Transcriptomic analysis of Mesoamerican and Andean Phaseolus vulgaris accessions revealed mRNAs and lncRNAs associated with strain selectivity during symbiosis

Abstract

Legume plants establish a nitrogen-fxing symbiosis with soil bacteria known as rhizobia. Compatibility between legumes and rhizobia is determined at species-specifc level, but variations in the outcome of the symbiotic process are also infuenced by the capacity of the plant to discriminate and select specifc strains that are better partners. We compared the transcriptional response of two genetically diverse accessions of Phaseolus vulgaris from Mesoamerica and South Andes to Rhizobium etli strains that exhibit variable degrees of symbiotic afnities. Our results indicate that the plant genotype is the major determinant of the transcriptional reprogramming occurring in roots at early stages of the symbiotic interaction. Diferentially expressed genes (DEGs) regulated in the Mesoamerican and the Andean accessions in response to specifc strains are diferent, but they belong to the same functional categories. The common and strain-specifc transcriptional responses to rhizobia involve distinct transcription factors and cis-elements present in the promoters of DEGs in each accession, showing that diversifcation and domestication of common bean at diferent geographic regions infuenced the evolution of symbiosis diferently in each genetic pool. Quantitative PCR analysis validated our transcriptional datasets, which constitute a valuable source of coding and non-coding candidate genes to further unravel the molecular determinants governing the mechanisms by which plants select bacterial strains that produce a better symbiotic outcome.