构建并行生物信息平台挖掘棉纤维发育的关键功能基因

Improving fiber quality is an important goal of cotton breeding. Gossypium barbadense, is a good gene pool to fiber quality improving of G. hirstum, for its high quality fiber. However, the functional genes of G. barbadense were little mined and the sequence resources were also very little collected..Before, we have constructed a local bioinformatics pipeline for ESTs analyis. Then, large-scale ESTs of G. barbadense were sequenced and analyzed to explore some of the important functions of candidate genes and, the function of some genes was verified through the technology of transgene..In this project, we will establish a high-throughput, parallel computational bioinformatics system for analyzing transcriptome and digital expression profiling of second generation sequencing. The fiber transcriptome and digital expression profiling will be sequenced through 454 and Solexa sequencing technology respectively. Through comprehensive annotation and analysis of transcriptome, transcriptional profiling of gene expression will be constructed. Then, the analysis of comparative genomics, gene expression pattern and, comparsion with transcriptome of Arabidopsis's root hairs and trichome will be carryied out. At last,a number of key candidate functional genes of fiber development were explored and confirmed through biology experiments preliminary. .The public resources of G. barbadense will be greatly enriched through this study. It also will significantly useful to reveal the mechanism of fiber development and fiber qulity formation, and provide a theoretical basis for the genetic improvement of cotton fiber.

纤维品质改良是棉花育种的重要目标之一。海岛棉纤维品质优良，是改良陆地棉纤维品质的优质基因库。但目前海岛棉的功能基因挖掘较少，相关的序列资源也非常稀缺。前期本实验室开展了大量海岛棉ESTs的测序及构建ESTs生物信息分析系统，发掘了一批重要候选基因并进行了基因功能验证。本项目拟采用454、Solexa测序技术分别对海岛棉纤维进行转录组、数字表达谱测序，构建对应的高通量、并行化生物信息分析软件平台，全面分析和注释序列，建立基因的转录谱和表达谱，阐释纤维发育的转录特征。比较拟南芥根毛及表皮毛发育调控网络、转录因子及细胞壁合成的数据库、纤维发育的重要代谢途径，结合基因表达模式分析，发掘一批纤维发育的重要候选功能基因，并进行初步实验验证。该研究将极大丰富海岛棉的公共资源，有助于揭示纤维发育和纤维品质形成的分子机制，为棉花纤维的遗传改良提供理论基础。

改良棉纤维品质是棉花育种者主要目标之一。海岛棉纤维品质优良，是优质基因库，也是研究棉花纤维发育和基因组进化的重要材料。但海岛棉由于其产量低、种植面积小等因素，其功能基因挖掘较少，基因组序列资源也非常缺乏。因此，本项目以海岛棉为研究对象，建立了一套本地化、高性能计算机集群环境下的并行生物信息分析系统（包括转录组、数字表达谱和序列注释等功能平台），开发了比较基因组学展示软件1个，系统分析了海岛棉8个组织和发育时期的转录组，阐释海岛棉纤维发育转录本的特征；并利用转录组数据开展了长链非编码RNA的鉴定工作。结果表明：类黄酮和木质素代谢在纤维发育过程中至关重要作用，在海岛棉中类黄酮代谢较陆地棉上调，而木质素较陆地棉是下调的。构建的纤维发育接力赛模型表明纤维伸长期是由A亚基因组和D亚基因组共同完成，而纤维素合成阶段全面A亚基因组接管。本项目的实施极大丰富了海岛棉的公共资源，为功能基因组学研究和棉花遗传改良输送了大量候选关键基因，这些基因对于揭示纤维发育和纤维品质形成，以及转移海岛棉基因到陆地棉有重要的理论和实践意义。