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Bian H, Song P, Gao Y, Deng Z, Huang C, Yu L, Wang H, Ye B, Cai Z, Pan Y, Wang F, Liu J, Gao X, Chen K, Jia G, Klee HJ, Zhang B. The m 6A reader SlYTH2 negatively regulates tomato fruit aroma by impeding the translation process. Proc Natl Acad Sci U S A 2024; 121:e2405100121. [PMID: 38950372 DOI: 10.1073/pnas.2405100121] [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: 03/20/2024] [Accepted: 05/29/2024] [Indexed: 07/03/2024] Open
Abstract
N6-methyladenosine (m6A) is a fundamentally important RNA modification for gene regulation, whose function is achieved through m6A readers. However, whether and how m6A readers play regulatory roles during fruit ripening and quality formation remains unclear. Here, we characterized SlYTH2 as a tomato m6A reader protein and profiled the binding sites of SlYTH2 at the transcriptome-wide level. SlYTH2 undergoes liquid-liquid phase separation and promotes RNA-protein condensate formation. The target mRNAs of SlYTH2, namely m6A-modified SlHPL and SlCCD1B associated with volatile synthesis, are enriched in SlYTH2-induced condensates. Through polysome profiling assays and proteomic analysis, we demonstrate that knockout of SlYTH2 expedites the translation process of SlHPL and SlCCD1B, resulting in augmented production of aroma-associated volatiles. This aroma enrichment significantly increased consumer preferences for CRISPR-edited fruit over wild type. These findings shed light on the underlying mechanisms of m6A in plant RNA metabolism and provided a promising strategy to generate fruits that are more attractive to consumers.
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Affiliation(s)
- Hanxiao Bian
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ying Gao
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhiping Deng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Chenyang Huang
- Key Laboratory of Macromolecular Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Lei Yu
- School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Hanqing Wang
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Bingbing Ye
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Zhihe Cai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yu Pan
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Southwest University, Chongqing 400715, China
| | - Fengqin Wang
- College of Animal Sciences, Key Laboratory of Animal Nutrition and Feed Sciences, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China
| | - Jianzhao Liu
- Key Laboratory of Macromolecular Synthesis and Functionalization of Ministry of Education, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Xiangwei Gao
- School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Kunsong Chen
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Center of RNA Biology, Peking University, Beijing 100871, China
| | - Harry J Klee
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Bo Zhang
- Zhejiang Key Laboratory of Horticultural Crop Quality Improvement, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya, Hainan 572000, China
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Zhao J, Xu Y, Li H, An W, Yin Y, Wang B, Wang L, Wang B, Duan L, Ren X, Liang X, Wang Y, Wan R, Huang T, Zhang B, Li Y, Luo J, Cao Y. Metabolite-based genome-wide association studies enable the dissection of the genetic bases of flavonoids, betaine and spermidine in wolfberry (Lycium). PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1435-1452. [PMID: 38194521 PMCID: PMC11123438 DOI: 10.1111/pbi.14278] [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: 12/22/2021] [Revised: 10/28/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024]
Abstract
Wolfberry is a plant with medicinal and food values. However, its bioactive ingredients and the corresponding genetic bases have not been determined. Here, we de novo generated a chromosome-level genome assembly for wolfberry, yielding a genome sequence of ~1.77 Gb with contig N50 of 50.55 Mb and 39 224 predicted gene models. A variation map, using 307 re-sequenced accessions, was called based on this genome assembly. Furthermore, the fruit metabolome of these accessions was profiled using 563 annotated metabolites, which separated Lycium barbarum L. and non-L. barbarum L. The flavonoids, coumarins, alkaloids and nicotinic acid contents were higher in the former than in the latter. A metabolite-based genome-wide association study mapped 156 164 significant single nucleotide polymorphisms corresponding to 340 metabolites. This included 19 219 unique lead single nucleotide polymorphisms in 1517 significant association loci, of which three metabolites, flavonoids, betaine and spermidine, were highlighted. Two candidate genes, LbUGT (evm.TU.chr07.2692) and LbCHS (evm.TU.chr07.2738), with non-synonymous mutations, were associated with the flavonoids content. LbCHS is a structural gene that interacts with a nearby MYB transcription factor (evm.TU.chr07.2726) both in L. barbarum and L. ruthenicum. Thus, these three genes might be involved in the biosynthesis/metabolism of flavonoids. LbSSADH (evm.TU.chr09.627) was identified as possibly participating in betaine biosynthesis/metabolism. Four lycibarbarspermidines (E-G and O) were identified, and only the lycibarbarspermidines O content was higher in L. barbarum varieties than in non-L. barbarum varieties. The evm.TU.chr07.2680 gene associated with lycibarbarspermidines O was annotated as an acetyl-CoA-benzylalcohol acetyltransferase, suggesting that it is a candidate gene for spermidine biosynthesis. These results provide novel insights into the specific metabolite profile of non-L. barbarum L. and the genetic bases of flavonoids, betaine and spermidine biosynthesis/metabolism.
