Functional and Sequence Analysis of Fiber Development in Allotetraploid Cotton

四倍体棉花纤维发育的功能和序列分析（作者：Z. Jeffrey Chen，德克萨斯大学奥斯汀分校）合作作者：Foo b张（美国J. Craig Venter研究所），Candace H. Haigler（北卡罗来纳州立大学），Brian E. Scheffler（奥尔康州立大学）和David M. Stelly（德克萨斯州A & M大学）棉花是天然纺织纤维的最大来源，也是主要的油料作物。每根棉纤维都是高度细长的种子毛，其次壁几乎由纯纤维素组成。棉纤维细胞数量多（每粒种子约2万个）且几乎同步发育，使其成为研究植物细胞分化、扩增和细胞壁生物合成的良好模型系统。纤维的分析提供了叶片毛状体、种子纤维、木质部成分和其他厚壁细胞的基因组信息。棉花属（Gossypium）也是植物基因组进化和多倍体研究的典范。对重复基因和基因组的遗传和表观遗传效应的研究将最终导致性状改良。该项目的目标是鉴定对纤维细胞发育和纤维素生物合成重要的棉花基因和调控序列。当代基因组资源将被开发用于测序、组装和注释两种主要的四倍体栽培物种（G. hirsutum和G. barbadense）的基因组，它们也分别被称为旱棉和皮马棉。新的测序技术将用于鉴定陆地棉和皮马棉纤维发育关键阶段的基因表达变化。比较分析棉花及相关属中与纤维品质性状相关的保守、独特基因及等位基因特异性表达模式。棉花基因的功能将通过基因组宽筛选在拟南芥和棉花突变体中进行测试。利用基于测序的指纹图谱技术，将开发高分辨率综合物理图谱，作为四倍体棉花的社区资源和测序模板。提高棉纤维产量和质量将为石油基合成纤维提供一种可持续的替代品。大多数作物都是多倍体起源，因此该项目开发的方法和原理也将促进其他具有复杂和多倍体基因组的作物的发展。提高对纤维发育和纤维素和壁生物合成的理解将广泛影响生物质作物和生物燃料生产的研究。基因组序列和基因表达数据将通过公共数据存储库提供，包括GenBank、基因表达Ominibus （GEO）、国家生物技术信息中心（NCBI）和J. Craig Venter研究所（JCVI）。植物和种子材料将通过棉花资源网站（CottonDB）分发。将为密西西比三角洲的初中和高中、两年制大学和本科院校开发植物基因组学、生物技术和生物信息学方面的创新和可扩展的教育和培训模块。通过与USDA-ARS K-12外展服务的合作，以及与奥尔康州立大学和密西西比河谷州立大学这两所传统黑人学院和大学的密切合作，将提高教育和外展服务的有效性。

Functional and Sequence Analysis of Fiber Development in Tetraploid CottonPI: Z. Jeffrey Chen (The University of Texas at Austin)Co-PIs: Foo Cheung (The J. Craig Venter Institute), Candace H. Haigler (North Carolina State University), Brian E. Scheffler (Alcorn State University) and David M. Stelly (Texas A & M University)Cotton is the largest source of natural textile fiber and a major oilseed crop. Each cotton fiber is a highly elongated seed hair with a secondary wall composed of almost pure cellulose. The large numbers (~20,000 per seed) and nearly synchronous development of cotton fiber cells make them an excellent model system to study plant cell differentiation, expansion, and wall biosynthesis. Analysis of fibers provides genomic information about leaf trichomes, seed fibers, xylem elements, and other cells with thick walls. The cotton genus Gossypium is also a model for research on plant genome evolution and polyploidy. The study of genetic and epigenetic effects on duplicate genes and genomes will ultimately lead to trait improvement. The project goals are to identify cotton genes and regulatory sequences that are important to fiber cell development and cellulose biosynthesis. Contemporary genomic resources will be developed for sequencing, assembling, and annotating the genomes of two major cultivated tetraploid species (G. hirsutum and G. barbadense), also known as Upland and Pima cotton, respectively. New sequencing technology will be used to identify gene expression changes at key stages of fiber development in Upland and Pima cotton. Conserved and unique genes as well as allele-specific expression patterns associated with fiber quality traits will be comparatively analyzed in cotton and in related genera. The function of cotton genes will be tested through genome wide screens in Arabidopsis and in mutants in cotton. Using sequencing-based fingerprinting techniques, a high-resolution integrated physical map will be developed as a community resource and as a sequencing template for tetraploid cotton.Improving cotton fiber yield and quality will provide a sustainable alternative to petroleum-based synthetic fibers. Most crops are of polyploid origin, so methods and principles being developed from this project will also advance other crops with complex and polyploid genomes. Improved comprehension of fiber development and cellulose and wall biosynthesis will broadly impact research on biomass crops and biofuel production. Genomic sequence and gene expression data will be made available through public data depositories, including GenBank, Gene Expression Ominibus (GEO), National Center for Biotechnology Information (NCBI), and the J. Craig Venter Institute (JCVI). Plant and seed materials will be distributed through the website for cotton resources, (CottonDB). Innovative and scalable education and training modules in plant genomics, biotechnology, and bioinformatics will be developed for middle and high schools, two year colleges and undergraduate institutions in the Mississippi Delta. The effectiveness of education and outreach will be enhanced through cooperation with USDA-ARS K-12 outreach services and augmented by close collaborations with two Historically Black Colleges and Universities (HBCUs), namely, Alcorn State University and Mississippi Valley State University.