Agriculture faces many challenges to maximize yields while it is required to operate in an environmentally sustainable manner. In the present study, we analyze the major agricultural challenges identified by European farmers (primarily related to biotic stresses) in 13 countries, namely Belgium, Bulgaria, the Czech Republic, France, Germany, Hungary, Italy, Portugal, Romania, Spain, Sweden, UK and Turkey, for nine major crops (barley, beet, grapevine, maize, oilseed rape, olive, potato, sunflower and wheat). Most biotic stresses (BSs) are related to fungi or insects, but viral diseases, bacterial diseases and even parasitic plants have an important impact on yield and harvest quality. We examine how these challenges have been addressed by public and private research sectors, using either conventional breeding, marker-assisted selection, transgenesis, cisgenesis, RNAi technology or mutagenesis. Both national surveys and scientific literature analysis followed by text mining were employed to evaluate genetic engineering (GE) and non-GE approaches. This is the first report of text mining of the scientific literature on plant breeding and agricultural biotechnology research. For the nine major crops in Europe, 128 BS challenges were identified with 40% of these addressed neither in the scientific literature nor in recent European public research programs. We found evidence that the private sector was addressing only a few of these "neglected" challenges. Consequently, there are considerable gaps between farmer's needs and current breeding and biotechnology research. We also provide evidence that the current political situation in certain European countries is an impediment to GE research in order to address these agricultural challenges in the future. This study should also contribute to the decision-making process on future pertinent international consortia to fill the identified research gaps.

AgroParisTech Paris and Université Paris Sud Collége d'Etudes Interdisciplinaires Sceaux France

b Crop Transformation Group John Innes Centre Norwich Research Park Norwich UK

c Institute of Entomology BC AS CR Faculty of Science University of South Bohemia České Budějovice Czech Republic

e Biotechnology and Biosecurity Department Institute of Biochemistry of the Romanian Academy Bucharest Romania

f University of Agronomic Science and Veterinary Medicine Bucharest Bucuresti Romania

g APOSOLO Associação Portuguesa de Mobilização e Conservação do Solo Évora Portugal

h Laboratory of Plant Cell Biotechnology ITQB Instituto de Tecnologia Química e Biológica Universidade Nova de Lisboa ITQB IBET Apt 127 Oeiras Portugal

i CRAG Centre de Recerca en AgriGenòmica Campus UAB Edifici CRAG Bellaterra Cerdanyola del Vallès Barcelona Spain

j Umeå Plant Science Center Umeå University UMEÅ Sweden

k Department of Biosciences Biophysics Institute of the National Research Council Università di Milano Milano Italy

l Faculty of Agronomy Agricultural University of Plovdiv Plovdiv Bulgaria

m Faculty of Engineering and Natural Sciences Sabanci University Istanbul Turkey

o InnoPlantae 5 OT Gatersleben Stadt Seeland Germany

p Institut für Pflanzengenetik Leibniz Universität Hannover Hannover Germany

Plant Cell Biology Department Center for Agricultural Research Hungarian Academy of Sciences Martonvásár Hungary

q Laboratoire de Physiologie Cellulaire Végétale CNRS CEA INRA Université Grenoble Alpes Grenoble France and

r INRA Direction de la Valorisation Information Scientifique et Technique Versailles France

VIB Ghent Belgium

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