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Affiliation(s)
- Jianhua Zhao
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd.UrumchiChina
| | - Haoxia Li
- Desertification Control Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Wei An
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Yue Yin
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Bin Wang
- Wuhan Matware Biotechnology Co., Ltd.WuhanChina
| | - Liping Wang
- School of breeding and multiplcation (Sanya Institute of Breeding and Multiplication)Hainan, UniversitySanyaChina
| | - Bi Wang
- School of breeding and multiplcation (Sanya Institute of Breeding and Multiplication)Hainan, UniversitySanyaChina
| | - Linyuan Duan
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Xiaoyue Ren
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Xiaojie Liang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Yajun Wang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Ru Wan
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Ting Huang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Bo Zhang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Yanlong Li
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
| | - Jie Luo
- School of breeding and multiplcation (Sanya Institute of Breeding and Multiplication)Hainan, UniversitySanyaChina
| | - Youlong Cao
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry SciencesYinchuanChina
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Cao X, Li X, Su Y, Zhang C, Wei C, Chen K, Grierson D, Zhang B. Transcription factor PpNAC1 and DNA demethylase PpDML1 synergistically regulate peach fruit ripening. PLANT PHYSIOLOGY 2024; 194:2049-2068. [PMID: 37992120 DOI: 10.1093/plphys/kiad627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/24/2023]
Abstract
Fruit ripening is accompanied by dramatic changes in color, texture, and flavor and is regulated by transcription factors (TFs) and epigenetic factors. However, the detailed regulatory mechanism remains unclear. Gene expression patterns suggest that PpNAC1 (NAM/ATAF1/2/CUC) TF plays a major role in peach (Prunus persica) fruit ripening. DNA affinity purification (DAP)-seq combined with transactivation tests demonstrated that PpNAC1 can directly activate the expression of multiple ripening-related genes, including ACC synthase1 (PpACS1) and ACC oxidase1 (PpACO1) involved in ethylene biosynthesis, pectinesterase1 (PpPME1), pectate lyase1 (PpPL1), and polygalacturonase1 (PpPG1) related to cell wall modification, and lipase1 (PpLIP1), fatty acid desaturase (PpFAD3-1), and alcohol acyltransferase1 (PpAAT1) involved in volatiles synthesis. Overexpression of PpNAC1 in the tomato (Solanum lycopersicum) nor (nonripening) mutant restored fruit ripening, and its transient overexpression in peach fruit induced target gene expression, supporting a positive role of PpNAC1 in fruit ripening. The enhanced transcript levels of PpNAC1 and its target genes were associated with decreases in their promoter mCG methylation during ripening. Declining DNA methylation was negatively associated with increased transcripts of DNA demethylase1 (PpDML1), whose promoter is recognized and activated by PpNAC1. We propose that decreased methylation of the promoter region of PpNAC1 leads to a subsequent decrease in DNA methylation levels and enhanced transcription of ripening-related genes. These results indicate that positive feedback between PpNAC1 and PpDML1 plays an important role in directly regulating expression of multiple genes required for peach ripening and quality formation.
