Genome-wide identification and expression analysis of rice NLR genes responsive to the infections of Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae

Li Ding,Xiameng Xu,Weiwen Kong,Xue Xia,Shengwei Zhang,Li-Wei Liu,Aixin Liu,Lifang Zou

doi:10.1016/j.pmpp.2020.101488

Abstract

Nucleotide-binding site, leucine-rich repeat (NLR) genes play a critical role in rice disease resistance. However, the transcriptional activities of rice NLR genes during pathogen invasions are still unclear. To uncover their activities, we identified 430 regular rice NLR genes with both NBS and LRR domains, consisting of 192 CNL and 238 XNL (without a CC motif) members. We performed individual and integrative analyses based on 69 samples from rice microarray after the infections of Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (Mor). Among the rice NLR genes, 397 were found to be expressed at low/medium level, while 10 NLR genes were observed to show high expression levels. A total of 400 NLR genes were discovered to be differentially expressed in at least one sample. Furthermore, 46 rice NLR genes were identified to be differentially expressed in response to the two pathogens and 38 of them could be validated using RNA-seq data. Six cis-regulatory elements (MYC, STRE, MYB, ABRE, G-box, and AS-1) were observed to occur frequently in the promoter regions of rice NLR genes. Ten NLR genes were selected for qPCR detection, and seven of the NLR genes verified the validity of the microarray and RNA-seq data. Our results are helpful in revealing expressions and regulations of NLR genes in rice resistance to Xoo and Mor.

Highlights

Nucleotide-binding site, leucine-rich repeat (NLR) genes play a critical role in rice disease resistance
We identified a total of 430 regular rice NLR genes with both nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains, consisting of 192 CNL and 238 XNL members
We performed individual and integrative analyses based on 69 samples from rice microarray after the infections of Xanthomonas oryzae pv. oryzae (Xoo) and Magnaporthe oryzae (Mor)

Summary

Methods

Identification of rice (Nipponbare) regular NLR genes at the genome levelNipponbare protein sequences were downloaded from the Rice Genome Annotation Project Release 7 (MSU 7.0, http://rice.plantbiology.msu.edu). Collection of the microarray datasets infected by Xoo and Mor in rice In this work, all the rice microarray data were obtained from the NCBI Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/). These data sets were selected on the basis of the following criteria: plant materials should come from different genotypes of rice; the platform source of microarray must be from the Affymetrix Rice Genome Array GPL2025; the experiments were all under the Xoo- or Mor-infected conditions. All the series consist of the samples from a variety of conditions, e.g., different growth conditions, tissues, and treatments (Table S2)

Results

Discussion

Conclusion