Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China.
BMC Genomics. 2013 Jan 16;14:26. doi: 10.1186/1471-2164-14-26.
The fertile and sterile plants were derived from the self-pollinated offspring of the F1 hybrid between the novel restorer line NR1 and the Nsa CMS line in Brassica napus. To elucidate gene expression and regulation caused by the A and C subgenomes of B. napus, as well as the alien chromosome and cytoplasm from Sinapis arvensis during the development of young floral buds, we performed a genome-wide high-throughput transcriptomic sequencing for young floral buds of sterile and fertile plants.
In this study, equal amounts of total RNAs taken from young floral buds of sterile and fertile plants were sequenced using the Illumina/Solexa platform. After filtered out low quality data, a total of 2,760,574 and 2,714,441 clean tags were remained in the two libraries, from which 242,163 (Ste) and 253,507 (Fer) distinct tags were obtained. All distinct sequencing tags were annotated using all possible CATG+17-nt sequences of the genome and transcriptome of Brassica rapa and those of Brassica oleracea as the reference sequences, respectively. In total, 3231 genes of B. rapa and 3371 genes of B. oleracea were detected with significant differential expression levels. GO and pathway-based analyses were performed to determine and further to understand the biological functions of those differentially expressed genes (DEGs). In addition, there were 1089 specially expressed unknown tags in Fer, which were neither mapped to B. oleracea nor to B. rapa, and these unique tags were presumed to arise basically from the added alien chromosome of S. arvensis. Fifteen genes were randomly selected and their expression levels were confirmed by quantitative RT-PCR, and fourteen of them showed consistent expression patterns with the digital gene expression (DGE) data.
A number of genes were differentially expressed between the young floral buds of sterile and fertile plants. Some of these genes may be candidates for future research on CMS in Nsa line, fertility restoration and improved agronomic traits in NR1 line. Further study of the unknown tags which were specifically expressed in Fer will help to explore desirable agronomic traits from wild species.
可育和不育植株是通过新型恢复系 NR1 与 NsaCMS 系的 F1 杂种自交得到的。为了阐明甘蓝型油菜 A、C 亚基因组以及白芥细胞质和外源染色体在幼小花芽发育过程中的基因表达和调控，我们对不育和可育植株的幼小花芽进行了全基因组高通量转录组测序。
本研究中，等量取自不育和可育植株幼小花芽的总 RNA 分别使用 Illumina/Solexa 平台进行测序。过滤掉低质量数据后，两个文库分别剩余 2,760,574 和 2,714,441 条清洁标签，从中分别获得 242,163（Ste）和 253,507（Fer）个独特标签。所有独特的测序标签均使用 Brassica rapa 和 Brassica oleracea 的基因组和转录组的所有可能的 CATG+17-nt 序列以及分别作为参考序列的 Brassica oleracea 的 CATG+17-nt 序列进行注释。总共检测到 3231 个 B. rapa 基因和 3371 个 B. oleracea 基因具有显著的差异表达水平。GO 和通路分析用于确定和进一步理解这些差异表达基因（DEGs）的生物学功能。此外，Fer 中还有 1089 个专门表达的未知标签，既不能映射到 B. oleracea 也不能映射到 B. rapa，这些独特的标签被认为基本上是来自白芥的添加的外源染色体。随机选择了 15 个基因，并通过定量 RT-PCR 验证了它们的表达水平，其中 14 个基因与数字基因表达（DGE）数据的表达模式一致。
不育和可育植株幼小花芽之间有许多基因差异表达。其中一些基因可能是 Nsa 系 CMS、NR1 系育性恢复和农艺性状改良未来研究的候选基因。进一步研究 Fer 中特异性表达的未知标签将有助于从野生种中探索理想的农艺性状。
