Transcriptomic Analysis for Indica and Japonica Rice Varieties under Aluminum Toxicity

Abstract

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., "Terpenoid backbone biosynthesis", "Ribosome", "Amino sugar and nucleotide sugar metabolism", "Plant hormone signal transduction", "TCA cycle", "Synthesis and degradation of ketone bodies", and "Butanoate metabolism" were found uniquely for Indica Al-tolerant varieties, while only one pathway (i.e., "Sulfur metabolism") 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 "Starch and sucrose metabolism", "Metabolic pathway", and "Amino sugar and nucleotide sugar metabolism".

Keywords: Indica; Japonica; aluminum toxicity; transcriptomic analysis.

Figure 1

Relative root elongation (RRE) of six varieties in this study.

Figure 2

The correlation coefficients among the three biological replications. R1, R2, R3, R4, R5, and R6 represent Ba shi zi, Chang ning wu qu nan tou zhan, Ai you, Kai xuan, Bnlastog and Hei ke da nuo, respectively.

Figure 3

Venn diagram showing the numbers of differentially expressed genes among the Al-tolerant and Al-sensitive varieties. (A). Comparison among three Al-tolerant varieties; (B). Comparison among three Al-sensitive varieties. T, S, and CK represents Al-tolerant varieties under Al toxicity after 24 hr, Al-sensitive varieties under Al toxicity after 24 hr, and without Al treatment, respectively.

Figure 4

Expression patterns of differentially expressed genes among six varieties. (A) Comparison based on the genes relating to Al-tolerance; (B) Comparison based on the genes relating to Al-sensitivity. SG1, SG2, and AD represent Indica, Japonica, and the mixed subgroup, respectively.

Figure 5

Gene ontology (GO) plot on genes with different expression patterns. (A). Genes with different expression patterns between Indica Al-tolerant and Japonica Al-tolerant sub-species; (B). Genes with different expression patterns between Indica Al-sensitive and Japonica Al-sensitive. SG1 and SG2 represent Indica and Japonica, respectively.

Figure 6

Enrichment analysis of differentially expressed genes of the KEGG pathway for Al-tolerant varieties. (A). Enrichment analysis for Al-tolerant variety in SG1 (Indica); (B). Enrichment analysis for Al-tolerant variety in SG2 (Japonica).

Figure 7

Expression of eight candidate genes in the rice root tip. * and ** represent significant differences at the p < 0.05 and p < 0.01 levels (t-test), respectively.