Transcriptome analysis of nematode-responsive genes in two susceptible Indica rice cultivars

Abstract

Summary Meloidogyne graminicola is a major plant pathogen damaging rice. Altering a plant susceptibility gene that critically facilitates compatibility is considered one of the most effective strategies to control plant pathogens. However, no resource is currently available regarding M. graminicola susceptibility genes in Indica rice cultivars. In this study, transcriptome analysis was used to elucidate nematode-responsive genes to the two susceptible Indica rice cultivars ‘Guinongzhan’ and ‘Wushansimiao (R534)’ with distinct levels of susceptibility to M. graminicola at 3 days post-inoculation (dpi). A total of 33157 transcripts corresponded to the predicted genes in the Indica rice genome. Among these, 2062 and 1386 differentially expressed genes (DEGs) were identified in ‘Guinongzhan’ and ‘Wushansimiao (R534)’, respectively, as a result of nematode infection. Cluster analysis showed that 2184 DEGs were commonly regulated and 503 DEGs were differentially regulated in ‘Guinongzhan’ and ‘Wushansimiao (R534)’. These DEGs were involved in defence responses, the Ca2+ signal pathway, cell wall, hormone pathways, the ubiquitin proteasome system and transcription factors. In addition, candidate genes that may be involved in rice defence responses and susceptibility to M. graminicola were identified, and some of them were further validated by quantitative real-time RT-PCR. The transcription data reveal insights into the susceptible rice gene expression pattern changes upon nematode infection, and provide a novel set of candidate defence-related and susceptibility genes in Indica rice cultivars for M. graminicola.