Alfalfa transcriptomic responses to the field pathobiome.

The pathobiome is a comprehensive biotic environment that includes a community of all disease-causing organisms within the plant, defining their mutual interactions and the resultant effects on plant health. The concept and understanding of alfalfa pathobiome and its impact on host fitness in natural ecosystems remain largely unexplored. We have previously reported on the diverse composition of the alfalfa pathobiome in the field production environment. In this study, using modern transcriptomics tools combined with computational analyses, we applied a novel 'field host genomics' approach to survey gene expression changes in visually healthy and diseased plants collected from commercial alfalfa fields. As a result of this work, genes and pathways involved in alfalfa responses to a diverse field pathobiome were identified and the genetic basis of the crop's resistance to multi-pathogenic infections was proposed. In addition to offering genetic insights into host resistance to multi-pathogenic infections in natural ecosystems, this strategy can facilitate identification of plants with tolerant genotypes adapted to field pathobiome, followed by their application in alfalfa breeding programs.