Comparative Transcriptome Analysis Reveals Novel Candidate Resistance Genes Involved in Defence against Phytophthora cactorum in Strawberry

Abstract

Crown rot, caused by Phytophthora cactorum, is a devastating disease of strawberry. While most commercial octoploid strawberry cultivars (Fragaria × ananassa Duch) are generally susceptible, the diploid species Fragaria vesca is a potential source of resistance genes to P. cactorum. We previously reported several F. vesca genotypes with varying degrees of resistance to P. cactorum. To gain insights into the strawberry defence mechanisms, comparative transcriptome profiles of two resistant genotypes (NCGR1603 and Bukammen) and a susceptible genotype (NCGR1218) of F. vesca were analysed by RNA-Seq after wounding and subsequent inoculation with P. cactorum. Differential gene expression analysis identified several defence-related genes that are highly expressed in the resistant genotypes relative to the susceptible genotype in response to P. cactorum after wounding. These included putative disease resistance (R) genes encoding receptor-like proteins, receptor-like kinases, nucleotide-binding sites, leucine-rich repeat proteins, RPW8-type disease resistance proteins, and ‘pathogenesis-related protein 1’. Seven of these R-genes were expressed only in the resistant genotypes and not in the susceptible genotype, and these appeared to be present only in the genomes of the resistant genotypes, as confirmed by PCR analysis. We previously reported a single major gene locus RPc-1 (Resistance to Phytophthora cactorum 1) in F. vesca that contributed resistance to P. cactorum. Here, we report that 4–5% of the genes (35–38 of ca 800 genes) in the RPc-1 locus are differentially expressed in the resistant genotypes compared to the susceptible genotype after inoculation with P. cactorum. In particular, we identified three defence-related genes encoding wall-associated receptor-like kinase 3, receptor-like protein 12, and non-specific lipid-transfer protein 1-like that were highly expressed in the resistant genotypes compared to the susceptible one. The present study reports several novel candidate disease resistance genes that warrant further investigation for their role in plant defence against P. cactorum.

Transcriptome analysis of Phytophthora cactorum infecting strawberry identified RXLR effectors that induce cell death when transiently expressed in Nicotiana benthamiana

“…Some additional plants, both zoospore inoculated and water control, were kept up to four weeks post inoculation to study the disease progression. Wilting and necrotic lesions were observed in the P. cactorum inoculated plants after two weeks while no symptoms were observed in the control plants (Gogoi et al, 2023a).…”

“…The rhizome samples were harvested 48 hours after inoculation, flash frozen in liquid nitrogen and stored at -80°C until RNA isolation. The 48 hour time point represents the early infection stage of P. cactorum based on a temporal expression study of defense related genes in the resistant and susceptible F. vesca genotypes as previously described (Toljamo et al, 2016;Chen et al, 2016a;Gogoi et al, 2023a). No visible symptoms were observed at the time of harvest.…”

“…Total RNA was extracted from the inoculated strawberry rhizomes using the Spectrum ™ Plant Total RNA Kit (Sigma-Aldrich, USA) according to the manufacturer's instructions. Oncolumn DNase digestion was performed for 30 minutes on the isolated RNA to remove traces of genomic DNA contamination (Sigma-Aldrich, USA), as described by Gogoi et al (2023a). Sequencing libraries were prepared using the TruSeq ™ stranded total RNA library prep Kit (Illumina), and sequencing was performed using four lanes on an Illumina HiSeq 3/4000 System (2 × 150 bp) at the Norwegian Sequencing Centre, Oslo, Norway.…”

Secondary Metabolites and Their Role in Strawberry Defense

“…Especially, the induction of PR1 gene expression is widely used as a signature for the activation of plant defense via the pathogen-triggered systemic acquired resistance (SAR) pathway [ 35 ]. For instance, in strawberry, a basic form of the PR1 gene was even upregulated in two resistant genotypes, while it was downregulated in a susceptible genotype after inoculation with P. cactorum [ 16 ].…”

“…This article focuses on three major specialized metabolites: terpenoids, flavonoids, and allergens, and discusses their phylogenetic and regulatory aspects, including in the context of beneficial microbes. We particularly focus on the diploid strawberry F. vesca due to the wide availability of its genomic resources [ 9 , 10 , 11 , 12 ], well-understood molecular mechanisms of defense, and relatively high number of available metabolomic and transcriptomic datasets [ 13 , 14 , 15 , 16 ], compared to the octoploid strawberry.…”