Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus

Abstract

BackgroundThe 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.ResultsIn 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.ConclusionsA 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.

Transcriptome Analysis to Understand the Toxicity of Latrodectus tredecimguttatus Eggs

“…The KEGG enrichment analysis of 280 unigenes was carried out by KOBAS software [84] and the unigenes that were annotated in KEGG databases were referred to as the universe of genes. The calculating formula used is as follows [85]: $P=1-{\displaystyle \sum }_{i=0}^{m-1}\frac{\left(\begin{array}{c}M\\ i\end{array}\right)\left(\begin{array}{c}N-M\\ n-i\end{array}\right)}{\left(\begin{array}{c}N\\ n\end{array}\right)}$ …”

Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)

“…To elucidate the mechanism of MS more comprehensively, the transcriptomes of many higher plants have been sequenced, including Arabidopsis [21], buckwheat [22], cotton [23–25], watermelon [26], soybean [27], Brassica napus [28–30] and Brassica oleracea [31]. In this study, fertile and sterile flower buds from DGMS line with a length of ~2.5 mm were sampled for RNA-seq, representing the first study of the sesame DGMS transcriptome.…”

Comparative transcript profiling of the fertile and sterile flower buds of pol CMS in B. napus

“…Nowadays, the transcriptomes of many higher plants have been sequenced for different purposes, including Arabidopsis thaliana [10,11], Myrica rubra [12], Fagopyrum [13], Citrus sinensis [14], Carthamus tinctorius [15], and even Brassica napus for fertility studies [16]. By RNA-Seq, researchers can obtain almost all of the expressed genes, especially genes with very low abundance.…”