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Genes 2019, 10(3), 224; https://doi.org/10.3390/genes10030224

Differential Alternative Splicing Genes in Response to Boron Deficiency in Brassica napus

1,2, 1,2, 1,2, 3, 3, 1,2, 1,2, 4,†, 3,*,† and 1,2,*,†
1
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
2
Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
3
School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham NG25 0QF, UK
4
State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
*
Authors to whom correspondence should be addressed.
These authors jointly supervised and contributed equally to this work.
Received: 19 February 2019 / Accepted: 7 March 2019 / Published: 18 March 2019
(This article belongs to the Special Issue Improving Plant Nutrient Use efficiency)
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Abstract

Alternative splicing (AS) can increase transcriptome diversity, protein diversity and protein yield, and is an important mechanism to regulate plant responses to stress. Oilseed rape (Brassica napus L.), one of the main oil crops in China, shows higher sensitivity to boron (B) deficiency than other species. Here, we demonstrated AS changes that largely increased the diversity of the mRNA expressed in response to B deficiency in B. napus. Each gene had two or more transcripts on average. A total of 33.3% genes in both Qingyou10 (QY10, B-efficient cultivar) and Westar10 (W10, B-inefficient cultivar) showed AS in both B conditions. The types of AS events were mainly intron retention, 3′ alternative splice site, 5′ alternative splice site and exon skipping. The tolerance ability of QY10 was higher than that of W10, possibly because there were far more differential alternative splicing (DAS) genes identified in QY10 at low B conditions than in W10. The number of genes with both DAS and differentially expressed (DE) was far lower than that of the genes that were either with DAS or DE in QY10 and W10, suggesting that the DAS and DE genes were independent. Four Serine/Arginine-rich (SR) splicing factors, BnaC06g14780D, BnaA01g14750D, BnaA06g15930D and BnaC01g41640D, underwent differentially alternative splicing in both cultivars. There existed gene–gene interactions between BnaC06g14780D and the genes associated with the function of B in oilseed rape at low B supply. This suggests that oilseed rape could regulate the alterative pre-mRNA splicing of SR protein related genes to increase the plant tolerance to B deficiency. View Full-Text
Keywords: boron deficiency; alternative splicing; differential expressed genes; differential alternative splicing genes; splicing factors; Brassica napus boron deficiency; alternative splicing; differential expressed genes; differential alternative splicing genes; splicing factors; Brassica napus
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Gu, J.; Li, W.; Wang, S.; Zhang, X.; Coules, A.; Ding, G.; Xu, F.; Ren, J.; Lu, C.; Shi, L. Differential Alternative Splicing Genes in Response to Boron Deficiency in Brassica napus. Genes 2019, 10, 224.

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