Aims 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. Methods 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 . Results 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. Conclusions 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.

中文翻译：

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水稻生根深度差异导致的可变剪接模式

目的 深根性状在水稻 ( Oryza sativa L. ) 中很重要，因为它们可以更好地从深层土壤中获取水分和养分。基因表达和选择性剪接 (AS) 的分析将有助于加速基因识别并了解 AS 在根深蒂固中的作用。方法 在营养液中种植具有极端深根率 (RDR) 的水稻品种。RNA-seq 分析使用 StringTie、SUPPA 和 3D RNA-seq 管道进行。通过 OsPIN1 的转基因过表达进行 AS 的功能验证。结果 基于参考的转录组组装转录本代表了水稻根系中 AS 的整体情况。百分比 (76.91%) 的组装基因包含至少一个预测的内含子。RNA-seq 单核苷酸多态性的主成分分析表明，遗传分化在高 RDR 品种的适应性驯化过程中产生了丰富的遗传多样性。获得的总数为：4392 个差异表达基因、3053 个差异可变剪接基因、5508 个差异转录本使用转录本和 1068 个差异 AS 事件转录本。这些基因的功能类别和 AS 调控转录本参与了 DNA 代谢过程、应激反应和细胞部分。含有保留内含子事件的 OsPIN1 的转基因过表达改善了水稻的 RDR。结论 AS增加了环境适应基因表达的复杂性，而基因表达水平没有显着变化。我们的研究结果为加强避免干旱提供了新的视角。