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Affiliation(s)
- Xiangmei Cao
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Xinzhao Li
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yike Su
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Chi Zhang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Chunyan Wei
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Desheng Middle Road No. 298, Hangzhou, Zhejiang Province 310021, China
| | - Kunsong Chen
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Donald Grierson
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Bo Zhang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
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Yan Y, Wang W, Hu T, Hu H, Wang J, Wei Q, Bao C. Metabolomic and Transcriptomic Analyses Reveal the Effects of Grafting on Nutritional Properties in Eggplant. Foods 2023; 12:3082. [PMID: 37628081 PMCID: PMC10453275 DOI: 10.3390/foods12163082] [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: 07/04/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Grafting has a significant impact on the botany properties, commercial character, disease resistance, and productivity of eggplants. However, the mechanism of phenotypic modulation on grafted eggplants is rarely reported. In this study, a widely cultivated eggplant (Solanum. melongena cv. 'Zheqie No.10') was selected as the scion and grafted, respectively, onto four rootstocks of TOR (S. torvum), Sa (S. aculeatissimum), SS (S. sisymbriifolium), and Sm64R (S. melongena cv. 'Qiezhen No. 64R') for phenotypic screening. Physiological and biochemical analysis showed the rootstock Sm64R could improve the fruit quality with the increasing of fruit size, yield, and the contents of total soluble solid, phenolic acid, total amino acid, total sugar, and vitamin C. To further investigate the improvement of fruit quality on Sm64R, a transcriptome and a metabolome between the Sm64R-grafted eggplant and self-grafted eggplant were performed. Significant differences in metabolites, such as phenolic acids, lipids, nucleotides and derivatives, alkaloids, terpenoids, and amino acids, were observed. Differential metabolites and differentially expressed genes were found to be abundant in three core pathways of nutritional qualities, including biosynthesis of phenylpropanoids, phospholipids, and nucleotide metabolism. Thus, this study may provide a novel insight into the effects of grafting on the fruit quality in eggplant.
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Affiliation(s)
| | | | | | | | | | | | - Chonglai Bao
- Institute of Vegetable, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China; (Y.Y.); (W.W.); (T.H.); (H.H.); (J.W.); (Q.W.)
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Zhang J, Liu S, Zhu X, Chang Y, Wang C, Ma N, Wang J, Zhang X, Lyu J, Xie J. A Comprehensive Evaluation of Tomato Fruit Quality and Identification of Volatile Compounds. PLANTS (BASEL, SWITZERLAND) 2023; 12:2947. [PMID: 37631159 PMCID: PMC10457953 DOI: 10.3390/plants12162947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 07/23/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023]
Abstract
Tomatoes (Lycopersicon esculentum) are the most valuable vegetable crop in the world. This study identified the morphological characteristics, vitamin content, etc., from 15 tomato varieties in total, that included five each from the three experimental types, during the commercial ripening period. The results showed that the hardness with peel and the moisture content of tasty tomatoes were 157.81% and 54.50%, and 3.16% and 1.90% lower than those of regular tomatoes and cherry tomatoes, respectively, while the soluble solids were 60.25% and 20.79% higher than those of the latter two types. In addition, the contents of vitamin C, lycopene, fructose, glucose, and total organic acids of tasty tomatoes were higher than those of regular tomatoes and cherry tomatoes. A total of 110 volatile compounds were detected in the 15 tomato varieties. The average volatile compound content of tasty tomatoes was 57.94% higher than that of regular tomatoes and 15.24% higher than that of cherry tomatoes. Twenty of the 34 characteristic tomato aroma components were identified in tasty tomatoes, with fruity and green being the main odor types. Ten characteristic aroma components in regular tomatoes were similar to those of tasty tomatoes; ten types of cherry tomatoes had floral and woody aromas as the main odor types. The flavor sensory score was significantly positively correlated with the content of soluble solids, fructose, glucose, citric acid, fumaric acid, and β-ionone (p < 0.01), and significantly negatively correlated with water content and firmness without peel. Regular, tasty, and cherry tomatoes were separated using principal component analysis, and the quality of tasty tomatoes was found to be better than cherry tomatoes, followed by regular tomatoes. These results provide valuable information for a comprehensive evaluation of fruit quality among tomato varieties to develop consumer guidelines.
