Transcriptomic Analysis for Indica and Japonica Rice Varieties under Aluminum Toxicity

Aluminum (Al) at high concentrations inhibits root growth, damage root systems, and causes significant reductions in rice yields. Indica and Japonica rice have been cultivated in distinctly different ecological environments with different soil acidity levels
thus, they might have different mechanisms of Al-tolerance. In the present study, transcriptomic analysis in the root apex for Al-tolerance in the seedling stage was carried out within Al-tolerant and -sensitive varieties belonging to different subpopulations (i.e., Indica, Japonica, and mixed). We found that there were significant differences between the gene expression patterns of Indica Al-tolerant and Japonica Al-tolerant varieties, while the gene expression patterns of the Al-tolerant varieties in the mixed subgroup, which was inclined to Japonica, were similar to the Al-tolerant varieties in Japonica. Moreover, after further GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses of the transcriptomic data, we found that eight pathways, i.e., &ldquo
Terpenoid backbone biosynthesis&rdquo
&ldquo
Ribosome&rdquo
Amino sugar and nucleotide sugar metabolism&rdquo
Plant hormone signal transduction&rdquo
TCA cycle&rdquo
Synthesis and degradation of ketone bodies&rdquo
and &ldquo
Butanoate metabolism&rdquo
were found uniquely for Indica Al-tolerant varieties, while only one pathway (i.e., &ldquo
Sulfur metabolism&rdquo
) was found uniquely for Japonica Al-tolerant varieties. For Al-sensitive varieties, one identical pathway was found, both in Indica and Japonica. Three pathways were found uniquely in &ldquo
Starch and sucrose metabolism&rdquo
Metabolic pathway&rdquo