Identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysis
Strawberries are one of the most economically important berry fruits worldwide and exhibit colours ranging from white to dark red, providing a rich genetic resource for strawberry quality improvement. In the present study, we conducted transcriptome analyses of three strawberry cultivars, namely, ‘B...
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PeerJ Inc.
2021-02-01
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| Online Access: | https://peerj.com/articles/10739.pdf |
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| author | Fengli Zhao Pan Song Xiangfen Zhang Gang Li Panpan Hu Ali Aslam Xia Zhao Houcheng Zhou |
| author_facet | Fengli Zhao Pan Song Xiangfen Zhang Gang Li Panpan Hu Ali Aslam Xia Zhao Houcheng Zhou |
| author_sort | Fengli Zhao |
| collection | DOAJ |
| description | Strawberries are one of the most economically important berry fruits worldwide and exhibit colours ranging from white to dark red, providing a rich genetic resource for strawberry quality improvement. In the present study, we conducted transcriptome analyses of three strawberry cultivars, namely, ‘Benihoppe’, ‘Xiaobai’, and ‘Snow White’, and compared their gene expression profiles. Among the high-quality sequences, 5,049 and 53,200 differentially expressed genes (DEGs) were obtained when comparing the diploid and octoploid strawberry genomes and analysed to identify anthocyanin-related candidate genes. Sixty-five DEGs in the diploid genome (transcriptome data compared to the diploid strawberry genome) and 317 DEGs in the octoploid genome (transcriptome data compared to the octoploid strawberry genome) were identified among the three cultivars. Among these DEGs, 19 and 70 anthocyanin pathway genes, six and 42 sugar pathway genes, 23 and 101 hormone pathway genes, and 17 and 104 transcription factors in the diploid and octoploid genomes, respectively, correlated positively or negatively with the anthocyanin accumulation observed among the three cultivars. Real-time qPCR analysis of nine candidate genes showed a good correlation with the transcriptome data. For example, the expression of PAL was higher in ‘Benihoppe’ and ‘Xiaobai’ than in ‘Snow White’, consistent with the RNA-seq data. Thus, the RNA-seq data and candidate DEGs identified in the present study provide a sound basis for further studies of strawberry fruit colour formation. |
| first_indexed | 2024-03-09T07:22:59Z |
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| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:22:59Z |
| publishDate | 2021-02-01 |
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| spelling | doaj.art-8d31a78883cf46f69b3d06729fe379e12023-12-03T07:13:22ZengPeerJ Inc.PeerJ2167-83592021-02-019e1073910.7717/peerj.10739Identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysisFengli Zhao0Pan Song1Xiangfen Zhang2Gang Li3Panpan Hu4Ali Aslam5Xia Zhao6Houcheng Zhou7Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, ChinaZhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, ChinaZhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, ChinaZhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, ChinaZhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, ChinaZhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, ChinaZhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, ChinaZhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, ChinaStrawberries are one of the most economically important berry fruits worldwide and exhibit colours ranging from white to dark red, providing a rich genetic resource for strawberry quality improvement. In the present study, we conducted transcriptome analyses of three strawberry cultivars, namely, ‘Benihoppe’, ‘Xiaobai’, and ‘Snow White’, and compared their gene expression profiles. Among the high-quality sequences, 5,049 and 53,200 differentially expressed genes (DEGs) were obtained when comparing the diploid and octoploid strawberry genomes and analysed to identify anthocyanin-related candidate genes. Sixty-five DEGs in the diploid genome (transcriptome data compared to the diploid strawberry genome) and 317 DEGs in the octoploid genome (transcriptome data compared to the octoploid strawberry genome) were identified among the three cultivars. Among these DEGs, 19 and 70 anthocyanin pathway genes, six and 42 sugar pathway genes, 23 and 101 hormone pathway genes, and 17 and 104 transcription factors in the diploid and octoploid genomes, respectively, correlated positively or negatively with the anthocyanin accumulation observed among the three cultivars. Real-time qPCR analysis of nine candidate genes showed a good correlation with the transcriptome data. For example, the expression of PAL was higher in ‘Benihoppe’ and ‘Xiaobai’ than in ‘Snow White’, consistent with the RNA-seq data. Thus, the RNA-seq data and candidate DEGs identified in the present study provide a sound basis for further studies of strawberry fruit colour formation.https://peerj.com/articles/10739.pdfStrawberryTranscriptomeAnthocyaninSugarsPhytohormones |
| spellingShingle | Fengli Zhao Pan Song Xiangfen Zhang Gang Li Panpan Hu Ali Aslam Xia Zhao Houcheng Zhou Identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysis PeerJ Strawberry Transcriptome Anthocyanin Sugars Phytohormones |
| title | Identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysis |
| title_full | Identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysis |
| title_fullStr | Identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysis |
| title_full_unstemmed | Identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysis |
| title_short | Identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysis |
| title_sort | identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysis |
| topic | Strawberry Transcriptome Anthocyanin Sugars Phytohormones |
| url | https://peerj.com/articles/10739.pdf |
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