Genomic Signatures of Common Bean Domestication and Phaseolus Inter-Species Introgression

Modern civilization depends on few of the world’s estimated 300,000 plant species for its nourishment, including common bean (Phaseolus vulgaris L.), the most important grain legume for human consumption. We determined the complete genome sequence of the P. vulgaris Mesoamerican breeding line BAT93 (549.6 Mb) and constructed an evolutionary model of its domestication history by re-sequencing twelve additional bean accessions from Mesoamerica and the Andes. A genome-scale screening of genetic diversity losses in domesticated accessions relative to wild genotypes, revealed selective sweeps (21.5Mb) spread across the eleven linkage groups and uncovered novel protein coding genes (PCGs) selected for during domestication that seem to affect plant architecture and fruit characters. Signal of selection was also detected on several miRNA precursors and lncRNA genes and, based on co-expression patterns of these elements with PCGs, we propose that the action of such transcriptional regulators also contributed to the emergence of domestication syndrome in P. vulgaris. Furthermore, the acquisition of adaptive traits has been associated to inter and intra species hybridizations, as described in maize. In spite of its preferential autogamy, Phaseolus species are able to hybridize with wild/domesticated relatives and phylogenetically related species. By sequencing the full genome of three sister species, P. dumosus, P. costarricensis and P. coccineus, we provide evidence of genomic introgression events within the Vulgaris group that will allow us to understand the genomic mosaicism of Phaseolus species, some of which have been suggested to be natural hybrids, and its relatedness to domestication and adaptation processes in common bean.