2008年11月，中科院北京基因組研究所基因組科學及信息重點實驗室研究成果——「Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines」論文在《BMC植物生物學》雜誌上發表。
水稻是一種重要的糧食作物，同時也是穀物研究的一種重要的模式生物。多年來，基因組所以超級雜交水稻（LYP9）及其親本（93-11和PA64s）為模式開展了一系列全基因組水平上的雜交優勢相關研究。作為所創新集體研究項目的一部分，該實驗室以水稻的成熟胚為材料，開展了相關研究。成熟胚在水稻的生命周期中具有重要的地位：它是發育到一定階段、擁有完整植株的營養器官雛形並且發育同步化的植物幼體，普遍認為其已經為後續的發育奠定了物質基礎，並且有研究表明擁有雜交優勢性狀的F1在較早的胚的階段就能表現出一些優勢的性狀。為了充分展示水稻成熟胚中基因的表達情況，了解其中的分子生物學過程以及鑑定在這一階段表現出的雜交優勢性狀和相關基因，我們以LYP9及其父母本的成熟胚為材料，利用EST分析的手段對其轉錄組進行了研究。
科研人員對每個樣品隨機測序（5』端）約一萬條，一共得到27，566條高質量的EST序列，並最終得到7，557條unigene（2,511條contig和5,046條singleton）。通過與公共資料庫內的序列進行比對，總共注釋了7，250（95.9%）個基因。通過基因表達豐度和功能分析（主要是GO和KAAS），對其基因表達譜特徵有了全面的認識：成熟胚中特徵性表達的基因集中在兩大功能類——抗逆和發育。大量的、種類全面的抗逆相關基因表達，包括抗水脅迫，抗氧化損傷，抗真菌等，同時，保證種子重新活化以及之後的快速啟動和後期發育所需的基因也大量表達。這與種子要在相當長的時間內、在完全乾燥的情況下保持發芽能力的生理特點十分符合。通過比較分析雜交水稻（F1）相對其父母本轉錄組基因表達水平的變化，鑑定出191個統計學上顯著的差異表達基因，對他們的表達模式和功能進行分析的結果表明：這些差異表達基因幾乎覆蓋了所有的表達模式，各種模式的差異表達基因有很大程度上的功能上的相關性；大部分在成熟胚中特異性積累的基因在子代中表現為上調，而表達量比較低的基因更多的表現為下調，使子代擁有一個更強的抗逆系統以及更有活力的後期發育。而這種組織特徵性功能的增強在對其他組織的雜交優勢相關研究中也有發現，可能是雜交優勢產生的原因之一。（生物谷Bioon.com）
生物谷推薦原始出處：
BMC Plant Biology， 2008, 8:114，Xiaomeng Ge，Jun Yu
Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines
Xiaomeng Ge* 1,2 , Weihua Chen* 1 , Shuhui Song1,2 , Weiwei Wang1,2 , Songnian Hu1 and Jun Yu1
1CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, PR China
2Graduate University of Chinese Academy of Sciences, Beijing, 100049, PR China
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.
Conclusion
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.