SIROtyping : siRNA and miRNA profiles of tomato

SIROtyping：番茄的 siRNA 和 miRNA 谱

• 批准号: BB/E007228/1
• 负责人: Kenneth Manning
• 金额: $ 2.18万
• 依托单位: University of Warwick
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2006
• 资助国家: 英国
• 起止时间: 2006 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FE007228%2F1
• 关键词: SIROtyping; siRNA; miRNA; profiles; tomato

Most of the RNA molecules in cells are involved in protein production (ribosomal, transfer or messenger RNAs), however there are RNA molecules with other functions. A recently discovered class of non-coding short RNAs (sRNA) regulate the level of protein production in a gene specific manner. These sRNAs can recognise specific mRNAs or DNA sequences because they have partially complementary sequences to them. As a result of this interaction expression of the targeted mRNAs is significantly reduced or transcription of the targeted DNA is suppressed. More than 70 000 different sRNAs were found in the model plant species Arabidopsis and we showed that these sRNAs are derived from more than 4000 clusters. We found that sRNAs are also produced from clusters in tomato fruits and that the expression of clusters was consistent between different samples of the same tomato type. Crop species have different cultivars that can be cross-fertilised but have different characteristics (e.g. fruit/seed size, colour, taste, texture, etc.). Arabidopsis - a non-cultivated model plant / also has different forms, which are called ecotypes. We tested the hypothesis that different clusters are active in different cultivars of tomato and different Arabidopsis ecotypes. In a preliminary experiment we found several sRNA clusters that accumulated at a different level between four Arabidopsis ecotypes and also between three tomato cultivars. Based on these data we propose to develop a tool that uses sRNAs as molecular markers of valuable characteristics in tomato. In the first phase of the project we will identify all the sRNA clusters in the tomato genome. Probes complementary to the identified sRNA clusters will be spotted on small glass plates. These microarrays will be used to profile sRNAs in a large number of tomato cultivars. Statistical analysis will then be used to establish the correlation between the phenotypes and production of specific sRNAs. Array based expression profile of sRNAs will identify a subset of sRNA clusters that are predictors of phenotypes. The proposed work will also evaluate the possibility that important agronomic traits can be modified when selected sRNAs are overexpressed or suppressed transgenically. These analyses and manipulations of sRNAs have the potential to establish a novel approach to crop improvement that is based on variation of regulatory RNAs rather than of protein coding genes.

细胞中的大多数RNA分子参与蛋白质的产生（核糖体、转移或信使RNA），但也有具有其他功能的RNA分子。最近发现的一类非编码短rna （sRNA）以一种基因特异性的方式调节蛋白质生产水平。这些sRNAs可以识别特定的mrna或DNA序列，因为它们有部分互补的序列。由于这种相互作用，靶mrna的表达显著减少或靶DNA的转录受到抑制。在模式植物拟南芥中发现了超过7万个不同的sRNAs，我们发现这些sRNAs来自4000多个集群。我们发现，在番茄果实中也可以从簇中产生sRNAs，并且簇的表达在同一番茄类型的不同样品之间是一致的。作物种类有不同的品种，这些品种可以杂交受精，但具有不同的特征（例如果实/种子大小、颜色、味道、质地等）。拟南芥-一种非栽培模式植物/也有不同的形式，称为生态型。我们验证了不同番茄品种和不同拟南芥生态型中不同簇具有不同活性的假设。在初步实验中，我们发现在4个拟南芥生态型和3个番茄品种之间有不同水平的sRNA聚集。基于这些数据，我们建议开发一种利用sRNAs作为番茄有价值特征的分子标记的工具。在项目的第一阶段，我们将确定番茄基因组中所有的sRNA簇。与已鉴定的sRNA簇互补的探针将被标记在小玻璃板上。这些微阵列将用于分析大量番茄品种的srna。然后将使用统计分析来建立表型和特定srna产生之间的相关性。基于阵列的sRNA表达谱将识别出作为表型预测因子的sRNA集群子集。拟议的工作还将评估当选择的sRNAs被转基因过表达或抑制时，重要农艺性状可以被修饰的可能性。这些对sRNAs的分析和操作有可能建立一种基于调控rna变异而不是蛋白质编码基因变异的作物改良新方法。