Tagging the signature of domestication in the common bean using RNA-seq genotyping

The introduction of next generation sequencing technologies has revolutionised geneticanalysis, creating new opportunities for plant research that can also be applied to non-modelspecies. Among the applications of next generation sequencing, genotyping by sequencing aims atthe identification of structural variants and polymorphisms in target regions or whole genomes. Weused RNA sequencing (RNA-Seq) technology to investigate the whole common bean (PhaseolusvulgarisL.) transcriptome of 21 wild and domesticated accessions, mostly from Mesoamerica. Thematerials were chosen on the basis of previous molecular analyses carried out using both multilocusmolecular markers and nucleotide data, which had highlighted greater genetic diversity in theMesoamerican than the Andean gene pool. We identified an high number of single nucleotidepolymorphisms and we used this large dataset for population genetics inference. In particular,variable RNA fragments in wild and domesticated forms were analysed, and we were able toidentify genes under selection during the domestication process. This information is crucial not onlyto reconstruct the evolutionary history of this species, but also for a more efficient conservation ofthe existing germplasm and for selective breeding programmes.