Insights into the population dynamics of Phytophthora species associated with arecanut fruit rot disease

Phytophthora, a ubiquitous filamentous oomycete, causes huge yield losses and is fatal to arecanut palms in case of severe infection. From 2014 onwards, a severe fruit rot epidemic has been recorded during the South-West monsoon season in major arecanut-growing states of South India. We have assessed the diversity and delineated the population structure of Phytophthora isolates infecting arecanut in India using a combination of morphological traits, multi-gene profiling, haplotype analysis, and pathogenicity. Ninety-eight Phytophthora isolates were obtained from infected samples collected from disease-endemic regions of Karnataka, Kerala, and Goa states in southern India from 2014 to 2019. Morphological traits coupled with phylogenetic analysis using the loci ITS, β-tub, TEF-1α, and Cox-II identified the A2 mating type of P. meadii as the predominant species together with two isolates of homothallic P. heveae. Linkage disequilibrium analysis revealed significant diversity in the form of single nucleotide polymorphisms (SNPs) from the concatenated sequence dataset. Population structure analysis using 590 SNPs demonstrated the existence of four population groups (sub-populations at K = 4 and K = 2) and significant diversity in the geo-distant Phytophthora populations. In summary, 22 haplotypes were identified from the representative 40 isolates with higher haplotype diversity of 1.23 and relatively varying haplotype frequency. Pathogenicity assays confirmed that both the species of Phytophthora were pathogenic to arecanut, while P. meadii coastal region isolates exhibited more virulence compared to others.