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 <it>Nsa</it> CMS line in <it>Brassica napus</it>
<p>Abstract</p> <p>Background</p> <p>The fertile and sterile plants were derived from the self-pollinated offspring of the F<sub>1</sub> hybrid between the novel restorer line NR1 and the <it>Nsa</it> CMS line in <it>Brassica napus</it&g...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2013-01-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/14/26 |
| _version_ | 1818843929479479296 |
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| author | Yan Xiaohong Dong Caihua Yu Jingyin Liu Wanghui Jiang Chenghong Liu Jia Hu Qiong Fang Xiaoping Wei Wenhui |
| author_facet | Yan Xiaohong Dong Caihua Yu Jingyin Liu Wanghui Jiang Chenghong Liu Jia Hu Qiong Fang Xiaoping Wei Wenhui |
| author_sort | Yan Xiaohong |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The fertile and sterile plants were derived from the self-pollinated offspring of the F<sub>1</sub> hybrid between the novel restorer line NR1 and the <it>Nsa</it> CMS line in <it>Brassica napus</it>. To elucidate gene expression and regulation caused by the A and C subgenomes of <it>B</it>. <it>napus</it>, as well as the alien chromosome and cytoplasm from <it>Sinapis arvensis</it> 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.</p> <p>Results</p> <p>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 <it>Brassica rapa</it> and those of <it>Brassica oleracea</it> as the reference sequences, respectively. In total, 3231 genes of <it>B</it>. <it>rapa</it> and 3371 genes of <it>B</it>. <it>oleracea</it> 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 <it>B</it>. <it>oleracea</it> nor to <it>B</it>. <it>rapa</it>, and these unique tags were presumed to arise basically from the added alien chromosome of <it>S</it>. <it>arvensis</it>. 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.</p> <p>Conclusions</p> <p>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 <it>Nsa</it> 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.</p> |
| first_indexed | 2024-12-19T05:05:41Z |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-19T05:05:41Z |
| publishDate | 2013-01-01 |
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| series | BMC Genomics |
| spelling | doaj.art-3d839ec808f14f4387684f3f101c85202022-12-21T20:34:56ZengBMCBMC Genomics1471-21642013-01-011412610.1186/1471-2164-14-26Transcriptome 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 <it>Nsa</it> CMS line in <it>Brassica napus</it>Yan XiaohongDong CaihuaYu JingyinLiu WanghuiJiang ChenghongLiu JiaHu QiongFang XiaopingWei Wenhui<p>Abstract</p> <p>Background</p> <p>The fertile and sterile plants were derived from the self-pollinated offspring of the F<sub>1</sub> hybrid between the novel restorer line NR1 and the <it>Nsa</it> CMS line in <it>Brassica napus</it>. To elucidate gene expression and regulation caused by the A and C subgenomes of <it>B</it>. <it>napus</it>, as well as the alien chromosome and cytoplasm from <it>Sinapis arvensis</it> 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.</p> <p>Results</p> <p>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 <it>Brassica rapa</it> and those of <it>Brassica oleracea</it> as the reference sequences, respectively. In total, 3231 genes of <it>B</it>. <it>rapa</it> and 3371 genes of <it>B</it>. <it>oleracea</it> 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 <it>B</it>. <it>oleracea</it> nor to <it>B</it>. <it>rapa</it>, and these unique tags were presumed to arise basically from the added alien chromosome of <it>S</it>. <it>arvensis</it>. 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.</p> <p>Conclusions</p> <p>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 <it>Nsa</it> 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.</p>http://www.biomedcentral.com/1471-2164/14/26 |
| spellingShingle | Yan Xiaohong Dong Caihua Yu Jingyin Liu Wanghui Jiang Chenghong Liu Jia Hu Qiong Fang Xiaoping Wei Wenhui 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 <it>Nsa</it> CMS line in <it>Brassica napus</it> BMC Genomics |
| title | 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 <it>Nsa</it> CMS line in <it>Brassica napus</it> |
| title_full | 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 <it>Nsa</it> CMS line in <it>Brassica napus</it> |
| title_fullStr | 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 <it>Nsa</it> CMS line in <it>Brassica napus</it> |
| title_full_unstemmed | 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 <it>Nsa</it> CMS line in <it>Brassica napus</it> |
| title_short | 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 <it>Nsa</it> CMS line in <it>Brassica napus</it> |
| title_sort | 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 it nsa it cms line in it brassica napus it |
| url | http://www.biomedcentral.com/1471-2164/14/26 |
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