Bean Adapt: The Genomics of Adaptation during Crop Expansion in Bean

BEAN_ADAPT is a three year project funded through the 2^nd ERA-CAPS call, ERA-NET for Coordinating Action in Plant Sciences.

The main aim of this project is to dissect out the genetic basis and phenotypic consequences of the adaptation to new environments of the common bean (Phaseolus vulgaris L.) and its sister species, the runner bean (Phaseolus coccineus L.), through the study of their introduction, from their respective centers of domestication in the Americas, and expansion through Europe, as a recent and historically well-defined event of rapid adaptation.

A large collection (11,500 accessions of both species) from three major genebanks, will be characterised by genotyping-by-sequencing (GBS), to define the population structure and to obtain subsets of genotypes for phenotyping (field and growth chamber) and for a deeper genomic–transcriptomic–metabolomic characterisation. We will use a multidisciplinary approach: genomics (WGS and RNAseq), population/ quantitative genetics, biochemistry, plant physiology on the subset of samples. Differential expression analysis, analysis of the co-expression patterns, and GWAS will be used to identify genes and metabolites putatively associated with adaptation, while genotypic information obtained from RNA-seq data will be used, with GBS and WGS data, to test for signatures of selection.

Among the main outcomes of the project are the development in P. vulgaris of haplotypes of all 10,000 accessions (HapBean), along with associated information and seed stocks, which will represent a unique tool for plant scientists and breeders. For P. coccineus, we will also have a well-defined set of information that will constitute the foundation for the development and application of its genomic resources.