|
1
|
Momo J, Islam K, Biswas S, Rawoof A, Ahmad I, Vishesh, Ramchiary N. Multi-omics analysis of non-pungent ( Capsicum annuum) and fiery hot ghost chili ( C. chinense) provides insights into proteins involved in fruit development and metabolites biosynthesis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2025; 31:453-475. [PMID: 40256276 PMCID: PMC12006620 DOI: 10.1007/s12298-025-01581-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 03/19/2025] [Accepted: 03/21/2025] [Indexed: 04/22/2025]
Abstract
Global omics offer extensive insights into the diversity of essential biomolecules across various plant developmental stages. Despite advancements in high-throughput technologies, the integrated analysis of global omics such as proteomics, transcriptomics, and metabolomics, is yet to be fully explored in fruits of Capsicum species. In this study, we used an integrated omics approach to identify proteins involved in fruit development, and metabolite biosynthesis in the placenta and pericarp tissues of two contrasting genotypes belonging to ghost chili (Capsicum chinense) and C. annuum. The mass spectrometry analysis identified a total of 4,473 and 2,012 proteins from the pericarp and placenta tissues of Capsicum fruits. We observed expression of developmental stage-specific proteins, such as kinases, transferases, ion transporters, F-box proteins, and transcription factors that were enriched in the biosynthesis of primary and secondary metabolites. The abundance of these proteins corresponded with RNAseq data. Key proteins related to capsaicinoids biosynthesis, such as Acyltransferase 3, 3-oxoacyl-[acyl-carrier protein], 4-coumaroyl co-A ligase, and 3-ketoacyl-coA synthase 3, were identified in placenta of highly pungent ghost chili, along with J-domain proteins and transcription factors such as MYB101, MYB 14-like, bHLH112, NAC, and Cyt p450 CYP82D47, suggesting their role in capsaicinoids and secondary metabolites biosynthesis. Further, we observed a correlation of the expression of genes and proteins with the abundance of primary and secondary metabolites, such as carbohydrates, alcohols, fatty acids, phenolics, glycerides, polyamines, and amino acids. Our findings provide a novel multiomics resources for future functional studies, with potential applications in breeding programs. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s12298-025-01581-7.
Collapse
Affiliation(s)
- John Momo
- School of Life Science, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Khushbu Islam
- School of Life Science, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Souparna Biswas
- School of Life Science, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Abdul Rawoof
- Department of Biological Sciences and Biodiscovery Institute, University of North Texas, Denton, TX USA
| | - Ilyas Ahmad
- Department of Plant Sciences, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, 82072 USA
| | - Vishesh
- School of Life Science, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Nirala Ramchiary
- School of Life Science, Jawaharlal Nehru University, New Delhi, 110067 India
| |
Collapse
|
|
2
|
Yang Y, Gao C, Ye Q, Liu C, Wan H, Ruan M, Zhou G, Wang R, Li Z, Diao M, Cheng Y. The Influence of Different Factors on the Metabolism of Capsaicinoids in Pepper ( Capsicum annuum L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:2887. [PMID: 39458834 PMCID: PMC11511365 DOI: 10.3390/plants13202887] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 10/11/2024] [Accepted: 10/14/2024] [Indexed: 10/28/2024]
Abstract
Pepper is a globally cultivated vegetable known for its distinct pungent flavor, which is derived from the presence of capsaicinoids, a class of unique secondary metabolites that accumulate specifically in pepper fruits. Since the accumulation of capsaicinoids is influenced by various factors, it is imperative to comprehend the metabolic regulatory mechanisms governing capsaicinoids production. This review offers a thorough examination of the factors that govern the metabolism of capsaicinoids in pepper fruit, with a specific focus on three primary facets: (1) the impact of genotype and developmental stage on capsaicinoids metabolism, (2) the influence of environmental factors on capsaicinoids metabolism, and (3) exogenous substances like methyl jasmonate, chlorophenoxyacetic acid, gibberellic acid, and salicylic acid regulate capsaicinoid metabolism. The findings of this study are expected to enhance comprehension of capsaicinoids metabolism and aid in the improvement of breeding and cultivation practices for high-quality pepper in the future.
