| Summary: | Improving <i>Brassica napus</i> via introgression of the genome components from its parental species, <i>B. oleracea</i> and <i>B. rapa</i>, is an important breeding strategy. Interspecific hybridization between <i>B. napus</i> and <i>B. rapa</i> is compatible with high rate of survival ovules, while the hybridization between <i>B. napus</i> and <i>B. oleracea</i> is incompatible with the high occurrence of embryo abortion. To understand the diverse embryo fate in the two interspecific hybridizations, here, the siliques of <i>B. napus</i> pollinated with <i>B. oleracea</i> (AE) and <i>B. rapa</i> (NE) were employed for transcriptome sequencing at 8 and 16 days after pollination. Compared to NE and the parental line of <i>B. napus</i>, more specific differentially expressed genes (DEGs) (1274 and 1698) were obtained in AE and the parental line of <i>B. napus</i> at 8 and 16 days after pollination (DAP). These numbers were 51 and 5.8 times higher than the number of specific DEGs in NE and parental line of <i>B. napus</i> at 8 and 16 DAP, respectively, suggesting more complex transcriptional changes in AE. Most of DEGs in the terms of cell growth and cell wall formation exhibited down-regulated expression patterns (96(down)/131(all) in AE8, 174(down)/235(all) in AE16), while most of DEGs in the processes of photosynthesis, photorespiration, peroxisome, oxidative stress, and systemic acquired resistance exhibited up-regulated expression patterns (222(up)/304(all) in AE8, 214(up)/287(all) in AE16). This is in accordance with a high level of reactive oxygen species (ROS) in the siliques of <i>B. napus</i> pollinated with <i>B. oleracea</i>. Our data suggest that the disorder of plant hormone metabolism, retardation of cell morphogenesis, and the accumulation of ROS may be associated with hybrid incompatibility between <i>B. napus</i> and <i>B. oleracea</i>.
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