Transcriptomics analysis of an EMS-induced bacterial blight resistant line of rice

An induced-mutant line derived from the elite rice cultivar, Samba Mahsuri, was identified to exhibit broad-spectrum resistance to BB. Using next-generation gene mapping approaches, we identified a genomic interval in chromosome 6 to be linked to BB resistance. Analysis of the SNPs in the locus and subsequent linkage analysis indicated that a missense SNP located in the second exon of the Mitogen-Activated Protein Kinase 6 (OsMAPK6) could be the causal mutation. A detailed examination of OsMAPK6 gene sequences in over 4000 rice genomes revealed that the mutant allele identified in this study is novel to rice germplasm. The candidate SNP causes the substitution of an invariant Serine residue with a Proline residue (S84P), thus likely affecting the protein function. Global transcriptome, metabolome, biochemical, and molecular analyses suggested that BB42 exhibit autoimmunity. Overall design: SM and BB42 plants were inoculated with the Xoo isolate IXO1221 during the maximum tillering stage. One-centimeter-long leaf samples from the site of clipping were collected at the time of infection as control (0 hour/Mock) and 24-hour post infection (Xoo) from both SM and BB42. The samples were collected from three independent plants and considered as biological replicates. The samples were flash-frozen immediately after collection and stored at -80? until further processing. RNA was isolated from the samples using RNeasy Plant RNA Isolation Kit (Qiagen, Germany) with on-column DNA digestion using RNase-Free DNase Set (Qiagen, Germany). Purified RNA was quantified using QubitTM RNA HS Assay Kit (Thermo Fisher Scientific, USA). RNA integrity was assessed using agarose gel electrophoresis and BioAnalyzer 2100 (Agilent Technologies, USA). 1 µg of intact total RNA samples were used for library preparation using Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, USA). Sequencing was performed on Illumina's NovaSeq6000 platform with cycling conditions to obtain 2x100bp reads on an S2 flow cell.