title: Comparative transcriptional profiling of three super-hybrid rice combinations.
abstract: 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.
authors.affiliation: 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. ygpeng@genetics.ac.cn.
authors.forename: Yonggang
authors.initials: Y
authors.lastname: Peng
authors.affiliation: 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. weigang2007@gmail.com.
authors.forename: Gang
authors.initials: G
authors.lastname: Wei
authors.affiliation: 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. lzhang@genetics.ac.cn.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China. gzhliu@genomics.org.cn.
authors.forename: Guozhen
authors.initials: G
authors.lastname: Liu
authors.affiliation: 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. xlwei@genetics.ac.cn.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Wei
authors.affiliation: 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. zzhu@genetics.ac.cn.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhu
mesh_terms: D002245:Carbon Dioxide / Q000378:metabolism; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant / Q000235:genetics; D006823:Hybrid Vigor / Q000235:genetics*; D006824:Hybridization, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D040641:Quantitative Trait Loci / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics
chemical_list: D010940:Plant Proteins; D002245:Carbon Dioxide