Multigene phylogeny and diversity of Phytophthora and Phytopythium species associated with avocado root rot in India and development of a point-of-care LAMP assay for Phytophthora cinnamomi and Phytopythium vexans

Abstract

Avocado root rot, predominantly caused by Phytophthora cinnamomi poses a major threat to avocado cultivation worldwide. However, the potential role of other Phytophthora and Phytophthora-like oomycete species in avocado decline remains largely unexplored. To address this knowledge gap, surveys were conducted across avocado orchards in the Western Ghats region of Karnataka, Kerala, and Tamil Nadu, India, to assess the diversity and pathogenicity of Phytophthora and Phytopythium species associated with root rot. Oomycete isolates were recovered from symptomatic root samples collected from 42 avocado orchards. Morphological characterization, coupled with multilocus sequence analysis targeting the internal transcribed spacer (ITS) region, cytochrome c oxidase subunit 1 (COX1), and β-tubulin (β-tub) genes, facilitated species identification. Furthermore, pathogenicity tests confirmed the virulence of the isolates. Among the surveyed orchards, Phytophthora species were isolated from 26 orchards, with P. cinnamomi being the most frequently detected, occurring in 22 orchards. Additionally, P. tropicalis was identified in 2 orchards, while P. nicotianae and P. kelmanii were each found in 1 orchard. In parallel, 9 Phytopythium isolates were recovered, with Phytopythium vexans detected in 7 orchards and Phytopythium chamaehyphon in 2 orchards. Among all isolates, P. cinnamomi exhibited the highest virulence, underscoring its primary role in avocado root rot. To facilitate early and accurate detection of the predominant pathogens, Phytophthora cinnamomi and Phytopythium vexans, in infected plants and nursery seedlings, a loop-mediated isothermal amplification (LAMP) assay was developed. The sensitivity of LAMP assay detection limits for P. cinnamomi was 25 pg, while for Pp. vexans was detected at 50 pg. This assay provides a rapid, highly sensitive, and reliable diagnostic tool, strengthening disease surveillance and management strategies for avocado cultivation in the region. This study highlighted the novel host record of P. Kelmanii and Pp. chamaehyphon in avocado root rot and Pp. vexans first report in India.