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Amalia F, Irifune T, Takegami T, Yusianto, Sumirat U, Putri SP, Fukusaki E. Identification of potential quality markers in Indonesia's Arabica specialty coffee using GC/MS-based metabolomics approach. Metabolomics 2023; 19:90. [PMID: 37880543 PMCID: PMC10600306 DOI: 10.1007/s11306-023-02051-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 09/08/2023] [Indexed: 10/27/2023]
Abstract
INTRODUCTION The cupping test is a widely used method for quality assessment of Arabica coffee. However, the cupping test is limited by the low number of certified panelists and the low throughput. Therefore, an analytical-based quality assessment may be a promising tool to complement the cupping test. A present, there is no report investigating quality marker candidates, focusing only on "specialty" grade Arabica coffee from Indonesia. OBJECTIVE This study identified the potential quality marker(s) in Arabica Specialty coffee at different stages (green beans, roasted beans, and brewed coffee. METHODS The metabolite profiles of ten different Arabica specialty-grade coffees were analyzed with different cup scores using gas chromatography-mass spectrometry (GC/MS). From the ten samples, green coffee beans, roasted coffee beans, and brewed coffee were selected. In addition, an orthogonal projection to latent structure (OPLS) regression analysis was conducted to obtain a potential quality marker based on the variable importance in projection (VIP). The potential quality marker(s) were validated by GC/MS metabolome profiling and OPLS analysis of different sets of samples consisting of 35 Arabica specialty-grade coffee samples. RESULTS In Arabica coffee samples, the OPLS model of the three stages showed galactinol to have a high VIP score. Galactinol showed a consistent positive correlation with cup scores at all stages of coffee production (green beans, roasted beans, and brewed coffee). The correlation suggests galactinol is a potential quality marker after further validation using different samples. CONCLUSION GC/MS combined with OPLS regression analysis suggested galactinol as a quality marker and provide an early screening method for Arabica coffee quality that complements the cupping test performed by certified panelists.
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Affiliation(s)
- Fitri Amalia
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomoya Irifune
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tetsuji Takegami
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yusianto
- Indonesian Coffee and Cocoa Research Institute, Jl. PB. Sudirman 90, Jember, East Java, 68118, Indonesia
| | - Ucu Sumirat
- Indonesian Coffee and Cocoa Research Institute, Jl. PB. Sudirman 90, Jember, East Java, 68118, Indonesia
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Industrial Biotechnology Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Industrial Biotechnology Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Osaka University Shimadzu Omics Innovation Research Laboratories, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Chen J, Nie Y, Xu J, Huang S, Sheng J, Wang X, Zhong J. Sensory and metabolite migration from tilapia skin to soup during the boiling process: fast and then slow. NPJ Sci Food 2022; 6:52. [DOI: 10.1038/s41538-022-00168-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/21/2022] [Indexed: 11/13/2022] Open
Abstract
AbstractThis study mainly studied sensory and metabolite migration from the skin to the soup in the boiling process of tilapia skin using content analysis, electronic nose technique, electronic tongue technique, and metabolomics technique based on ultra-high performance liquid chromatography-mass spectrometry/mass spectrometry and gas chromatography-time-of-flight-mass spectrometry. The content changes, flavor changes, taste changes, metabolite numbers and differential metabolite numbers for both tilapia skin and soup mainly occurred in the initial 30 min. Moreover, the initial 10 min was the key period for the metabolite changes in the boiling process. Further, the differential metabolites in these three periods (0–10, 10–30, and 30–60 min) were identified to show the metabolites migration process. Six (adenine, gingerol, terephthalic acid, vanillin, pentanenitrile, and 2-pyrrolidinonede) and seven (butyramide, lysope(0:0/20:4(5z,8z,11z,14z)), lysope(22:6(4z,7z,10z,13z,16z,19z)/0:0), linoleic acid, N-acetylneuraminic acid, L-threose, and benzoin) chemicals were screened out in the differential metabolites of tilapia skin and soup, respectively, with Variable Importance in the Projection of >1 and p value of <0.05. This work would be beneficial to understand the sensory and metabolite migration in the preparation process of fish soup and provided a metabolomic analysis route to analyze metabolites migration in food.