Collapse
Affiliation(s)
- Yuanling Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.G.); (Q.Y.); (C.L.); (H.W.); (M.R.); (G.Z.); (R.W.); (Z.L.)
- College of Agriculture, Shihezi University, Shihezi 832003, China
| | - Chengan Gao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.G.); (Q.Y.); (C.L.); (H.W.); (M.R.); (G.Z.); (R.W.); (Z.L.)
- College of Horticultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Qingjing Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.G.); (Q.Y.); (C.L.); (H.W.); (M.R.); (G.Z.); (R.W.); (Z.L.)
| | - Chenxu Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.G.); (Q.Y.); (C.L.); (H.W.); (M.R.); (G.Z.); (R.W.); (Z.L.)
| | - Hongjian Wan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.G.); (Q.Y.); (C.L.); (H.W.); (M.R.); (G.Z.); (R.W.); (Z.L.)
| | - Meiying Ruan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.G.); (Q.Y.); (C.L.); (H.W.); (M.R.); (G.Z.); (R.W.); (Z.L.)
| | - Guozhi Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.G.); (Q.Y.); (C.L.); (H.W.); (M.R.); (G.Z.); (R.W.); (Z.L.)
| | - Rongqing Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.G.); (Q.Y.); (C.L.); (H.W.); (M.R.); (G.Z.); (R.W.); (Z.L.)
| | - Zhimiao Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.G.); (Q.Y.); (C.L.); (H.W.); (M.R.); (G.Z.); (R.W.); (Z.L.)
| | - Ming Diao
- College of Agriculture, Shihezi University, Shihezi 832003, China
| | - Yuan Cheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.Y.); (C.G.); (Q.Y.); (C.L.); (H.W.); (M.R.); (G.Z.); (R.W.); (Z.L.)
| |
Collapse
|
|
3
|
Liu W, He G, Deng XW. Toward understanding and utilizing crop heterosis in the age of biotechnology. iScience 2024; 27:108901. [PMID: 38533455 PMCID: PMC10964264 DOI: 10.1016/j.isci.2024.108901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Heterosis, a universal phenomenon in nature, mainly reflected in the superior productivity, quality, and fitness of F1 hybrids compared with their inbred parents, has been exploited in agriculture and greatly benefited human society in terms of food security. However, the flexible and efficient utilization of heterosis has remained a challenge in hybrid breeding systems because of the limitations of "three-line" and "two-line" methods. In the past two decades, rapidly developed biotechnologies have provided unprecedented conveniences for both understanding and utilizing heterosis. Notably, "third-generation" (3G) hybrid breeding technology together with high-throughput sequencing and gene editing greatly promoted the efficiency of hybrid breeding. Here, we review emerging ideas about the genetic or molecular mechanisms of heterosis and the development of 3G hybrid breeding system in the age of biotechnology. In addition, we summarized opportunities and challenges for optimal heterosis utilization in the future.
Collapse
Affiliation(s)
- Wenwen Liu
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| | - Guangming He
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| |
Collapse
|
|
4
|
Wang P, Li Y, Liu Z, Zhang W, Li D, Wang X, Wen X, Feng Y, Zhang X. Analysis of DNA Methylation Differences during the JIII Formation of Bursaphelenchus xylophilus. Curr Issues Mol Biol 2023; 45:9656-9673. [PMID: 38132449 PMCID: PMC10742416 DOI: 10.3390/cimb45120603] [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: 11/13/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
DNA methylation is a pivotal process that regulates gene expression and facilitates rapid adaptation to challenging environments. The pinewood nematode (PWN; Bursaphelenchus xylophilus), the causative agent of pine wilt disease, survives at low temperatures through third-stage dispersal juvenile, making it a major pathogen for pines in Asia. To comprehend the impact of DNA methylation on the formation and environmental adaptation of third-stage dispersal juvenile, we conducted whole-genome bisulfite sequencing and transcriptional sequencing on both the third-stage dispersal juvenile and three other propagative juvenile stages of PWN. Our findings revealed that the average methylation rate of cytosine in the samples ranged from 0.89% to 0.99%. Moreover, we observed significant DNA methylation changes in the third-stage dispersal juvenile and the second-stage propagative juvenile of PWN, including differentially methylated cytosine (DMCs, n = 435) and regions (DMRs, n = 72). In the joint analysis of methylation-associated transcription, we observed that 23 genes exhibited overlap between differentially methylated regions and differential gene expression during the formation of the third-stage dispersal juvenile of PWN. Further functional analysis of these genes revealed enrichment in processes related to lipid metabolism and fatty acid synthesis. These findings emphasize the significance of DNA methylation in the development of third-stage dispersal juvenile of PWN, as it regulates transcription to enhance the probability of rapid expansion in PWN.
