Laccase directed lignification is one of the major processes associated with the defense response against Pythium ultimum infection in apple roots

Authors: Zhu, Yanmin; LI, GUANLIANG - South China Agricultural University; SINGH, JUGPREET - Cornell University; KHAN, AWAIS - Cornell University; Fazio, Gennaro; SALTZGIVER, MELODY - Former ARS Employee; XIA, RUI - South China Agricultural Univerisity

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/9/2021
Publication Date: 9/7/2021
Citation: Zhu, Y., Li, G., Singh, J., Khan, A., Fazio, G., Saltzgiver, M., Xia, R. 2021. Laccase directed lignification is one of the major processes associated with the defense response against Pythium ultimum infection in apple roots. Frontiers in Plant Science. 12. Article 629776. https://doi.org/10.3389/fpls.2021.629776.
DOI: https://doi.org/10.3389/fpls.2021.629776

Interpretive Summary: Plant gene functions in combating pathogen infection are both complicated and intriguing. The current study investigates apple root response to infection from P. ultimum, one of several pathogens causing apple replant disease. The focus in this study is to investigate the small RNAs (sRNAs), which are short (20-24 nucleotides) and noncoding (no proteins will be translated from). The primary roles of these tiny molecules are believed to induce gene silencing through cleavage of specific target genes (which encode proteins), or suppression of their translation process. By doing so, these sRNAs and their related RNA silencing pathways can crucially regulate apple root defense activation to pathogen infection from Pythium ultimum. Analysis of such dataset could assist the identification of the key components controlling apple root resistance. Using large-scale and high-throughput NextGen sequencing technology, the population, abundance of sRNA and their corresponding targets were compared between three pairs of apple rootstock genotypes of contrasting resistance traits. Among 43 known and 39 novel sRNA families, several of them were identified as potential key players in differentiating resistance and susceptibility. For example, the expression of miR397 family members exhibited different expression patterns between resistant and susceptible genotypes, their targets are laccase encoding genes with annotated functions for tissue lignification. This observation suggested that the tissue fortification by laccase activities may be a key process to thwart pathogen penetration at the initial infection stage. Another example is the detailed analysis of miR482 which was known to target a large family of resistance (R) genes. Out of a few hundred R genes existed in the apple genome, our results pinpointed a handful of them which may specifically regulate interactions between apple root and P. ultimum. The identified target genes (those being cleaved by sRNAs) are a valuable resource for subsequent functional analysis to verify their roles in differentiating apple root resistance from susceptibility to P. ultimum infection.

Technical Abstract: Apple replant disease (ARD), incited by a pathogen complex including Pythium ultimum, causes stunted growth or death of newly planted trees at replant sites. Development and deployment of resistant or tolerant rootstocks offers a cost-effective, ecologically friendly, and durable approach for ARD management. Maximized exploitation of natural resistance demands the integrated efforts to identify key components and regulation mechanisms underlying resistance traits in apple. In this study, miRNA profiling and degradome sequencing identified major miRNA pathways and candidate genes using six apple rootstock genotypes with contrasting phenotypes to P. ultimum infection. The comprehensive RNAseq dataset offered an expansive view of post-transcriptional regulation of apple root defense activation in response to infection from P. ultimum. Several pairs of miRNA families and their corresponding targets were identified for their roles in defense response in apple root, including miR397-laccase, miR398-superoxide dismutase, miR10986-polyphenol oxidase, miR482-resistance genes and miR160-auxin response factor. Of these families, the genotype-specific expression patterns of miR397 indicated its fundamental role in developing defense response patterns to P. ultimum infection. Combined with other identified copper proteins, the importance of cellular fortification, such as lignification of root tissues by the action of laccase, may critically contribute to genotype-specific resistance traits. Our findings suggest that a quick and enhanced lignification of apple root may have significantly impeded pathogen penetration and minimizes the disruption of effective defense activation in root of resistant genotypes. The identified target miRNA species and target genes consist of a valuable resource for subsequent functional analysis of their roles during interaction between apple root and P. ultimum.