title: Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines.
abstract: BACKGROUND
  The mature embryo of rice (Oryza sativa, L.) is a synchronized and integrated tissue mass laying the foundation at molecular level for its growth, development, and differentiation toward a developing and ultimately a mature plant. We carried out an EST (expressed-sequence-tags)-based transcriptomic study, aiming at gaining molecular insights into embryonic development of a rice hybrid triad-an elite hybrid rice LYP9 and its parental lines (93-11 and PA64s)-and possible relatedness to heterosis.
  
  
  RESULTS
  We generated 27,566 high-quality ESTs from cDNA libraries made from mature rice embryos. We classified these ESTs into 7,557 unigenes (2,511 contigs and 5,046 singletons) and 7,250 (95.9%) of them were annotated. We noticed that the high-abundance genes in mature rice embryos belong to two major functional categories, stress-tolerance and preparation-for-development, and we also identified 191 differentially-expressed genes (General Chi-squared test, P-value <= 0.05) between LYP9 and its parental lines, representing typical expression patterns including over-dominance, high- and low-parent dominance, additivity, and under-dominance. In LYP9, the majority of embryo-associated genes were found not only abundantly and specifically enriched but also significantly up-regulated.
  
  
  CONCLUSIONS
  Our results suggested that massively strengthening tissue-(or stage-) characteristic functions may contribute to heterosis rather than a few simple mechanistic explanations at the individual gene level. In addition, the large collection of rice embryonic ESTs provides significant amount of data for future comparative analyses on plant development, especially for the important crops of the grass family.
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, PR China. gexiaomeng@big.ac.cn
authors.forename: Xiaomeng
authors.initials: X
authors.lastname: Ge
authors.forename: Weihua
authors.initials: W
authors.lastname: Chen
authors.forename: Shuhui
authors.initials: S
authors.lastname: Song
authors.forename: Weiwei
authors.initials: W
authors.lastname: Wang
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D001947:Breeding; D016009:Chi-Square Distribution; D016000:Cluster Analysis; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant; D018745:Genome, Plant; D006823:Hybrid Vigor; D012275:Oryza / Q000196:embryology / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012639:Seeds / Q000196:embryology / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018749:RNA, Plant