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Yin B, Jia J, Sun X, Hu X, Ao M, Liu W, Tian Z, Liu H, Li D, Tian W, Hao Y, Xia X, Sade N, Brotman Y, Fernie AR, Chen J, He Z, Chen W. Dynamic metabolite QTL analyses provide novel biochemical insights into kernel development and nutritional quality improvement in common wheat. PLANT COMMUNICATIONS 2024; 5:100792. [PMID: 38173227 PMCID: PMC11121174 DOI: 10.1016/j.xplc.2024.100792] [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: 08/20/2023] [Revised: 12/20/2023] [Accepted: 01/01/2024] [Indexed: 01/05/2024]
Abstract
Despite recent advances in crop metabolomics, the genetic control and molecular basis of the wheat kernel metabolome at different developmental stages remain largely unknown. Here, we performed widely targeted metabolite profiling of kernels from three developmental stages (grain-filling kernels [FKs], mature kernels [MKs], and germinating kernels [GKs]) using a population of 159 recombinant inbred lines. We detected 625 annotated metabolites and mapped 3173, 3143, and 2644 metabolite quantitative trait loci (mQTLs) in FKs, MKs, and GKs, respectively. Only 52 mQTLs were mapped at all three stages, indicating the high stage specificity of the wheat kernel metabolome. Four candidate genes were functionally validated by in vitro enzymatic reactions and/or transgenic approaches in wheat, three of which mediated the tricin metabolic pathway. Metabolite flux efficiencies within the tricin pathway were evaluated, and superior candidate haplotypes were identified, comprehensively delineating the tricin metabolism pathway in wheat. Finally, additional wheat metabolic pathways were re-constructed by updating them to incorporate the 177 candidate genes identified in this study. Our work provides new information on variations in the wheat kernel metabolome and important molecular resources for improvement of wheat nutritional quality.
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Affiliation(s)
- Bo Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingqi Jia
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xu Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Min Ao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Wenfei Tian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanfeng Hao
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nir Sade
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yariv Brotman
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Yazhouwan National Laboratory, Sanya 572025, China.
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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Deng M, Zeng Q, Liu S, Jin M, Luo H, Luo J. Combining association with linkage mapping to dissect the phenolamides metabolism of the maize kernel. FRONTIERS IN PLANT SCIENCE 2024; 15:1376405. [PMID: 38681218 PMCID: PMC11047430 DOI: 10.3389/fpls.2024.1376405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Phenolamides are important secondary metabolites in plant species. They play important roles in plant defense responses against pathogens and insect herbivores, protection against UV irradiation and floral induction and development. However, the accumulation and variation in phenolamides content in diverse maize lines and the genes responsible for their biosynthesis remain largely unknown. Here, we combined genetic mapping, protein regulatory network and bioinformatics analysis to further enhance the understanding of maize phenolamides biosynthesis. Sixteen phenolamides were identified in multiple populations, and they were all significantly correlated with one or several of 19 phenotypic traits. By linkage mapping, 58, 58, 39 and 67 QTLs, with an average of 3.9, 3.6, 3.6 and 4.2 QTLs for each trait were mapped in BBE1, BBE2, ZYE1 and ZYE2, explaining 9.47%, 10.78%, 9.51% and 11.40% phenotypic variation for each QTL on average, respectively. By GWAS, 39 and 36 significant loci were detected in two different environments, 3.3 and 2.8 loci for each trait, explaining 10.00% and 9.97% phenotypic variation for each locus on average, respectively. Totally, 58 unique candidate genes were identified, 31% of them encoding enzymes involved in amine and derivative metabolic processes. Gene Ontology term analysis of the 358 protein-protein interrelated genes revealed significant enrichment in terms relating to cellular nitrogen metabolism, amine metabolism. GRMZM2G066142, GRMZM2G066049, GRMZM2G165390 and GRMZM2G159587 were further validated involvement in phenolamides biosynthesis. Our results provide insights into the genetic basis of phenolamides biosynthesis in maize kernels, understanding phenolamides biosynthesis and its nutritional content and ability to withstand biotic and abiotic stress.
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Affiliation(s)
- Min Deng
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Qingping Zeng
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Songqin Liu
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Min Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Hongbing Luo
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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Cao P, Yang J, Xia L, Zhang Z, Wu Z, Hao Y, Liu P, Wang C, Li C, Yang J, Lai J, Li X, Deng M, Wang S. Two gene clusters and their positive regulator SlMYB13 that have undergone domestication-associated negative selection control phenolamide accumulation and drought tolerance in tomato. MOLECULAR PLANT 2024; 17:579-597. [PMID: 38327054 DOI: 10.1016/j.molp.2024.02.003] [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: 08/22/2023] [Revised: 01/01/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Among plant metabolites, phenolamides, which are conjugates of hydroxycinnamic acid derivatives and polyamines, play important roles in plant adaptation to abiotic and biotic stresses. However, the molecular mechanisms underlying phenolamide metabolism and regulation as well as the effects of domestication and breeding on phenolamide diversity in tomato remain largely unclear. In this study, we performed a metabolite-based genome-wide association study and identified two biosynthetic gene clusters (BGC7 and BGC11) containing 12 genes involved in phenolamide metabolism, including four biosynthesis genes (two 4CL genes, one C3H gene, and one CPA gene), seven decoration genes (five AT genes and two UGT genes), and one transport protein gene (DTX29). Using gene co-expression network analysis we further discovered that SlMYB13 positively regulates the expression of two gene clusters, thereby promoting phenolamide accumulation. Genetic and physiological analyses showed that BGC7, BGC11 and SlMYB13 enhance drought tolerance by enhancing scavenging of reactive oxygen species and increasing abscisic acid content in tomato. Natural variation analysis suggested that BGC7, BGC11 and SlMYB13 were negatively selected during tomato domestication and improvement, leading to reduced phenolamide content and drought tolerance of cultivated tomato. Collectively, our study discovers a key mechanism of phenolamide biosynthesis and regulation in tomato and reveals that crop domestication and improvement shapes metabolic diversity to affect plant environmental adaptation.
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Affiliation(s)
- Peng Cao
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Haikou 572208, China
| | - Jun Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Haikou 572208, China.
| | - Linghao Xia
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China
| | - Zhonghui Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China
| | - Zeyong Wu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China
| | - Yingchen Hao
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China
| | - Penghui Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China
| | - Chao Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China
| | - Chun Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China
| | - Jie Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China
| | - Jun Lai
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China
| | - Xianggui Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China
| | - Meng Deng
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China
| | - Shouchuang Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; College of Tropical Agriculture and Forestry, Hainan University, Haikou 572208, China; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, Hainan University, Haikou 572208, China.
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Qiao J, Cai W, Wang K, Haubruge E, Dong J, El-Seedi HR, Xu X, Zhang H. New Insights into Identification, Distribution, and Health Benefits of Polyamines and Their Derivatives. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5089-5106. [PMID: 38416110 DOI: 10.1021/acs.jafc.3c08556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Polyamines and their derivatives are ubiquitously present in free or conjugated forms in various foods from animal, plant, and microbial origins. The current knowledge of free polyamines in foods and their contents is readily available; furthermore, conjugated polyamines generate considerable recent research interest due to their potential health benefits. The structural diversity of conjugated polyamines results in challenging their qualitative and quantitative analysis in food. Herein, we review and summarize the knowledge published on polyamines and their derivatives in foods, including their identification, sources, quantities, and health benefits. Particularly, facing the inherent challenges of isomer identification in conjugated polyamines, this paper provides a comprehensive overview of conjugated polyamines' structural characteristics, including the cleavage patterns and characteristic ion fragments of MS/MS for isomer identification. Free polyamines are present in all types of food, while conjugated polyamines are limited to plant-derived foods. Spermidine is renowned for antiaging properties, acclaimed as antiaging vitamins. Conjugated polyamines highlight their anti-inflammatory properties and have emerged as the mainstream drugs for antiprostatitis. This paper will likely help us gain better insight into polyamines and their derivatives to further develop functional foods and personalized nutraceuticals.
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Affiliation(s)
- Jiangtao Qiao
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
- Terra Research Center, Gembloux Agro-Bio Tech, University of Liege, Gembloux 5030, Belgium
| | - Wenwen Cai
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
- College of Food Engineering, Harbin University of Commerce, Harbin 155023, China
| | - Kai Wang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
- Terra Research Center, Gembloux Agro-Bio Tech, University of Liege, Gembloux 5030, Belgium
| | - Eric Haubruge
- Terra Research Center, Gembloux Agro-Bio Tech, University of Liege, Gembloux 5030, Belgium
| | - Jie Dong
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
- Key Laboratory of Bee Products for Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Beijing 100093, China
| | - Hesham R El-Seedi
- Pharmacognosy Group, Department of Pharmaceutical Biosciences, BMC, Uppsala University, Box 591, SE 75124 Uppsala, Sweden
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Department of Chemistry, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia
| | - Xiang Xu
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Hongcheng Zhang
- Key Laboratory of Bee Products for Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Beijing 100093, China
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Naake T, Zhu F, Alseekh S, Scossa F, Perez de Souza L, Borghi M, Brotman Y, Mori T, Nakabayashi R, Tohge T, Fernie AR. Genome-wide association studies identify loci controlling specialized seed metabolites in Arabidopsis. PLANT PHYSIOLOGY 2024; 194:1705-1721. [PMID: 37758174 PMCID: PMC10904349 DOI: 10.1093/plphys/kiad511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/01/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023]
Abstract
Plants synthesize specialized metabolites to facilitate environmental and ecological interactions. During evolution, plants diversified in their potential to synthesize these metabolites. Quantitative differences in metabolite levels of natural Arabidopsis (Arabidopsis thaliana) accessions can be employed to unravel the genetic basis for metabolic traits using genome-wide association studies (GWAS). Here, we performed metabolic GWAS on seeds of a panel of 315 A. thaliana natural accessions, including the reference genotypes C24 and Col-0, for polar and semi-polar seed metabolites using untargeted ultra-performance liquid chromatography-mass spectrometry. As a complementary approach, we performed quantitative trait locus (QTL) mapping of near-isogenic introgression lines between C24 and Col-0 for specific seed specialized metabolites. Besides common QTL between seeds and leaves, GWAS revealed seed-specific QTL for specialized metabolites, indicating differences in the genetic architecture of seeds and leaves. In seeds, aliphatic methylsulfinylalkyl and methylthioalkyl glucosinolates associated with the ALKENYL HYDROXYALKYL PRODUCING loci (GS-ALK and GS-OHP) on chromosome 4 containing alkenyl hydroxyalkyl producing 2 (AOP2) and 3 (AOP3) or with the GS-ELONG locus on chromosome 5 containing methylthioalkyl malate synthase (MAM1) and MAM3. We detected two unknown sulfur-containing compounds that were also mapped to these loci. In GWAS, some of the annotated flavonoids (kaempferol 3-O-rhamnoside-7-O-rhamnoside, quercetin 3-O-rhamnoside-7-O-rhamnoside) were mapped to transparent testa 7 (AT5G07990), encoding a cytochrome P450 75B1 monooxygenase. Three additional mass signals corresponding to quercetin-containing flavonols were mapped to UGT78D2 (AT5G17050). The association of the loci and associating metabolic features were functionally verified in knockdown mutant lines. By performing GWAS and QTL mapping, we were able to leverage variation of natural populations and parental lines to study seed specialized metabolism. The GWAS data set generated here is a high-quality resource that can be investigated in further studies.
