A semi-dominant mutation in a CC-NB-LRR-type protein leads to a short-root phenotype in rice

The mechanisms of plant defense against pathogen attack in plant leaves have been extensively studied. However, our understanding of plant defense mechanisms in plant roots is still limited. In this study, a semi-dominant mutant nrtp1-D (necrotic root tip 1), with a short-root phenotype, was characterized in rice. Map-based cloning revealed that NRTP1 encoded a typical coiled-coil nucleotide binding leucine rich repeat (CC-NB-LRR) type protein and the mutation caused an amino acid substitution in the Nucleotide-Binding adaptor shared by Apaf1, certain R genes and CED4 (NB-ARC) domain, which may cause constitutive auto-activation of the NRTP1 protein. Gene expression analysis revealed that NRTP1 was preferentially expressed in rice roots. Expression of mutant nrtp1-D in tobacco leaves induced necrotic lesions, which indicated a common mechanism of plant defense response between leaves and roots. Transcriptome analysis revealed that many typical defense-response genes were differentially expressed in homozygous nrtp1-D. In addition, we also found differential expression of genes in pathways which had not previously been described as being associated with pathogen response. Histochemical analysis showed that the level of nitric oxide (NO), but not reactive oxygen species (ROS), was increased in homozygous nrtp1-D mutant roots. These results indicate that, in addition to the mechanism of defense response common to both roots and shoots, a novel pathway may also exist in rice roots, which does not operate in shoots. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12284-018-0250-1) contains supplementary material, which is available to authorized users.