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Affiliation(s)
- Jing Zhang
- College of Horticulture, Gansu Agricultural University, Anning District, Yingmeng Village, Lanzhou 730070, China; (J.Z.); (S.L.); (Y.C.); (C.W.); (N.M.); (J.W.); (X.Z.); (J.L.)
| | - Sitian Liu
- College of Horticulture, Gansu Agricultural University, Anning District, Yingmeng Village, Lanzhou 730070, China; (J.Z.); (S.L.); (Y.C.); (C.W.); (N.M.); (J.W.); (X.Z.); (J.L.)
| | - Xiumei Zhu
- Gansu Inspection and Testing Center for Agricultural Product Quality and Safety, Lanzhou 730000, China;
| | - Youlin Chang
- College of Horticulture, Gansu Agricultural University, Anning District, Yingmeng Village, Lanzhou 730070, China; (J.Z.); (S.L.); (Y.C.); (C.W.); (N.M.); (J.W.); (X.Z.); (J.L.)
| | - Cheng Wang
- College of Horticulture, Gansu Agricultural University, Anning District, Yingmeng Village, Lanzhou 730070, China; (J.Z.); (S.L.); (Y.C.); (C.W.); (N.M.); (J.W.); (X.Z.); (J.L.)
| | - Ning Ma
- College of Horticulture, Gansu Agricultural University, Anning District, Yingmeng Village, Lanzhou 730070, China; (J.Z.); (S.L.); (Y.C.); (C.W.); (N.M.); (J.W.); (X.Z.); (J.L.)
| | - Junwen Wang
- College of Horticulture, Gansu Agricultural University, Anning District, Yingmeng Village, Lanzhou 730070, China; (J.Z.); (S.L.); (Y.C.); (C.W.); (N.M.); (J.W.); (X.Z.); (J.L.)
| | - Xiaodan Zhang
- College of Horticulture, Gansu Agricultural University, Anning District, Yingmeng Village, Lanzhou 730070, China; (J.Z.); (S.L.); (Y.C.); (C.W.); (N.M.); (J.W.); (X.Z.); (J.L.)
| | - Jian Lyu
- College of Horticulture, Gansu Agricultural University, Anning District, Yingmeng Village, Lanzhou 730070, China; (J.Z.); (S.L.); (Y.C.); (C.W.); (N.M.); (J.W.); (X.Z.); (J.L.)
| | - Jianming Xie
- College of Horticulture, Gansu Agricultural University, Anning District, Yingmeng Village, Lanzhou 730070, China; (J.Z.); (S.L.); (Y.C.); (C.W.); (N.M.); (J.W.); (X.Z.); (J.L.)
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Li X, Tieman D, Alseekh S, Fernie AR, Klee HJ. Natural variations in the Sl-AKR9 aldo/keto reductase gene impact fruit flavor volatile and sugar contents. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1134-1150. [PMID: 37243881 DOI: 10.1111/tpj.16310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/29/2023]
Abstract
The unique flavors of different fruits depend upon complex blends of soluble sugars, organic acids, and volatile organic compounds. 2-Phenylethanol and phenylacetaldehyde are major contributors to flavor in many foods, including tomato. In the tomato fruit, glucose, and fructose are the chemicals that most positively contribute to human flavor preferences. We identified a gene encoding a tomato aldo/keto reductase, Sl-AKR9, that is associated with phenylacetaldehyde and 2-phenylethanol contents in fruits. Two distinct haplotypes were identified; one encodes a chloroplast-targeted protein while the other encodes a transit peptide-less protein that accumulates in the cytoplasm. Sl-AKR9 effectively catalyzes reduction of phenylacetaldehyde to 2-phenylethanol. The enzyme can also metabolize sugar-derived reactive carbonyls, including glyceraldehyde and methylglyoxal. CRISPR-Cas9-induced loss-of-function mutations in Sl-AKR9 significantly increased phenylacetaldehyde and lowered 2-phenylethanol content in ripe fruit. Reduced fruit weight and increased soluble solids, glucose, and fructose contents were observed in the loss-of-function fruits. These results reveal a previously unidentified mechanism affecting two flavor-associated phenylalanine-derived volatile organic compounds, sugar content, and fruit weight. Modern varieties of tomato almost universally contain the haplotype associated with larger fruit, lower sugar content, and lower phenylacetaldehyde and 2-phenylethanol, likely leading to flavor deterioration in modern varieties.
