Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed
Yellow seed coat color is a desirable characteristic in rapeseed (<i>Brassica napus</i>), 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 or...
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MDPI AG
2020-07-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/9/8/977 |
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| author | Ai Lin Jinqi Ma Fei Xu Wen Xu Huanhuan Jiang Haoran Zhang Cunmin Qu Lijuan Wei Jiana Li |
| author_facet | Ai Lin Jinqi Ma Fei Xu Wen Xu Huanhuan Jiang Haoran Zhang Cunmin Qu Lijuan Wei Jiana Li |
| author_sort | Ai Lin |
| collection | DOAJ |
| description | Yellow seed coat color is a desirable characteristic in rapeseed (<i>Brassica napus</i>), 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 <i>B. napus</i>, we compared 31 RNA-seq libraries of yellow- and black-seeded <i>B. napus</i> 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 <i>TT8</i> (<i>BnaC09g24870D</i>), <i>TT5</i> (<i>BnaA09g34840D</i> and <i>BnaC08g26020D</i>), <i>TT12</i> (<i>BnaC06g17050D</i> and <i>BnaA07g18120D</i>), <i>AHA10</i> (<i>BnaA08g23220D</i> and <i>BnaC08g17280D</i>), <i>CHI</i> (<i>BnaC09g50050D</i>), <i>BAN</i> (<i>BnaA03g60670D</i>) and <i>DFR</i> (<i>BnaC09g17150D</i>). Gene <i>BnaC03g23650D</i>, 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 <i>B. napus</i>. This study provides insight into the formation of seed coat color in <i>B. napus</i>. |
| first_indexed | 2024-03-10T18:02:49Z |
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| id | doaj.art-0e344c9a50c647a7a910257f26bcf721 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T18:02:49Z |
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| spelling | doaj.art-0e344c9a50c647a7a910257f26bcf7212023-11-20T08:43:03ZengMDPI AGPlants2223-77472020-07-019897710.3390/plants9080977Differences in Alternative Splicing between Yellow and Black-Seeded RapeseedAi Lin0Jinqi Ma1Fei Xu2Wen Xu3Huanhuan Jiang4Haoran Zhang5Cunmin Qu6Lijuan Wei7Jiana Li8Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, ChinaChongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, ChinaChongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, ChinaChongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, ChinaChongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, ChinaChongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, ChinaChongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, ChinaChongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, ChinaChongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, ChinaYellow seed coat color is a desirable characteristic in rapeseed (<i>Brassica napus</i>), 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 <i>B. napus</i>, we compared 31 RNA-seq libraries of yellow- and black-seeded <i>B. napus</i> 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 <i>TT8</i> (<i>BnaC09g24870D</i>), <i>TT5</i> (<i>BnaA09g34840D</i> and <i>BnaC08g26020D</i>), <i>TT12</i> (<i>BnaC06g17050D</i> and <i>BnaA07g18120D</i>), <i>AHA10</i> (<i>BnaA08g23220D</i> and <i>BnaC08g17280D</i>), <i>CHI</i> (<i>BnaC09g50050D</i>), <i>BAN</i> (<i>BnaA03g60670D</i>) and <i>DFR</i> (<i>BnaC09g17150D</i>). Gene <i>BnaC03g23650D</i>, 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 <i>B. napus</i>. This study provides insight into the formation of seed coat color in <i>B. napus</i>.https://www.mdpi.com/2223-7747/9/8/977alternative splicingRNA-seqWGCNAyellow seed<i>Brassica napus</i> |
| spellingShingle | Ai Lin Jinqi Ma Fei Xu Wen Xu Huanhuan Jiang Haoran Zhang Cunmin Qu Lijuan Wei Jiana Li Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed Plants alternative splicing RNA-seq WGCNA yellow seed <i>Brassica napus</i> |
| title | Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed |
| title_full | Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed |
| title_fullStr | Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed |
| title_full_unstemmed | Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed |
| title_short | Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed |
| title_sort | differences in alternative splicing between yellow and black seeded rapeseed |
| topic | alternative splicing RNA-seq WGCNA yellow seed <i>Brassica napus</i> |
| url | https://www.mdpi.com/2223-7747/9/8/977 |
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