Comparative transcriptional profiling and preliminary study on heterosis mechanism of super-hybrid rice

Abstract

Heterosis is a biological phenomenon whereby the offspring from two parents show improved and superior performance than either inbred parental lines. Hybrid rice is one of the most successful apotheoses in crops utilizing heterosis. Transcriptional profiling of F(1) super-hybrid rice Liangyou-2186 and its parents by serial analysis of gene expression (SAGE) revealed 1183 differentially expressed genes (DGs), among which DGs were found significantly enriched in pathways such as photosynthesis and carbon-fixation, and most of the key genes involved in the carbon-fixation pathway exhibited up-regulated expression in F(1) hybrid rice. Moreover, increased catabolic activity of corresponding enzymes and photosynthetic efficiency were also detected, which combined to indicate that carbon fixation is enhanced in F(1) hybrid, and might probably be associated with the yield vigor and heterosis in super-hybrid rice. By correlating DGs with yield-related quantitative trait loci (QTL), a potential relationship between differential gene expression and phenotypic changes was also found. In addition, a regulatory network involving circadian-rhythms and light signaling pathways was also found, as previously reported in Arabidopsis, which suggest that such a network might also be related with heterosis in hybrid rice. Altogether, the present study provides another view for understanding the molecular mechanism underlying heterosis in rice.

Figure 1.

Overview of Serial Analysis of Gene Expression (SAGE) Libraries and Differentially Expressed Tags. (A) Venn diagram of tags shared among three SAGE libraries. (B) Venn diagram of tags with significant differential expression (P < 0.05) between LY2186 and its parental lines. (C) Expression patterns of tags with significant differential expression (P < 0.05) between F₁ hybrid and parents. AHP, above high-parent; HPL, high-parent level; MPL, mid-parent level; LPL, low-parent level; BLP, below low-parent.

Figure 2.

Comparison of Gene Ontology (GO) Classification between Differentially Expressed Genes (DGs) and All Genes from the Rice Genome. The gene ontology slims are from the Rice Genome Annotation (Ouyang et al., 2007). GO terms at level 2 are plotted. Star (*) indicates remarkable relationship, if the P-value is below the significant level of 0.05.

Figure 3.

Real-Time Quantitative PCR of DGs in the Carbon-Fixation Pathway. (A) Hybrid rice combination LY2186, (B) LYP9, and (C) SY63. Data are means ± SE of three replicates.

Figure 4.

Principal Component Analysis (PCA) of Enzyme Activity Patterns in LY2186 Combination. BIPLOT visualization of PCA of enzyme activity patterns of the carbon-fixation pathway. The rice lines are indicated in red (LY2186), green (SE21s), or blue (MH86), and the contribution of the enzymes to positioning in the plot is provided. The two parent lines (MH86 and SE21s) are more similar to each other than either to the hybrid line (LY2186). The positioning of the hybrid line towards the right side of the plot (indicated by an arrow) underpins the increase in the carbon-fixation-related enzyme activity as compared with its parents.

Figure 5.

Comparisons of Photosynthesis Characters in Three Hybrid Rice Combinations. (A–C) Photosynthesis characters of hybrid rice combination Liangyou-2186, (D–F) Liangyou-pei9, and (G–I) Shanyou-63. (A, D, G) Net photosynthetic rate (P_n); (B, E, H) light response curve; (C, F, I) CO₂ response curve. PAR, photosynthetic activity rate; C_i, CO₂ concentration. Data are means ± SE of three replicates.

Figure 6.

Distribution of DGs Located in Yield-Category QTL of Small Intervals. Yield-category QTL of small intervals (number of genes ≤ 100) that harbor DGs were aligned with the gene coordinates in Rice Genome Annotation release 6.1. The long horizontal lines represent the rice chromosomes, the short horizontal lines in different colors QTL intervals, and the short vertical lines DGs.

Figure 7.

Gene Network of DGs in Hybrid Rice by Pathway Studio Analysis. DGs were used for direct interaction analysis by Pathway Studio 6.2. Interaction searching includes promoter binding, expression, regulation, and binding. APRR, PSEUDO-RESPONSE REGULATOR; CAB1, CHLOROPHYLL A/B BINDING PROTEIN 1; CAT3, CATALASE 3; CHS, CHALCONE SYNTHASE; DND1, DEFENSE NO DEATH 1; GBSSI, GRANULE-BOUND STARCH SYNTHASE I; GI, GIGANTEA; HOG1, HOMOLOGY-DEPENDENT GENE SILENCING 1; LHY, LATE ELONGATED HYPOCOTYL; PAT1, PHYTOCHROME A SIGNAL TRANSDUCTION 1; PIF3, PHYTOCHROME INTERACTING FACTOR 3; RBCS1A, RUBISCO SMALL SUBUNIT 1A; RCD1, RADICAL-INDUCED CELL DEATH1; STO, SALT TOLERANCE.