Reprogramming of Strawberry (Fragaria vesca) Root Transcriptome in Response to Phytophthora cactorum

Abstract

Crown rot (Phytophthora cactorum) 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 (Fragaria × ananassa) challenging. The diploid wild strawberry Fragaria vesca 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 P. cactorum in a novel in vitro 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 P. cactorum. 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 P. cactorum resistance locus RPc-1. These new findings help to target the breeding efforts aiming at more resistant strawberry cultivars.

Fig 1. Several genes involved in flavonoid biosynthesis were up-regulated in F. vesca upon P. cactorum inoculation.

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.

Fig 2. P. cactorum inoculation changes isoprenoid metabolism in F. vesca roots.

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.