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Zhang L, Jiang G, Wang X, Bai Y, Zhang P, Liu J, Li L, Huang L, Qin P. Identifying Core Genes Related to Low-Temperature Stress Resistance in Quinoa Seedlings Based on WGCNA. Int J Mol Sci 2024; 25:6885. [PMID: 38999994 DOI: 10.3390/ijms25136885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024] Open
Abstract
Quinoa is a nutritious crop that is tolerant to extreme environmental conditions; however, low-temperature stress can affect quinoa growth, development, and quality. Considering the lack of molecular research on quinoa seedlings under low-temperature stress, we utilized a Weighted Gene Co-Expression Network Analysis to construct weighted gene co-expression networks associated with physiological indices and metabolites related to low-temperature stress resistance based on transcriptomic data. We screened 11 co-expression modules closely related to low-temperature stress resistance and selected 12 core genes from the two modules that showed the highest associations with the target traits. Following the functional annotation of these genes to determine the key biological processes and metabolic pathways involved in low-temperature stress, we identified four important transcription factors involved in resistance to low-temperature stress: gene-LOC110731664, gene-LOC110736639, gene-LOC110684437, and gene-LOC110720903. These results provide insights into the molecular genetic mechanism of quinoa under low-temperature stress and can be used to breed lines with tolerance to low-temperature stress.
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Affiliation(s)
- Lingyuan Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Guofei Jiang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Xuqin Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Yutao Bai
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Li Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Liubin Huang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
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Cun Z, Zhang JY, Hong J, Yang J, Gao LL, Hao B, Chen JW. Integrated metabolome and transcriptome analysis reveals the regulatory mechanism of low nitrogen-driven biosynthesis of saponins and flavonoids in Panax notoginseng. Gene 2024; 901:148163. [PMID: 38224922 DOI: 10.1016/j.gene.2024.148163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/30/2023] [Accepted: 01/11/2024] [Indexed: 01/17/2024]
Abstract
BACKGROUND Nitrogen (N) is an important macronutrient involved in the biosynthesis of primary and secondary metabolites in plants. However, the metabolic regulatory mechanism of low-N-induced triterpenoid saponin and flavonoid accumulation in rhizomatous medicinal Panax notoginseng (Burk.) F. H. Chen remains unclear. METHODS To explore the potential regulatory mechanism and metabolic basis controlling the response of P. notoginseng to N deficiency, the transcriptome and metabolome were analysed in the roots. RESULTS The N content was significantly reduced in roots of N0-treated P. notoginseng (0 kg·N·667 m-2). The C/N ratio was enhanced in the N-deficient P. notoginseng. N deficiency promotes the accumulation of amino acids (L-proline, L-leucine, L-isoleucine, L-norleucine, L-arginine, and L-citrulline) and sugar (arabinose, xylose, glucose, fructose, and mannose), thus providing precursor metabolites for the biosynthesis of flavonoids and triterpenoid saponins. Downregulation of key structural genes (PAL, PAL3, ACC1, CHS2, PPO, CHI3, F3H, DFR, and FGT), in particular with the key genes of F3H, involved in the flavonoid biosynthesis pathway possibly induced the decrease in flavonoid content with increased N supply. Notoginsenoside R1, ginsenoside Re, Rg1, Rd, F1, R1 + Rg1 + Rb1 and total triterpenoid saponins were enhanced in the N0 groups than in the N15 (15 kg·N·667 m-2) plants. Higher phosphoenolpyruvate (an intermediate of glycolyticwith pathway metabolism) and serine (an intermediate of photorespiration) levels induced by N deficiency possibly promote saponin biosynthesis through mevalonic acid (MVA) and methylerythritol (MEP) pathways. Genes (MVD2, HMGS, HMGR1, HMGR2, DXR, and HMGR1) encoding the primary enzymes HMGS, HMGR, DXR, and MVD in the MVA and MEP pathways were significantly upregulated in the N0-treated P. notoginseng. The saponin biosynthesis genes DDS, DDS, CYP716A52, CYP716A47, UGT74AE2, and FPS were upregulated in the N-deficient plants. Upregulation of genes involved in saponin biosynthesis promotes the accumulation of triterpenoid saponins in the N0-grown P. notoginseng. CONCLUSIONS N deficiency enhances primary metabolisms, such as amino acids and sugar accumulation, laying the foundation for the synthesis of flavonoids and triterpenoid saponins in P. notoginseng. F3H, DDS, FPS, HMGR, HMGS and UGT74AE2 can be considered as candidates for functional characterisation of the N-regulated accumulation of triterpenoid saponins and flavonoids in future.
