Genome‐wide discovery of natural variation in pre‐mRNA splicing and prioritising causal alternative splicing to salt stress response in rice

Abstract

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 visualise 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 prioritise 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. In total, 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 prioritising candidate causal pre-mRNA splicing and corresponding genomic variations in GWAS.

Serrate‐Associated Protein 1, a splicing‐related protein, promotes miRNA biogenesis in Arabidopsis

“…Only the genes with standard deviation of expression larger than one among all samples were used in the analysis and the genes with statistic Q-value ≤ 0.05 were considered as differentially expressed genes (DEGs). Differential mRNA splicing analysis was conducted using R package VASP (Yu et al, 2021). The Single Splicing Strength (3S) score, which is junction reads normalized by gene-level average read coverage, was calculated for each annotated intron (Yu et al, 2021).…”

“…Differential mRNA splicing analysis was conducted using R package VASP (Yu et al, 2021). The Single Splicing Strength (3S) score, which is junction reads normalized by gene-level average read coverage, was calculated for each annotated intron (Yu et al, 2021). Only the introns supported with at least five junction reads in at least one sample were considered, and only the genes with the average read coverage larger than one in all samples were used in the analysis.…”

Genetic, Epigenetic, Genomic and Microbial Approaches to Enhance Salt Tolerance of Plants: A Comprehensive Review

“…More comprehensive GWAS studies involving a larger population of plant genotypes derived from crossing multiple parents called Multi-parent Advanced Generation Inter Crosses (MAGIC) lines are proposed for in-depth identification of marker-trait associations [ 133 , 134 ]. In addition to conventional trait mapping, NGS technologies have also been used for transcriptomics [ 135 , 136 , 137 , 138 ], proteomics [ 139 ], and pre-mRNA splicing [ 140 ] analysis for the identification of genes associated with salt stress responses.…”

Identifying stress responsive genes using overlapping communities in co-expression networks

“…The 19 selected genes were also enriched by contrasting them with findings reported in the literature [ 25 – 28 ], which applied different approaches to study the same RNA-seq dataset GSE98455. In [ 27 ], 11 of the 19 selected genes were reported to have conserved heritability for both control and salt stress conditions.…”