Comparative analysis of the apple root transcriptome as affected by rootstock genotype and Brassicaceae seed meal soil amendment: Implications for plant health

Authors: WANG, LIKUN - Washington State University; Somera, Tracey; Hargarten, Heidi; Honaas, Loren; MAZZOLA, MARK - Stellenbosch University

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/31/2021
Publication Date: 4/6/2021
Citation: Wang, L., Somera, T.S., Hargarten, H.L., Honaas, L.A., Mazzola, M. 2021. Comparative analysis of the apple root transcriptome as affected by rootstock genotype and Brassicaceae seed meal soil amendment: Implications for plant health. Microorganisms. 9(4). Article 763. https://doi.org/10.3390/microorganisms9040763.
DOI: https://doi.org/10.3390/microorganisms9040763

Interpretive Summary: Replant disease refers to the poor growth of trees when attempting to establish the same or related species on old orchard sites. Apple replant disease (ARD) results primarily from plant-induced changes in the soil microbiota leading to a build-up of multiple soil-borne pathogens over time prior to removal of the old orchard. One promising strategy for the control of ARD is the use of pre-plant Brassicaceae seed meal (SM) soil amendments. This disease control method requires both biologically- and chemically-based mechanisms that function in response to the seed meal amendment. Rootstock genetics may also be a valuable tool in the management of ARD. This study examined differential gene expression in roots of an ARD tolerant (G.210) and a susceptible (M.26) apple rootstock in the presence and absence of the SM soil treatment. Genes functioning in plant defense related processes and biosynthesis of phytohormones were found associated with SM treatment for both rootstock genotypes. SM-induced changes in rhizosphere fungal densities and bacterial community composition were associated with the initiation of plant defense responses. In G.210 (but not M.26), there was a large accumulation of genes which were expressed at higher levels when planted in the non-treated soil relative to SM-amended soil at 7 days. At this later time point, the number of defense genes exhibiting increased expression was higher in G.210 relative to M.26 in non-treated soil, suggesting that G.210 was eliciting a defense response against ARD pathogens at 7 days. The timing of the plant defense response appeared to be earlier and similar in G.210 and M.26 when grown in SM-amended soil. The growth data suggests that both genotypes benefitted from an earlier defense response and reduced pathogen loads in SM amended soil.

Technical Abstract: Brassicaceae seed meal (SM) amendment is utilized as an alternative to pre-plant soil fumigation for the control of soil-borne plant diseases. SM amendment transforms the soil microbiome and provides a concomitant beneficial influence on plant growth and productivity. SM from particular Brassicaceae species can afford long lasting disease control through both chemical and biological mechanisms of pathogen suppression. This study examined apple root gene expression in response to SM amendments and sought to elucidate whether such changes were associated with modifications of the rhizosphere microbiome. Transcriptome analysis was performed using root tissue from an apple replant disease (ARD) susceptible (M.26) and tolerant (G.210) rootstock cultivated in non-treated orchard replant soil or the same soil amended with a 1:1 formulation of Brassica juncea and Sinapis alba SM. SM-amended soil induced differential gene expression in both rootstock genotypes – interestingly in the ARD susceptible genotype M.26 the number of differentially expressed genes (DEG) peaked at 72h, while the number of DEG continued to increase through the 7 d timepoint in the resistant genotype G.210. DEG associated with defense-related hormone signaling were induced in both genotypes providing insight into the phenotype changes for rootstocks planted in SM-treated soil. The changes in rhizosphere microbiome density and composition were temporally associated with initiation of plant defense responses in SM-treated soil. A follow-up gene expression analysis showed genotype-specific responses when established in non-treated soil (pathogen-infested), which suggested trade-offs between growth and defense may be modulated by rootstock genetic factors. In non-treated soil, considerably more genes associated with signaling, cell regulation and defense were upregulated in M.26 versus G.210 root tissue. Conversely, genes involved in processes related to basic cellular functions and oxidation-reduction processes were downregulated in M.26 relative to G.210.