A generic tool for managing and exploiting genetic association studies results using high throughput genotyping data and high throughput phenotyping – GnpAsso

Over several years, large efforts have been made to produce crop genetic and genomic data at genome scale. Bioinformatics and data
integration was more and more required to take full advantage of these data [1]. Several databases were developed at national and international levels, dedicated to one species in particular or dedicated to one type of data.
Association genetic methods, based on the exploitation of linkage disequilibrium (LD), are valuable tools for the dissection of complex traits. In many plant species indeed, they have shown to be useful for the analysis of the genetic determinism of quantitative traits and to pinpoint the genes involved in the variation of traits of agronomic interest.

With the increase of genome sequencing and resequencing plant projects and the rapid decrease of cost in molecular typing, with at the same time, the set up of high-throughput genotyping methods, it is now possible to genotype a lot of SNP polymorphisms to conduct exhaustive association mapping approaches at the whole-genome scale “Whole genome association mapping” or in regions in which QTL have been detected by linkage approaches, no longer focusing only on candidate genes putatively involved in the variation of traits of interest. This strategy is today possible for an increasing number of crops.
By combining this method with traditional ones, as QTL mapping, it is now possible to i) fine map QTL, ii) identify faster new markers useful for selection, iii) to find interesting alleles in genetic resources collections and to use them in new material dedicated to selection.

The rationale of GnpAsso project is to create a new bioinformatics database resource dedicated to the storage and the query of genome association mapping results in relation with highthroughput sequencing data (in particular third generation markers “Single Nucleotide Polymorphism, SNP data). This resource will also give access ii) in details to all the data linked to these association studies results (the genetic resources, genotypes, SNP, traits, alleles, QTL, gene annotation, gene expression…) via links to other existing resources in GnpIS, URGI information system.