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Song S, Zhang L, Zhao Y, Sheng C, Zhou W, Dossou SSK, Wang L, You J, Zhou R, Wei X, Zhang X. Metabolome genome-wide association study provides biochemical and genetic insights into natural variation of primary metabolites in sesame. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1051-1069. [PMID: 36176211 DOI: 10.1111/tpj.15995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/19/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Plants' primary metabolites are of great importance from the survival and nutritional perspectives. However, the genetic bases underlying the profiles of primary metabolites in oilseed crops remain largely unclear. As one of the main oilseed crops, sesame (Sesamum indicum L.) is a potential model plant for investigating oil metabolism in plants. Therefore, the objective of this study is to disclose the genetic variants associated with variation in the content of primary metabolites in sesame. We performed a comprehensive metabolomics analysis of primary metabolites in 412 diverse sesame accessions using gas chromatography-mass spectrometry and identified a total of 45 metabolites, including fatty acids, monoacylglycerols (MAGs), and amino acids. Genome-wide association study unveiled 433 significant single-nucleotide polymorphism loci associated with variation in primary metabolite contents in sesame. By integrating diverse genomic analyses, we identified 10 key candidate causative genes of variation in MAG, fatty acid, asparagine, and sucrose contents. Among them, SiDSEL was significantly associated with multiple traits. SiCAC3 and SiKASI were strongly associated with variation in oleic acid and linoleic acid contents. Overexpression of SiCAC3, SiKASI, SiLTPI.25, and SiLTPI.26 in transgenic Arabidopsis and Saccharomyces cerevisiae revealed that SiCAC3 is a potential target gene for improvement of unsaturated fatty acid levels in crops. Furthermore, we found that it may be possible to breed several quality traits in sesame simultaneously. Our results provide valuable genetic resources for improving sesame seed quality and our understanding of oilseed crops' primary metabolism.
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Affiliation(s)
- Shengnan Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Liangxiao Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yan Zhao
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Chen Sheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Wangyi Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Senouwa Segla Koffi Dossou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
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Singh DP, Bisen MS, Shukla R, Prabha R, Maurya S, Reddy YS, Singh PM, Rai N, Chaubey T, Chaturvedi KK, Srivastava S, Farooqi MS, Gupta VK, Sarma BK, Rai A, Behera TK. Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops. Int J Mol Sci 2022; 23:ijms232012062. [PMID: 36292920 PMCID: PMC9603451 DOI: 10.3390/ijms232012062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.
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Affiliation(s)
- Dhananjaya Pratap Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
- Correspondence:
| | - Mansi Singh Bisen
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Renu Shukla
- Indian Council of Agricultural Research (ICAR), Krishi Bhawan, Dr. Rajendra Prasad Road, New Delhi 110001, India
| | - Ratna Prabha
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudarshan Maurya
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Yesaru S. Reddy
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Prabhakar Mohan Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Nagendra Rai
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Tribhuwan Chaubey
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Krishna Kumar Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Mohammad Samir Farooqi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland’s Rural College, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Birinchi K. Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Tusar Kanti Behera
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
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Genome-Wide Identification and Characterization of Chinese Cabbage S1fa Transcription Factors and Their Roles in Response to Salt Stress. Antioxidants (Basel) 2022; 11:antiox11091782. [PMID: 36139856 PMCID: PMC9495863 DOI: 10.3390/antiox11091782] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/24/2022] Open
Abstract
The S1fa transcription factor is part of a small family involved in plant growth and development and abiotic stress tolerance. However, the roles of the S1fa genes in abiotic stress tolerance in Chinese cabbage are still unclear. In this study, four S1fa genes in the Chinese cabbage genome were identified and characterized for abiotic stress tolerance. Tissue-specific expression analysis suggested that three of these four S1fa genes were expressed in all tissues of Chinese cabbage, while Bra006994 was only expressed in the silique. Under Hg and Cd stresses, the S1fa genes were significantly expressed but were downregulated under NaCl stresses. The Bra034084 and Bra029784 overexpressing yeast cells exhibited high sensitivity to NaCl stresses, which led to slower growth compared with the wild type yeast cells (EV) under 1 M NaCl stress. In addition, the growth curve of the Bra034084 and Bra029784 overexpressing cells shows that the optical density was reduced significantly under salt stresses. The activities of the antioxidant enzymes, SOD, POD and CAT, were decreased, and the MDA, H2O2 and O2− contents were increased under salt stresses. The expression levels of cell wall biosynthesis genes Ccw14p, Cha1p, Cwp2p, Sed1p, Rlm1p, Rom2p, Mkk1p, Hsp12p, Mkk2p, Sdp1p and YLR194c were significantly enhanced, while Bck1p, and Ptc1p were downregulated under salt stresses. These results suggest that the Bra034084 and Bra029784 genes regulate cell wall biosynthesis and the defense regulatory system under salt stresses. These findings provide a fundamental basis for the further investigation of crop genetic modification to improve crop production and abiotic stress tolerance in Chinese cabbage.
