Transcriptomic Evidence of a Link between Cell Wall Biogenesis, Pathogenesis, and Vigor in Walnut Root and Trunk Diseases.

Crown gall disease (), crown/root rot disease ( spp.), root lesion disease () and tree vigor are key traits affecting the productivity and quality of walnuts in California. Unchallenged hybrid rootstocks were analyzed by RNA-seq to examine pre-formed factors affecting these traits. Enrichment analysis of the differentially expressed genes revealed that the increased expression of cell wall biogenesis-related genes plays a key role in susceptibility to , susceptibility to spp. and increased vigor. Analysis of the predicted subcellular loci of the encoded proteins revealed that many gene products associated with vigor and susceptibility were targeted to the plasma membrane and extracellular space, connecting these traits to sustaining barrier function. We observed that RNA processing and splicing, along with predicted nuclear targeting, were associated with resistance to , resistance to spp. and low vigor. Four genes within the QTL region for resistance to and spp. were represented among our transcripts, with two of the genes being differentially expressed in association with resistance to and decreased vigor. No differential expression related to spp. or resistance was observed in this region. Additionally, the haplotype expressed more transcripts associated with resistance to , spp. and low vigor, but not , than the haplotype. We also report unique and shared hormone and defense responses associated with each trait. This research suggests a link between cell wall biogenesis, vigor and critical root diseases of walnut.