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Sajjad M, Xue S, Zhou M, Li G, Xu Y, Liu L, Zhu J, Meng Q, Jin Q, Du H, Yao C, Zhong Y. Decoding comparative taste and nutrition regulation in Chinese cabbage via integrated metabolome and transcriptome analysis. Food Res Int 2024; 195:114943. [PMID: 39277221 DOI: 10.1016/j.foodres.2024.114943] [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: 05/22/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/17/2024]
Abstract
Chinese cabbage (Brassica rapa L. ssp. pekinensis) is a widely consumed leafy vegetable known for its various health-beneficial nutrients. Caixin (ET and JY) represent distinct cultivars of Chinese cabbage that exhibit differential consumer preference attributed to variations in taste and nutritional content, with ET being characterized as sweeter and more nutritionally superior compared to JY. However, limited research has been conducted to explore regulation of flavor and nutrition-related quality traits in Chinese cabbage. In this pioneer study, comprehensive trans-meta-analysis was used to compare the metabolic and molecular underpinnings behind unique taste and nutritional profiles of ET and JY. 8-Methylsulfonyloctyl glucosinolates and Uridine 5'-diphospho-D-glucose exhibited the highest correlation coefficient in Pearson meta-meta-association, which modulate flavor and nutrition processes. While DAMs primarily featured L-Homomethionine, saccharic acid, 1,6-Di-O-caffeoyl-β-D-glucose, and Rutin, with notable variations in expression between ET and JY. Conspicuously, DEGs encoding structural enzymes i.e. Glucosinolates (MAM, CYP, UGT), flavonoids (CHS, CHI, F3H) and sucrose (SPS, SPP, SUS) synthases were identified as key players in nutrient and flavor production. Multi-omics conjoint analysis revealed that saccharides, amino acids, ascorbates, flavonoids, organic acids and vitamins were positively correlated with taste and nutrition, and were found to be overexpressed in ET. While aliphatic glucosinolates were abundant in JY compared to ET, they might play a critical role in regulating quality traits. Besides, HPLC and RT-qPCR corroborated multi-omics data reliability. These findings offer novel insights into the mechanisms governing the regulation of taste and nutritional levels in Chinese cabbage.
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Affiliation(s)
- Muhammad Sajjad
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Shudan Xue
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Meijiang Zhou
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Guihua Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Yingchao Xu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Ling Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Jitong Zhu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Qitao Meng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Qingmin Jin
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Hu Du
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Chunpeng Yao
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China
| | - Yujuan Zhong
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, PR China.
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Li XH, Kang XJ, Zhang XY, Su LN, Bi X, Wang RL, Xing SY, Sun LM. Formation mechanism and regulation analysis of trumpet leaf in Ginkgo biloba L. FRONTIERS IN PLANT SCIENCE 2024; 15:1367121. [PMID: 39086912 PMCID: PMC11288918 DOI: 10.3389/fpls.2024.1367121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/24/2024] [Indexed: 08/02/2024]
Abstract
Introduction The research on plant leaf morphology is of great significance for understanding the development and evolution of plant organ morphology. As a relict plant, the G. biloba leaf morphology typically exhibits bifoliate and peltate forms. However, throughout its long evolutionary history, Ginkgo leaves have undergone diverse changes. Methods This study focuses on the distinct "trumpet" leaves and normal fan-shaped leaves of G. biloba for analysis of their phenotypes, photosynthetic activity, anatomical observations, as well as transcriptomic and metabolomic analyses. Results The results showed that trumpet-shaped G. biloba leaves have fewer cells, significant morphological differences between dorsal and abaxial epidermal cells, leading to a significantly lower net photosynthetic rate. Additionally, this study found that endogenous plant hormones such as GA, auxin, and JA as well as metabolites such as flavonoids and phenolic acids play roles in the formation of trumpet-shaped G. biloba leaves. Moreover, the experiments revealed the regulatory mechanisms of various key biological processes and gene expressions in the trumpet-shaped leaves of G. biloba. Discussion Differences in the dorsal and abdominal cells of G. biloba leaves can cause the leaf to curl, thus reducing the overall photosynthetic efficiency of the leaves. However, the morphology of plant leaves is determined during the primordia leaf stage. In the early stages of leaf development, the shoot apical meristem (SAM) determines the developmental morphology of dicotyledonous plant leaves. This process involves the activity of multiple gene families and small RNAs. The establishment of leaf morphology is complexly regulated by various endogenous hormones, including the effect of auxin on cell walls. Additionally, changes in intracellular ion concentrations, such as fluctuations in Ca2+ concentration, also affect cell wall rigidity, thereby influencing leaf growth morphology.
