Genomic Access to Adaptive Diversity in Echinochloa Species

Echinochloa is a major weed in rice field. Ecotype difference in Echinochloa drew our attention because its adaptive diversity confers a range of competitiveness against rice. We selected three species of Echinochloa (E. crus-galli var. praticola, E. crus-galli var. crus-galli, and E. oryzicola), which response differently to the environmental condition from dry to flooding, to explore their transcriptomes. Using next generation sequencing, we obtained leaf transcriptome of 30,048 unigen set from E. crus-galli var. praticola, 28,814 from E. crus-galli var. crus-galli, and 31,160 from E. oryzicola. These transcriptomes were accessed in two aspects: polymorphism diversity and differential gene expression pattern. First, we investigated polymorphic diversity across three species using SSRs: 3,234 SSRs/2,958 contigs, 3,021 SSRs/2,776 contigs, and 1,722 SSRs/1,589 contigs were retrieved from E. crus-galli var. praticola, E. crus-galli var. crus-galli, and E. oryzicola, respectively. Of them, E. oryzicola exhibited approximately half number of SSRs among three species. Second, we investigated the differential gene expression (DE) in pair-wise manner with 2-fold difference (q<0.05). Interestingly, E. oryzicola exhibited twice number of significant up-regulation in the comparison with two other species. Considering the greatest flooding tolerance of E. oryzicola among three species, E. oryzicola appears to have evolved with distinct pattern compared to E. crus-galli. To identify upstream regulators from DE, we classified 86 transcription factors (TFs) into 6 groups by clustering pattern, which would give a clue about specific genes/pathways involved in adaptation. These information will provide a basis for future study on adaptive traits in Echinochloa and weed control.