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Open AccessArticle

Comparative Transcriptional Profiling of Three Super-Hybrid Rice Combinations

by Yonggang Peng 1,†, Gang Wei 1,2,†, Lei Zhang 1,†, Guozhen Liu 3, Xiaoli Wei 1 and Zhen Zhu 1,*
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Int. J. Mol. Sci. 2014, 15(3), 3799-3815;
Received: 24 January 2014 / Revised: 17 February 2014 / Accepted: 17 February 2014 / Published: 3 March 2014
(This article belongs to the Section Biochemistry)
Utilization of heterosis has significantly increased rice yields. However, its mechanism remains unclear. In this study, comparative transcriptional profiles of three super-hybrid rice combinations, LY2163, LY2186 and LYP9, at the flowering and filling stages, were created using rice whole-genome oligonucleotide microarray. The LY2163, LY2186 and LYP9 hybrids yielded 1193, 1630 and 1046 differentially expressed genes (DGs), accounting for 3.2%, 4.4% and 2.8% of the total number of genes (36,926), respectively, after using the z-test (p < 0.01). Functional category analysis showed that the DGs in each hybrid combination were mainly classified into the carbohydrate metabolism and energy metabolism categories. Further analysis of the metabolic pathways showed that DGs were significantly enriched in the carbon fixation pathway (p < 0.01) for all three combinations. Over 80% of the DGs were located in rice quantitative trait loci (QTLs) of the Gramene database, of which more than 90% were located in the yield related QTLs in all three combinations, which suggested that there was a correlation between DGs and rice heterosis. Pathway Studio analysis showed the presence of DGs in the circadian regulatory network of all three hybrid combinations, which suggested that the circadian clock had a role in rice heterosis. Our results provide information that can help to elucidate the molecular mechanism underlying rice heterosis. View Full-Text
Keywords: rice; transcriptional profiling; heterosis; photosynthesis; circadian clock rice; transcriptional profiling; heterosis; photosynthesis; circadian clock
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Peng, Y.; Wei, G.; Zhang, L.; Liu, G.; Wei, X.; Zhu, Z. Comparative Transcriptional Profiling of Three Super-Hybrid Rice Combinations. Int. J. Mol. Sci. 2014, 15, 3799-3815.

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