RNA-seq analysis of Arabidopsis thaliana wild-type roots and type-A arr3,4,5,6,7,8,9,15 mutant roots non-infected and infected with Heterodera schachtii nematodes

Plant-parasitic cyst nematodes induce the formation of hypermetabolic feeding sites, termed syncytia, as their sole source of nutrients. The formation of the syncytium is orchestrated by the nematode in part by modulation of phytohormone responses, including cytokinin. In response to infection by the nematode H. schachtii, cytokinin signaling is transiently induced at the site of infection and in the developing syncytium. Arabidopsis lines with reduced cytokinin sensitivity show reduced susceptibility to nematode infection, indicating that cytokinin signaling is required for optimal nematode development. Furthermore, lines with increased cytokinin sensitivity also exhibit reduced nematode susceptibility. To ascertain why cytokinin hypersensitivity reduces nematode parasitism, we examined the transcriptomes in wild-type and a cytokinin-hypersensitive type-A arr Arabidopsis mutant in response to H. schachtii infection. Genes involved in the response to biotic stress and defense response were elevated in the type-A arr mutant in the absence of nematodes and were hyper-induced following H. schachtii infection, which suggests that the Arabidopsis type-A arr mutants impede nematode development because they are primed to respond to pathogen infection. These results suggest that cytokinin signaling is required for optimal H. schachtii parasitism of Arabidopsis, but that elevated cytokinin signaling triggers a heightened immune response to nematode infection. Overall design: Wild-type Col-0 and type-A arr3,4,5,6,7,8,9,15 octuple mutant Arabidopsis thaliana roots were infected with Heterodera schachti nematodes and whole root tissue was collected at 4 days post infection (dpi) and 10 dpi, along with the corresponding control roots that were not infected with nematodes. We had tissue for collected for 4 experimental groups at 4 dpi and 10 dpi, wild-type non-infected, wild-type infeced, octuple mutant non-infected and octuple mutant infected. Tissue was collected for 3 biological replicates. Therefore we had 12 samples at 4dpi and 12 samples at 10 dpi making a total of 24 samples that we used for sequencing.