Pattern of alternative splicing different associated with difference in rooting depth in rice

Deep root traits are important in rice (Oryza sativa L.) because of their implications for better ability to reach water and nutrients from deep soil. Analysis of gene expression and alternative splicing (AS) will help speed gene identification and understand the role of AS in deep rooting. Rice varieties displaying extreme ratio of deep rooting (RDR) were grown in nutrient solutions. RNA-seq analysis was conducted using StringTie, SUPPA, and 3D RNA-seq pipeline. Functional validation of AS was performed by transgenic overexpression of OsPIN1. The reference-based transcriptome assembly transcripts represented an overall portrait of AS in rice roots. A percentage (76.91%) of assembled genes contained at least one predicted intron. Principal component analysis of single-nucleotide polymorphisms from RNA-seq indicated that genetic differentiation generated abundant genetic diversity during adaptive domestication of high RDR varieties. Totals obtained were: 4392 differentially expressed genes, 3053 differentially alternatively spliced genes, 5508 differential transcript usage transcripts, and 1068 differential AS event transcripts. Functional categories of these genes and AS regulation transcripts were involved in DNA metabolic processes, stress responses and cell part. Transgenic overexpression of OsPIN1 containing retained intron events improved RDR in rice. AS increased the complexity of gene expression for environmental adaptation while the gene expression level did not change significantly. Our findings provide new perspectives for enhancing drought avoidance.