Tagging the Signature of Domestication in the Common Bean Using RNA-Seq Genotyping

The introduction of next generation sequencing technologies has revolutionised genetic analysis, creating new opportunities for plant research that can also be applied to non-model species. Among the applications of next generation sequencing, genotyping by sequencing aims at the identification of structural variants and polymorphisms in target regions or whole genomes. We used RNA sequencing (RNA-Seq) technology to investigate the whole common bean (Phaseolus vulgaris L.) transcriptome of 21 wild and domesticated accessions, mostly from Mesoamerica. The materials were chosen on the basis of previous molecular analyses carried out using both multilocus molecular markers and nucleotide data, which had highlighted greater genetic diversity in the Mesoamerican than the Andean gene pool. We identified an high number of single nucleotide polymorphisms 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 to identify genes under selection during the domestication process. This information is crucial not only to reconstruct the evolutionary history of this species, but also for a more efficient conservation of the existing germplasm and for selective breeding programmes.