Epigenetic control of strawberry secondary metabolism- a small fruit with a complex genome

在英国和世界范围内，越来越需要促进新鲜农产品的消费，因为它与预防几种类型的癌症和心血管疾病的保护作用有关。然而，软水果如草莓在收获后具有非常短的货架期，导致对消费者的营养价值降低和大量浪费。草莓中产生的次级代谢物是促进健康的关键，也是草莓风味和香气的关键。这种小分子鸡尾酒对所有草莓品种都是独一无二的，在收获前后的果实成熟过程中会发生变化。因此，编码不同代谢途径的生物合成基因受到动态调节。本项目将从表观遗传学的角度研究草莓果实次生代谢的调控。首先，与模式植物不同，许多经济作物具有复杂的多倍体基因组。商业草莓（草莓）具有二倍体基因组，因此我们需要了解组分基因组之间的相互作用是如何调节的。其次，最近发现许多代谢途径基因被组织成邻近基因的簇，并受到染色质构型变化的调节。在初步的表达和代谢实验中，我们已经确定了几个代谢途径的基因和小分子调控的商业草莓收获后。现在，我们建议分析F. ananassa中的转录水平，并将其与一个更简单的二倍体野生近缘种F. vesca，使用RNAseq分析基因表达的总体变化，然后使用真实的时间PCR进行更详细的靶向分析。这将导致调查的表观遗传控制基因表达的商业草莓使用技术，如染色质免疫沉淀。我们的长期目标是确定植物育种者使用的过程和基因靶点。因此，我们与草莓育种者和种植者建立了联系，他们将为学生提供进一步的见解，了解优化水果质量的商业优先事项，以及如何将项目结果整合到育种计划中。

There is an increasing need to promote the consumption of fresh produce in the UK and world-wide as it is associated with a protective role against several types of cancer and cardiovascular diseases. However, soft fruit such as strawberries have a very short shelf-life after harvest resulting in reduced nutritional value to the consumer and in substantial waste. Central to the health-promoting properties as well as to the flavour and aroma of strawberries are the secondary metabolites produced in the fruit. This cocktail of small molecules is unique for all strawberry varieties, and changes during fruit ripening pre and post-harvest. Accordingly, the biosynthesis genes encoding the diverse metabolic pathways are dynamically regulated. This project will investigate the regulation of secondary metabolism in strawberry fruit at an epigenetic level. Firstly, unlike model plants, many commercial crops have complex polyploid genomes. Commercial strawberries (Fragaria ananassa) have octoploid genomes, so we need to understand how interactions between the component genomes are regulated. Secondly, it has been recently discovered that many metabolic pathway genes are organised in clusters of neighbouring genes and are regulated by changes in chromatin configuration. In preliminary expression and metabolite experiments, we have identified several metabolic pathway genes and small molecules that are regulated in commercial strawberry post-harvest. Now, we propose to analyse the contribution of the separate genomes of F. ananassa to this expression pattern and compare it to the transcription in a simpler diploid wild relative, F. vesca, using RNAseq to analyse global changes in gene expression followed by more detailed targeted analyses using real time PCR. This will lead on to investigating the epigenetic control of gene expression in the commercial strawberry using techniques such as chromatin immunoprecipitation. Our long- term aim is to identify processes and gene targets of use to plant breeders. We have therefore made links with a strawberry breeder and grower who will provide the student with further insights into the commercial priorities for optimising fruit quality and how to integrate results from the project into breeding programmes.