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Zhang M, Jian H, Shang L, Wang K, Wen S, Li Z, Liu R, Jia L, Huang Z, Lyu D. Transcriptome Analysis Reveals Novel Genes Potentially Involved in Tuberization in Potato. Plants (Basel) 2024; 13:795. [PMID: 38592791 PMCID: PMC10975680 DOI: 10.3390/plants13060795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
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.
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Affiliation(s)
- Meihua Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Hongju Jian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing 400715, China
| | - Lina Shang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Ke Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Shiqi Wen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Zihan Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Rongrong Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Lijun Jia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Zhenlin Huang
- Chongqing Agricultural Technical Extension Station, Chongqing 401121, China;
| | - Dianqiu Lyu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 401329, China; (M.Z.); (H.J.); (L.S.); (S.W.); (Z.L.); (R.L.); (L.J.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing 400715, China
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