Peronosporales amplicon sequencing in UK raspberries. Survey and characterisation of Peronosporales species associated with root rot in UK red raspberry

Phytophthora rubi has previously been reported as the primary causal agent of raspberry root rot (RRR) in the United Kingdom, resulting in severe economic losses for growers. Recent observations by UK plant pathologists suggest the RRR complex may be more diverse than previously thought. This study aims to determine the species of Peronosporales present in UK raspberry plants and factors affecting their diversity and abundance. Eighty-six symptomatic root and cane samples were collected from seven grower farms in the UK in 2020 and 2021. Five additional samples were collected from blackberry roots. Symptomatic tissue was plated onto selective media and resultant isolates were identified by morphological observations and ribosomal internal transcribed spacer (ITS) barcoding. Twelve isolates of five species of Phytophthora; P. citrophthora, P. pini, P. erythroseptica, P. cryptogea, P. pseudocryptogea, and seven isolates of two Phytopythium species; Pp. vexans and Pp. litorale species were collected. The pathogenicity of the isolates were assessed using a detached leaf method. High throughput sequencing of the ITS region of symptomatic root samples was conducted to determine Peronosporales community composition and the effects of farm location and plant variety on the abundance of taxa. This study presents new potential pathogens of interest for further pathogenicity studies. Furthermore, we note the importance of the inclusion of other Peronosporales species into raspberry breeding programme resistance screen’s to produce genotypes which are more resilient to community composition shifts in the raspberry root pathosphere observed in the UK.