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Affiliation(s)
- Thomas Naake
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Saleh Alseekh
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Federico Scossa
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
- Research Center for Genomics and Bioinformatics (CREA-GB), Council for Agricultural Research and Economics, Via Ardeatina 546, 00178 Rome, Italy
| | - Leonardo Perez de Souza
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
| | - Monica Borghi
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84321-5305, USA
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Be’er Sheva, Israel
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource Science, Tsurumi, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, Tsurumi, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Takayuki Tohge
- Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Alisdair R Fernie
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [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: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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Han S, Shen Z, Gao Q, Jin N, Lou Y. Knocking Out OsRLK7-1 Impairs Rice Growth and Development but Enhances Its Resistance to Planthoppers. Int J Mol Sci 2023; 24:14569. [PMID: 37834016 PMCID: PMC10572756 DOI: 10.3390/ijms241914569] [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: 08/31/2023] [Revised: 09/21/2023] [Accepted: 09/24/2023] [Indexed: 10/15/2023] Open
Abstract
Leucine-rich repeat receptor-like kinases (LRR-RLKs) are an important subfamily of receptor-like kinases (RLKs) in plants that play key roles in sensing different biotic and abiotic stress. However, the role of LRR-RLKs in herbivore-induced plant defense remains largely elusive. Here, we found that the expression of a rice gene, OsRLK7-1, was induced by mechanical wounding, but was slightly suppressed by the infestation of gravid females of brown planthopper (BPH, Nilaparvata lugens) or white-backed planthopper (WBPH, Sogatella furcifera). Through targeted disruption of OsRLK7-1 (resulting in the ko-rlk lines), we observed an augmentation in transcript levels of BPH-induced OsMPK3, OsWRKY30, OsWRKY33, and OsWRKY45, alongside heightened levels of planthopper-induced jasmonic acid, JA-isoleucine, and abscisic acid in plant tissues. These dynamic changes further facilitated the biosynthesis of multiple phenolamides within the rice plants, culminating in an enhanced resistance to planthopper infestations under both lab and field conditions. In addition, knocking out OsRLK7-1 impaired plant growth and reproduction. These results suggest that OsRLK7-1 plays an important role in regulating rice growth, development, and rice-planthopper interactions.
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Affiliation(s)
- Shanjie Han
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agriculture Key Lab of Agricultural Entomology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhifan Shen
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agriculture Key Lab of Agricultural Entomology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qing Gao
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agriculture Key Lab of Agricultural Entomology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Nuo Jin
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agriculture Key Lab of Agricultural Entomology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yonggen Lou
- State Key Laboratory of Rice Biology and Breeding & Ministry of Agriculture Key Lab of Agricultural Entomology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
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8
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Wang W, Xie X, Lv Y, Guan H, Liu L, Huang Q, Bao Y, Zhou J, Bao L, Gong C, Yu Y. Identification and profile of phenolamides with anthracnose resistance potential in tea ( Camellia sinensis). HORTICULTURE RESEARCH 2023; 10:uhad154. [PMID: 37719276 PMCID: PMC10500153 DOI: 10.1093/hr/uhad154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/25/2023] [Indexed: 09/19/2023]
Abstract
Tea anthracnose is a prevalent disease in China that can lead to reduced tea production and lower quality, yet there is currently a lack of effective means for controlling this disease. In this study, we identified 46 phenolamides (including 27 isomers) in different tissues and organs of tea plants based on a developed workflow, and the secondary mass spectra of all these compounds have been documented. It was revealed that tea plants predominantly accumulate protonated aliphatic phenolamides, rather than aromatic phenolamides. The profile of phenolamides indicate that their buildup in tea plants is specific to certain tissues and acyl-acceptors, and this distribution is associated with the extent of phenolamide acyl-modification. Additionally, it was observed that N-Feruloylputrescine (Fer-Put, a type of phenolamides) was responsive to the stimulated accumulation of the tea anthracnose pathogen. The findings of anti-anthracnose experiments in vitro and on tea leaf demonstrated that Fer-Put was capable of significantly inhibiting the growth of anthracnose pathogen colony, effectively prevented tea leaf disease. Furthermore, it was observed that Fer-Put treatment can enhance the antioxidant enzyme activity of tea leaves. TEA002780.1 and TEA013165.1 gene may be responsible for the biosynthesis of Fer-Put in the disease resistance process in tea plants. Through these studies, the types and distribution of phenolamides in tea plants have been elucidated, and Fer-Put's ability to resist anthracnose has been established, providing new insights into the resistance of tea anthracnose.
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Affiliation(s)
- Wenzhao Wang
- College of Horticulture, Northwest A&F University, Yangling 712100 Shaanxi, China
| | - Xingcui Xie
- College of Horticulture, Northwest A&F University, Yangling 712100 Shaanxi, China
| | - Yuanyuan Lv
- College of Tropical Crops, Hainan University, Haikou 570228 Hainan, China
| | - Haonan Guan
- College of Horticulture, Northwest A&F University, Yangling 712100 Shaanxi, China
| | - Lu Liu
- College of Horticulture, Northwest A&F University, Yangling 712100 Shaanxi, China
| | - Qian Huang
- College of Horticulture, Northwest A&F University, Yangling 712100 Shaanxi, China
| | - Yumeng Bao
- College of Horticulture, Northwest A&F University, Yangling 712100 Shaanxi, China
| | - Jie Zhou
- College of Horticulture, Northwest A&F University, Yangling 712100 Shaanxi, China
| | - Lu Bao
- College of Horticulture, Northwest A&F University, Yangling 712100 Shaanxi, China
| | - Chunmei Gong
- College of Horticulture, Northwest A&F University, Yangling 712100 Shaanxi, China
| | - Youben Yu
- College of Horticulture, Northwest A&F University, Yangling 712100 Shaanxi, China
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9
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Alseekh S, Karakas E, Zhu F, Wijesingha Ahchige M, Fernie AR. Plant biochemical genetics in the multiomics era. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4293-4307. [PMID: 37170864 PMCID: PMC10433942 DOI: 10.1093/jxb/erad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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10
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Shu W, Shi M, Zhang Q, Xie W, Chu L, Qiu M, Li L, Zeng Z, Han L, Sun Z. Transcriptomic and Metabolomic Analyses Reveal Differences in Flavonoid Pathway Gene Expression Profiles between Two Dendrobium Varieties during Vernalization. Int J Mol Sci 2023; 24:11039. [PMID: 37446217 DOI: 10.3390/ijms241311039] [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: 05/16/2023] [Revised: 06/24/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Dendrobium (Orchidaceae, Epidendoideae) plants have flowers with a wide variety of colors that persist for a long period throughout the year. The yellow coloration of Dendrobium flowers is mainly determined by the flavonol pathway and the flavone pathway, but the relevant biosynthesis mechanisms during vernalization remain unclear. To explore the similarities and differences in flavonoid biosynthesis in different tissues during vernalization, we selected two species of Dendrobium for a flower color study: Dendrobium capillipes Rchb (which has yellow flowers) and Dendrobium nobile Lindl (which has white flowers). We collected a total of 36 samples from six tissue types and both Dendrobium species during vernalization and subjected the samples to metabolic profiling and transcriptome sequencing. A total of 31,504 differentially expressed genes (DEGs) were identified between different tissues of the two Dendrobium species by transcriptomic analysis. However, many differentially accumulated metabolites (DAMs) and DEGs were enriched not only in the general pathway of "flavonoid biosynthesis" but also in multiple subpathways of "flavone and flavonol biosynthesis". According to a combined transcriptome and metabolome analysis, Putrescine hydroxycinnamoyl transferase 1 (LOC110093422) may be the main gene responsible for the differences in flavonoid accumulation during vernalization, which is closely associated with yellow flowers. Taken together, the results of our study preliminarily revealed the metabolites responsible for and the key genes regulating flavonoid biosynthesis during vernalization. These results provide a basis for the further study of the molecular mechanism of flavonoid synthesis during vernalization.
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Affiliation(s)
- Wenbo Shu
- National Key Laboratory for Germplasm Innovation and Utilization Crops, College of Horticulture and Forestry, Huazhong Agriculture University, Wuhan 430070, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Meirong Shi
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Qiqi Zhang
- National Key Laboratory for Germplasm Innovation and Utilization Crops, College of Horticulture and Forestry, Huazhong Agriculture University, Wuhan 430070, China
| | - Wenyu Xie
- National Key Laboratory for Germplasm Innovation and Utilization Crops, College of Horticulture and Forestry, Huazhong Agriculture University, Wuhan 430070, China
| | - Liwei Chu
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Mingxuan Qiu
- National Key Laboratory for Germplasm Innovation and Utilization Crops, College of Horticulture and Forestry, Huazhong Agriculture University, Wuhan 430070, China
| | - Linyan Li
- National Key Laboratory for Germplasm Innovation and Utilization Crops, College of Horticulture and Forestry, Huazhong Agriculture University, Wuhan 430070, China
| | - Zhixin Zeng
- National Key Laboratory for Germplasm Innovation and Utilization Crops, College of Horticulture and Forestry, Huazhong Agriculture University, Wuhan 430070, China
| | - Lei Han
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhenyuan Sun
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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11
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Brouckaert M, Peng M, Höfer R, El Houari I, Darrah C, Storme V, Saeys Y, Vanholme R, Goeminne G, Timokhin VI, Ralph J, Morreel K, Boerjan W. QT-GWAS: A novel method for unveiling biosynthetic loci affecting qualitative metabolic traits. MOLECULAR PLANT 2023; 16:1212-1227. [PMID: 37349988 PMCID: PMC7614782 DOI: 10.1016/j.molp.2023.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/06/2023] [Accepted: 06/16/2023] [Indexed: 06/24/2023]
Abstract
Although the plant kingdom provides an enormous diversity of metabolites with potentially beneficial applications for humankind, a large fraction of these metabolites and their biosynthetic pathways remain unknown. Resolving metabolite structures and their biosynthetic pathways is key to gaining biological understanding and to allow metabolic engineering. In order to retrieve novel biosynthetic genes involved in specialized metabolism, we developed a novel untargeted method designated as qualitative trait GWAS (QT-GWAS) that subjects qualitative metabolic traits to a genome-wide association study, while the conventional metabolite GWAS (mGWAS) mainly considers the quantitative variation of metabolites. As a proof of the validity of QT-GWAS, 23 and 15 of the retrieved associations identified in Arabidopsis thaliana by QT-GWAS and mGWAS, respectively, were supported by previous research. Furthermore, seven gene-metabolite associations retrieved by QT-GWAS were confirmed in this study through reverse genetics combined with metabolomics and/or in vitro enzyme assays. As such, we established that CYTOCHROME P450 706A5 (CYP706A5) is involved in the biosynthesis of chroman derivatives, UDP-GLYCOSYLTRANSFERASE 76C3 (UGT76C3) is able to hexosylate guanine in vitro and in planta, and SULFOTRANSFERASE 202B1 (SULT202B1) catalyzes the sulfation of neolignans in vitro. Collectively, our study demonstrates that the untargeted QT-GWAS method can retrieve valid gene-metabolite associations at the level of enzyme-encoding genes, even new associations that cannot be found by the conventional mGWAS, providing a new approach for dissecting qualitative metabolic traits.
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Affiliation(s)
- Marlies Brouckaert
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Meng Peng
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - René Höfer
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Ilias El Houari
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Chiarina Darrah
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Véronique Storme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Yvan Saeys
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, 9000 Ghent, Belgium; VIB Center for Inflammation Research, 9052 Ghent, Belgium
| | - Ruben Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert Goeminne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium; VIB Metabolomics Core, 9052 Ghent, Belgium
| | - Vitaliy I Timokhin
- Department of Biochemistry, and US Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John Ralph
- Department of Biochemistry, and US Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kris Morreel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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12
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Xiang J, Yuan Y, Du L, Zhang Y, Li C, Beta T. Modification on phenolic profiles and enhancement of antioxidant activity of proso millets during germination. Food Chem X 2023; 18:100628. [PMID: 36949751 PMCID: PMC10025011 DOI: 10.1016/j.fochx.2023.100628] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023] Open
Abstract
Changes in phenolic profiles and antioxidant activity of three varieties of proso millet during germination were investigated. Total phenolic content (TPC) and total flavonoid content (TFC) increased significantly with prolongation in germination period. After germination for 6 days, TPC of the free and bound fractions increased 6.30-8.66-fold and 77.65-116.18%, respectively. The free and bound phenolic compounds identified by UPLC-MS/MS, displayed significant variations. Feruloylquinic acid and N,N'-bis-(p-coumaroyl)-putrescine biosynthesized during germination, are reported for the first time in proso millets. Other phenolics including trans- and cis-ferulic, trans-p-coumaric, vanillic acid and ferulic acid dimers (DFAs) were increased significantly along with a new DFA (8,5'-DFA) seemingly produced during germination. The germinated proso milllets displayed superior antioxidant activity than the corresponding ungerminated samples indicating that germination could be one applicable method for improving phenolic profiles and antioxidant capacity of proso millets. Thus germinated proso millet could be exploited as a functional ingredient in several products.
