Using targeted phenomics and environmental proxies to understand Phytophthora medicaginis and Phytophthora root rot resistance in Australian chickpea

Abstract

Australian chickpea production is constrained by Phytophthora root rot (PRR), caused by the soil-borne oomycete Phytophthora medicaginis. Yield penalties are exacerbated by waterlogging resulting in partial or complete crop losses with few control options. Higher levels of PRR resistance have been identified in wild Cicer species but are associated with undesirable traits due to genetic linkage drag. Understanding the mechanisms involved in waterlogging tolerance and PRR resistance traits is necessary to determine if they can be uncoupled from poor agronomic traits when breeding improved varieties. The aims of this research were to; (1) investigate and characterise the response of both chickpea and the PRR causing organism, P. medicaginis, to waterlogging stress, (2) identify mechanisms of resistance using waterlogging as a proxy, (3) phenotype flavonoid phytoalexin metabolite accumulation associated with resistance following PRR infection, and (4) identify associated quantitative trait loci (QTL) with discoverable traits. Under waterlogging conditions, oxygen levels in soil are reduced and the plant itself compromised through physiological and structural changes that increase the sensitivity of chickpea to PRR infection. This research found that late waterlogging in combination with PRR reduced total plant biomass in chickpea by an average of 94%; however, waterlogging alone accounted for 88% of loss. Further experimentation found that under hypoxic conditions associated with waterlogging, P. medicaganis did not proliferate as determined by zoospore counts and DNA quantification using qPCR, due to oxygen requirements of the pathogen. These results demonstrate that waterlogging alone can result in plant stunting, yield loss and a reduced ability to express resistance. Chickpea genotypes demonstrated variability in phenotype, such as plant biomass and root parameters, when exposed to waterlogging stress. Following waterlogging conditions, the PRR moderately susceptible chickpea variety, Yorker, had an eightfold increase in adventitious root growth when compared with the PRR moderately resistant interspecific backcross line, 04067- 81-2-1-1. Phytophthora spp. are reportedly attracted to branch sites and leached exudates. It is proposed that compromised root barriers at emergence sites of adventitious roots under waterlogging increases chemotaxis and hastens hyphal entry, increasing susceptibility to PRR. Screening under waterlogging conditions may offer a novel proxy phenotyping method for PRR resistance traits at early stages of chickpea breeding. This research explored the genetic relationship between waterlogging phenotype, metabolite accumulation, and their association with PRR disease resistance QTL. An F6 bi-parental population of recombinant inbred lines derived from 04067-81-2-1-1 and Yorker was used to gather waterlogging response measures following 14 days of soil saturation, including dry root weight (DRW), dry shoot weight, plant height, primary root length (PRL) and adventitious root count (RC). Previously published QTL for field PRR resistance co-located closely with QTL mapped in this research for DRW, PRL and RC. The second component of this research explored the influence of P. medicaginis infection on the accumulation of flavonoid metabolites in chickpea root exudates following eight days of P. medicaginis infection. QTL were identified for formononetin, maackiain, biochanin A, morin and genistin (genistein-7-Oglucoside) biosynthesis. Two previously published QTL for field PRR resistance co-located closely with QTL for morin biosynthesis. In vitro tests demonstrated that this compound reduced P. medicaginis mycelial growth. The genetic mapping of waterlogging tolerance and metabolite QTL to regions near to those reported for PRR resistance suggests that a single genetic mechanism may have pleiotropic effects on both waterlogging and PRR response. This information can be used in future to identify flanking markers to facilitate targeted breeding for waterlogging tolerance and PRR disease resistance in chickpea.