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Affiliation(s)
- Xiang Li
- Horticultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Denise Tieman
- Horticultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Harry J Klee
- Horticultural Sciences, Genetics Institute, University of Florida, Gainesville, Florida, 32611, USA
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Kaur G, Abugu M, Tieman D. The dissection of tomato flavor: biochemistry, genetics, and omics. FRONTIERS IN PLANT SCIENCE 2023; 14:1144113. [PMID: 37346138 PMCID: PMC10281629 DOI: 10.3389/fpls.2023.1144113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/02/2023] [Indexed: 06/23/2023]
Abstract
Flavor and quality are the major drivers of fruit consumption in the US. However, the poor flavor of modern commercial tomato varieties is a major cause of consumer dissatisfaction. Studies in flavor research have informed the role of volatile organic compounds in improving overall liking and sweetness of tomatoes. These studies have utilized and applied the tools of molecular biology, genetics, biochemistry, omics, machine learning, and gene editing to elucidate the compounds and biochemical pathways essential for good tasting fruit. Here, we discuss the progress in identifying the biosynthetic pathways and chemical modifications of important tomato volatile compounds. We also summarize the advances in developing highly flavorful tomato varieties and future steps toward developing a "perfect tomato".
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Affiliation(s)
- Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Modesta Abugu
- Department of Horticulture Science, North Carolina State University, Raleigh, NC, United States
| | - Denise Tieman
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
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Guo S, Ji Y, Zheng Y, Watkins CB, Ma L, Wang Q, Liang H, Bai C, Fu A, Li L, Meng D, Liu M, Zuo J. Transcriptomic, metabolomic, and ATAC-seq analysis reveal the regulatory mechanism of senescence of post-harvest tomato fruit. FRONTIERS IN PLANT SCIENCE 2023; 14:1142913. [PMID: 36968400 PMCID: PMC10032333 DOI: 10.3389/fpls.2023.1142913] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Several physiological changes occur during fruit storage, which include the regulation of genes, metabolisms and transcription factors. In this study, we compared 'JF308' (a normal tomato cultivar) and 'YS006' (a storable tomato cultivar) to determine the difference in accumulated metabolites, gene expression, and accessible chromatin regions through metabolome, transcriptome, and ATAC-seq analysis. A total of 1006 metabolites were identified in two cultivars. During storage time, sugars, alcohols and flavonoids were found to be more abundant in 'YS006' compared to 'JF308' on day 7, 14, and 21, respectively. Differentially expressed genes, which involved in starch and sucrose biosynthesis were observed higher in 'YS006'. 'YS006' had lower expression levels of CesA (cellulose synthase), PL (pectate lyase), EXPA (expansin) and XTH (xyglucan endoglutransglucosylase/hydrolase) than 'JF308'. The results showed that phenylpropanoid pathway, carbohydrate metabolism and cell wall metabolism play important roles in prolonging the shelf life of tomato (Solanum lycopersicum) fruit. The ATAC-seq analysis revealed that the most significantly up-regulated transcription factors during storage were TCP 2,3,4,5, and 24 in 'YS006' compared to 'JF308' on day 21. This information on the molecular regulatory mechanisms and metabolic pathways of post-harvest quality changes in tomato fruit provides a theoretical foundation for slowing post-harvest decay and loss, and has theoretical importance and application value in breeding for longer shelf life cultivars.
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Affiliation(s)
- Susu Guo
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanhai Ji
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanyan Zheng
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Christopher B. Watkins
- School of Integrative Plant Science, Horticulture Section, College of Agriculture and Life Science, Cornell University, NY, Ithaca, United States
| | - Lili Ma
- College of Food Science and Biotechnology, Tianjin Agricultural University, Tianjin, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hao Liang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunmei Bai
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Anzhen Fu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ling Li
- College of Food Science and Biotechnology, Tianjin Agricultural University, Tianjin, China
| | - Demei Meng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China
| | - Mingchi Liu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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9
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Vegetable biology and breeding in the genomics era. SCIENCE CHINA. LIFE SCIENCES 2023; 66:226-250. [PMID: 36508122 DOI: 10.1007/s11427-022-2248-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize, thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.
