Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data

Abstract

Background: It was proposed that differentially-expressed genes, aside from genetic variations affecting protein processing and functioning, between hybrid and its parents provide essential candidates for studying heterosis or hybrid vigor. Based our serial analysis of gene expression (SAGE) data from an elite Chinese super-hybrid rice (LYP9) and its parental cultivars (93-11 and PA64s) in three major tissue types (leaves, roots and panicles) at different developmental stages, we analyzed the transcriptome and looked for candidate genes related to rice heterosis.

Results: By using an improved strategy of tag-to-gene mapping and two recently annotated genome assemblies (93-11 and PA64s), we identified 10,268 additional high-quality tags, reaching a grand total of 20,595 together with our previous result. We further detected 8.5% and 5.9% physically-mapped genes that are differentially-expressed among the triad (in at least one of the three stages) with P-values less than 0.05 and 0.01, respectively. These genes distributed in 12 major gene expression patterns; among them, 406 up-regulated and 469 down-regulated genes (P < 0.05) were observed. Functional annotations on the identified genes highlighted the conclusion that up-regulated genes (some of them are known enzymes) in hybrid are mostly related to enhancing carbon assimilation in leaves and roots. In addition, we detected a group of up-regulated genes related to male sterility and 442 down-regulated genes related to signal transduction and protein processing, which may be responsible for rice heterosis.

Conclusion: We improved tag-to-gene mapping strategy by combining information from transcript sequences and rice genome annotation, and obtained a more comprehensive view on genes that related to rice heterosis. The candidates for heterosis-related genes among different genotypes provided new avenue for exploring the molecular mechanism underlying heterosis.

Figure 1

Description of the strategy used to construct the conceptual transcript. The high-quality genome assembly of 93-11 (Oryza sativa L. subsp. indica; [48] and a collection of transcriptome information (FL-cDNA, UniGene, and ST; see Materials and Methods) were used for the construction of virtual transcripts. When the transcript sequences extend beyond the predicated coding sequence were available, the UTR sequences were aligned and determined (A). When the information was not available, the theoretical 3' UTR sequences were determined based on a stepwise (100-, 200-, 300-, 400-, and 500 bp) assessment of the genome sequences and added after the stop codons (B). Nearly 58.7% of the assigned tags have a 3'-UTR length of 300 bp.

Figure 2

Expression patterns and fold changes of differentially-expressed genes. Differentially-expressed genes in panicle, leaf, and root, among 93-11 (N), PA64s (P), and their F1 hybrid LYP9 (L) are shown. Twelve different patterns were labeled in each slice and their graphical indicators were displayed surrounding the three panels. The radius at which a gene is plotted represents log₂ of the fold change between the high and low values among three rice cultivars, and the angle represents the relationships between LYP9 and its parents. Differential expressed genes with significance intervals of 0.01 <P < 0.05 and P < 0.01 are shown in blue and green, respectively. Only tags that exhibited changes of <16-fold are plotted since those beyond the fold value are very limited in numbers (listed in Additional file 5). Note (1) genes harbored by the five patterns above the horizontal lines in each panel are up-regulated (positive heterosis) in hybrid, (2) genes in the five patterns in each panel below the horizontal lines are down-regulated (negative heterosis) in hybrid, and (3) two mid-parent patterns are on the horizontal lines.

Figure 3

Functional categories of differentially-expressed genes (P < 0.05) among the three cultivars.

Figure 4

Functional Categories of up-regulated and down-regulated genes in panicles, leaves, and roots.

Figure 5

Differentially-expressed genes that are involved in selected key metabolic pathways among three major cellular compartments. Genes involved in photosynthesis, glycolysis/gluconeogenesis, citrate cycle (TCA cycle), anaerobic respiration, glycolic acid oxidation, and fatty acid β-oxdidation pathways are shown. The enzymes (^# denotes key or rate-limiting enzymes) are: E1^#, fructose-1,6-bisphosphatase; E2, fructose-bisphosphate aldolase; E3, glyceraldehyde 3-phosphate dehydrogenase; E4, phosphoglycerate kinase; E5^#, pyruvate kinase; E6^#, alcohol dehydrogenase; E7, catalase; E8, acyl-CoA dehydrogenase; E9, succinyl-CoA ligase; E10, malate dehydrogenase; E11^#, ribulose bisphosphate carboxylase; E12, transketolase; E13, ribulose-phosphate 3-epimerase; E14, phosphoribulokinase; E15, beta-phosphoglucomutase, 1,4-alpha-glucan branching enzyme; E16^#, sucrose phosphate synthase; E17^#, sucrose synthase. Proteins and enzymes in the light reaction complex are plastocyanin, ferredoxin [2Fe-2S], chlorophyll A-B binding protein, photosystem II protein PsbX, photosystem II protein PsbW, photosystem II protein PsbY, photosystem II oxygen evolving complex protein PsbP, photosystem II protein PsbR, photosystem II manganese-stabilizing protein PsbO, photosystem II oxygen evolving complex protein PsbQ, photosystem I reaction centre (subunit XI PsaL), photosystem I psaG/psaK protein, photosystem I reaction centre subunit N, photosystem I reaction center protein PsaF (subunit III), NADH:flavin oxidoreductase/NADH oxidase, and cytochrome b ubiquinol oxidase. The ratios of up- (+) or down (-) -regulated tags are indicated. Detailed information for light reaction complexes is listed in Additional file 6. Note that the key enzymes are either up- or down-regulated in three tissues; this behavior suggests active yet unique regulations in the hybrid.