ena-STUDY-CRI-FEM-10-01-2019-11:07:12:465-748
Apple as a Model for Genomic Information Exchange.
Crop genetic improvement is fundamental not only to meet customer preferences but also to cope with the consequences of climate change like the temperature rise or the extreme weather events. To achieve this goal, the first step is the identification of the available genetic diversity. During the past few years, the FruitBreedomics EU project (http://www.fruitbreedomics.com/), has developed tools that have genetically characterised almost all the cultivated apple varieties, an effort that has returned, among other results, 2 commercially available SNP genotyping arrays as well as a substantial amount of genome re-sequencing data for 63 apple cultivars, ranging from 30x to 50x coverage of the genome. The output of this re-sequencing project has provided nearly two million SNPs per cultivar. Moreover, an Italian-French collaboration recently produced a new high quality reference genome for one of these strains. However, at the present time, none of these data are included in ELIXIR data resources negatively impacting the adoption of apple data and limiting the community for ELIXIR resources for apple and related fruit communities (peach, pear, grape and strawberry). Here we propose a data implementation study (IS) using ELIXIR-supported data archives such as BioSamples, ENA, EVA, and value added data resources such as ORCAE and Ensembl Plants, as a case study for managing the growing number of projects cataloguing the diversity of fruit genomes and streamlining the associated data management.
Crop genetic improvement is fundamental not only to meet customer preferences but also to cope with the consequences of climate change like the temperature rise or the extreme weather events. To achieve this goal, the first step is the identification of the available genetic diversity. During the past few years, the FruitBreedomics EU project (http://www.fruitbreedomics.com/), has developed tools that have genetically characterised almost all the cultivated apple varieties, an effort that has returned, among other results, 2 commercially available SNP genotyping arrays as well as a substantial amount of genome re-sequencing data for 63 apple cultivars, ranging from 30x to 50x coverage of the genome. The output of this re-sequencing project has provided nearly two million SNPs per cultivar. Moreover, an Italian-French collaboration recently produced a new high quality reference genome for one of these strains. However, at the present time, none of these data are included in ELIXIR data resources negatively impacting the adoption of apple data and limiting the community for ELIXIR resources for apple and related fruit communities (peach, pear, grape and strawberry). Here we propose a data implementation study (IS) using ELIXIR-supported data archives such as BioSamples, ENA, EVA, and value added data resources such as ORCAE and Ensembl Plants, as a case study for managing the growing number of projects cataloguing the diversity of fruit genomes and streamlining the associated data management.