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

Authors

Huihui Yu, University of Nebraska - LincolnFollow
Qian Du, University of Nebraska - LincolnFollow
Malachy Campbell, University of Nebraska - Lincoln
Bin Yu, University of Nebraska - LincolnFollow
Harkamal Walia, University of Nebraska - LincolnFollow
Chi Zhang, University of Nebraska - LincolnFollow

ORCID IDs

Huihui Yu

Qian Du

Malachy Campbell

Bin Yu

Harkamal Walia

Chi Zhang

Document Type

Article

Date of this Version

1-4-2021

Citation

New Phytologist (2021) 230: 1273–1287 doi: 10.1111/nph.17189

Comments

OPEN ACCESS

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 GW