Identification of a ‘Candidatus Phytoplasma citri’ strain associated with phyllody disease of cumin

Cumin is a key export spice of India, widely used in cooking and as herbal medicine. Since 2019, phytoplasma symptoms, including yellowing, phyllody, witches’ broom, and seed elongation, have been observed in cumin crop at the Agricultural Research Station in Mandor, and farmers field of Jodhpur, Barmer and Nagaur districts of Rajasthan. Symptoms appeared 7075 days after sowing, with disease incidence increasing from 0.25% to 10.6% in 2022. Screening of 80 cumin genotypes, GC 4, MCU 73, MCU 105, and MCU 32 showed low disease incidence (0.5-1.5%), while MCU 78 had the highest incidence (10.6%). Phytoplasma presence was confirmed in 80 cumin symptomatic germplasm accessions by employing phytoplasma specific primers. Pairwise sequence identity and phylogeny of 16S rRNA gene sequences of CuPP-Jod strains in the study indicated the presence of ‘Candidatus Phytoplasma citri’ (16SrII-C subgroup). Chickpea, lentil and weeds growing in and nearby cumin fields were also presenting phytoplasma symptoms and were also analysed for phytoplasma presence. Phylogenetic and virtual RFLP analysis of 16S rRNA gene sequences confirmed the identity of cumin and chickpea phytoplasmas as ‘Ca. P. citri’.