期刊
G3-GENES GENOMES GENETICS
卷 11, 期 7, 页码 -出版社
OXFORD UNIV PRESS INC
DOI: 10.1093/g3journal/jkab162
关键词
soybean; alternative splicing; nitrate; transcriptome; root development
资金
- Key R&D project of Jiangsu Province [BE2019376]
- Natural Science Foundation of Jiangsu Province [BK20191438]
- Project of Special Funding for Crop Science Discipline Development [yzuxk202006]
- Jiangsu Agriculture Science and Technology Innovation Fund [CX(20)2007]
In this study, we investigated the genome-wide alternative splicing events in soybean roots in response to different levels of nitrate supply using high-quality high-throughput RNA-sequencing data. Our results identified 355 nitrate-responsive AS events between optimal and high nitrate levels, 335 nitrate-responsive AS events between optimal and low nitrate levels, and 588 nitrate-responsive AS events between low and high nitrate levels. The most common AS types were RI and A355, which accounted for 67% of all AS events under all conditions.
In plants, nitrate acts not only as a signaling molecule that affects plant development but also as a nutrient. The development of plant roots, which directly absorb nutrients, is greatly affected by nitrate supply. Alternative gene splicing plays a crucial role in the plant stress response by increasing transcriptome diversity. The effects of nitrate supply on alternative splicing (AS), however, have not been investigated in soybean roots. We used high-quality high-throughput RNA-sequencing data to investigate genome-wide AS events in soybean roots in response to various levels of nitrate supply. In total, we identified 355 nitrate-responsive AS events between optimal and high nitrate levels (NH), 335 nitrate-responsive AS events between optimal and low nitrate levels (NL), and 588 nitrate-responsive AS events between low and high nitrate levels (NLH). RI and A355 were the most common AS types; in particular, they accounted for 67% of all AS events under all conditions. This increased complex and diversity of AS events regulation might be associated with the soybean response to nitrate. Functional ontology enrichment analysis suggested that the differentially splicing genes were associated with several pathways, including spliceo-some, base excision repair, mRNA surveillance pathway and so on. Finally, we validated several AS events using reverse transcription-polymerase chain reaction to confirm our RNA-seq results. In summary, we characterized the features and patterns of genome-wide AS in the soybean root exposed to different nitrate levels, and our results revealed that AS is an important mechanism of nitrate-response regulation in the soybean root.
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