetic beads / Vélez-Bermúdez, Isabel Cristina (Academia Sinica (Taiwan). Institute of Plant and Microbial Biology) ; Salazar-Henao, Jorge Enrique (Academia Sinica (Taiwan). Institute of Plant and Microbial Biology) ; Riera, Marta (Centre de Recerca en Agrigenòmica) ; Caparros Ruíz, David (Centre de Recerca en Agrigenòmica) ; Schmidt, Wolfgang (National Taiwan University. College of Life Science)
    Co-immunoprecipitation (Co-IP) is a widely used and powerful approach for studying protein-protein interactions in vivo. Here, we describe a protocol for antibody purification and immobilization followed by immunoprecipitation from plant tissue extracts using magnetic beads. [...]
    2022 - 10.1016/j.xpro.2022.101449
    STAR Protocols, Vol. 3, Issue 2 (June 2022) , art. 101449  
    2 p, 530.8 KB ICTV Virus Taxonomy Profile : Potyviridae 2022 / Inoue-Nagata, Alice K. (Embrapa Vegetables) ; Jordan, Ramon (U.S. Department of Agriculture (USDA)) ; Kreuze, Jan (International Potato Center (CIP)) ; Li, Fan (Yunnan Agricultural University) ; Lopez-Moya, Juan Jose (Centre de Recerca en Agrigenòmica) ; Mäkinen, Kristiina (University of Helsinki) ; Ohshima, Kazusato (Saga University) ; Wylie, Stephen (Murdoch University) ; ICTV Report Consortium
    The family Potyviridae includes plant viruses with single-stranded, positive-sense RNA genomes of 8-11 kb and flexuous filamentous particles 650-950 nm long and 11-20 nm wide. Genera in the family are distinguished by the host range, genomic features and phylogeny of the member viruses. [...]
    2022 - 10.1099/jgv.0.001738
    The Journal of general virology, Vol. 103, Issue 5 (May 2022)  
    13 p, 3.1 MB BRAVO self-confined expression through WOX5 in the Arabidopsis root stem-cell niche / Mercadal Melià, Josep (Universitat de Barcelona. Departament de Física de la Matèria Condensada) ; Betegon Putze, Isabel (Centre de Recerca en Agrigenòmica) ; Bosch, Nadja (Centre de Recerca en Agrigenòmica) ; Caño Delgado, Ana I (Centre de Recerca en Agrigenòmica) ; Ibañes, Marta (Universitat de Barcelona. Institute of Complex Systems)
    In animals and plants, stem-cell niches are local microenvironments that are tightly regulated to preserve their unique identity while communicating with adjacent cells that will give rise to specialized cell types. [...]
    2022 - 10.1242/dev.200510
    Development (Cambridge), Vol. 149, Issue 15 (August 2022) , art. dev200510  
    12 p, 7.2 MB Loss-of-function of NITROGEN LIMITATION ADAPTATION confers disease resistance in Arabidopsis by modulating hormone signaling and camalexin content / Val-Torregrosa, Beatriz (Centre de Recerca en Agrigenòmica) ; Bundó Barberà, Mireia (Centre de Recerca en Agrigenòmica) ; Mallavarapu, Mani Deepika (Centre de Recerca en Agrigenòmica) ; Chiou, Tzyy-Jen (Academia Sinica. Agricultural Biotechnology Research Center) ; Flors, Victor (Univesitat Jaume I. Departament de Ciències Agràries i del Medi Natural) ; San Segundo, Blanca (Centre de Recerca en Agrigenòmica)
    Phosphorus is an important macronutrient required for plant growth and development. It is absorbed by the roots in the form of inorganic phosphate (Pi). Under Pi limiting conditions, plants activate the Phosphate Starvation Response (PSR) system to enhance Pi acquisition. [...]
    2022 - 10.1016/j.plantsci.2022.111374
    Plant science, Vol. 323 (October 2022) , art. 111374  
    14 p, 2.8 MB Genomic analysis of emmer wheat shows a complex history with two distinct domestic groups and evidence of differential hybridization with wild emmer from the western Fertile Crescent / Iob, Alice (Centre de Recerca en Agrigenòmica) ; Botigué, Laura (Centre de Recerca en Agrigenòmica)
    Triticum turgidum ssp. dicoccoides (wild emmer wheat) was one of the first plants that gave rise to domestic wheat forms in southwest Asia. The details of the domestication of emmer and its early dispersal routes out of southwest Asia remain elusive, especially with regard to its dispersal to the east. [...]
    2022 - 10.1007/s00334-022-00898-7
    Vegetation History and Archaeobotany, 2022