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10
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Zhang H, Zhu X, Xu R, Yuan Y, Abugu MN, Yan C, Tieman D, Li X. Postharvest chilling diminishes melon flavor via effects on volatile acetate ester biosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 13:1067680. [PMID: 36684781 PMCID: PMC9853462 DOI: 10.3389/fpls.2022.1067680] [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: 10/12/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
In postharvest handling systems, refrigeration can extend fruit shelf life and delay decay via slowing ripening progress; however, it selectively alters the biosynthesis of flavor-associated volatile organic compounds (VOCs), which results in reduced flavor quality. Volatile esters are major contributors to melon fruit flavor. The more esters, the more consumers enjoy the melon fruit. However, the effects of chilling on melon flavor and volatiles associated with consumer liking are yet to be fully understood. In the present study, consumer sensory evaluation showed that chilling changed the perception of melon fruit. Total ester content was lower after chilling, particularly volatile acetate esters (VAEs). Transcriptomic analysis revealed that transcript abundance of multiple flavor-associated genes in fatty acid and amino acid pathways was reduced after chilling. Additionally, expression levels of the transcription factors (TFs), such as NOR, MYB, and AP2/ERF, also were substantially downregulated, which likely altered the transcript levels of ester-associated pathway genes during cold storage. VAE content and expression of some key genes recover after transfer to room temperature. Therefore, chilling-induced changes of VAE profiles were consistent with expression patterns of some pathway genes that encode specific fatty acid- and amino acid-mobilizing enzymes as well as TFs involved in fruit ripening, metabolic regulation, and hormone signaling.
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Affiliation(s)
- Huijun Zhang
- School of Life Science, Huaibei Normal University, Huaibei, Anhui, China
| | - Xiuxiu Zhu
- School of Life Science, Huaibei Normal University, Huaibei, Anhui, China
| | - Runzhe Xu
- School of Life Science, Huaibei Normal University, Huaibei, Anhui, China
| | - Yushu Yuan
- School of Life Science, Huaibei Normal University, Huaibei, Anhui, China
| | - Modesta N. Abugu
- Horticultural Sciences, North Carolina State University, Raleigh, NC, United States
| | - Congsheng Yan
- Horticultural Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Denise Tieman
- Horticultural Sciences, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Xiang Li
- Horticultural Sciences, Genetics Institute, University of Florida, Gainesville, FL, United States
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11
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Yang S, Sun Z, Zhang G, Wang L, Zhong Q. Identification of the key metabolites and related genes network modules highly associated with the nutrients and taste components among different Pepino (Solanum muricatum) cultivars. Food Res Int 2023; 163:112287. [PMID: 36596193 DOI: 10.1016/j.foodres.2022.112287] [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: 04/15/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
There is considerable knowledge about plant compounds that produce flavor, scent, and aroma. Aside from the similarities, however, groups of plant-produced nutrients and taste components have little in common with each other. Network analysis holds promise for metabolic gene discovery, which is especially important in plant systems where metabolic networks are not yet fully resolved. To bridge this gap, we propose a joint model of gene regulation and metabolic reactions in two different pepino varieties. Differential metabolomics analysis is carried out for detection of eventual interaction of compound. We adopted a multi-omics approach to profile the transcriptome and metabolome analyze differences in phenolic acids, flavonoids, organic acids, lipids, alkaloids, and sugars between LOF and SRF. The two most predominant classes of metabolites are phenolic acids and lipids in pepino. Overall results show enrichment in most DEGs was carbohydrate and biosynthesis of secondary metabolites pathway. Results of DEMs predominantly comprised N-p-coumaroyl agmatine and tryptamine, and significant differences were observed in their expression between LOF and SRF. Integrated DEMs and DEGs specific networks were constructed by combining two types of networks: transcriptional regulatory networks composed of interactions between DEMs and the regulated genes, and pepino metabolite-metabolite interaction networks. Newly discovered features, such as DEGs (USPA, UBE2 and DELLA) involved in the production of secondary metabolites are found in coregulated gene clusters. Moreover, lipid metabolites were most involved in DEMs correlations by OPLS-DA while identifying a significant number of DEGs co-regulated by SENP1, HMGCS et al. These results further that the metabolite discrepancies result from characterized the nutrients and taste components between two pepino genotype. Among the possible causes of the differences between species in pepino metabolite concentrations is co-regulated by these DEGs, continue to suggest that novel features of metabolite biosynthetic pathway remain to be uncovered. Finally, the integrated metabolome and transcriptome analyses have revealed that many important metabolic pathways are regulated at the transcriptional level. The metabolites content differences observed among varieties of the same species mainly originates from different regulated genes and enzymes expression. Overall, this study provides new insights into the underlying causes of differences in the plant metabolites and suggests that genetic data can be used to improve its nutrients and taste components.