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Affiliation(s)
- Jinle Xiang
- Henan University of Science & Technology, Faculty of Food & Bioengineering, Luoyang, Henan 471000, China
- Henan University of Science & Technology, Henan International Joint Laboratory of Food Green Processing and Safety Control, Luoyang, Henan 471000, China
| | - Yuan Yuan
- Henan University of Science & Technology, Faculty of Food & Bioengineering, Luoyang, Henan 471000, China
| | - Lin Du
- Henan University of Science & Technology, Faculty of Food & Bioengineering, Luoyang, Henan 471000, China
| | - Youyang Zhang
- Henan University of Science & Technology, Faculty of Food & Bioengineering, Luoyang, Henan 471000, China
| | - Chunqiu Li
- Henan University of Science & Technology, Faculty of Food & Bioengineering, Luoyang, Henan 471000, China
- Henan University of Science & Technology, Henan International Joint Laboratory of Food Green Processing and Safety Control, Luoyang, Henan 471000, China
| | - Trust Beta
- University of Manitoba, Department of Food & Human Nutritional Sciences, Winnipeg, Manitoba R3T 2N2, Canada
- Corresponding author at: Department of Food & Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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13
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Hong J, Rosental L, Xu Y, Xu D, Orf I, Wang W, Hu Z, Su S, Bai S, Ashraf M, Hu C, Zhang C, Li Z, Xu J, Liu Q, Zhang H, Zhang F, Luo Z, Chen M, Chen X, Betts N, Fernie A, Liang W, Chen G, Brotman Y, Zhang D, Shi J. Genetic architecture of seed glycerolipids in Asian cultivated rice. PLANT, CELL & ENVIRONMENT 2023; 46:1278-1294. [PMID: 35698268 DOI: 10.1111/pce.14378] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/30/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
Glycerolipids are essential for rice development and grain quality but its genetic regulation remains unknown. Here we report its genetic base using metabolite-based genome-wide association study and metabolite-based quantitative traits locus (QTL) analyses based on lipidomic profiles of seeds from 587 Asian cultivated rice accessions and 103 chromosomal segment substitution lines, respectively. We found that two genes encoding phosphatidylcholine (PC):diacylglycerol cholinephosphotransferase (OsLP1) and granule-bound starch synthase I (Waxy) contribute to variations in saturated triacylglycerol (TAG) and lyso-PC contents, respectively. We demonstrated that allelic variation in OsLP1 sequence between indica and japonica results in different enzymatic preference for substrate PC-16:0/16:0 and different saturated TAG levels. Further evidence demonstrated that OsLP1 also affects heading date, and that co-selection of OsLP1 and a flooding-tolerant QTL in Aus results in the abundance of saturated TAGs associated with flooding tolerance. Moreover, we revealed that the sequence polymorphisms in Waxy has pleiotropic effects on lyso-PC and amylose content. We proposed that rice seed glycerolipids have been unintentionally shaped during natural and artificial selection for adaptive or import seed quality traits. Collectively, our findings provide valuable genetic resources for rice improvement and evolutionary insights into seed glycerolipid variations in rice.
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Affiliation(s)
- Jun Hong
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Leah Rosental
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Yang Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Dawei Xu
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Isabel Orf
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Wengsheng Wang
- Department of Rice Molecular Design Technology and Application, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiqiang Hu
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Su Su
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoxing Bai
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mohammed Ashraf
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chaoyang Hu
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Changquan Zhang
- Department of Agronomy, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Zhikang Li
- Department of Rice Molecular Design Technology and Application, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianlong Xu
- Department of Rice Molecular Design Technology and Application, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiaoquan Liu
- Department of Agronomy, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Hui Zhang
- Department of Plant Science, School of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Fengli Zhang
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhijing Luo
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mingjiao Chen
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaofei Chen
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Natalie Betts
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Alisdair Fernie
- Department of Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Wanqi Liang
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Dabing Zhang
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Jianxin Shi
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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14
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Wang Y, Shi C, Ge P, Li F, Zhu L, Wang Y, Tao J, Zhang X, Dong H, Gai W, Wang F, Ye Z, Grierson D, Xu W, Zhang Y. A 21-bp InDel in the promoter of STP1 selected during tomato improvement accounts for soluble solid content in fruits. HORTICULTURE RESEARCH 2023; 10:uhad009. [PMID: 36960428 PMCID: PMC10028405 DOI: 10.1093/hr/uhad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Domestication and improvement are important processes that generate the variation in genome and phonotypes underlying crop improvement. Unfortunately, during selection for certain attributes, other valuable traits may be inadvertently discarded. One example is the decline in fruit soluble solids content (SSC) during tomato breeding. Several genetic loci for SSC have been identified, but few reports on the underlying mechanisms are available. In this study we performed a genome-wide association study (GWAS) for SSC of the red-ripe fruits in a population consisting of 481 tomato accessions with large natural variations and found a new quantitative trait locus, STP1, encoding a sugar transporter protein. The causal variation of STP1, a 21-bp InDel located in the promoter region 1124 bp upstream of the start codon, alters its expression. STP1 Insertion accessions with an 21-bp insertion have higher SSC than STP1 Deletion accessions with the 21-bp deletion. Knockout of STP1 in TS-23 with high SSC using CRISPR/Cas9 greatly decreased SSC in fruits. In vivo and in vitro assays demonstrated that ZAT10-LIKE, a zinc finger protein transcription factor (ZFP TF), can specifically bind to the promoter of STP1 Insertion to enhance STP1 expression, but not to the promoter of STP1 Deletion , leading to lower fruit SSC in modern tomatoes. Diversity analysis revealed that STP1 was selected during tomato improvement. Taking these results together, we identified a naturally occurring causal variation underlying SSC in tomato, and a new role for ZFP TFs in regulating sugar transporters. The findings enrich our understanding of tomato evolution and domestication, and provide a genetic basis for genome design for improving fruit taste.
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Affiliation(s)
- Ying Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunmei Shi
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Pingfei Ge
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangman Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Lihui Zhu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Yaru Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinbao Tao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingyu Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Haiqiang Dong
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenxian Gai
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhibiao Ye
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Donald Grierson
- Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Wei Xu
- Corresponding authors. E-mail: ;
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15
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Chakraborty M, Gautam A, Das O, Masid A, Bhaumik M. Prenatal arsenic exposure stymies gut butyrate production and enhances gut permeability in post natal life even in absence of arsenic deftly through miR122-Occludin pathway. Toxicol Lett 2023; 374:19-30. [PMID: 36473683 DOI: 10.1016/j.toxlet.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 12/11/2022]
Abstract
This discourse attempts to capture a few important dimensions of gut physiology like microbial homeostasis, short chain fatty acid (SCFA) production, occludin expression, and gut permeability in post-natal life of mice those received arsenic only during pre-natal life. Adult Balb/c mice were fed with 4 ppm arsenic trioxide in drinking water during breeding and gestation. After the birth of the pups, the arsenic water was withdrawn and replaced with clean drinking water. The pups were allowed to grow for 28 days (pAs-mice) and age matched Balb/c mice which were never exposed to arsenic served as control The pAs-mice showed a striking reduction in Firmicutes to Bacteroidetes (F/B) ratio coupled with a decrease in tight junction protein, occludin resulting in an increase in gut permeability, increased infiltration of inflammatory cells in the colon and decrease in common SCFAs in which butyrate reduction was quite prominent in fecal samples as compared to normal control. The above phenotypes of pAs-mice were mostly reversed by supplementing 5% sodium butyrate (w/w) with food from 21st to 28th day. The ability of butyrate in enhancing occludin expression, in particular, was dissected further. As miR122 causes degradation of Occludin mRNA, we transiently overexpressed miR122 by injecting appropriate plasmids and showed reversal of butyrate effects in pAs-mice. Thus, pre-natal arsenic exposure orchestrates variety of effects by decreasing butyrate in pAs-mice leading to increased permeability due to reduced occludin expression. Our research adds a new dimension to our understanding that pre-natal arsenic exposure imprints in post-natal life while there was no further arsenic exposure.
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Affiliation(s)
- Mainak Chakraborty
- Division of Immunology, ICMR-National Institute of Cholera and Enteric Diseases, Beleghata, Kolkata 700010, India
| | - Anupam Gautam
- Department of Algorithms in Bioinformatics, Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany; International Max Planck Research School "From Molecules to Organisms'', Max Planck Institute for Biology Tübingen, Max-Planck-Ring∼5, 72076 Tübingen, Germany
| | - Oishika Das
- Division of Immunology, ICMR-National Institute of Cholera and Enteric Diseases, Beleghata, Kolkata 700010, India
| | - Aaheli Masid
- Division of Immunology, ICMR-National Institute of Cholera and Enteric Diseases, Beleghata, Kolkata 700010, India
| | - Moumita Bhaumik
- Division of Immunology, ICMR-National Institute of Cholera and Enteric Diseases, Beleghata, Kolkata 700010, India.
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The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis. Int J Mol Sci 2022; 23:ijms232415932. [PMID: 36555572 PMCID: PMC9781956 DOI: 10.3390/ijms232415932] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.
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Ghosh S, Bollinedi H, Gopala Krishnan S, Kundu A, Singh A, Bhowmick PK, Singh A, Nagarajan M, Vinod KK, Ellur RK, Singh AK. From farm to plate: Spatio-temporal characterization revealed compositional changes and reduced retention of γ-oryzanol upon processing in rice. Front Nutr 2022; 9:1040362. [DOI: 10.3389/fnut.2022.1040362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022] Open
Abstract
BackgroundAntioxidants detain the development and proliferation of various non-communicable diseases (NCDs). γ-oryzanol, a group of steryl ferulates and caffeates, is a major antioxidant present in rice grain with proven health benefits. The present study evaluated the distribution and dynamics of γ-oryzanol and its components in spatial and temporal scales and also delineated the effect of processing and cooking on its retention.MethodsSix rice varieties (four Basmati and two non-Basmati) belonging to indica group were analyzed at spatial scale in four different tissues (leaf blades, leaf sheaths, peduncle and spikelets) and temporal scale at three developmental stages (booting, milky and dough). Additionally, the matured grains were fractioned into husk, embryo, bran, and endosperm to assess differential accumulation in these tissues. Further, milling and cooking of the samples was done to assess the retention upon processing. After extraction of γ-oryzanol by solvent extraction method, individual components were identified by UPLC-QToF-ESI-MS and quantified by RP-HPLC.ResultsThe non-seed tissues were significantly different from the seed tissues for composition and quantitative variation of γ-oryzanol. Cycloartenyl caffeate was predominant in all the non-seed tissues during the three developmental stages while it showed significant reduction during the growth progression toward maturity and was totally absent in the matured grains. In contrary, the 24-methylenecycloartanyl ferulate, campesteryl ferulate and β-sitosteryl ferulate showed significant increment toward the growth progression to maturity. Milling caused significant reduction, retaining only an average of 58.77% γ-oryzanol. Cooking of brown rice in excess water showed relatively lower average retention (43.31%) to samples cooked in minimal water (54.42%). Cooked milled rice showed least mean retention of 21.66%.ConclusionThe results demonstrate prominent compositional variation of γ-oryzanol during different growth stages. For the first time, the study demonstrated that ferulate esters of γ-oryzanol were predominant in the seed tissues while caffeate esters were dominant in non-seed tissues. Basmati cultivars show differential expression of γ-oryzanol and its components compared to non-Basmati cultivars. Cooking in excess water causes maximum degradation of γ-oryzanol. Post-harvest losses due to milling and cooking indicate the necessity of biofortification for γ-oryzanol content in rice grain.
