Page 1 Page 2 Page 3 Page 4 Page 5 Page 6 Page 7 Page 8 Page 9 Page 10 Page 11 Page 12 Page 13 Page 14 Page 15 Page 16 Page 17 Page 18 Page 19 Page 20 Page 21 Page 22 Page 23 Page 24 Page 25 Page 26 Page 27 Page 28 Page 29 Page 30 Page 31 Page 32 Page 33 Page 34 Page 35 Page 36 Page 37 Page 38 Page 39 Page 40 Page 41 Page 42 Page 43 Page 44 Page 45 Page 46 Page 47 Page 48 Page 49 Page 50 Page 51 Page 52EUROPEAN-SEED.COM I EUROPEAN SEED I 33 • to perform an association study that can exploit the genomic data available on the 10,000 pure lines; and • to select any subset of germplasm on the basis of the data available from the project, and from the data that will be contributed by the associated partner. Indeed, as will be described later, BEAN_ADAPT is an open project which is also willing to contribute to the development of a ‘bean community’, which can include both private and public sectors. STRATEGY AND ACHIEVEMENTS BEAN_ADAPT aims to provide the scientific community, breeders and the seed industry with knowledge of the genes, quantitative trait loci, and genetic mechanisms that contribute to the phenotypic adaptation associated with environmental conditions, along with their mapping along the reference genome. These will be useful genetic tools for geneticists and breeders for the construction of novel varieties. With the activities started in the second half of 2015, BEAN_ADAPT aims to develop an integrated approach to efficient exploitation of plant genetic resources preserved ex situ in genebanks, to maximise their use for plant genetics and plant breeding. The molecular characterisation of a large collection from the major genebanks, including 11,500 accessions of both the common bean and the runner bean, has started. The genotyping-by-sequencing technique will be used, a procedure that identifies polymorphisms due to differences in single nucleotides (i.e. single nucleotide polymorphism markers), which are now essential tools for genetic analysis. This allows definition of the population structures of these species, and provides subsets of genotypes for phenotyping and for deeper genomic, transcriptomic, and metabolomic characterisation. A multidisciplinary approach will be used, including genomics (e.g. sequencing of the whole genome and transcriptome, RNA sequencing techniques), population/quantitative genetics, biochemistry and plant physiology. To identify genes and metabolites that are putatively associated with adaptation, we will apply differential expression analysis, analysis of co-expression patterns, and genome-wide association studies. The genotypic information obtained from genotyping-by- sequencing, whole genome sequencing, and RNA sequencing will be used to test for signatures of selection and to identify regions of the genome associated with adaptive and important agronomic traits (e.g. flowering time, photoperiod sensitiveness, yield, and others). Another important aspect of the BEAN_ADAPT project is promotion of the efficient use of Phaseolus plant genetic resources through the development of an integrated information system. This will be linked to genebank management and enhanced by development and characterisation of the 10,000 P. vulgaris purified lines, part of which will be deeply investigated by sequencing the whole genome, analysis of the transcriptome and metabolome, and characterisation of phenotype. BEAN_ADAPT will also develop a unified information system that will integrate the huge amounts of data being generated within the project, linking the genomic data with information on plant genetic resources. This will also facilitate data sharing, with connection of data to the European Genetic Resources Search Catalogue (EURISCO). The BEAN_ ADAPT project is already participating in international initiatives on the conservation and use of plant genetic resources as DivSeek, and is actively collaborating with the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) and Crop Trust. BEAN_ADAPT CONSORTIUM The integration of different types of expertise, through combination of all novel tools of genomics, along with molecular and standard phenotyping, is fundamental to the activities of the project. The BEAN_ADAPT partnership involves five research groups of public European and American institutions and universities, with unique and highly complementary expertise in different fields of plant science. These include genomics, bioinformatics, metabolomics, new molecular phenotyping technologies, field trials, plant breeding, applied population genomics, evolutionary processes analysis, in addition to the largest Phaseolus collection in Europe. Research groups from three European organisations and two U.S. universities make up this consortium, and include the following: • The Agricultural Genetics Group, the Department of Agricultural, Food and Environmental Sciences of the Polytechnic University of Marche in Ancona, Italy. This group is led by Roberto Papa, who is also the BEAN_ADAPT coordinator. This team will contribute mostly with their expertise on Phaseolus and in applied population genomics to analyse the large amount of data that will be obtained. • The Central Metabolism Group led by Alisdair R. Fernie at the Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. The group has in-depth expertise in metabolomics, which guarantees innovative support for the project through the integration of genomics with new molecular phenotyping technologies. • Andreas Graner, head of the genome diversity group at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), and the federal ex situ genebank at Gatersleben, Germany. They host the largest Phaseolus collection in Europe, and its genetic characterisation will be a fundamental tool for breeders and plant scientists.