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Affiliation(s)
- Shipeng Yang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China; College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100, China
| | - Zhu Sun
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China
| | - Guangnan Zhang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China
| | - Lihui Wang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China
| | - Qiwen Zhong
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China.
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12
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Deng Y, Liu R, Zheng M, Wang Z, Yu S, Zhou Y, Zhou Z, Diao J. From the First to Third Generation of Neonicotinoids: Implication for Saving the Loss of Fruit Quality and Flavor by Pesticide Applications. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15415-15429. [PMID: 36451590 DOI: 10.1021/acs.jafc.2c06055] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Neonicotinoids can control crop pests with high efficiency and low cost and have quickly swept one-fourth of the global insecticide market since the launch of imidacloprid in 1991. Imidacloprid and acetamiprid, the first generation of neonicotinoids, and dinotefuran, the representative of third generation of neonicotinoids, were applied on tomato plants individually to investigate neonicotinoid effects on tomato fruit quality, especially on appearance parameters, sugar, acid, and aroma compounds. Compared with the control, fewer differences in the transcriptome profile, sugar, acid, and volatile organic compound (VOC) contents, and sensory analysis results were shown in dinotefuran treatments than in the other two treatments. Therefore, dinotefuran was more recommended to control pests of tomatoes with less loss of fruit flavor and quality as well as lower ecological risks.
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Affiliation(s)
- Yue Deng
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing 400715, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Beijing 100193, P.R. China
| | - Rui Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Beijing 100193, P.R. China
| | - Meiling Zheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Beijing 100193, P.R. China
| | - Zikang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Beijing 100193, P.R. China
| | - Simin Yu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Beijing 100193, P.R. China
| | - Yihui Zhou
- Center of Disease Control and Prevention, Shijingshan District, Beijing 100043, China
| | - Zhiqiang Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Beijing 100193, P.R. China
| | - Jinling Diao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Applied Chemistry, China Agricultural University, Beijing 100193, P.R. China
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13
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Rajewski A, Maheepala DC, Le J, Litt A. Multispecies transcriptomes reveal core fruit development genes. FRONTIERS IN PLANT SCIENCE 2022; 13:954929. [PMID: 36407608 PMCID: PMC9673247 DOI: 10.3389/fpls.2022.954929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
During angiosperm evolution there have been repeated transitions from an ancestral dry fruit to a derived fleshy fruit, often with dramatic ecological and economic consequences. Following the transition to fleshy fruits, domestication may also dramatically alter the fruit phenotype via artificial selection. Although the morphologies of these fruits are well documented, relatively less is known about the molecular basis of these developmental and evolutionary shifts. We generated RNA-seq libraries from pericarp tissue of desert tobacco and both cultivated and wild tomato species at common developmental time points and combined this with corresponding, publicly available data from Arabidopsis and melon. With this broadly sampled dataset consisting of dry/fleshy fruits and wild/domesticated species, we applied novel bioinformatic methods to investigate conserved and divergent patterns of gene expression during fruit development and evolution. A small set of 121 orthologous "core" fruit development genes show a common pattern of expression across all five species. These include key players in developmental patterning such as orthologs of KNOLLE, PERIANTHIA, and ARGONAUTE7. GO term enrichment suggests that these genes function in basic cell division processes, cell wall biosynthesis, and developmental patterning. We furthermore uncovered a number of "accessory" genes with conserved expression patterns within but not among fruit types, and whose functional enrichment highlights the conspicuous differences between these phenotypic classes. We observe striking conservation of gene expression patterns despite large evolutionary distances, and dramatic phenotypic shifts, suggesting a conserved function for a small subset of core fruit development genes.