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Wang S, Qiang Q, Xiang L, Fernie AR, Yang J. Targeted approaches to improve tomato fruit taste. HORTICULTURE RESEARCH 2022; 10:uhac229. [PMID: 36643745 PMCID: PMC9832879 DOI: 10.1093/hr/uhac229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/30/2022] [Indexed: 06/17/2023]
Abstract
Tomato (Solanum lycopersicum) is the most valuable fruit and horticultural crop species worldwide. Compared with the fruits of their progenitors, those of modern tomato cultivars are, however, often described as having unsatisfactory taste or lacking flavor. The flavor of a tomato fruit arises from a complex mix of tastes and volatile metabolites, including sugars, acids, amino acids, and various volatiles. However, considerable differences in fruit flavor occur among tomato varieties, resulting in mixed consumer experiences. While tomato breeding has traditionally been driven by the desire for continual increases in yield and the introduction of traits that provide a long shelf-life, consumers are prepared to pay a reasonable premium for taste. Therefore, it is necessary to characterize preferences of tomato flavor and to define its underlying genetic basis. Here, we review recent conceptual and technological advances that have rendered this more feasible, including multi-omics-based QTL and association analyses, along with the use of trained testing panels, and machine learning approaches. This review proposes how the comprehensive datasets compiled to date could allow a precise rational design of tomato germplasm resources with improved organoleptic quality for the future.
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Affiliation(s)
- Shouchuang Wang
- To whom correspondence should be addressed. E-mail: , or . Tel: 86-0898-66184571. Fax number: 0898-66184571
| | | | - Lijun Xiang
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Alisdair R Fernie
- To whom correspondence should be addressed. E-mail: , or . Tel: 86-0898-66184571. Fax number: 0898-66184571
| | - Jun Yang
- To whom correspondence should be addressed. E-mail: , or . Tel: 86-0898-66184571. Fax number: 0898-66184571
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Genome-wide association mapping reveals genes underlying population-level metabolome diversity in a fungal crop pathogen. BMC Biol 2022; 20:224. [PMID: 36209159 PMCID: PMC9548119 DOI: 10.1186/s12915-022-01422-z] [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] [Received: 05/25/2022] [Accepted: 09/27/2022] [Indexed: 11/12/2022] Open
Abstract
Background Fungi produce a wide range of specialized metabolites (SMs) involved in biotic interactions. Pathways for the production of SMs are often encoded in clusters of tightly arranged genes identified as biosynthetic gene clusters. Such gene clusters can undergo horizontal gene transfers between species and rapid evolutionary change within species. The acquisition, rearrangement, and deletion of gene clusters can generate significant metabolome diversity. However, the genetic basis underlying variation in SM production remains poorly understood. Results Here, we analyzed the metabolite production of a large population of the fungal pathogen of wheat, Zymoseptoria tritici. The pathogen causes major yield losses and shows variation in gene clusters. We performed untargeted ultra-high performance liquid chromatography-high resolution mass spectrometry to profile the metabolite diversity among 102 isolates of the same species. We found substantial variation in the abundance of the detected metabolites among isolates. Integrating whole-genome sequencing data, we performed metabolite genome-wide association mapping to identify loci underlying variation in metabolite production (i.e., metabolite-GWAS). We found that significantly associated SNPs reside mostly in coding and gene regulatory regions. Associated genes encode mainly transport and catalytic activities. The metabolite-GWAS identified also a polymorphism in the 3′UTR region of a virulence gene related to metabolite production and showing expression variation. Conclusions Taken together, our study provides a significant resource to unravel polymorphism underlying metabolome diversity within a species. Integrating metabolome screens should be feasible for a range of different plant pathogens and help prioritize molecular studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01422-z.
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Tsafack PB, Tsopmo A. Effects of bioactive molecules on the concentration of biogenic amines in foods and biological systems. Heliyon 2022; 8:e10456. [PMID: 36105466 PMCID: PMC9465362 DOI: 10.1016/j.heliyon.2022.e10456] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/14/2022] [Accepted: 08/22/2022] [Indexed: 11/20/2022] Open
Abstract
Biogenic amines (BAs) are a group of molecules naturally present in foods that contain amino acids, peptides, and proteins as well as in biological systems. In foods, their concentrations typically increase during processing and storage because of exposure to microorganisms that catalyze their formation by releasing amino acid decarboxylases. The concentrations of BAs above certain values are indicative of unsafe foods due to associate neuronal toxicity, allergenic reactions, and increase risks of cardiovascular diseases. There are therefore various strategies that focus on the control of BAs in foods mostly through elimination, inactivation, or inhibition of the growth of microorganisms. Increasingly, there are works on bioactive compounds that can decrease the concentration of BAs through their antimicrobial activity as well as the inhibition of decarboxylating enzymes that control their formation in foods or amine oxidases and N-acetyltransferase that control the degradation in vivo. This review focusses on the role of food-derived bioactive compounds and the mechanism by which they regulate the concentration of BAs. The findings are that most active molecules belong to polyphenols, one of the largest groups of plant secondary metabolites, additionally other useful +compounds are present in extracts of different herbs and spices. Different mechanisms have been proposed for the effects of polyphenols depending on the model system. Studies on the effects in vivo are limited and there is a lack of bioavailability and transport data which are important to assess the importance of the bioactive molecules.
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Affiliation(s)
- Patrick Blondin Tsafack
- Nutrition and Functional Food, School of Biosciences and Veterinary Medicine, University of Camerino, Via A. D'Accorso, 16, Camerino, Italy
| | - Apollinaire Tsopmo
- Food Science and Nutrition Program, Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, K1S 5B6, Ottawa, ON, Canada
- Corresponding author.
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Zhang F, Zhang X, Luo Y, Li H, Qin X. Biosynthetic mechanisms of isoflavone accumulation affected by different growth patterns in Astragalus mongholicus products. BMC PLANT BIOLOGY 2022; 22:410. [PMID: 35996112 PMCID: PMC9396891 DOI: 10.1186/s12870-022-03769-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND At present, Astragalus mongholicus products on the market represent two growth patterns: imitative wild A. mongholicus (WAM) and cultivated A. mongholicus (CAM). The 6-year-old WAM (A6) and 2-year-old CAM (B2) products are often sold as commodities. This study aimed to explore the effects of the abovementioned growth patterns on the biosynthetic mechanisms of isoflavone accumulation in A. mongholicus products. RESULTS In this paper, the content of calycosin-7-O-β-D-glucoside in 6-year-old WAM (A6) was significantly higher than that in 2-year-old CAM (B2) based on high-performance liquid chromatography. Tissue anatomy indicated that A6 has developed phloem fibers, thickened secondary walls, and a more well-developed vascular system than B2. Thirteen differentially accumulated metabolites were found in A6 and B2 by UHPLC-ESI-Q-TOF-MS/MS, of which isoflavones were highly and significantly enriched in A6. By combining transcriptomics and metabolomics analysis, we found that the metabolomics profile was the same as the transcriptomics profile in both A6 and B2. In total, 11 novel isoflavone-related genes were isolated using BLAST and functional annotation through RNA-Seq and Iso-Seq. The results of integrated analysis, Short Time-series Expression Miner analysis, and Pearson correlation analysis showed that the regulation of four key enzymes, cinnamate 4-hydroxylase, 6-deoxychalcone synthase, chalcone reductase, and chalcone isomerase, led to the high accumulation of isoflavones in A6. In addition, AmUFGT (c778119) and AmUCGT (c303354) were predicted to be 7-O-glycosyltransferases by phylogenetic analysis; these genes catalyze formononetin and calycosin, respectively. CONCLUSIONS The findings of this work will clarify the differences in the biosynthetic mechanism of isoflavone accumulation between A6 and B2, which will guide the cultivation of A. mongholicus.
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Affiliation(s)
- Fusheng Zhang
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China.
| | - Xuan Zhang
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Yangyang Luo
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Huijuan Li
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China.
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Xu X, Wang Z, Xu S, Xu M, He L, Zhang J, Luo Z, Xie X, Wu M, Yang J. Identifying loci controlling total starch content of leaf in Nicotiana tabacum through genome-wide association study. Funct Integr Genomics 2022; 22:537-552. [PMID: 35404023 DOI: 10.1007/s10142-022-00851-x] [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: 11/19/2021] [Revised: 03/07/2022] [Accepted: 03/22/2022] [Indexed: 11/04/2022]
Abstract
Starch is an important primary metabolite in plants, which can provide bioenergy for fuel ethanol production. There are many studies focusing on starch metabolism in Arabidopsis, maize, and rice, but few reports have been made on the starch content of tobacco leaves. Hence, to identify the marker-trait associations and isolate the candidate genes related to starch content of tobacco leaf, the genome-wide association study (GWAS) was performed using a multiparent advanced generation intercross (MAGIC) population consisting of 276 accessions genotyped by a 430 K SNP array. In this study, we detected the leaf starch content of tobacco plants cultivated in two places (Zhucheng and Chenzhou), which showed a wide variation of starch content in the population. A total of 28 and 45 significant single-nucleotide polymorphism (SNP) loci associated with leaf starch content were identified by single-locus and multi-locus GWAS models, respectively, and the phenotypic variance explained by these loci varied from 1.80 to - 14.73%. Furthermore, among these quantitative trait loci (QTLs), one SNP, AX-106011713 located on chromosome 19, was detected repeatedly in multiple models and two environments, which was selected for linkage disequilibrium (LD) analysis to obtain the target candidate region. Through gene annotation, haplotype, and gene expression analysis, two candidate genes encoding E3 ubiquitin-protein ligase (Ntab0823160) and fructose-bisphosphate aldolase (Ntab0375050) were obtained. Results showed that the variety carrying the beneficial alleles of the two candidate genes had higher gene expression level and leaf starch content, suggesting the potential role of candidate genes in enhancing the level of tobacco leaf starch content. Furthermore, silencing of Ntab0823160 in tobacco leaves reduced the content of total starch to 39.41-69.75% of that in the wide type plants. Taken together, our results provide useful resources for further investigation of the starch metabolic pathway and are also beneficial for the creation of eco-friendly cultivars with increased accumulation of leaf starch content.
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Affiliation(s)
- Xin Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Zhong Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Shixiao Xu
- Henan Agricultural University, Zhengzhou, 450002, China
| | - Min Xu
- Henan Tobacco Company of CNTC, Zhengzhou, 450018, China
| | - Lei He
- Henan Tobacco Company of CNTC, Zhengzhou, 450018, China
| | - Jianfeng Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Zhaopeng Luo
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Xiaodong Xie
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Mingzhu Wu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China.
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Mutations in Rht-B1 Locus May Negatively Affect Frost Tolerance in Bread Wheat. Int J Mol Sci 2022; 23:ijms23147969. [PMID: 35887316 PMCID: PMC9324540 DOI: 10.3390/ijms23147969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/08/2022] [Accepted: 07/16/2022] [Indexed: 02/01/2023] Open
Abstract
The wheat semi-dwarfing genes Rht (Reduced height) are widely distributed among the contemporary wheat varieties. These genes also exert pleiotropic effects on plant tolerance towards various abiotic stressors. In this work, frost tolerance was studied in three near-isogenic lines of the facultative variety ‘April Bearded’ (AB), carrying the wild type allele Rht-B1a (tall phenotype), and the mutant alleles Rht-B1b (semi-dwarf) and Rht-B1c (dwarf), and was further compared with the tolerance of a typical winter type variety, ‘Mv Beres’. The level of freezing tolerance was decreasing in the order ‘Mv Beres’ > AB Rht-B1a > AB Rht-B1b > AB Rht-B1c. To explain the observed differences, cold acclimation-related processes were studied: the expression of six cold-related genes, the phenylpropanoid pathway, carbohydrates, amino acids, polyamines and compounds in the tricarboxylic acid cycle. To achieve this, a comprehensive approach was applied, involving targeted analyses and untargeted metabolomics screening with the help of gas chromatography/liquid chromatography—mass spectrometry setups. Several cold-related processes exhibited similar changes in these genotypes; indeed, the accumulation of eight putrescine and agmatine derivatives, 17 flavones and numerous oligosaccharides (max. degree of polymerization 18) was associated with the level of freezing tolerance in the ‘April Bearded’ lines. In summary, the mutant Rht alleles may further decrease the generally low frost tolerance of the Rht-B1a, and, based on the metabolomics study, the mechanisms of frost tolerance may differ for a typical winter variety and a facultative variety. Present results point to the complex nature of frost resistance.