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Affiliation(s)
- Zhu Cun
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China; Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jin-Yan Zhang
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China; Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jie Hong
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China; Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jing Yang
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China; Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Li-Lin Gao
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China; Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China
| | - Bing Hao
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China; Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China.
| | - Jun-Wen Chen
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China; Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, 650201, China.
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Cheng T, Zhou X, Lin J, Zhou X, Wang H, Chen T. Transcriptomic and Metabolomic Analyses Reveal the Response Mechanism of Ophiopogon japonicus to Waterlogging Stress. BIOLOGY 2024; 13:197. [PMID: 38534466 DOI: 10.3390/biology13030197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Ophiopogon japonicus, a plant that thrives in river alluvial dams, often faces waterlogging stress due to sustained rainfall and flood seasons, which significantly impacts its growth and development. Currently, the mechanisms of waterlogging tolerance in Ophiopogon japonicus are still unclear. This study analyzed the transcriptome and metabolome data for Ophiopogon japonicus in the Sichuan region (referred to as CMD) under varying degrees of waterlogging stress: mild, moderate, and severe. The results indicate that the group exposed to flooding stress exhibited a higher number of differentially expressed genes (DEGs) compared to the control group. Notably, most DEGs were downregulated and primarily enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction pathways. A total of 5151 differentially accumulated metabolites (DAMs) were identified, with significantly upregulated DAMs annotated to two clusters, namely flavonoids such as apiin, pelargonin, and others. Furthermore, our study revealed significant upregulation in the expression of C2H2 (C2H2 zinc finger proteins) and AP2/ERF-ERF (the subfamily ERF proteins of APETALA2/ethylene-responsive element binding factors) transcription factors in CMD under flooding stress, suggesting their critical roles in enabling CMD to adapt to these conditions. In conclusion, this research provides insights into the intricate molecular mechanisms underlying CMD's response to flooding stress and reports valuable genetic data for the development of transgenic plants with improved waterlogging tolerance.
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Affiliation(s)
- Tingting Cheng
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Xia Zhou
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Juan Lin
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Xianjian Zhou
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Hongsu Wang
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Tiezhu Chen
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
- Sichuan Provincial Key Laboratory of Quality and Innovation Research of Chinese Materia Medica, Chengdu 610041, China
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Li H, Wang Q, Huang T, Liu J, Zhang P, Li L, Xie H, Wang H, Liu C, Qin P. Transcriptome and Metabolome Analyses Reveal Mechanisms Underlying the Response of Quinoa Seedlings to Nitrogen Fertilizers. Int J Mol Sci 2023; 24:11580. [PMID: 37511340 PMCID: PMC10380953 DOI: 10.3390/ijms241411580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/09/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Quinoa (Chenopodium quinoa Willd.) is a dicotyledonous annual amaranth herb that belongs to the family Chenopodiaceae. Quinoa can be cultivated across a wide range of climatic conditions. With regard to its cultivation, nitrogen-based fertilizers have a demonstrable effect on the growth and development of quinoa. How crops respond to the application of nitrogen affects grain quality and yield. Therefore, to explore the regulatory mechanisms that underlie the responses of quinoa seedlings to the application of nitrogen, we selected two varieties (i.e., Dianli-1299 and Dianli-71) of quinoa seedlings and analyzed them using metabolomic and transcriptomic techniques. Specifically, we studied the mechanisms underlying the responses of quinoa seedlings to varying concentrations of nitrogen by analyzing the dynamics of metabolites and genes involved in arginine biosynthesis; carbon fixation; and alanine, aspartate, and glutamate biosynthetic pathways. Overall, we found that differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) of quinoa are affected by the concentration of nitrogen. We detected 1057 metabolites, and 29,012 genes were annotated for the KEGG. We also found that 15 DEMs and 8 DEGs were key determinants of the differences observed in quinoa seedlings under different nitrogen concentrations. These contribute toward a deeper understanding of the metabolic processes of plants under different nitrogen treatments and provide a theoretical basis for improving the nitrogen use efficiency (NUE) of quinoa.
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Affiliation(s)
- Hanxue Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Qianchao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Tingzhi Huang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Li Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Heng Xie
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Hongxin Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Chenghong Liu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
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