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Hanifah A, Firmanto H, Putri SP, Fukusaki E. Unique metabolite profiles of Indonesian cocoa beans from different origins and their correlation with temperature. J Biosci Bioeng 2022; 134:125-132. [PMID: 35654674 DOI: 10.1016/j.jbiosc.2022.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/14/2022] [Accepted: 05/02/2022] [Indexed: 12/27/2022]
Abstract
Chocolate flavors vary depending on the origin of the cocoa beans used. Differences in soil, microorganisms, and environmental factors contribute to the formation of flavor precursors in cocoa beans. During cocoa bean fermentation, environmental temperature has been shown to alter metabolite concentrations. However, the correlation between the metabolite profile of cocoa beans and the temperature of their region of origin has not been fully defined. In this study, the metabolite profiles of Indonesian cocoa beans of various origins were evaluated using gas chromatography/mass spectrometry-based analysis, and were found to differ depending on the origin of the bean. Subsequently, the correlation between metabolite profile and environmental temperature of the origin was assessed using orthogonal projection to latent structure regression (OPLS-R) analysis. The analysis revealed that seven metabolites were associated with temperature: γ-aminobutyric acid (GABA), ethanolamine, glycerol, isocitric acid + citric acid, succinic acid, malic acid, and saccharic acid. The findings of this study will be valuable to chocolate industries for the production of single-origin chocolates.
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Affiliation(s)
- Abu Hanifah
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hendy Firmanto
- Indonesian Coffee and Cocoa Research Institute, Jl. PB. Sudirman 90, Jember, Jawa Timur 68118, Indonesia
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan; Osaka University-Shimadzu Omics Innovation Research Laboratories, Osaka University, Osaka 565-0871, Japan
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Zayed A, Sheashea M, Kassem IAA, Farag MA. Red and white cabbages: An updated comparative review of bioactives, extraction methods, processing practices, and health benefits. Crit Rev Food Sci Nutr 2022; 63:7025-7042. [PMID: 35174750 DOI: 10.1080/10408398.2022.2040416] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Red and white cabbages (Brassica oleracea var. capitata f. alba and rubra, respectively) are two of the most commercially valued vegetables in crucifers, well-recognized for their unique sensory and nutritive attributes in addition to a myriad of health-promoting benefits. The current review addressed the differential qualitative/quantitative phytochemical make-ups for the first time for better utilization as nutraceuticals and to identify potential uses based on the chemical makeup of both cultivars (cvs.). In addition, extraction methods are compared highlighting their advantages and/or limitations with regards to improving yield and stability of cabbage bioactives, especially glucosinolates. Besides, the review recapitulated detailed action mechanism and safety of cabbage bioactives, as well as processing technologies to further improve their effects are posed as future perspectives. White and red cabbage cvs. revealed different GLSs profile which affected by food processing, including enzymatic hydrolysis, thermal breakdown, and leaching. In addition, the red cultivar provides high quality pigment for industrial applications. Moreover, non-conventional modern extraction techniques showed promising techniques for the recovery of their bioactive constituents compared to solvent extraction. All these findings pose white and red cabbages as potential candidates for inclusion in nutraceuticals and/or to be commercialized as functional foods prepared in different culinary forms.
