Fungal Etiology of Storage Rot in Carrot Taproots and the Role of the Newly Established Pathogen Rhexocercosporidium carotae in Lithuania

Rhexocercosporidium carotae (Årsvoll) U. Braun has been discovered for the first time in Lithuania and significantly influences the quality of harvested carrots. This study was conducted in the Šiauliai, Kėdainiai, and Pasvalys districts from 2016 to 2017. The aim was to identify fungal pathogens of stored carrots in Lithuania and to assess the effect of farming system and storage environment (controlled chamber vs. uncontrolled storage) on rot development, with emphasis on R. carotae. Two checks were conducted in spring to study the fungi present. Twelve pathogen taxa were detected as being involved in the decay process through morphological analysis. In 2016–2017, Alternaria radicina was the predominant pathogen in Pasvalys, accounting for 20.2–37.4% (2016) and 25.0–51.9% (2017) of the isolates obtained from stored carrot taproots, followed by Pythium spp. (17.6–28.2% in 2016) and Sclerotinia sclerotiorum, which accounted for 44.4% of the isolates from the ‘Niland’ cultivar in 2017. Storage conditions and farming systems affected the pathogen complex: in ‘Narbone’, A. radicina increased from 24.4% to 41.5% under uncontrolled storage versus 20.2% to 33.0% in a controlled chamber, and in organically grown ‘Nipomo’ taproots, S. sclerotiorum rose from 43.6% to 85.5% in 2017. In Šiauliai, the incidence of A. radicina declined significantly during storage (from 33.3% to 17.1% in 2016 and from 17.9% to 2.5% in 2017) in the ‘Niland’ cultivar, while Rhizoctonia spp. increased (3.7% to 25.7% in 2016; 10.7% to 20.0% in 2017). B. cinerea emerged as a late-season pathogen only in the ‘Niland’ cultivar in 2016 (31.4% at the second sampling), and S. sclerotiorum appeared in this cultivar in 2017 at 10.0%. In 2016, the pathogen complex in stored ‘Nerac’ carrots at the Kėdainiai farm was dominated by S. sclerotiorum, which accounted for 50.0% and 52.0% of the isolates at the first and second sampling, respectively. Alternaria radicina (20.0% to 18.68%), Pythium spp. (10.0% to 11.1%), and Fusarium spp. (20.0% to 17.20%) remained almost stable during storage. Rhexocercosporidium carotae showed pronounced farm-to-farm variation: it was the predominant pathogen at the Šiauliai farm in both years (14.3–63.3% of isolates in 2016 and 30.0–55.0% in 2017), a minor but regular component of the pathogen complex in the Pasvalys district (2.3–7.6% in 2016 and 2.2–6.1% in 2017) and completely absent at the Kėdainiai farm. These results indicate that the role of this pathogen in carrot storage rot depends strongly on the farm, and that it was detected only in conventionally grown taproots. This is, to our knowledge, the first detection of R. carotae in stored carrots in Lithuania, and its role in storage rot appears to depend strongly on the farm.