GENOMIC INSIGHTS INTO DIDYMELLA RHEI AND ITS IMPACT ON RHUBARB CULTIVATION

The major goalof this projectis to advancethe current understanding of rhubarb leaf spot biology by analyzing populationstructure, reproductive strategies, and host interactions of Didymella rhei, a causal agent of rhubarb leaf spot. This research will test the hypotheses that D. rhei (1) has a clonal population structure, (2) does not undergo observable sexual reproduction despite carrying both mating type loci in populations, (3) can only infect rhubarb and several close relatives, and (4) is differentially virulent across rhubarb cultivars. The goals of this research comprise four parts: 1.) describe the structure of D. rhei populations collected across three years, 2.) resolve cryptic sexual reproduction in D. rhei, 3.) clarify the host range of D. rhei within and beyond the Polygonaceae, and 4.) screen for resistance in commercially available rhubarb cultivars. The proposed research will provide insights into the biology of D. rhei and identify potential strategies to manage rhubarb leaf spot. Project outcomes will provide recommendations for improved management of rhubarb leaf spot to advance the production of an emerging crop.Rhubarb (Rheum) is an emerging perennial crop for many small farms in the northeast US. Culinary rhubarb is grown for consumption of the fleshy leafstalk (petiole) and is propagated either by seed or rhizome divisions. Growers commonly divide from previous plantings to maintain cultivars. In the US, petioles are typically harvested between May and August and sold by the pound in the fresh market. The USDA grading standards suggest that fresh market rhubarb should be disease or damage-free (USDA AMS 2016); if these standards are not met, stalks can be sold for reduced prices as a frozen product (USDA AMS 1945). Currently, the USDA National Agricultural Statistics Service has not published production statistics on rhubarb. In the northeast US, growers are enthusiastic to increase rhubarb acreage. They highlight its contributions to early season income as rhubarb is harvested before many other fruits and vegetables reach maturity. Members of craft beverage and baked goods industries cite challenges in sourcing large quantities of local rhubarb. Some have imported the stalks from as far as Poland (personal communication from growers and producers in New York [NY]). Many growers have sought recommendations on cultural and disease management practices to support local rhubarb production.Rhubarb leaf spot (RLS), caused by the fungal pathogen Didymella rhei, has been documented in New Zealand (Aveskamp et al 2010), China(Liu et al 2014), South Korea (Lee et al 2021), and the United States (Indermaur et al 2023). In the northeast US, leaf spot is the most common disease of rhubarb. Initial symptoms are small, circular lesions with concentric rings and red margins. Lesions often coalesce and perforate, and affected leaves become chlorotic (Fig. 1A). Lesions also form on petioles. Under high humidity, pycnidia can develop in host tissue and serve as an asexual inoculum source (Fig. 1B). In NY, symptoms begin in May with leaf emergence and persist until senescence in late fall. RLS likely reduces productivity and can limit fresh market sales of infected stalks. Currently, there are no known sources of resistance to RLS in cultivated rhubarb or its relatives.Didymella is theis the type genus of the Didymellaceae (de Gruyter et al 2009). Members of the family are cosmopolitan and occupy several important lifestyles including endophytes, saprobes, and pathogens of mammals and plants (Hou et al 2020). In phytopathogenic Didymella species, recent studies have determined the presence of sexual morphs (Pearce et al 2016), assessed population structure (Ozkilinc et al 2015, Pearce et al 2019), and clarified the host range (Barilli et al 2016, Keirnan et al 2021). Several congeneric species with broad host ranges are also of quarantine concern (Zhao et al 2021).This project proposes to examine research areas that remain unexplored in D. rhei: population structure, reproductive strategies, and host interactions. The goal of this research is to advance rhubarb production in the northeast US by expanding our knowledge of pathogen biology, enabling the identification of management strategies to reduce disease incidence and spread. Research objectives include: (1) Describe the population structure of D. rhei, (2) resolve potential cryptic sexual reproduction, (3) clarify the host range within theCaryophyllales, and (4) screen for resistance in commercially available rhubarb cultivars.In summary, much of the biology of D. rhei remains unknown which limits growers' success and effective disease management. To address this, Objective 1 aims to determine how genetically diverse populations of D. rhei are and if they can overwinter asexually in rhubarb crowns. This can directly impact grower's cultivation practices including sanitation and propagation. Objective 2 aims to investigate the likelihood of sexual reproduction occurring within these populations. If this reproductive mode is possible, this would require that management strategies consider long-distance spread of sexual spores and genetic recombination contributing to breakdown of host resistance or fungicide sensitivity. Objective 3 aims to determine which weeds, including common co-ordinal species, serve as alternative hosts of D. rhei. This can directly inform growers' weed management practices to reduce disease pressure. Objective 4 aims to identify rhubarb varieties that are less susceptible to D. rhei. This can immediately aid growers and inform future breeding efforts to develop resistant varieties. Together, each objective contributes to the development of more sustainable management of RLS and the advancement of an emerging crop.