New Phytologist|一种软件工具来量化和可视化植物群体剪接变异（VaSP）

mRNA前剪接是调节基因表达的重要步骤。 为了专门捕获植物中的剪接变体以进行全基因组关联研究（GWAS），我们开发了一种软件工具来量化和可视化群体剪接变异（VaSP）。 

VaSP可以从短读RNA-seq数据集中量化剪接变体，并发现基因型特异性剪接（GSS）事件，可用于对GWAS中的因果性pre-mRNA剪接事件进行优先级排序。

我们将我们的方法应用于RNA-seq数据集，该数据集来自暴露于最佳和盐分生长条件下的水稻多样性研究小组的82个基因型的328个样本。 

在盐胁迫条件下共鉴定出764个重大GSS事件。 GSS事件被用作带有芽Na +积累的GWAS的标记物，该标记在与地上部分Na +含量显着相关的五个基因中鉴定出六个GSS事件。 这些基因中的两个OsNUC1和OsRAD23作为具有剪接变体的顶级候选基因出现，这些变体之间在盐胁迫条件下的枝条生长表现出显着的差异。 VaSP是一种用于植物中可变剪接分析的多功能工具，也是一种功能强大的工具，可用于优先排序候选因果前mRNA剪接和GWAS中相应的基因组变异。

Pre‐mRNA splicing is an essential step for the regulation of gene expression. In order to specifically capture splicing variants in plants for genome‐wide association studies (GWAS), we developed a software tool to quantify and visualize Variations of Splicing in Population (VaSP).

VaSP can quantify splicing variants from short‐read RNA‐seq datasets and discover genotype‐specific splicing (GSS) events, which can be used to prioritize causal pre‐mRNA splicing events in GWAS. We applied our method to an RNA‐seq dataset with 328 samples from 82 genotypes from a rice diversity panel exposed to optimal and saline growing conditions.

A total of 764 significant GSS events were identified in salt stress conditions. GSS events were used as markers for a GWAS with the shoot Na+ accumulation, which identified six GSS events in five genes significantly associated with the shoot Na+ content. Two of these genes, OsNUC1 and OsRAD23 emerged as top candidate genes with splice variants that exhibited significant divergence between the variants for shoot growth under salt stress conditions.

VaSP is a versatile tool for alternative splicing analysis in plants and a powerful tool for prioritizing candidate causal pre‐mRNA splicing and corresponding genomic variations in GWAS.

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