Reference Annotations for Small RNA-producing Genes in Plants

植物中产生小RNA的基因的参考注释

• 批准号: 1339207
• 负责人: Michael Axtell
• 金额: $ 88.54万
• 依托单位: Pennsylvania State Univ University Park
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-05-15 至 2019-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1339207&HistoricalAwards=false
• 关键词: Reference; Annotations; Small; RNA; producing

PI: Michael J. Axtell (Pennsylvania State University - University Park)CoPI: Matthew Jones-Rhoades (Knox College)Genes are discrete sections of DNA within chromosomes that encode specific functional products. Gene expression is the production of RNA copies of these discrete DNA sections that are then either used to encode for proteins, or are functional as RNAs in their own right. Gene annotations identify and characterize the location of genes throughout a complete genome sequence. Annotations of protein-coding genes have received a great deal of attention, and are at a relatively advanced state for many plant species of agricultural and economic interest. In contrast, annotations for many other types of genes are much less developed. Regulatory small RNAs are short bits of RNA that function to turn off the expression of other genes in the genome and have been implicated as key players in several important plant traits, including disease resistance, tolerance to adverse environmental conditions, and plant growth traits affecting yield. One sub-type of regulatory small RNA genes, the microRNAs, are well-studied and well-annotated. However, microRNAs account for a very small fraction of the overall small RNA gene population in plants; preliminary data indicate that a typical plant genome has just a few hundred microRNA genes, but tens of thousands of genes encoding other types of regulatory small RNAs. This project seeks to provide systematic annotations of plant genes that produce all types regulatory small RNAs for several plants of agricultural and societal interest, including rice, maize, tomato, and apple.Knowing where in the genome the genes are, and what types of products they produce, is key information for genetic approaches to plant improvement. Regulatory small RNAs are clearly a major type of gene in plants, but their annotation is currently under-developed. Systematic and reliable gene annotations for regulatory small RNA genes will accelerate genetic, genomic, and breeding experiments to identify superior plant varieties to meet the challenge of feeding a growing population and maintaining the astounding productivity of American agriculture in the face of a changing climate. This project is also training graduate and undergraduate students in modern plant genetics through mentored research experience, and allowing the development of novel undergraduate courses. All project outcomes from this project will be made available without restriction via the project website at http://plantsmallrnagenes.psu.edu/. Sequence data will be available through long-term repositories (GEO, SRA) and small RNA gene models will be provided to community portals such as Gramene and MaizeGDB.

PI：Michael J. Axtell（宾夕法尼亚州立大学 - 大学公园）COPI：Matthew Jones -Rhoades（Knox College）基因是编码特定功能产品的染色体内DNA的离散部分。基因表达是这些离散DNA切片的RNA拷贝的产生，然后用来编码蛋白质，或者本身可以用作RNA。基因注释在整个基因组序列中识别并表征基因的位置。蛋白质编码基因的注释受到了很多关注，并且对于许多农业和经济利益的植物种类处于相对先进的状态。相比之下，许多其他类型的基因的注释的发展要少得多。调节性的小RNA是RNA的短位，其功能可以关闭基因组中其他基因的表达，并被牵涉到几种重要植物特征的关键参与者，包括抗病性，对不利环境条件的耐受性以及影响产量的植物生长特征。调节性的小RNA基因（microRNAS）的一个亚型是经过充分研究且被宣布良好的。但是，microRNA占植物中总小RNA基因群的一小部分。初步数据表明，典型的植物基因组只有几百个microRNA基因，但是编码其他类型的调节性小RNA的基因数万。该项目旨在提供植物基因的系统注释，这些注释为几种农业和社会兴趣的植物生产所有类型的调节小型RNA，包括大米，玉米，玉米，番茄和苹果。基因组中的基因组是哪种类型的基因组以及它们产生的产品类型，是基因改进的基因方法的关键信息。 调节性小型RNA显然是植物中的主要基因，但是它们的注释目前尚未发育。调节性小RNA基因的系统和可靠的基因注释将加速遗传，基因组和育种实验，以鉴定出较高的植物品种，以应对面对不断变化的气候下的美国农业生产力的挑战，并保持美国农业的惊人生产力。该项目还通过指导的研究经验培训现代植物遗传学的毕业生和本科生，并允许开发新的本科课程。该项目的所有项目成果将通过项目网站http://plantsmallrrnagenes.psu.edu/提供限制。 序列数据将通过长期存储库（GEO，SRA）获得，并且将向Gramene和MaizeGDB等社区门户提供小的RNA基因模型。