Reprogramming of Strawberry (<i>Fragaria vesca</i>) Root Transcriptome in Response to <i>Phytophthora cactorum</i>

<div><p>Crown rot (<i>Phytophthora cactorum</i>) causes significant economic losses in strawberry production. The best control strategy would be to use resistant cultivars, but polygenically inherited resistance makes the breeding of the garden strawberry (<i>Fragaria</i> × <i>ananassa</i>) challenging. The diploid wild strawberry <i>Fragaria vesca</i> Hawaii 4 genotype was shown previously to have resistance against crown rot. To explore the resistance mechanisms, we inoculated the roots of Hawaii 4 with <i>P</i>. <i>cactorum</i> in a novel <i>in vitro</i> hydroponic system to minimize interference caused by other microbes. Major reprogramming of the root transcriptome occurred, involving 30% of the genes. The surveillance system of the plant shifted from the development mode to the defense mode. Furthermore, the immune responses as well as many genes involved in the biosynthesis of the defense hormones jasmonic acid, ethylene and salicylic acid were up-regulated. Several major allergen-like genes encoding PR-10 proteins were highly expressed in the inoculated plants, suggesting that they also have a crucial role in the defense responses against <i>P</i>. <i>cactorum</i>. Additionally, flavonoids and terpenoids may be of vital importance, as several genes involved in their biosynthesis were up-regulated. The cell wall biosynthesis and developmental processes were down-regulated, possibly as a result of the down-regulation of the key genes involved in the biosynthesis of growth-promoting hormones brassinosteroids and auxin. Of particular interest was the expression of potential resistance genes in the recently identified <i>P</i>. <i>cactorum</i> resistance locus <i>RPc-1</i>. These new findings help to target the breeding efforts aiming at more resistant strawberry cultivars.</p></div

Genes in <i>P</i>. <i>cactorum</i> resistance locus <i>RPc-1</i> expressed in the roots of <i>F</i>. <i>vesca</i>.

<p>Genes in <i>P</i>. <i>cactorum</i> resistance locus <i>RPc-1</i> expressed in the roots of <i>F</i>. <i>vesca</i>.</p

Receptor-like kinases expressed in the wild strawberry <i>F</i>. <i>vesca</i>.

<p>Receptor-like kinases expressed in the wild strawberry <i>F</i>. <i>vesca</i>.</p

Effect of <i>P</i>. <i>cactorum</i> inoculation of <i>F</i>. <i>vesca</i> roots on the expression of genes involved in cell wall synthesis.

<p>Effect of <i>P</i>. <i>cactorum</i> inoculation of <i>F</i>. <i>vesca</i> roots on the expression of genes involved in cell wall synthesis.</p

Summary of RNA sequencing results.

<p>Controls 1 to 3 refer to water control replicates, inoculated 1 to 3 to replicate plants inoculated with <i>P</i>. <i>cactorum</i> 407; each replicate represents roots collected from one individual plant.</p

Several genes involved in flavonoid biosynthesis were up-regulated in <i>F</i>. <i>vesca</i> upon <i>P</i>. <i>cactorum</i> inoculation.

<p>PAL, phenylalanine ammonia-lyase; C4H, cinnamic acid 4-hydroxylase; 4CL, 4-coumarate:coenzyme A ligase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavonoid 3-hydroxylase; F3’H, flavanone 3’-hydroxylase; DFR, dihydroflavanol 4-reductase; ANS, anthocyanidin synthase; GT, glycosyltransferase; FLS, flavonol synthase; LAR, leucoanthocyanidin reductase. GT1 was expressed at low level and it was excluded from the analysis in the filtering step. The expression level of ANR is not known, since it is not included in the annotation version used in this study.</p

<i>P</i>. <i>cactorum</i> inoculation changes isoprenoid metabolism in <i>F</i>. <i>vesca</i> roots.

<p>Several genes involved in MVA pathway were up-regulated, whereas none of the MEP pathway genes were up-regulated. Products of the MVA pathway appear to be targeted to sesquiterpenoid and triterpenoid biosynthesis rather than to sterol biosynthesis. AACT, acetoacetyl-CoA thiolase; HMGS, 3-hydroxy-3-methylglutaryl-CoA synthase; HMGR, 3-hydroxy-3-methylglutaryl-CoA reductase; MVK, mevalonate kinase; PMK, phosphomevalonate kinase; MPDC, diphosphomevalonate decarboxylase; IDI, isopentenyl-diphosphate Delta-isomerase; DXS, 1-deoxy-D-xylulose-5-phosphate synthase; DXR, 1-deoxy-D-xylulose 5-phosphate reductoisomerase; MCT, 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase; CMK, 4-(cytidine 5’-diphospho)-2-C-methyl-D-erythritol kinase; MDS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; HDS, 1-hydroxy-2-methyl-2-butenyl 4-diphosphate synthase; HDR, 1-hydroxy-2-methyl-2-butenyl 4-diphosphate reductase; FPS, farnesyl diphosphate synthase; GPPS, geranyl diphosphate synthase; GGPPS, geranylgeranyl diphosphate synthase; SQS, squalene synthase; SQE, squalene epoxidase; GDS, (-)-germacrene D synthase-like; BAS, beta-amyrin synthase-like; CAS, cycloartenol synthase -like; APS, (-)-alpha-pinene synthase-like.</p

LCk32 transcriptome annotation

Annotation of the LCK32 (La Calamine accession) de novo assembly. Annotation was performed using the Trinotate pipeline. Ortholog clustering was performed using OrthoFinder. Ortholog groups and the corresponding A thaliana TAIR codes have been combined with the Trinotate annotation

LEk32 transcriptome annotation

Annotation of the LEK32 (Lellingen accession) de novo assembly. Annotation was performed using the Trinotate pipeline. Ortholog clustering was performed using OrthoFinder. Ortholog groups and the corresponding A thaliana TAIR codes have been combined with the Trinotate annotation

MPk32 transcriptome annotation

Annotation of the MPK32 (Monte Prinzera accession) de novo assembly. Annotation was performed using the Trinotate pipeline. Ortholog clustering was performed using OrthoFinder. Ortholog groups and the corresponding A thaliana TAIR codes have been combined with the Trinotate annotation