Collapse
Affiliation(s)
- Peng Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (P.W.); (Z.L.); (W.Z.); (D.L.); (X.W.); (X.W.); (Y.F.); (X.Z.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yongxia Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (P.W.); (Z.L.); (W.Z.); (D.L.); (X.W.); (X.W.); (Y.F.); (X.Z.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Zhenkai Liu
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (P.W.); (Z.L.); (W.Z.); (D.L.); (X.W.); (X.W.); (Y.F.); (X.Z.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (P.W.); (Z.L.); (W.Z.); (D.L.); (X.W.); (X.W.); (Y.F.); (X.Z.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Dongzhen Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (P.W.); (Z.L.); (W.Z.); (D.L.); (X.W.); (X.W.); (Y.F.); (X.Z.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xuan Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (P.W.); (Z.L.); (W.Z.); (D.L.); (X.W.); (X.W.); (Y.F.); (X.Z.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiaojian Wen
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (P.W.); (Z.L.); (W.Z.); (D.L.); (X.W.); (X.W.); (Y.F.); (X.Z.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yuqian Feng
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (P.W.); (Z.L.); (W.Z.); (D.L.); (X.W.); (X.W.); (Y.F.); (X.Z.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xingyao Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (P.W.); (Z.L.); (W.Z.); (D.L.); (X.W.); (X.W.); (Y.F.); (X.Z.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| |
Collapse
|
|
5
|
Ahmad I, Rawoof A, Islam K, Momo J, Anju T, Kumar A, Ramchiary N. Diversity and expression analysis of ZIP transporters and associated metabolites under zinc and iron stress in Capsicum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:415-430. [PMID: 36758289 DOI: 10.1016/j.plaphy.2023.01.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/16/2022] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
The members of ZRT, IRT-like protein (ZIP) family are involved in the uptake and transportation of several metal ions. Here, we report a comprehensive identification of ZIP transporter genes from Capsicum annuum, C. chinense, and C. baccatum, and their expression analysis under Zn and Fe stress. Changes in root morphology and differential accumulation of several metabolites from sugars, amino acids, carboxylic acids, and fatty acids in root and leaf tissues of plants in the absence of Zn and Fe were observed. Further, metabolites such as L-aspartic acid, 2-ketoglutaric acids, β-L-fucopyranose, quininic acid, chlorogenic acid, and aucubin were significantly upregulated in root and leaf tissues under Zn/Fe deprived conditions. qRT-PCR analysis of 17 CaZIPs in different tissues revealed tissue-specific expression of CaZIP1-2, CaZIP4-8, CaZIP13, and CaZIP16-17 under normal conditions. However, the absence of Zn and Fe significantly induced the expression of CaZIP4-5, CaZIP7-9, and CaZIP14 genes in root and leaf tissues. Additionally, in the absence of Fe, upregulation of CaZIP4-5 and CaZIP8 and increased uptake of mineral elements Cu, Zn, Mg, P, and S were observed in roots, suggesting their potential role in metal-ion uptake in Capsicum. The identified genes provide the basis for future studies of mineral uptake and their biofortification to increase the nutritional values in Capsicum.
Collapse
Affiliation(s)
- Ilyas Ahmad
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Abdul Rawoof
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Khushbu Islam
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - John Momo
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Thattantavide Anju
- Department of Plant Science, School of Biological Sciences, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - Ajay Kumar
- Department of Plant Science, School of Biological Sciences, Central University of Kerala, Kasaragod, 671316, Kerala, India
| | - Nirala Ramchiary
- Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|