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Isolation and Characterisation of Hordatine-Rich Fractions from Brewer’s Spent Grain and Their Biological Activity on α-Glucosidase and Glycogen Phosphorylase α. SUSTAINABILITY 2022. [DOI: 10.3390/su14148421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hordatines are a characteristic class of secondary metabolites found in barley which have been reported to be present in barley malt, beer and, recently, brewer´s spent grain (BSG). However, little is known about their biological activities such as antioxidative effects in beer or antifungal activity as their main task within the plants. We conducted an in vitro investigation of the activity of hordatines isolated from BSG towards enzymes of glucose metabolism. Hordatine-rich fractions from BSG were prepared by solid-liquid extraction (SLE) with 60% acetone followed by purification and fractionation. The fractions were characterised and investigated for their in vitro inhibitory potential on α-glucosidase and glycogen phosphorylase α (GPα). Both enzymes are relevant within the human glucose metabolism regarding the digestion of carbohydrates as well as the liberation of glucose from the liver. In total, 10 hordatine-rich fractions varying in the composition of different hordatines were separated and analysed by mass spectrometry. Hordatine A, B and C, as well as hydroxylated aglycons and many glycosides, were detected in the fractions. The total hordatine content was analysed by HPLC-DAD using a semi-quantitative approach and ranged from 60.7 ± 3.1 to 259.6 ± 6.1 µg p-coumaric acid equivalents/mg fraction. Regarding the biological activity of fractions, no inhibitory effect on GPα was observed, whereas an inhibitory effect on α-glucosidase was detected (IC50 values: 77.5 ± 6.5–194.1 ± 2.6 µg/mL). Overall, the results confirmed that hordatines are present in BSG in relatively high amounts and provided evidence that they are potent inhibitors of α-glucosidase. Further research is needed to confirm these results and identify the active hordatine structure.
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Zhuang Y, Wang X, Llorca LC, Lu J, Lou Y, Li R. Role of jasmonate signaling in rice resistance to the leaf folder Cnaphalocrocis medinalis. PLANT MOLECULAR BIOLOGY 2022; 109:627-637. [PMID: 34709485 DOI: 10.1007/s11103-021-01208-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Jasmonate-induced accumulation of anti-herbivore compounds mediates rice resistance to the leaf folder Cnaphalocrocis medinalis. The rice leaf folder (LF), Cnaphalocrocis medinalis, is one of the most destructive insect pests in the paddy field. LF larvae induces leaf folding and scrapes the upper epidermis and mesophyll tissues reducing photosynthesis and yield in rice. Identifying plant defense pathways and genes involved in LF resistance is essential to understand better this plant-insect interaction and develop new control strategies for this pest. Jasmonate (JA) signaling controls a plethora of plant defenses against herbivores. Using RNA-seq time series analysis, we characterized changes in the transcriptome of wild-type (WT) leaves in response to LF damage and measured the dynamics of accumulation of JA phytohormone pools in time-course experiments. Genes related to JA signaling and responses, known to mediate resistance responses to herbivores, were induced by LF and were accompanied by an increment in the levels of JA pools in damaged leaves. The accumulation of defense compounds such as phenolamides and trypsin proteinase inhibitor (TPI) also increased after LF infestation in WT but not in JA mutant plants impaired in JA biosynthesis (aoc-2) and signaling (myc2-5). Consistent with all these responses, we found that LF larvae performed better in the JA mutant backgrounds than in the WT plants. Our results show that JA signaling regulates LF-induced accumulation of TPI and phenolamides and that these compounds are likely an essential part of the defense arsenal of rice plants against this insect pest.
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Affiliation(s)
- Yunqi Zhuang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xinjue Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Lucas Cortés Llorca
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Jing Lu
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yonggen Lou
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Ran Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.
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Sestari I, Campos ML. Into a dilemma of plants: the antagonism between chemical defenses and growth. PLANT MOLECULAR BIOLOGY 2022; 109:469-482. [PMID: 34843032 DOI: 10.1007/s11103-021-01213-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/28/2021] [Indexed: 05/21/2023]
Abstract
Chemical defenses are imperative for plant survival, but their production is often associated with growth restrictions. Here we review the most recent theories to explain this complex dilemma of plants. Plants are a nutritional source for a myriad of pests and pathogens that depend on green tissues to complete their life cycle. Rather than remaining passive victims, plants utilize an arsenal of chemical defenses to fend off biotic attack. While the deployment of such barriers is imperative for survival, the production of these chemical defenses is typically associated with negative impacts on plant growth. Here we discuss the most recent theories which explain this highly dynamic growth versus defense dilemma. Firstly, we discuss the hypothesis that the antagonism between the accumulation of chemical defenses and growth is rooted in the evolutionary history of plants and may be a consequence of terrestrialization. Then, we revise the different paradigms available to explain the growth versus chemical defense antagonism, including recent findings that update these into more comprehensive and plausible theories. Finally, we highlight state-of-the-art strategies that are now allowing the activation of growth and the concomitant production of chemical barriers in plants. Growth versus chemical defense antagonism imposes large ecological and economic costs, including increased crop susceptibility to pests and pathogens. In a world where these plant enemies are the main problem to increase food production, we believe that this review will summarize valuable information for future studies aiming to breed highly defensive plants without the typical accompanying penalties to growth.
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Affiliation(s)
- Ivan Sestari
- Coordenadoria Especial de Ciências Biológicas e Agronômicas, Universidade Federal de Santa Catarina, Curitibanos, SC, Brazil
| | - Marcelo Lattarulo Campos
- Integrative Plant Research Laboratory, Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.
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Eragam A, Shukla V, Kola VS, Latha P, Akkareddy S, Kommana ML, Ramireddy E, Vemireddy LR. Yield-associated putative gene regulatory networks in Oryza sativa L. subsp. indica and their association with high-yielding genotypes. Mol Biol Rep 2022; 49:7649-7663. [PMID: 35612779 DOI: 10.1007/s11033-022-07581-0] [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: 01/27/2022] [Accepted: 05/06/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND With the increase in population and economies of developing countries in Asia and Africa, the research towards securing future food demands is an imminent need. Among japonica and indica genotypes, indica rice varieties are largely cultivated across the globe. However, our present understanding of yield-contributing gene information stems mainly from japonica and studies on the yield potential of indica genotypes are limited. METHODS AND RESULTS In the present study, yield contributing orthologous genes previously characterized from japonica varieties were identified in the indica genome and analysed with binGO tool for GO biological processes categorization. Transcription factor binding site enrichment analysis in the promoters of yield-related genes of indica was performed with MEME-AME tool that revealed putative common TF regulators are enriched in flower development, two-component signalling and water deprivation biological processes. Gene regulatory networks revealed important TF-target interactions that might govern yield-related traits. Some of the identified candidate genes were validated by qRT-PCR analysis for their expression and association with yield-related traits among 16 widely cultivated popular indica genotypes. Further, SNP-metabolite-trait association analysis was performed using high-yielding indica variety Rasi. This resulted in the identification of putative SNP variations in TF regulators and targeted yield genes significantly linked with metabolite accumulation. CONCLUSIONS The study suggests some of the high yielding indica genotypes such as Ravi003, Rasi and Kavya could be used as potential donors in breeding programs based on yield gene expression analysis and SNP-metabolites associations.
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Affiliation(s)
- Aparna Eragam
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India
- Biology Division, Indian Institute of Science Education and Research Tirupati (IISER Tirupati), Tirupati, 517507, India
| | - Vishnu Shukla
- Biology Division, Indian Institute of Science Education and Research Tirupati (IISER Tirupati), Tirupati, 517507, India
| | - Vijaya Sudhakararao Kola
- Biology Division, Indian Institute of Science Education and Research Tirupati (IISER Tirupati), Tirupati, 517507, India
| | - P Latha
- Regional Agricultural Research Station (RARS), ANGRAU, Tirupati, India
| | | | - Madhavi L Kommana
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India
| | - Eswarayya Ramireddy
- Biology Division, Indian Institute of Science Education and Research Tirupati (IISER Tirupati), Tirupati, 517507, India.
| | - Lakshminarayana R Vemireddy
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India.
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Wang W, Sang S. Biotransformation of Barley Phenolamide by Mice and the Human Gut Microbiota and Quantitative Analysis of the Major Metabolites in Mice. Mol Nutr Food Res 2022; 66:e2200134. [PMID: 35532207 DOI: 10.1002/mnfr.202200134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/31/2022] [Indexed: 11/06/2022]
Abstract
SCOPE This study investigates the metabolism of p-coumaroylagmatine (pCAA), one of the phenolamides in barley, in mice, and by human gut microbiota, and measures the concentrations of its main metabolites in mice. METHODS AND RESULTS Nine major metabolites are identified from fecal and urinary samples collected from pCAA treated mice via analysis of their LC chromatograms and tandem mass spectra compared to the commercial and synthesized standards. These nine metabolites are generated through four different biotransformation pathways: double bond reduction, amide bond hydrolyzation, cleavage of guanidine, and oxidation of guanidine. Furthermore, interindividual differences in the formation of dihydro-pCAA (M3), high and low metabolizers, are observed in human in vitro intestinal microbial conversion. Moreover, significant amount of pCAA is detected in mice (29.33 ± 1.58 µmol g-1 in feces and 2020.44 ± 130.07 µM in urine), and the concentrations of agmatine (M1) are increased to 177.6 times and 3.2 times in mouse feces and urine, respectively. CONCLUSION This study demonstrates that pCAA is metabolized in mice and by human gut microbiota to generate potential bioactive metabolites through four major metabolic pathways. pCAA and its metabolites have the potential to be used as the exposure biomarkers to reflect the intake of whole grain barley.
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Affiliation(s)
- Weixin Wang
- Laboratory for Functional Foods and Human Health, Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural and Technical State University, North Carolina Research Campus, 500 Laureate Way, Kannapolis, NC, 28081, USA
| | - Shengmin Sang
- Laboratory for Functional Foods and Human Health, Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural and Technical State University, North Carolina Research Campus, 500 Laureate Way, Kannapolis, NC, 28081, USA
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Integrated Metabolomics and Transcriptomics Analyses Reveal the Metabolic Differences and Molecular Basis of Nutritional Quality in Landraces and Cultivated Rice. Metabolites 2022; 12:metabo12050384. [PMID: 35629888 PMCID: PMC9142891 DOI: 10.3390/metabo12050384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/07/2022] [Accepted: 04/20/2022] [Indexed: 02/01/2023] Open
Abstract
Rice (Oryza sativa L.) is one of the most globally important crops, nutritionally and economically. Therefore, analyzing the genetic basis of its nutritional quality is a paramount prerequisite for cultivating new varieties with increased nutritional health. To systematically compare the nutritional quality differences between landraces and cultivated rice, and to mine key genes that determine the specific nutritional traits of landraces, a seed metabolome database of 985 nutritional metabolites covering amino acids, flavonoids, anthocyanins, and vitamins by a widely targeted metabolomic approach with 114 rice varieties (35 landraces and 79 cultivars) was established. To further reveal the molecular mechanism of the metabolic differences in landrace and cultivated rice seeds, four cultivars and six landrace seeds were selected for transcriptome and metabolome analysis during germination, respectively. The integrated analysis compared the metabolic profiles and transcriptomes of different types of rice, identifying 358 differentially accumulated metabolites (DAMs) and 1982 differentially expressed genes (DEGs), establishing a metabolite–gene correlation network. A PCA revealed anthocyanins, flavonoids, and lipids as the central differential nutritional metabolites between landraces and cultivated rice. The metabolite–gene correlation network was used to screen out 20 candidate genes postulated to be involved in the structural modification of anthocyanins. Five glycosyltransferases were verified to catalyze the glycosylation of anthocyanins by in vitro enzyme activity experiments. At the same time, the different mechanisms of the anthocyanin synthesis pathway and structural diversity in landrace and cultivated rice were systematically analyzed, providing new insights for the improvement and utilization of the nutritional quality of rice landrace varieties.