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Affiliation(s)
- Xin-hui Li
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Forestry College of Shandong Agricultural University, Tai’an, Shandong, China
| | - Xiao-jing Kang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Forestry College of Shandong Agricultural University, Tai’an, Shandong, China
| | - Xin-yue Zhang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Forestry College of Shandong Agricultural University, Tai’an, Shandong, China
| | - Li-ning Su
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Forestry College of Shandong Agricultural University, Tai’an, Shandong, China
| | - Xing Bi
- Department of Publicity, The Second Affiliated Hospital of Shandong First Medical University, Tai’an, Shandong, China
| | - Rui-long Wang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Forestry College of Shandong Agricultural University, Tai’an, Shandong, China
| | - Shi-yan Xing
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Forestry College of Shandong Agricultural University, Tai’an, Shandong, China
| | - Li-min Sun
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Forestry College of Shandong Agricultural University, Tai’an, Shandong, China
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Lv B, Li Y, Wu X, Zhu C, Cao Y, Duan Q, Huang J. Brassica rapa Nitrate Transporter 2 ( BrNRT2) Family Genes, Identification, and Their Potential Functions in Abiotic Stress Tolerance. Genes (Basel) 2023; 14:1564. [PMID: 37628616 PMCID: PMC10454591 DOI: 10.3390/genes14081564] [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: 06/19/2023] [Revised: 07/23/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Nitrate transporter 2 (NRT2) proteins play vital roles in both nitrate (NO3-) uptake and translocation as well as abiotic stress responses in plants. However, little is known about the NRT2 gene family in Brassica rapa. In this study, 14 NRT2s were identified in the B. rapa genome. The BrNRT2 family members contain the PLN00028 and MATE_like superfamily domains. Cis-element analysis indicated that regulatory elements related to stress responses are abundant in the promoter sequences of BrNRT2 genes. BrNRT2.3 expression was increased after drought stress, and BrNRT2.1 and BrNRT2.8 expression were significantly upregulated after salt stress. Furthermore, protein interaction predictions suggested that homologs of BrNRT2.3, BrNRT2.1, and BrNRT2.8 in Arabidopsis thaliana may interact with the known stress-regulating proteins AtNRT1.1, AtNRT1.5, and AtNRT1.8. In conclusion, we suggest that BrNRT2.1, BrNRT2.3, and BrNRT2.8 have the greatest potential for inducing abiotic stress tolerance. Our findings will aid future studies of the biological functions of BrNRT2 family genes.
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Affiliation(s)
| | | | | | | | | | | | - Jiabao Huang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271000, China
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Comparative Metabolomic Studies of Siberian Wildrye ( Elymus sibiricus L.): A New Look at the Mechanism of Plant Drought Resistance. Int J Mol Sci 2022; 24:ijms24010452. [PMID: 36613896 PMCID: PMC9820681 DOI: 10.3390/ijms24010452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Drought is one of the most important factors affecting plant growth and production due to ongoing global climate change. Elymus sibiricus has been widely applied for ecological restoration and reseeding of degraded grassland in the Qinghai-Tibetan Plateau (QTP) because of its strong adaptability to barren, salted, and drought soils. To explore the mechanism of drought resistance in E. sibiricus, drought-tolerant and drought-sensitive genotypes of E. sibiricus were used in metabolomic studies under simulated long-term and short-term drought stress. A total of 1091 metabolites were detected, among which, 27 DMs were considered to be the key metabolites for drought resistance of E. sibiricus in weighted gene co-expression network analysis (WGCNA). Ten metabolites, including 3-amino-2-methylpropanoic acid, coniferin, R-aminobutyrate, and so on, and 12 metabolites, including L-Proline, L-histidine, N-acetylglycine, and so on, showed differential accumulation patterns under short-term and long-term drought stress, respectively, and thus, could be used as biomarkers for drought-tolerant and drought-sensitive E. sibiricus. In addition, different metabolic accumulation patterns and different drought response mechanisms were also found in drought-tolerant and drought-sensitive genotypes of E. sibiricus. Finally, we constructed metabolic pathways and metabolic patterns for the two genotypes. This metabolomic study on the drought stress response of E. sibiricus can provide resources and a reference for the breeding of new drought-tolerant cultivars of E. sibiricus.
