de Jong Grant W, Adams Keith L
Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
Plant J. 2023 Apr;114(1):142-158. doi: 10.1111/tpj.16127. Epub 2023 Feb 18.
Polyploidy has played an extensive role in the evolution of flowering plants. Allopolyploids, with subgenomes containing duplicated gene pairs called homeologs, can show rapid transcriptome changes including novel alternative splicing (AS) patterns. The extent to which abiotic stress modulates AS of homeologs is a nascent topic in polyploidy research. We subjected both resynthesized and natural lines of polyploid Brassica napus, along with the progenitors Brassica rapa and Brassica oleracea, to infection with the fungal pathogen Sclerotinia sclerotiorum. RNA-sequencing analyses revealed widespread divergence between polyploid subgenomes in both gene expression and AS patterns. Resynthesized B. napus displayed significantly more A and C subgenome biased homeologs under pathogen infection than during uninfected growth. Differential AS (DAS) in response to infection was highest in natural B. napus (12 709 DAS events) and lower in resynthesized B. napus (8863 DAS events). Natural B. napus had more upregulated events and fewer downregulated events. There was a global expression bias towards the B. oleracea-derived (C) subgenome in both resynthesized and natural B. napus, enhanced by widespread non-parental downregulation of the B. rapa-derived (A) homeolog. In the resynthesized B. napus, this resulted in a disproportionate C subgenome contribution to the pathogen defense response, characterized by biases in both transcript expression levels and the proportion of induced genes. Our results elucidate the complex ways in which Sclerotinia infection affects expression and AS of homeologous genes in resynthesized and natural B. napus.
多倍体在开花植物的进化过程中发挥了广泛作用。异源多倍体的亚基因组包含被称为同源基因对的重复基因对，可能会出现快速的转录组变化，包括新的可变剪接（AS）模式。非生物胁迫对同源基因可变剪接的调控程度是多倍体研究中的一个新兴课题。我们让人工合成的和天然的多倍体甘蓝型油菜品系，以及其亲本油菜和甘蓝，感染真菌病原体核盘菌。RNA测序分析显示，多倍体亚基因组在基因表达和可变剪接模式上普遍存在差异。与未感染时相比，人工合成的甘蓝型油菜在病原体感染下，A和C亚基因组偏向的同源基因明显更多。天然甘蓝型油菜对感染的差异可变剪接（DAS）事件最多（12709个DAS事件），人工合成的甘蓝型油菜则较少（8863个DAS事件）。天然甘蓝型油菜上调事件更多，下调事件更少。在人工合成的和天然的甘蓝型油菜中，都存在对甘蓝来源的（C）亚基因组的全局表达偏向，油菜来源的（A）同源基因广泛的非亲本下调增强了这种偏向。在人工合成的甘蓝型油菜中，这导致C亚基因组对病原体防御反应的贡献不成比例，其特征是转录本表达水平和诱导基因比例都存在偏向。我们的结果阐明了核盘菌感染影响人工合成的和天然的甘蓝型油菜中同源基因表达和可变剪接的复杂方式。