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Liu B, Ju Y, Xia C, Zhong R, Christensen MJ, Zhang X, Nan Z. The effect of Epichloë endophyte on phyllosphere microbes and leaf metabolites in Achnatherum inebrians. iScience 2022; 25:104144. [PMID: 35402863 PMCID: PMC8991375 DOI: 10.1016/j.isci.2022.104144] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 01/09/2022] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
Upon exposure to the prevailing environment, leaves become increasingly colonized by fungi and bacteria located on the surface (epiphytic) or within (endophytic) the leaves. Many cool season grasses, including Achnatherum inebrians, host a seed-borne, intercellular, mutualistic Epichloë fungal endophyte, the growth of which is synchronized with the host grass. A study utilizing illumina sequencing was used to examine the epiphytic and endophytic microbial communities in Epichloë endophyte-infected and endophyte-free A. inebrians plants growing under hot dry field conditions. The presence of Epichloë endophyte increased the Shannon and decreased Simpson diversity of bacterial and fungal communities. Sphingomonas and Hymenobacter bacteria and Filobasidium and Mycosphaerella fungi were growing largely epiphytically, whereas Methylobacterium, Escherichia-Shigella, and the fungus Blumeria were mostly found within leaves with the location of colonization influenced by the Epichloë endophyte. In addition, leaf metabolites in Epichloë-infected and Epichloë-free leaves were examined using LC/MS. Epichloë was significantly correlated with 132 metabolites. Epichloë altered the composition and diversity of phyllosphere microbial communities 414 detected metabolites were annotated, of which the 132 differential metabolites There were 229 significant correlations between metabolites and microbial phyla
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Affiliation(s)
- Bowen Liu
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Yawen Ju
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Chao Xia
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Rui Zhong
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | | | - Xingxu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
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Sun Y, Liu Q, Shang S, Chen J, Lu P, Zang Y, Tang X. Physiological Responses and Metabonomics Analysis of Male and Female Sargassum thunbergii Macroalgae Exposed to Ultraviolet-B Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:778602. [PMID: 35481140 PMCID: PMC9037290 DOI: 10.3389/fpls.2022.778602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Ultraviolet-B (UV-B) radiation is a major environmental stress that suppresses or activates defense responses in organisms. UV-B radiation affecting growth and development in intertidal species have been researched for a long time, but a series of unknown knowledge remain in the male and female macroalgae comparison. To compare the different responses of male and female Sargassum thunbergii macroalgae under UV-B radiation, PSII photochemical efficiency determination, metabolomic analysis, and main carbon-based metabolites (including soluble sugar, total amino acid, and lipid) content measuring have been performed in our experiments. Results showed that males have significantly superiority performance in the chlorophyll fluorescence parameters of F v/F m, Y(II), and Y(NO) either low or high UV-B radiation treatments. Metabolomics analysis revealed that carbon and nitrogen metabolism pathways in male and female S. thunbergii were significant components responding to enhanced UV-B radiation. Based on measuring, female S. thunbergii lipid content expressed higher than males without any stimulation. Additionally, under low UV-B radiation stimulation, females total amino acid content shown significantly higher than control group and their lipid content also significantly higher than males. Under high UV-B radiation, males soluble sugar, total amino acid, and lipid content significantly varied from females, which meant that enhancing UV-B stress might altered mainly carbon-based metabolites flowing directions. The present study elucidated the potential role of enhanced UV-B radiation in regulating macroalgae physiological responses, metabolites changing, and reflecting differences between male and female S. thunbergii, contributing to understanding of brown-macroalgae diecious adopting mechanisms in defending intertidal UV-B stresses.
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Affiliation(s)
- Yan Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qian Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shuai Shang
- College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Peiyao Lu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yu Zang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Hamany Djande CY, Steenkamp PA, Piater LA, Tugizimana F, Dubery IA. Hordatines and Associated Precursors Dominate Metabolite Profiles of Barley (Hordeum vulgare L.) Seedlings: A Metabolomics Study of Five Cultivars. Metabolites 2022; 12:metabo12040310. [PMID: 35448497 PMCID: PMC9030721 DOI: 10.3390/metabo12040310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 02/06/2023] Open
Abstract
In the process of enhancing crop potential, metabolomics offers a unique opportunity to biochemically describe plant metabolism and to elucidate metabolite profiles that govern specific phenotypic characteristics. In this study we report an untargeted metabolomic profiling of shoots and roots of barley seedlings performed to reveal the chemical makeup therein at an early growth stage. The study was conducted on five cultivars of barley: ‘Overture’, ‘Cristalia’, ‘Deveron’, ‘LE7′ and ‘Genie’. Seedlings were grown for 16 days post germination under identical controlled conditions, and methanolic extracts were analysed on an ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC–HRMS) system. In addition, an unsupervised pattern identification technique, principal component analysis (PCA), was performed to process the generated multidimensional data. Following annotation of specific metabolites, several classes were revealed, among which phenolic acids represented the largest group in extracts from both shoot and root tissues. Interestingly, hordatines, barley-specific metabolites, were not found in the root tissue. In addition, metabolomic profiling revealed metabolites potentially associated with the plants’ natural protection system against potential pathogens. The study sheds light on the chemical composition of barley at a young developmental stage and the information gathered could be useful in plant research and biomarker-based breeding programs.
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Medina-Lozano I, Díaz A. Applications of Genomic Tools in Plant Breeding: Crop Biofortification. Int J Mol Sci 2022; 23:3086. [PMID: 35328507 PMCID: PMC8950180 DOI: 10.3390/ijms23063086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 12/02/2022] Open
Abstract
Crop breeding has mainly been focused on increasing productivity, either directly or by decreasing the losses caused by biotic and abiotic stresses (that is, incorporating resistance to diseases and enhancing tolerance to adverse conditions, respectively). Quite the opposite, little attention has been paid to improve the nutritional value of crops. It has not been until recently that crop biofortification has become an objective within breeding programs, through either conventional methods or genetic engineering. There are many steps along this long path, from the initial evaluation of germplasm for the content of nutrients and health-promoting compounds to the development of biofortified varieties, with the available and future genomic tools assisting scientists and breeders in reaching their objectives as well as speeding up the process. This review offers a compendium of the genomic technologies used to explore and create biodiversity, to associate the traits of interest to the genome, and to transfer the genomic regions responsible for the desirable characteristics into potential new varieties. Finally, a glimpse of future perspectives and challenges in this emerging area is offered by taking the present scenario and the slow progress of the regulatory framework as the starting point.
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Affiliation(s)
- Inés Medina-Lozano
- Departamento de Ciencia Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, Avda. Montañana 930, 50059 Zaragoza, Spain;
- Instituto Agroalimentario de Aragón—IA2, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Aurora Díaz
- Departamento de Ciencia Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, Avda. Montañana 930, 50059 Zaragoza, Spain;
- Instituto Agroalimentario de Aragón—IA2, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Universidad de Zaragoza, 50013 Zaragoza, Spain
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Zhang Z, Shi Q, Wang B, Ma A, Wang Y, Xue Q, Shen B, Hamaila H, Tang T, Qi X, Fernie AR, Luo J, Li X. Jujube metabolome selection determined the edible properties acquired during domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1116-1133. [PMID: 34862996 DOI: 10.1111/tpj.15617] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/11/2021] [Accepted: 11/27/2021] [Indexed: 05/26/2023]
Abstract
Plants supply both food and medicinal compounds, which are ascribed to diverse metabolites produced by plants. However, studies on domestication-driven changes in the metabolome and genetic basis of bioactive molecules in perennial fruit trees are generally lacking. Here, we conducted multidimensional analyses revealing a singular domestication event involving the genomic and metabolomic selection of jujube trees (Ziziphus jujuba Mill.). The genomic selection for domesticated genes was highly enriched in metabolic pathways, including carbohydrates and specialized metabolism. Domesticated metabolome profiling indicated that 187 metabolites exhibited significant divergence as a result of directional selection. Malic acid was directly selected during domestication, and the simultaneous selection of specialized metabolites, including triterpenes, consequently lead to edible properties. Cyclopeptide alkaloids (CPAs) were specifically targeted for the divergence between dry and fresh cultivars. We identified 1080 significantly associated loci for 986 metabolites. Among them, 15 triterpenes were directly selected at six major loci, allowing the identification of a homologous cluster containing seven 2,3-oxidosqualene cyclases (OSCs). An OSC gene was found to contribute to the reduction in the content of triterpenes during domestication. The complete pathway for synthesizing ursolic acid was dissected by integration of the metabolome and transcriptome. Additionally, an N-methyltransferase involved in the biosynthesis of CPA and responsible for inter-cultivar content variation was identified. The present study promotes our understanding of the selection process of the global metabolome subsequent to fruit tree domestication and facilitates the genetic manipulation of specialized metabolites to enhance their edible traits.
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Affiliation(s)
- Zhong Zhang
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Qianqian Shi
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Bin Wang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, 430070, China
| | - Aimin Ma
- Key Laboratory of Plant Molecular, Physiology Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yongkang Wang
- Pomology Institute, Shanxi Academy of Agricultural Sciences, Taigu, 030815, China
| | - Qingtun Xue
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Bingqi Shen
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Halina Hamaila
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
| | - Tang Tang
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, 430070, China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular, Physiology Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Xingang Li
- College of Forestry, Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, 712100, China
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Metabolomic Analysis Reveals Nutritional Diversity among Three Staple Crops and Three Fruits. Foods 2022; 11:foods11040550. [PMID: 35206028 PMCID: PMC8870860 DOI: 10.3390/foods11040550] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/09/2022] [Accepted: 02/13/2022] [Indexed: 12/15/2022] Open
Abstract
More than 2 billion people worldwide are under threat of nutritional deficiency. Thus, an in-depth comprehension of the nutritional composition of staple crops and popular fruits is essential for health. Herein, we performed LC-MS-based non-targeted and targeted metabolome analyses with crops (including wheat, rice, and corn) and fruits (including grape, banana, and mango). We detected a total of 2631 compounds by using non-targeted strategy and identified more than 260 nutrients. Our work discovered species-dependent accumulation of common present nutrients in crops and fruits. Although rice and wheat lack vitamins and amino acids, sweet corn was rich in most amino acids and vitamins. Among the three fruits, mango had more vitamins and amino acids than grape and banana. Grape and banana provided sufficient 5-methyltetrahydrofolate and vitamin B6, respectively. Moreover, rice and grape had a high content of flavonoids. In addition, the three crops contained more lipids than fruits. Furthermore, we also identified species-specific metabolites. The crops yielded 11 specific metabolites, including flavonoids, lipids, and others. Meanwhile, most fruit-specific nutrients were flavonoids. Our work discovered the complementary pattern of essential nutrients in crops and fruits, which provides metabolomic evidence for a healthy diet.
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Yang C, Shen S, Zhou S, Li Y, Mao Y, Zhou J, Shi Y, An L, Zhou Q, Peng W, Lyu Y, Liu X, Chen W, Wang S, Qu L, Liu X, Fernie AR, Luo J. Rice metabolic regulatory network spanning the entire life cycle. MOLECULAR PLANT 2022; 15:258-275. [PMID: 34715392 DOI: 10.1016/j.molp.2021.10.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/09/2021] [Accepted: 10/21/2021] [Indexed: 05/18/2023]
Abstract
As one of the most important crops in the world, rice (Oryza sativa) is a model plant for metabolome research. Although many studies have focused on the analysis of specific tissues, the changes in metabolite abundance across the entire life cycle have not yet been determined. In this study, combining both targeted and nontargeted metabolite profiling methods, a total of 825 annotated metabolites were quantified in rice samples from different tissues covering the entire life cycle. The contents of metabolites in different tissues of rice were significantly different, with various metabolites accumulating in the plumule and radicle during seed germination. Combining these data with transcriptome data obtained from the same time period, we constructed the Rice Metabolic Regulation Network. The metabolites and co-expressed genes were further divided into 12 clusters according to their accumulation patterns, with members within each cluster displaying a uniform and clear pattern of abundance across development. Using this dataset, we established a comprehensive metabolic profile of the rice life cycle and used two independent strategies to identify novel transcription factors-namely the use of known regulatory genes as bait to screen for new networks underlying lignin metabolism and the unbiased identification of new glycerophospholipid metabolism regulators on the basis of tissue specificity. This study thus demonstrates how guilt-by-association analysis of metabolome and transcriptome data spanning the entire life cycle in cereal crops provides novel resources and tools to aid in understanding the mechanisms underlying important agronomic traits.
