Yellow seed coat color is a desirable characteristic in rapeseed (Brassica napus), as it is associated with higher oil content and higher quality of meal. Alternative splicing (AS) is a vital post-transcriptional regulatory process contributing to plant cell differentiation and organ development. To identify novel transcripts and differences at the isoform level that are associated with seed color in B. napus, we compared 31 RNA-seq libraries of yellow- and black-seeded B. napus at five different developmental stages. AS events in the different samples were highly similar, and intron retention accounted for a large proportion of the observed AS pattern. AS mainly occurred in the early and middle stage of seed development. Weighted gene co-expression network analysis (WGCNA) identified 23 co-expression modules composed of differentially spliced genes, and we picked out two of the modules whose functions were highly associated with seed color. In the two modules, we found candidate DAS (differentially alternative splicing) genes related to the flavonoid pathway, such as TT8 (BnaC09g24870D), TT5 (BnaA09g34840D and BnaC08g26020D), TT12 (BnaC06g17050D and BnaA07g18120D), AHA10 (BnaA08g23220D and BnaC08g17280D), CHI (BnaC09g50050D), BAN (BnaA03g60670D) and DFR (BnaC09g17150D). Gene BnaC03g23650D, encoding RNA-binding family protein, was also identified. The splicing of the candidate genes identified in this study might be used to develop stable, yellow-seeded B. napus. This study provides insight into the formation of seed coat color in B. napus.

中文翻译：

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黄籽油菜和黑籽油菜选择性剪接的差异。

黄色种皮颜色是油菜籽（甘蓝型油菜）的理想特征，因为它与较高的含油量和较高的粗粉质量相关。选择性剪接（AS）是一种重要的转录后调控过程，有助于植物细胞分化和器官发育。为了识别与甘蓝型油菜种子颜色相关的新转录本和异构体水平的差异，我们比较了黄色和黑色种子甘蓝型油菜在五个不同发育阶段的 31 个 RNA-seq 文库。不同样本中的AS事件高度相似，内含子保留占观察到的AS模式的很大一部分。AS主要发生在种子发育的早中期。加权基因共表达网络分析（WGCNA）鉴定了23个由差异剪接基因组成的共表达模块，我们选出了其中两个功能与种子颜色高度相关的模块。在这两个模块中，我们发现了与类黄酮通路相关的候选DAS（差异选择性剪接）基因，例如TT8（BnaC09g24870D）、TT5（BnaA09g34840D和BnaC08g26020D）、TT12（BnaC06g17050D和BnaA07g18120D）、AHA10（BnaA0） 8g23220D 和 BnaC08g17280D)、CHI (BnaC09g50050D)、BAN (BnaA03g60670D) 和 DFR (BnaC09g17150D)。编码RNA结合家族蛋白的基因BnaC03g23650D也被鉴定出来。本研究中确定的候选基因的剪接可用于培育稳定的黄籽甘蓝型油菜。这项研究提供了对甘蓝型油菜种皮颜色形成的深入了解。