Elucidating the molecular responses of apple rootstock resistant to ARD pathogens: challenges and opportunities for development of genomics-assisted breeding tools

Abstract

Apple replant disease (ARD) is a major limitation to the establishment of economically viable orchards on replant sites due to the buildup and long-term survival of pathogen inoculum. Several soilborne necrotrophic fungi and oomycetes are primarily responsible for ARD, and symptoms range from serious inhibition of growth to the death of young trees. Chemical fumigation has been the primary method used for control of ARD, and manipulating soil microbial ecology to reduce pathogen density and aggressiveness is being investigated. To date, innate resistance of apple rootstocks as a means to control this disease has not been carefully explored, partly due to the complex etiology and the difficulty in phenotyping the disease resistance. Molecular defense responses of plant roots to soilborne necrotrophic pathogens are largely elusive, although considerable progress has been achieved using foliar disease systems. Plant defense responses to necrotrophic pathogens consist of several interacting modules and operate as a network. Upon pathogen detection by plants, cellular signals such as the oscillation of Ca2+ concentration, reactive oxygen species (ROS) burst and protein kinase activity, lead to plant hormone biosynthesis and signaling. Jasmonic acid (JA) and ethylene (ET) are known to be fundamental to the induction and regulation of defense mechanisms toward invading necrotrophic pathogens. Complicated hormone crosstalk modulates the fine-tuning of transcriptional reprogramming and metabolic redirection, resulting in production of antimicrobial metabolites, enzyme inhibitors and cell wall refortification to restrict further pathogenesis. Transcriptome profiling of apple roots in response to inoculation with Pythium ultimum demonstrated that there is a high degree of conservation regarding the molecular framework of defense responses compared with those observed with foliar tissues. It is conceivable that the timing and intensity of genotype-specific defense responses may lead to different outcomes between rootstocks in response to invasion by necrotrophic pathogens. Elucidation of host defense mechanisms is critical in developing molecular tools for genomics-assisted breeding of resistant apple rootstocks. Due to their perennial nature, use of resistant rootstocks as a component for disease management might offer a durable and cost-effective benefit to tree performance than the standard practice of soil fumigation for control of ARD.

Genes Involved in Stress Response and Especially in Phytoalexin Biosynthesis Are Upregulated in Four Malus Genotypes in Response to Apple Replant Disease

“…This corresponds well with the findings, that parasitic fungi and oomycetes of the genera Cylindrocarpon (Tewoldemedhin et al, 2011b;Mazzola and Manici, 2012;Franke-Whittle et al, 2015;Manici et al, 2015), Phytophthora (Tewoldemedhin et al, 2011a;Mazzola and Manici, 2012), Pythium (Tewoldemedhin et al, 2011a;Mazzola and Manici, 2012;Manici et al, 2013), and Rhizoctonia (Tewoldemedhin et al, 2011a;Mazzola and Manici, 2012;Manici et al, 2013) are enriched in ARD soil in comparison to healthy or disinfected soil. In particular, genes of the biphenyl biosynthetic pathway were rapidly activated in the roots of apple plants grown in ARD soil (Zhu et al, 2014;Zhu et al, 2016;Weiß et al, 2017a;Weiß et al, 2017b). Phytoalexins like biphenyls and dibenzofurans are known to act in an induced defense mechanism against biotic stressors, such as fungi and bacteria (Ahuja et al, 2012;Chizzali et al, 2012b;Chizzali and Beerhues, 2012;Chizzali et al, 2013).…”

Apple Replant Disease: Causes and Mitigation Strategies

“…94 hormone metabolism (Shin et al, 2014(Shin et al, , 2016Zhu et al, 2014). Comparative transcriptomic studies of roots of the sensitive rootstock M26 grown either in ARD or gamma irradiated ARD soils revealed several differences in the expression of genes involved in stress responses (Weiß et al, 2017a, b).…”

Root system traits impact early fire blight susceptibility in apple (Malus × domestica)

“…Earlier studies have reported that rootstocks and rootstock system architecture influence various important traits of scion genotypes grafted onto these rootstocks [20,21]. As it has been demonstrated that rootstocks confer enhanced tolerance to salinity, drought, and disease in various crops [21,22,23], efforts have been undertaken to develop resistant rootstocks, which in turn can enhance disease tolerance of grafted scion cultivars [11,24,25]. In this study, it is observed that root traits of an apple rootstock (M.7), including root dry mass (g) and average roots per node (count), are indeed variable, and they do in turn influence shoot and leaf traits, including leaf chlorophyll contents, of different scion genotypes grafted onto this rootstock.…”

“…For example, resistant rootstocks have been selected and used to enhance disease tolerance of grafted scion cultivars [11,24,25,26] for sustainable disease management in commercial apple orchards. It has been proposed that rootstocks can modify scion phenotypes by altering levels of abscisic acid, cytokinin, auxin, and other hormones through long-distance signaling between roots and shoots [27,28,29,30].…”