Transcriptome Analysis of Rice Near-Isogenic Lines Inoculated with Two Strains of Xanthomonas oryzae pv. oryzae, AH28 and PXO99A

Rice bacterial blight (BB), caused by <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> (<i>Xoo</i>), is a major threat to rice production and food security. Exploring new resistance genes and developing varieties with broad-spectrum and high resistance has been a key focus in rice disease resistance research. In a preliminary study, rice cultivar Fan3, exhibiting high resistance to PXO99^A and susceptibility to AH28, was developed by enhancing the resistance of Yuehesimiao (YHSM) to BB. This study performed a transcriptome analysis on the leaves of Fan3 and YHSM following inoculation with <i>Xoo</i> strains AH28 and PXO99^A. The analysis revealed significant differential expression of 14,084 genes. Among the transcription factor (TF) families identified, bHLH, WRKY, and ERF were prominent, with notable differences in the expression of <i>OsWRKY62</i>, <i>OsWRKY76</i>, and <i>OsbHLH6</i> across samples. Over 100 genes were directly linked to disease resistance, including nearly 30 NBS-LRR family genes. Additionally, 11 SWEET family protein genes, over 750 protein kinase genes, 63 peroxidase genes, and eight phenylalanine aminolysase genes were detected. Gene ontology (GO) analysis showed significant enrichment in pathways related to defense response to bacteria and oxidative stress response. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis and diterpenoid biosynthesis pathways. Gene expression results from qRT-PCR were consistent with those from RNA-Seq, underscoring the reliability of the findings. Candidate genes identified in this study that may be resistant to BB, such as NBS-LRR family genes <i>LOC_Os11g11960</i> and <i>LOC_Os11g12350</i>, SWEET family genes <i>LOC_Os01g50460</i> and <i>LOC_Os01g12130</i>, and protein kinase-expressing genes <i>LOC_Os01g66860</i> and <i>LOC_Os02g57700</i>, will provide a theoretical basis for further experiments. These results suggest that the immune response of rice to the two strains may be more concentrated in the early stage, and there are more up-regulated genes in the immune response of the high-resistant to PXO99A and medium-resistant to AH28, respectively, compared with the highly susceptible rice. This study offers a foundation for further research on resistance genes and the molecular mechanisms in Fan3 and YHSM.