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Wang J, Li Y, Wang Y, Du F, Zhang Y, Yin M, Zhao X, Xu J, Yang Y, Wang W, Fu B. Transcriptome and Metabolome Analyses Reveal Complex Molecular Mechanisms Involved in the Salt Tolerance of Rice Induced by Exogenous Allantoin. Antioxidants (Basel) 2022; 11:antiox11102045. [PMID: 36290768 PMCID: PMC9598814 DOI: 10.3390/antiox11102045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Allantoin is crucial for plant growth and development as well as adaptations to abiotic stresses, but the underlying molecular mechanisms remain unclear. In this study, we comprehensively analyzed the physiological indices, transcriptomes, and metabolomes of rice seedlings following salt, allantoin, and salt + allantoin treatments. The results revealed that exogenous allantoin positively affects the salt tolerance by increasing the contents of endogenous allantoin with antioxidant activities, increasing the reactive oxygen species (ROS)–scavenging capacity, and maintaining sodium and potassium homeostasis. The transcriptome analysis detected the upregulated expression genes involved in ion transport and redox regulation as well as the downregulated expression of many salt-induced genes related to transcription and post-transcriptional regulation, carbohydrate metabolism, chromosome remodeling, and cell wall organization after the exogenous allantoin treatment of salt-stressed rice seedlings. Thus, allantoin may mitigate the adverse effects of salt stress on plant growth and development. Furthermore, a global metabolite analysis detected the accumulation of metabolites with antioxidant activities and intermediate products of the allantoin biosynthetic pathway in response to exogenous allantoin, implying allantoin enhances rice salt tolerance by inducing ROS scavenging cascades. These results have clarified the transcript-level and metabolic processes underlying the allantoin-mediated salt tolerance of rice.
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Affiliation(s)
- Juan Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Life Sciences, China Agricultural University, Beijing 100193, China
| | - Yingbo Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yinxiao Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fengping Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yue Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ming Yin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuqin Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongqing Yang
- College of Life Sciences, China Agricultural University, Beijing 100193, China
- Correspondence: (Y.Y.); (W.W.); (B.F.)
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
- Correspondence: (Y.Y.); (W.W.); (B.F.)
| | - Binying Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Correspondence: (Y.Y.); (W.W.); (B.F.)
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Zhao Y, Guo Q, Cao S, Tian Y, Han K, Sun Y, Li J, Yang Q, Ji Q, Sederoff R, Li Y. Genome-wide identification of the AlkB homologs gene family, PagALKBH9B and PagALKBH10B regulated salt stress response in Populus. FRONTIERS IN PLANT SCIENCE 2022; 13:994154. [PMID: 36204058 PMCID: PMC9530910 DOI: 10.3389/fpls.2022.994154] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
The AlkB homologs (ALKBH) gene family regulates N6-methyladenosine (m6A) RNA methylation and is involved in plant growth and the abiotic stress response. Poplar is an important model plant for studying perennial woody plants. Poplars typically have a long juvenile period of 7-10 years, requiring long periods of time for studies of flowering or mature wood properties. Consequently, functional studies of the ALKBH genes in Populus species have been limited. Based on AtALKBHs sequence similarity with Arabidopsis thaliana, 23 PagALKBHs were identified in the genome of the poplar 84K hybrid genotype (P. alba × P. tremula var. glandulosa), and gene structures and conserved domains were confirmed between homologs. The PagALKBH proteins were classified into six groups based on conserved sequence compared with human, Arabidopsis, maize, rice, wheat, tomato, barley, and grape. All homologs of PagALKBHs were tissue-specific; most were highly expressed in leaves. ALKBH9B and ALKBH10B are m6A demethylases and overexpression of their homologs PagALKBH9B and PagALKBH10B reduced m6A RNA methylation in transgenic lines. The number of adventitious roots and the biomass accumulation of transgenic lines decreased compared with WT. Therefore, PagALKBH9B and PagALKBH10B mediate m6A RNA demethylation and play a regulatory role in poplar growth and development. Overexpression of PagALKBH9B and PagALKBH10B can reduce the accumulation of H2O2 and oxidative damage by increasing the activities of SOD, POD, and CAT, and enhancing protection for Chl a/b, thereby increasing the salt tolerance of transgenic lines. However, overexpression lines were more sensitive to drought stress due to reduced proline content. This research revealed comprehensive information about the PagALKBH gene family and their roles in growth and development and responsing to salt stress of poplar.
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Affiliation(s)
- Ye Zhao
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Qi Guo
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Sen Cao
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Yanting Tian
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Kunjin Han
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Yuhan Sun
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Juan Li
- Natural Resources and Planning Bureau of Yanshan County, Cangzhou, Hebei, China
| | - Qingshan Yang
- Shandong Academy of Forestry, Jinan, Shandong, China
| | - Qingju Ji
- Cangzhou Municipal Forestry Seeding and Cutting Management Center, Cangzhou, China
| | - Ronald Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Yun Li
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, National Engineering Research Center of Tree Breeding and Ecological Restoration, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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