2008年11月，中科院北京基因组研究所基因组科学及信息重点实验室研究成果——“Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines”论文在《BMC植物生物学》杂志上发表。
水稻是一种重要的粮食作物，同时也是谷物研究的一种重要的模式生物。多年来，基因组所以超级杂交水稻（LYP9）及其亲本（93-11和PA64s）为模式开展了一系列全基因组水平上的杂交优势相关研究。作为所创新集体研究项目的一部分，该实验室以水稻的成熟胚为材料，开展了相关研究。成熟胚在水稻的生命周期中具有重要的地位：它是发育到一定阶段、拥有完整植株的营养器官雏形并且发育同步化的植物幼体，普遍认为其已经为后续的发育奠定了物质基础，并且有研究表明拥有杂交优势性状的F1在较早的胚的阶段就能表现出一些优势的性状。为了充分展示水稻成熟胚中基因的表达情况，了解其中的分子生物学过程以及鉴定在这一阶段表现出的杂交优势性状和相关基因，我们以LYP9及其父母本的成熟胚为材料，利用EST分析的手段对其转录组进行了研究。
科研人员对每个样品随机测序（5’端）约一万条，一共得到27，566条高质量的EST序列，并最终得到7，557条unigene（2,511条contig和5,046条singleton）。通过与公共数据库内的序列进行比对，总共注释了7，250（95.9%）个基因。通过基因表达丰度和功能分析（主要是GO和KAAS），对其基因表达谱特征有了全面的认识：成熟胚中特征性表达的基因集中在两大功能类——抗逆和发育。大量的、种类全面的抗逆相关基因表达，包括抗水胁迫，抗氧化损伤，抗真菌等，同时，保证种子重新活化以及之后的快速启动和后期发育所需的基因也大量表达。这与种子要在相当长的时间内、在完全干燥的情况下保持发芽能力的生理特点十分符合。通过比较分析杂交水稻（F1）相对其父母本转录组基因表达水平的变化，鉴定出191个统计学上显著的差异表达基因，对他们的表达模式和功能进行分析的结果表明：这些差异表达基因几乎覆盖了所有的表达模式，各种模式的差异表达基因有很大程度上的功能上的相关性；大部分在成熟胚中特异性积累的基因在子代中表现为上调，而表达量比较低的基因更多的表现为下调，使子代拥有一个更强的抗逆系统以及更有活力的后期发育。而这种组织特征性功能的增强在对其他组织的杂交优势相关研究中也有发现，可能是杂交优势产生的原因之一。（生物谷Bioon.com）
生物谷推荐原始出处：
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.