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Affiliation(s)
- Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shen Zhou
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Yufei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyuan Mao
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Junjie Zhou
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Yuheng Shi
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Longxu An
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qianqian Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Wenju Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanyuan Lyu
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Xuemei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shouchuang Wang
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Lianghuan Qu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianqing Liu
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China.
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Zhang F, Huang J, Guo H, Yang C, Li Y, Shen S, Zhan C, Qu L, Liu X, Wang S, Chen W, Luo J. OsRLCK160 contributes to flavonoid accumulation and UV-B tolerance by regulating OsbZIP48 in rice. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1380-1394. [PMID: 35079956 DOI: 10.1007/s11427-021-2036-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/12/2021] [Indexed: 12/23/2022]
Abstract
Plants produce specialized metabolites to adapt to the ever-changing environments. Flavonoids are antioxidants essential for growth, development, and breeding with increased stress resistance in crops. However, the mechanism of the involvement of flavonoids in ultraviolet-B (UV-B) stress in rice (Oryza sativa) is largely unknown. In this study, we cloned and functionally identified a receptor-like kinase (OsRLCK160) and a bZIP transcription factor (OsbZIP48) positively regulating flavonoid accumulation through metabolite-based genome-wide association study of the flavonoid content in rice. Meanwhile, OsRLCK160 interacted with and phosphorylated OsbZIP48 to regulate the flavonoid accumulation and participate in UV-B tolerance in rice. Our study indicates the importance of applying OsRLCK160 and OsbZIP48 to advance the fundamental understanding of stable rice production and breed UV-B-tolerant rice varieties, which may contribute to breeding high-yield rice varieties.
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Affiliation(s)
- Feng Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiacheng Huang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Guo
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
| | - Chenkun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yufei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuansong Zhan
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
| | - Lianghuan Qu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianqing Liu
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
| | - Shouchuang Wang
- College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China. .,College of Tropical Crops, Hainan University, Haikou, Hainan, 570288, China.
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Yuan Z, Dong F, Pang Z, Fallah N, Zhou Y, Li Z, Hu C. Integrated Metabolomics and Transcriptome Analyses Unveil Pathways Involved in Sugar Content and Rind Color of Two Sugarcane Varieties. FRONTIERS IN PLANT SCIENCE 2022; 13:921536. [PMID: 35783968 PMCID: PMC9244704 DOI: 10.3389/fpls.2022.921536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/18/2022] [Indexed: 05/02/2023]
Abstract
Metabolic composition can have potential impact on several vital agronomic traits, and metabolomics, which represents the bioactive compounds in plant tissues, is widely considered as a powerful approach for linking phenotype-genotype interactions. However, metabolites related to cane traits such as sugar content, rind color, and texture differences in different sugarcane cultivars using metabolome integrated with transcriptome remain largely inconclusive. In this study, metabolome integrated with transcriptome analyses were performed to identify and quantify metabolites composition, and have better insight into the molecular mechanisms underpinning the different cane traits, namely, brix, rind color, and textures in the stems (S) and leaves (L) of sugarcane varieties FN41 and 165402. We also identified metabolites and associated genes in the phenylpropanoid and flavonoid biosynthesis pathways, starch and sucrose metabolism. A total of 512 metabolites from 11 classes, with the vast majority (122) belonging to flavonoids were identified. Moreover, the relatively high amount of D-fructose 6-p, D-glucose6-p and glucose1-p detected in FN41L may have been transported and distributed by source and sink of the cane, and a majority of them reached the stem of sugarcane FN41L, thereby promoting the high accumulation of sugar in FN41S. Observations also revealed that genes such as C4H, CHS, F3H, F3'H, DFR, and FG2 in phenylpropanoid and flavonoid biosynthesis pathways were the major factors impacting the rind color and contrasting texture of FN41 and 165204. Further analysis revealed that weighted gene co-expression network analysis (WGCNA) hub genes and six transcription factors, namely, Tify and NAC, MYB-related, C2C2-Dof, WRKY, and bHLH play a key role in phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, starch and sucrose metabolism. Additionally, metabolites such as L-phenylalanine, tyrosine, sinapaldehyde, pinobanksin, kaempferin, and nictoflorin were the potential drivers of phenotypic differences. Our finding also demonstrated that genes and metabolites in the starch and sucrose metabolism had a significant effect on cane sugar content. Overall, this study provided valuable insight into the molecular mechanisms underpinning high sugar accumulation and rind color in sugarcane, which we believe is important for future sugarcane breeding programs and the selection of high biomass varieties.
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Affiliation(s)
- Zhaonian Yuan
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
- Province and Ministry Co-sponsored Collaborative Innovation Center of Sugar Industry, Nanning, China
- *Correspondence: Zhaonian Yuan,
| | - Fei Dong
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongmei Zhou
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhi Li
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chaohua Hu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou, China
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Li Z, Gao L, Chang P, Chen Z, Zhang X, Yin W, Fan Y, Wang X. The Impact of Elsinoë ampelina Infection on Key Metabolic Properties in Vitis vinifera 'Red Globe' Berries via Multiomics Approaches. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:15-27. [PMID: 34533970 DOI: 10.1094/mpmi-09-21-0225-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Grape anthracnose caused by Elsinoë ampelina (Shear) is one of the most serious fungal diseases that lead to the quality reduction and yield losses of grape (Vitis vinifera 'Red Globe') berries. In the present study, metabolome and transcriptome analyses were conducted using grape berries in the field after infection with E. ampelina at 7, 10, and 13 days to identify the metabolic properties of berries. In total, 132 metabolites with significant differences and 6,877 differentially expressed genes were detected and shared by three comparisons. The analyses demonstrated that phenylpropanoid, flavonoid, stilbenoid, and nucleotide metabolisms were enriched in E. ampelina-infected grape berries but not amino acid metabolism. Phenolamide, terpene, and polyphenole contents also accumulated during E. ampelina infection. The results provided evidence of the enhancement of secondary metabolites such as resveratrol, α-viniferin, ε-viniferin, and lignins involved in plant defense. The results showed the plant defense-associated metabolic reprogramming caused by E. ampelina infection in grape berry and provided a global metabolic mechanism under E. ampelina stimulation.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linlin Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pingping Chang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ziqiu Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiuming Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wuchen Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanchun Fan
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Identification of α-Glucosidase Inhibitors from Leaf Extract of Pepper ( Capsicum spp.) through Metabolomic Analysis. Metabolites 2021; 11:metabo11100649. [PMID: 34677364 PMCID: PMC8538662 DOI: 10.3390/metabo11100649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/15/2021] [Accepted: 09/18/2021] [Indexed: 12/11/2022] Open
Abstract
Metabolomics and in vitro α-glucosidase inhibitory (AGI) activities of pepper leaves were used to identify bioactive compounds and select genotypes for the management of type 2 diabetes mellitus (T2DM). Targeted metabolite analysis using UPLC-DAD-QToF-MS was employed and identified compounds that belong to flavone and hydroxycinnamic acid derivatives from extracts of pepper leaves. A total of 21 metabolites were detected from 155 samples and identified based on MS fragmentations, retention time, UV absorbance, and previous reports. Apigenin-O-(malonyl) hexoside, luteolin-O-(malonyl) hexoside, and chrysoeriol-O-(malonyl) hexoside were identified for the first time from pepper leaves. Pepper genotypes showed a huge variation in their inhibitory activity against α-glucosidase enzyme(AGE) ranging from 17% to 79%. Genotype GP38 with inhibitory activity of 79% was found to be more potent than the positive control acarbose (70.8%.). Orthogonal partial least square (OPLS) analyses were conducted for the prediction of the AGI activities of pepper leaves based on their metabolite composition. Compounds that contributed the most to the bioactivity prediction model (VIP >1.5), showed a strong inhibitory potency. Caffeoyl-putrescine was found to show a stronger inhibitory potency (IC50 = 145 µM) compared to acarbose (IC50 = 197 µM). The chemometric procedure combined with high-throughput AGI screening was effective in selecting polyphenols of pepper leaf for T2DM management.
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Liu J, Shi K, Shi J, Feng Y, Hao C, Peng J, Chen S. A simple strategy to monitor the temporal and spatial distribution of alkaloids in sacred lotus leaves. Biosci Biotechnol Biochem 2021; 85:1332-1340. [PMID: 33713113 DOI: 10.1093/bbb/zbab038] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/01/2021] [Indexed: 11/13/2022]
Abstract
Owing to the high degree of diversity of metabolite pools and complexity of spatial and temporal distributions within biological tissues, currently available methods for metabolite characterization face large challenges. In this study, the temporal and spatial distributions of the alkaloid components of the medicinal plant lotus (Nelumbo nucifera) were investigated over various growth phases. The results showed that alkaloid biosynthesis in lotus leaf is regulated by development and that there is maximum accumulation of alkaloids when the lotus leaf was completely expanded. Furthermore, alkaloid content tended to be stable in mature lotus leaves. However, there was significant variation in the alkaloid content of lotus leaves with different genotypes, suggesting that genetic background is an important factor that affects the temporal and spatial distributions of alkaloids in sacred lotus leaves. The dynamic contents of alkaloids during the growth and development of lotus leaves provide insight into basic biological differences when sampling.
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Affiliation(s)
- Jing Liu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongzhimennei, Beijing, China
| | - Kaifeng Shi
- Wang Jing Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jia Shi
- National Institutes for Food and Drug Control, Beijing, China
| | - Yunluan Feng
- The Experimental High School Attached to Beijing Normal University, Beijing, China
| | - Chenyang Hao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongzhimennei, Beijing, China
| | - Jing Peng
- Institute of Plant Protection, Hunan Academy of Agriculture Sciences, Furong District, Changsha, Hunan Province, P. R. China
| | - Sha Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongzhimennei, Beijing, China
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Hamany Djande CY, Piater LA, Steenkamp PA, Tugizimana F, Dubery IA. A Metabolomics Approach and Chemometric Tools for Differentiation of Barley Cultivars and Biomarker Discovery. Metabolites 2021; 11:metabo11090578. [PMID: 34564394 PMCID: PMC8466441 DOI: 10.3390/metabo11090578] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/04/2021] [Accepted: 08/20/2021] [Indexed: 12/15/2022] Open
Abstract
One of the ultimate goals of plant breeding is the development of new crop cultivars capable of withstanding increasing environmental stresses, to sustain the constantly growing population and economic demands. Investigating the chemical composition of the above and underground tissues of cultivars is crucial for the understanding of common and specific traits thereof. Using an untargeted metabolomics approach together with appropriate chemometrics tools, the differential metabolite profiles of leaf and root extracts from five cultivars of barley (‘Erica’, ‘Elim’, ‘Hessekwa’, ‘S16’ and ‘Agulhas’) were explored and potential signatory biomarkers were revealed. The study was conducted on seedlings grown for 21 days under identical controlled conditions. An ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) was employed to analyse hydromethanolic leaf and root extracts of barley cultivars. Furthermore, unsupervised and supervised learning algorithms were applied to mine the generated data and to pinpoint cultivar-specific metabolites. Among all the classes of metabolites annotated, phenolic acids and derivatives formed the largest group and also represented the most discriminatory metabolites. In roots, saponarin, an important allelochemical differentially distributed across cultivars, was the only flavonoid annotated. The application of an untargeted metabolomics approach in phenotyping grain crops such as barley was demonstrated, and the metabolites responsible for differentiating between the selected cultivars were revealed. The study provides insights into the chemical architecture of barley, an agro-economically relevant cereal crop; and reiterates the importance of metabolomics tools in plant breeding practices for crop improvement.
