RNA-Seq-Based Transcriptomic and SNP Discovery Analysis for Neck Blast Resistance in Rice (Oryzae sativa)

Neck blast, a severe form of rice blast disease caused by the fungal pathogen Magnaporthe oryzae (also known as Pyricularia oryzae), poses a significant threat to rice production, especially in hotspot regions like Chhattisgarh, India. While genetic markers have been identified for leaf and panicle blast resistance, molecular markers specifically associated with neck blast resistance remain limited. To bridge this critical knowledge gap, this study utilized RNA sequencing (RNA-Seq) to investigate transcriptomic changes in resistant and susceptible rice genotypes in response to infection by M. oryzae. Resistant and susceptible lines were artificially inoculated with the neck blast pathogen, and total RNA was extracted from panicle tissues at 3 days post-inoculation (3 dpi). High-throughput Illumina RNA-Seq was then employed to generate detailed transcriptomic profiles, aiming to unravel the molecular mechanisms underlying resistance to neck blast disease.