SIROtyping : siRNA and miRNA profiles of tomato

细胞中的大多数RNA分子都参与蛋白质的产生（核糖体，转移或信使RNA），但也有其他功能的RNA分子。最近发现的一类非编码短RNA（sRNA）以基因特异性方式调节蛋白质产生水平。这些sRNA可以识别特定的mRNA或DNA序列，因为它们具有与它们部分互补的序列。作为这种相互作用的结果，靶向mRNA的表达显著降低或靶向DNA的转录被抑制。在模式植物拟南芥中发现了超过70000种不同的sRNA，我们发现这些sRNA来自4000多个簇。我们发现，sRNA也产生于番茄果实中的簇，并且簇的表达在相同番茄类型的不同样品之间是一致的。作物物种具有不同的栽培品种，这些栽培品种可以交叉受精，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-非栽培模式植物/也有不同的形式，这被称为生态型。我们测试的假设，不同的集群是活跃在不同品种的番茄和不同的拟南芥生态型。在一个初步的实验中，我们发现了几个sRNA簇，积累在不同的水平之间的四个拟南芥生态型和三个番茄品种。基于这些数据，我们建议开发一种工具，使用sRNAs作为分子标记的有价值的特征，在番茄。在该项目的第一阶段，我们将鉴定番茄基因组中的所有sRNA簇。将与鉴定的sRNA簇互补的探针点样在小玻璃板上。这些微阵列将被用于在大量的番茄栽培品种的sRNA的概况。然后将使用统计分析来建立表型与特定sRNA产生之间的相关性。基于阵列的sRNA表达谱将鉴定作为表型预测因子的sRNA簇的子集。拟议的工作还将评估重要的农艺性状可以被修改时，选择的sRNA过表达或抑制转基因的可能性。这些sRNA的分析和操作有可能建立一种基于调节RNA而不是蛋白质编码基因变异的作物改良新方法。

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.