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Wei W, Li S, Wang Y, Wang B, Fan G, Zeng Q, Zhao F, Xu C, Zhang X, Tang T, Feng X, Shi J, Shi G, Zhang W, Song G, Li H, Wang F, Zhang Y, Li X, Wang D, Zhang W, Pei J, Wang X, Zhao Z. Metabolome-Based Genome-Wide Association Study Provides Genetic Insights Into the Natural Variation of Foxtail Millet. FRONTIERS IN PLANT SCIENCE 2021; 12:665530. [PMID: 34386024 PMCID: PMC8353534 DOI: 10.3389/fpls.2021.665530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/20/2021] [Indexed: 05/23/2023]
Abstract
The plant metabolome is considered as a bridge between the genome and the phenome and is essential for the interaction between plant growth and the plant environment. Here, we used the liquid chromatography-tandem mass spectrometry method to perform a widely targeted metabolomics analysis of 150 millet germplasm and simultaneous identification and quantification of 330 annotated metabolites. Comparing the metabolic content of different millets revealed significant natural variation of both primary and secondary metabolites, including flavonoids, phenolamides, hydroxycinnamoyl derivatives, nucleotides, and lipids, in the millets from India and the north and south of China; among them, some of the flavonoids are the most prominent. A total of 2.2 TB sequence data were obtained by sequencing 150 accessions of foxtail millet using the Illumina platform. Further digging into the genetic basis of metabolites by mGWAS analysis found that cyanidin 3-O-glucoside and quercetin O-acetylhexside are concentratedly located at 43.55 Mb on chromosome 5 and 26.9 Mb on chromosome 7, and two Lc were mined as candidate genes, respectively. However, the signals of luteolin 7-O-glucoside and kaempferol 3-O-glucoside were also detected at 14.36 Mb on chromosome 3, and five glycosyltransferase genes on this loci were deemed to regulate their content. Our work is the first research to use mGWAS in millet, and it paves the way for future dissection of complex physiological traits in millet.
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Affiliation(s)
- Wei Wei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Shuangdong Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Yixiang Wang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Bin Wang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Guangyu Fan
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Qisen Zeng
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Fang Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Congping Xu
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Xiaolei Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Tang Tang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Xiaolei Feng
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Jian Shi
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Gaolei Shi
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Weiqin Zhang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Guoliang Song
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Huan Li
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Feng Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Yali Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xinru Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Dequan Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Wenying Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Jingjing Pei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xiaoming Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Zhihai Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
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Pál M, Szalai G, Gondor OK, Janda T. Unfinished story of polyamines: Role of conjugation, transport and light-related regulation in the polyamine metabolism in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 308:110923. [PMID: 34034871 DOI: 10.1016/j.plantsci.2021.110923] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 05/27/2023]
Abstract
Polyamines play a fundamental role in the functioning of all cells. Their regulatory role in plant development, their function under stress conditions, and their metabolism have been well documented as regards both synthesis and catabolism in an increasing number of plant species. However, the majority of these studies concentrate on the levels of the most abundant polyamines, sometimes providing data on the enzyme activity or gene expression levels during polyamine synthesis, but generally making no mention of the fact that changes in the polyamine pool are very dynamic, and that other processes are also involved in the regulation of actual polyamine levels. Differences in the distribution of individual polyamines and their conjugation with other compounds were described some time ago, but these have been given little attention. In addition, the role of polyamine transporters in plants is only now being recognised. The present review highlights the importance of conjugated polyamines and also points out that investigations should not only deal with the polyamine metabolism itself, but should also cover other important questions, such as the relationship between light perception and the polyamine metabolism, or the involvement of polyamines in the circadian rhythm.
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Affiliation(s)
- Magda Pál
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Brunszvik u. 2, Martonvásár, H-2462, Hungary.
| | - Gabriella Szalai
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Brunszvik u. 2, Martonvásár, H-2462, Hungary
| | - Orsolya Kinga Gondor
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Brunszvik u. 2, Martonvásár, H-2462, Hungary
| | - Tibor Janda
- Department of Plant Physiology, Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, Brunszvik u. 2, Martonvásár, H-2462, Hungary
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Roumani M, Besseau S, Gagneul D, Robin C, Larbat R. Phenolamides in plants: an update on their function, regulation, and origin of their biosynthetic enzymes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2334-2355. [PMID: 33315095 DOI: 10.1093/jxb/eraa582] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Phenolamides represent a family of specialized metabolites, consisting of the association of hydroxycinnamic acid derivatives with aliphatic or aromatic amines. Since the discovery of the first phenolamide in the late 1940s, decades of phytochemical analyses have revealed a high structural diversity for this family and a wide distribution in the plant kingdom. The occurrence of structurally diverse phenolamides in almost all plant organs has led to early hypotheses on their involvement in floral initiation and fertility, as well as plant defense against biotic and abiotic stress. In the present work, we critically review the literature ascribing functional hypotheses to phenolamides and recent evidence on the control of their biosynthesis in response to biotic stress. We additionally provide a phylogenetic analysis of the numerous N-hydroxycinnamoyltransferases involved in the synthesis of phenolamides and discuss the potential role of other enzyme families in their diversification. The data presented suggest multiple evolutionary events that contributed to the extension of the taxonomic distribution and diversity of phenolamides.
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Affiliation(s)
- Marwa Roumani
- UMR 1121, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine- INRAe, Nancy, France
| | - Sébastien Besseau
- EA 2106, Biomolécules et biotechnologies végétales (BBV), Université de Tours, Tours, France
| | - David Gagneul
- UMR 1158, BioEcoAgro, Université de Lille, INRAe, Université de Liège, UPJV, YNCREA, Université d'Artois, Université Littoral Côte d'Opale, Institut Charles Viollette (ICV), Lille, France
| | - Christophe Robin
- UMR 1121, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine- INRAe, Nancy, France
| | - Romain Larbat
- UMR 1121, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine- INRAe, Nancy, France
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Mass spectrometry based untargeted metabolomics for plant systems biology. Emerg Top Life Sci 2021; 5:189-201. [DOI: 10.1042/etls20200271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022]
Abstract
Untargeted metabolomics enables the identification of key changes to standard pathways, but also aids in revealing other important and possibly novel metabolites or pathways for further analysis. Much progress has been made in this field over the past decade and yet plant metabolomics seems to still be an emerging approach because of the high complexity of plant metabolites and the number one challenge of untargeted metabolomics, metabolite identification. This final and critical stage remains the focus of current research. The intention of this review is to give a brief current state of LC–MS based untargeted metabolomics approaches for plant specific samples and to review the emerging solutions in mass spectrometer hardware and computational tools that can help predict a compound's molecular structure to improve the identification rate.
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Metabolomics Intervention Towards Better Understanding of Plant Traits. Cells 2021; 10:cells10020346. [PMID: 33562333 PMCID: PMC7915772 DOI: 10.3390/cells10020346] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other-omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).
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Li Q, Xu K, Wang S, Li M, Jiang Y, Liang X, Niu J, Wang C. Enzymatic Browning in Wheat Kernels Produces Symptom of Black Point Caused by Bipolaris sorokiniana. Front Microbiol 2020; 11:526266. [PMID: 33362724 PMCID: PMC7756095 DOI: 10.3389/fmicb.2020.526266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 11/17/2020] [Indexed: 01/17/2023] Open
Abstract
To understand the blackening mechanism in black point diseased kernels, ultraviolet–visible light (UV–Vis) and Fourier-transform infrared (FT-IR) absorbance spectra of extracts made from the blackening parts of black point-affected (BP) kernels and the analogous part of black point-free (BPF) kernels were measured using susceptible wheat genotypes “PZSCL6” inoculated with Bipolaris sorokiniana (the dominant pathogen causing this disease). In addition, metabolite differences between BP and BPF kernels were identified by a method that combines gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-high resolution mass spectrometry (LC-MS). Successively, symptoms of black point were produced in vitro. The results showed (i) the spectroscopic properties of the extracts from BP and BPF kernels were very similar, with an absorption peak at 235 nm and a small shoulder at 280–300 nm in both UV–Vis spectra and shared vibrations at 3400–3300, 2925 and 2852, 1512 and 1463, 1709, 1220, 600–860 cm–1 in FT-IR spectra that are consistent with similar bonding characteristics. In contrast, spectroscopic properties of extracts from wheat kernels were different from those of synthetic melanin and extracellular and intracellular melanin produced by B. sorokiniana. (ii) Levels of 156 metabolites in BP kernels were different from those in BPF kernels. Among those 156 metabolites, levels of phenolic acids (ferulic acid and p-coumaric acid), 11 phenolamides compounds, and four benzoxazinone derivatives were significantly higher in BP kernels than in BPF kernels. (iii) Symptom of black point could be produced in vitro in wheat kernels with supplement of phenol substrate (catechol) and H2O2. This result proved that blackening substance causing symptom of black point was produced by enzymatic browning in wheat kernels instead of by B. sorokiniana.
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Affiliation(s)
- Qiaoyun Li
- National Engineering Research Centre for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Kaige Xu
- National Engineering Research Centre for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Siyu Wang
- National Engineering Research Centre for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Mengyu Li
- National Engineering Research Centre for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Yumei Jiang
- National Engineering Research Centre for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Xiaolong Liang
- National Engineering Research Centre for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Jishan Niu
- National Engineering Research Centre for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Chenyang Wang
- National Engineering Research Centre for Wheat/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
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Schaarschmidt S, Fischer A, Lawas LMF, Alam R, Septiningsih EM, Bailey-Serres J, Jagadish SVK, Huettel B, Hincha DK, Zuther E. Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. Int J Mol Sci 2020; 21:ijms21218148. [PMID: 33142722 PMCID: PMC7663775 DOI: 10.3390/ijms21218148] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/20/2020] [Accepted: 10/30/2020] [Indexed: 01/05/2023] Open
Abstract
The wide natural variation present in rice is an important source of genes to facilitate stress tolerance breeding. However, identification of candidate genes from RNA-Seq studies is hampered by the lack of high-quality genome assemblies for the most stress tolerant cultivars. A more targeted solution is the reconstruction of transcriptomes to provide templates to map RNA-seq reads. Here, we sequenced transcriptomes of ten rice cultivars of three subspecies on the PacBio Sequel platform. RNA was isolated from different organs of plants grown under control and abiotic stress conditions in different environments. Reconstructed de novo reference transcriptomes resulted in 37,500 to 54,600 plant-specific high-quality isoforms per cultivar. Isoforms were collapsed to reduce sequence redundancy and evaluated, e.g., for protein completeness (BUSCO). About 40% of all identified transcripts were novel isoforms compared to the Nipponbare reference transcriptome. For the drought/heat tolerant aus cultivar N22, 56 differentially expressed genes in developing seeds were identified at combined heat and drought in the field. The newly generated rice transcriptomes are useful to identify candidate genes for stress tolerance breeding not present in the reference transcriptomes/genomes. In addition, our approach provides a cost-effective alternative to genome sequencing for identification of candidate genes in highly stress tolerant genotypes.
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Affiliation(s)
- Stephanie Schaarschmidt
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
- Correspondence: (S.S.); (E.Z.)
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
| | - Lovely Mae F. Lawas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Rejbana Alam
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (R.A.); (J.B.-S.)
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA;
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (R.A.); (J.B.-S.)
| | - S. V. Krishna Jagadish
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines;
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, 50829 Cologne, Germany;
| | - Dirk K. Hincha
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (A.F.); (L.M.F.L.); (D.K.H.)
- Correspondence: (S.S.); (E.Z.)
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Samulski GB, Gontijo DC, Moreira NC, Brandão GC, Braga de Oliveira A. Dereplication of Palicourea sessilis ethanol extracts by UPLC-DAD-ESI-MS/MS discloses the presence of hydroxycinnamic acid amides and the absence of monoterpene indole alkaloids. BIOCHEM SYST ECOL 2020. [DOI: 10.1016/j.bse.2020.104114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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