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Affiliation(s)
- Ahmed Zayed
- Pharmacognosy Department, College of Pharmacy, Tanta University, Tanta, Egypt
- Institute of Bioprocess Engineering, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Mohamed Sheashea
- Aromatic and Medicinal Plants Department, Desert Research Center, Cairo, Egypt
| | - Iman A A Kassem
- Chemistry of Natural Compounds Department, National Research Centre, Dokki, Giza, Egypt
| | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Cairo, Egypt
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Putri SP, Ikram MMM, Sato A, Dahlan HA, Rahmawati D, Ohto Y, Fukusaki E. Application of gas chromatography-mass spectrometry-based metabolomics in food science and technology. J Biosci Bioeng 2022; 133:425-435. [DOI: 10.1016/j.jbiosc.2022.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 12/23/2022]
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AMINUDIN A, ANDARWULAN N, PALUPI NS, ARIFIANTINI RI. Identification of antioxidant bioactive compounds as potential functional food ingredient from kebar grass (Biophytum petersianum) by metabolomic approach. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.71520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Aminudin AMINUDIN
- Agricultural Development Polytechnic of Bogor, Indonesia; IPB University, Indonesia
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Hosni H, Diallo A, Morcillo F, Vaissayre V, Collin M, Tranchant-Dubreuil C, Dussert S, Joët T, Castaño F, Marquínez X, Stauffer FW, Hodel DR, Castillo Mont JJ, Adam H, Jouannic S, Tregear JW. Redox-related gene expression and sugar accumulation patterns are altered in the edible inflorescence produced by the cultivated form of pacaya palm (Chamaedorea tepejilote). ANNALS OF BOTANY 2021; 128:231-240. [PMID: 33978714 PMCID: PMC8324030 DOI: 10.1093/aob/mcab060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/07/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS The pacaya palm is a dioecious neotropical palm species that is exploited in Latin America for its male inflorescence, which is edible when immature. It is cultivated, in a non-intensive manner, in Guatemala, where a morphotype occurs that produces much larger, more highly branched inflorescences compared with wild palms. We sought to identify molecular factors underlying this phenotypic divergence, which is likely to be a product of domestication. METHODS We performed RNA-seq-based studies on immature pacaya palm male inflorescences in order to identify genes that might be directly or indirectly affected in their expression in relation to domestication. We also measured the accumulation of a range of soluble sugar molecules to provide information on the biochemical status of the two different types of material. KEY RESULTS A total of 408 genes were found to display significantly different expression levels between the wild and cultivated morphotypes. Three different functional categories were found to be enriched in the gene set that was upregulated in the cultivated morphotype: redox balance; secondary metabolism; and transport. Several sugars were found to accumulate at higher levels in inflorescences of the cultivated morphotype, in particular myo-inositol, fructose and glucose. CONCLUSIONS The observed upregulation of redox-related genes in the cultivated morphotype is corroborated by the observation of higher myo-inositol accumulation, which has been shown to be associated with enhanced scavenging of reactive oxygen species in other plants and which may affect meristem activity.
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Affiliation(s)
- Hanene Hosni
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Abdoulaye Diallo
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Fabienne Morcillo
- CIRAD, DIADE, Montpellier, France
- DIADE, Université de Montpellier, Institut de Recherche pour le Développement, Montpellier, France
| | - Virginie Vaissayre
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Myriam Collin
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | | | - Stéphane Dussert
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Thierry Joët
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Felipe Castaño
- Universidad Industrial de Santander, Escuela de Biología, Calle, Bucaramanga, Colombia
| | - Xavier Marquínez
- Universidad Nacional de Colombia, Departamento de Biología, Carrera, Bogotá, Colombia
| | - Fred W Stauffer
- Conservatoire et Jardin botaniques de la Ville de Genève, Université de Genève, Laboratoire de Systématique Végétale et Biodiversité, Chambésy, Switzerland
| | - Donald R Hodel
- University of California, Cooperative Extension, Alhambra, CA, USA
| | | | - Hélène Adam
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Stefan Jouannic
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - James W Tregear
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
- For correspondence. E-mail
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