Multilocus genotyping of sugarcane white leaf phytoplasma in Thailand

Abstract
One hundred and seventy-four symptomatic sugarcane samples infected with sugarcane white leaf (SCWL) phytoplasma were collected from sugarcane growing areas in ten provinces across the North, Northeastern and Central plain of Thailand. Genotyping was performed using 16S rRNA and ITS sequence and multilocus sequence typing (MLST) based on six genes including tuf, secY, leuS, secA, AAA1 and groES. The 16S rRNA sequence analysis indicated that the SCWL phytoplasma population showed nucleotide sequence identity of 99.74% to 99.80% to ‘Candidatus Phytoplasma sacchari’. In silico RFLP analysis clustered the strains into 16SrXI-B and 16SrXI-D subgroups. Most strains (77%) were in the 16SrXI-D group, while 16SrXI-B strains were only found in the Northeastern regions. The 16SrXI-D group coexisted with the 16SrXI-B group in Roi Et, Kalasin, and Mookdahan provinces, but it was found alone in Surin province. Multilocal sequence typing showed genetic variations in six genes including tuf, secY, leuS, secA, AAA1, and groES. These variations resulted in the SCWL population being divided into two distinct groups, that are consistent with the 16SrXI subgroups. Additionally, five strains in this population exhibited recombinant DNA in the tuf, secA, leuS, AAA1 and groES genes. This information about the genetic variability of SCWL phytoplasma in Thailand could be used to develop detection methods and monitoring strategies for the disease management.