Molecular characterization of internal transcribed spacer (ITS) of ribosomal RNA gene, haplotypes and pathogenicity of potato rot nematode Ditylenchus destructor in China

Abstract

Potato rot nematode Ditylenchus destructor is one of the most damaging pests in potato-producing regions and causes severe yield losses worldwide. However, D. destructor has been rarely reported in potato crops in China. We collected 542 samples from 17 Chinese provinces during 2016–2020 for the detection of D. destructor using species-specific primers and universal primers targeting ribosomal internal transcribed spacer (ITS) or 28S ribosomal RNA (rRNA) sequences. D. destructor was detected in 14.94% of total samples, primarily in Inner Mongolia Autonomous Region (43 sites), Jilin Province (12 sites), and Shaanxi Province (9 sites). The nematode was for the first time detected in Guizhou Province and Ningxia Hui Autonomous Region. Phylogenetic analysis of 33 ITS sequences along with the prediction of the secondary structure of the helix H9 of ITS1 sequences revealed that haplotypes A, B, and C accounted for 6.06%, 9.09%, and 69.70% of our detections, respectively, while 15.15% were comprised of haplotypes H–L, and extensive genetic diversity of ITS sequences was detected in samples from Gansu Province. Using RNAfold software, we analyzed the haplotypes of 124 Chinese D. destructor populations based on their ITS sequences, and the results showed that haplotypes A, B, C, E, F, and new haplotypes M–P accounted for 49.19%, 12.10%, 15.32%, 3.23%, 1.61%, and 18.55% of the total sequences, respectively. Infection tests on the potato cultivar ‘Helan 15’ showed significant difference in infection capacity among different D. destructor populations. The information obtained in this study on spatial patterns of D. destructor haplotypes in China provides valuable insights into the development of an integrated approach for the management of this plant-parasitic nematode.