Transcriptome Analysis Reveals Novel Genes Potentially Involved in Tuberization in Potato
The formation and development of tubers, the primary edible and economic organ of potatoes, directly affect their yield and quality. The regulatory network and mechanism of tuberization have been preliminarily revealed in recent years, but plenty of relevant genes remain to be discovered. A few cand...
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| Format: | Article |
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MDPI AG
2024-03-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/13/6/795 |
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| author | Meihua Zhang Hongju Jian Lina Shang Ke Wang Shiqi Wen Zihan Li Rongrong Liu Lijun Jia Zhenlin Huang Dianqiu Lyu |
| author_facet | Meihua Zhang Hongju Jian Lina Shang Ke Wang Shiqi Wen Zihan Li Rongrong Liu Lijun Jia Zhenlin Huang Dianqiu Lyu |
| author_sort | Meihua Zhang |
| collection | DOAJ |
| description | The formation and development of tubers, the primary edible and economic organ of potatoes, directly affect their yield and quality. The regulatory network and mechanism of tuberization have been preliminarily revealed in recent years, but plenty of relevant genes remain to be discovered. A few candidate genes were provided due to the simplicity of sampling and result analysis of previous transcriptomes related to tuberization. We sequenced and thoroughly analyzed the transcriptomes of thirteen tissues from potato plants at the tuber proliferation phase to provide more reference information and gene resources. Among them, eight tissues were stolons and tubers at different developmental stages, which we focused on. Five critical periods of tuberization were selected to perform an analysis of differentially expressed genes (DEGs), according to the results of the tissue correlation. Compared with the unswollen stolons (Sto), 2751, 4897, 6635, and 9700 DEGs were detected in the slightly swollen stolons (Sto1), swollen stolons (Sto2), tubers of proliferation stage 1 (Tu1), and tubers of proliferation stage 4 (Tu4). A total of 854 transcription factors and 164 hormone pathway genes were identified in the DEGs. Furthermore, three co-expression networks associated with Sto–Sto1, Sto2–Tu1, and tubers of proliferation stages two to five (Tu2–Tu5) were built using the weighted gene co-expression network analysis (WGCNA). Thirty hub genes (HGs) and 30 hub transcription factors (HTFs) were screened and focalized in these networks. We found that five HGs were reported to regulate tuberization, and most of the remaining HGs and HTFs co-expressed with them. The orthologs of these HGs and HTFs were reported to regulate processes (e.g., flowering, cell division, hormone synthesis, metabolism and signal transduction, sucrose transport, and starch synthesis) that were also required for tuberization. Such results further support their potential to control tuberization. Our study provides insights and countless candidate genes of the regulatory network of tuberization, laying the foundation for further elucidating the genetic basis of tuber development. |
| first_indexed | 2024-04-24T17:53:30Z |
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| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-04-24T17:53:30Z |
| publishDate | 2024-03-01 |
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| series | Plants |
| spelling | doaj.art-0ba4906a85ba447d9f1d1c9cd4a8967a2024-03-27T14:00:40ZengMDPI AGPlants2223-77472024-03-0113679510.3390/plants13060795Transcriptome Analysis Reveals Novel Genes Potentially Involved in Tuberization in PotatoMeihua Zhang0Hongju Jian1Lina Shang2Ke Wang3Shiqi Wen4Zihan Li5Rongrong Liu6Lijun Jia7Zhenlin Huang8Dianqiu Lyu9Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, ChinaChongqing Agricultural Technical Extension Station, Chongqing 401121, ChinaIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, ChinaThe formation and development of tubers, the primary edible and economic organ of potatoes, directly affect their yield and quality. The regulatory network and mechanism of tuberization have been preliminarily revealed in recent years, but plenty of relevant genes remain to be discovered. A few candidate genes were provided due to the simplicity of sampling and result analysis of previous transcriptomes related to tuberization. We sequenced and thoroughly analyzed the transcriptomes of thirteen tissues from potato plants at the tuber proliferation phase to provide more reference information and gene resources. Among them, eight tissues were stolons and tubers at different developmental stages, which we focused on. Five critical periods of tuberization were selected to perform an analysis of differentially expressed genes (DEGs), according to the results of the tissue correlation. Compared with the unswollen stolons (Sto), 2751, 4897, 6635, and 9700 DEGs were detected in the slightly swollen stolons (Sto1), swollen stolons (Sto2), tubers of proliferation stage 1 (Tu1), and tubers of proliferation stage 4 (Tu4). A total of 854 transcription factors and 164 hormone pathway genes were identified in the DEGs. Furthermore, three co-expression networks associated with Sto–Sto1, Sto2–Tu1, and tubers of proliferation stages two to five (Tu2–Tu5) were built using the weighted gene co-expression network analysis (WGCNA). Thirty hub genes (HGs) and 30 hub transcription factors (HTFs) were screened and focalized in these networks. We found that five HGs were reported to regulate tuberization, and most of the remaining HGs and HTFs co-expressed with them. The orthologs of these HGs and HTFs were reported to regulate processes (e.g., flowering, cell division, hormone synthesis, metabolism and signal transduction, sucrose transport, and starch synthesis) that were also required for tuberization. Such results further support their potential to control tuberization. Our study provides insights and countless candidate genes of the regulatory network of tuberization, laying the foundation for further elucidating the genetic basis of tuber development.https://www.mdpi.com/2223-7747/13/6/795potatotranscriptome sequencingtuberizationWGCNAnetwork |
| spellingShingle | Meihua Zhang Hongju Jian Lina Shang Ke Wang Shiqi Wen Zihan Li Rongrong Liu Lijun Jia Zhenlin Huang Dianqiu Lyu Transcriptome Analysis Reveals Novel Genes Potentially Involved in Tuberization in Potato Plants potato transcriptome sequencing tuberization WGCNA network |
| title | Transcriptome Analysis Reveals Novel Genes Potentially Involved in Tuberization in Potato |
| title_full | Transcriptome Analysis Reveals Novel Genes Potentially Involved in Tuberization in Potato |
| title_fullStr | Transcriptome Analysis Reveals Novel Genes Potentially Involved in Tuberization in Potato |
| title_full_unstemmed | Transcriptome Analysis Reveals Novel Genes Potentially Involved in Tuberization in Potato |
| title_short | Transcriptome Analysis Reveals Novel Genes Potentially Involved in Tuberization in Potato |
| title_sort | transcriptome analysis reveals novel genes potentially involved in tuberization in potato |
| topic | potato transcriptome sequencing tuberization WGCNA network |
| url | https://www.mdpi.com/2223-7747/13/6/795 |
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