Transcriptomic Access to Adaptive Diversity in Echinochloa Accessions in Korea

Echinochloa is known for the most troublesome weed in rice field in Korea due to its competitiveness in flooding. Interestingly, three major Echinochloa crus-galli (ECC) accessions (ECC-SNU1, ECC-SNU2, and ECC-SNU3) collected in Korea exhibited a wide range of adaptabilities from dry to flooding. To investigate the molecular components responsible for the adaptive diversity among three Echinochloa accessions, we performed de novo assembly using next generation sequencing and searched differentially expressed genes (DEGs) in pair-wise comparison of three transcriptomes. We discovered five protein categories (serine/threonine kinase, leucine-rich repeat kinase, signaling-related, glycoprotein, and glycosidase) were significantly (FDR, q < 0.05) enriched in up-regulated DEGs from EC-SNU1, the most tolerant accession in flooding response. Our result implied that DEGs in upstream of signal transduction led to adaptive diversity among Echinochloa crus-galli during evolution.