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| Status |
Public on Oct 01, 2007 |
| Title |
Gene expression non-additivity in immature ears of a heterotic F1 maize hybrid |
| Organism |
Zea mays |
| Experiment type |
Expression profiling by array
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| Summary |
Non-additive gene regulation has been recently suggested as an important factor promoting phenotypic variation and plasticity. In order to obtain a description of gene expression status at an early stage of ear development in a maize (Zea mays L.) F1 hybrid as relative to its parental inbreds, we compared gene expression profiles in immature ears of elite inbred lines B73 and H99 to one of their F1 hybrids (B73xH99) using cDNA microarray technology. Results show several genes expressed at a significantly different level between both inbred lines and their hybrid. In addition, gene expression non-additivity in the hybrid was detected on a broad scale, consisting of both dominance and over-dominance components, indicating that complex non-additive interactions at the molecular level exist in the developing ear of the studied maize hybrid. Non-additively regulated genes belong to a wide range of molecular functions, indicating that several regulatory and metabolic patterns are possibly affected during ear development in the investigated hybrid. We discuss the possibility that observed gene expression non-additivity in immature ear might be an early molecular manifestation of hybrid vigor, the most exploited factor for maize agronomic improvement.
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| Overall design |
We directly contrasted both B73 and H99 inbred lines vs. their F1 heterotic hybrid transcriptomes in immature ear. Our experimental design consisted of 10 cDNA microarray hybridizations, 5 for each combination of hybrid vs. inbred genotypes, involving 20 separate labeling reactions. Labeling dyes were swapped in two of the five replicates for each combination. In each hybridization, control channel was assigned to the F1 hybrid, and differences in transcriptional levels between B73 and H99 were inferred using the hybrid as a common reference sample in an indirect experimental design. To take in account variability in transcript population among individuals, total RNA coming from different isolations, each collected on multiple individuals, were mixed before poly(A+) RNA purification. All hybridizations on microarray slides were then performed using cDNA independently labeled from the poly(A+) RNA purification product for each genotype.
Base-two logarithms of expression ratios were subjected to one-class response significance analysis in SAM v. 2.20 software [Tusher et al. 2001]. For each EST the estimates of additive parameter "a" and dominance parameter "d" (middle-parent heterosis) were obtained as
a = (L2 – L1)/2
d = (L1 + L2)/2
(where L1 and L2 are mean base-two logarithms of expression ratios of F1 vs. B73 and F1 vs. H99, respectively). Positive values of "a" indicate expression values bigger in B73 than in H99. The dominance/additivity ratio (d/|a|) was also calculated [Falconer 1989]. Evaluation of statistical significance of parameters was done by calculating standard errors of the estimates "a" and "d" as standard errors of linear functions of the means. Significance testing was done correspondingly, using an F-test for linear contrasts. P-values for the families of tests corresponding to each parameter were subjected to global error analyses using a method based on fitting mixture distribution [Allison et al. 2002], allowing to estimate the false discovery rates (FDR) and false negative rates (FNR). Confidence intervals for d/|a| ratios were obtained by Fieller’s method [Piepho and Emrich 2005], allowing to classify the genes into different dominance type classes.
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| Contributor(s) |
Pea G, Ferron S, Gianfranceschi L, Krajewski P, Pe' ME |
| Citation |
Giorgio Pea, Simona Ferron, Luca Gianfranceschi, Pawel Krajewski and M. Enrico Pè. Gene expression non-additivity in immature ears of a heterotic F1 maize hybrid. Plant Science 174(1), January 2008, pp. 17-24. http://dx.doi.org/10.1016/j.plantsci.2007.09.005 doi:10.1016/j.plantsci.2007.09.005.
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| Submission date |
Jun 06, 2005 |
| Last update date |
Mar 16, 2012 |
| Contact name |
Giorgio Pea |
| E-mail(s) |
giorgio.pea@unimi.it
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| Phone |
+390250315013
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| Fax |
+390250315044
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| URL |
http://users.unimi.it/camelot/
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| Organization name |
University of Milan
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| Department |
Department of Biomolecular Sciences and Biotechnology
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| Street address |
via Celoria 26
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| City |
Milan |
| ZIP/Postal code |
20133 |
| Country |
Italy |
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| Platforms (1) |
| GPL372 |
ZmDB 606-Immature Ear Microarray (2 cm) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA92303 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE2771_RAW.tar |
1002.0 Mb |
(http)(custom) |
TAR (of TIFF) |
| Processed data included within Sample table |
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