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14
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Matsui K, Engelberth J. Green Leaf Volatiles-The Forefront of Plant Responses Against Biotic Attack. PLANT & CELL PHYSIOLOGY 2022; 63:1378-1390. [PMID: 35934892 DOI: 10.1093/pcp/pcac117] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/27/2022] [Accepted: 08/07/2022] [Indexed: 05/23/2023]
Abstract
Green leaf volatiles (GLVs) are six-carbon volatile oxylipins ubiquitous in vascular plants. GLVs are produced from acyl groups in the biological membranes via oxygenation by a pathway-specific lipoxygenase (LOX) and a subsequent cleavage reaction by hydroperoxide lyase. Because of the universal distribution and ability to form GLVs, they have been anticipated to play a common role in vascular plants. While resting levels in intact plant tissues are low, GLVs are immediately synthesized de novo in response to stresses, such as insect herbivory, that disrupt the cell structure. This rapid GLV burst is one of the fastest responses of plants to cell-damaging stresses; therefore, GLVs are the first plant-derived compounds encountered by organisms that interact with plants irrespective of whether the interaction is competitive or friendly. GLVs should therefore be considered important mediators between plants and organisms that interact with them. GLVs can have direct effects by deterring herbivores and pathogens as well as indirect effects by attracting predators of herbivores, while other plants can recruit them to prepare their defenses in a process called priming. While the beneficial effects provided to plants by GLVs are often less dramatic and even complementary, the buildup of these tiny effects due to the multiple functions of GLVs can amass to levels that become substantially beneficial to plants. This review summarizes the current understanding of the spatiotemporal resolution of GLV biosynthesis and GLV functions and outlines how GLVs support the basic health of plants.
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Affiliation(s)
- Kenji Matsui
- Graduate School of Sciences and Technology for Innovation (Agriculture), Yamaguchi University, Yoshida, Yamaguchi 753-8515, Japan
| | - Jurgen Engelberth
- Department of Integrative Biology, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA
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15
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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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16
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Gao Y, Lin Y, Xu M, Bian H, Zhang C, Wang J, Wang H, Xu Y, Niu Q, Zuo J, Fu DQ, Pan Y, Chen K, Klee H, Lang Z, Zhang B. The role and interaction between transcription factor NAC-NOR and DNA demethylase SlDML2 in the biosynthesis of tomato fruit flavor volatiles. THE NEW PHYTOLOGIST 2022; 235:1913-1926. [PMID: 35686614 DOI: 10.1111/nph.18301] [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] [Received: 02/17/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Flavor-imparting volatile chemicals accumulate as fruits ripen, making major contributions to taste. The NAC transcription factor nonripening (NAC-NOR) and DNA demethylase 2 (SlDML2) are essential for tomato fruit ripening, but details of the potential roles and the relationship between these two regulators in the synthesis of volatiles are lacking. Here, we show substantial reductions in fatty acid and carotenoid-derived volatiles in tomato slnor and sldml2 mutants. An unexpected finding is the redundancy and divergence in volatile profiles, biosynthetic gene expression, and DNA methylation in slnor and sldml2 mutants relative to wild-type tomato fruit. Reduced transcript levels are accompanied by hypermethylation of promoters, including the NAC-NOR target gene lipoxygenase (SlLOXC) that is involved in fatty acid-derived volatile synthesis. Interestingly, NAC-NOR activates SlDML2 expression by directly binding to its promoter both in vitro and in vivo. Meanwhile, reduced NAC-NOR expression in the sldml2 mutant is accompanied by hypermethylation of its promoter. These results reveal a relationship between SlDML2-mediated DNA demethylation and NAC-NOR during tomato fruit ripening. In addition to providing new insights into the metabolic modulation of flavor volatiles, the outcome of our study contributes to understanding the genetics and control of fruit ripening and quality attributes in tomato.
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Affiliation(s)
- Ying Gao
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Yujing Lin
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Min Xu
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Hanxiao Bian
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Chi Zhang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Jingyu Wang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Hanqing Wang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Yaping Xu
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qingfeng Niu
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jinhua Zuo
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Da-Qi Fu
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yu Pan
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Kunsong Chen
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Harry Klee
- Horticultural Sciences, Genetic Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Bo Zhang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
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17
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Li X, Qi L, Zang N, Zhao L, Sun Y, Huang X, Wang H, Yin Z, Wang A. Integrated metabolome and transcriptome analysis of the regulatory network of volatile ester formation during fruit ripening in pear. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 185:80-90. [PMID: 35661588 DOI: 10.1016/j.plaphy.2022.04.030] [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: 01/13/2022] [Revised: 04/04/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
'Nanguo' pear (Pyrus ussuriensis Maxim.) is a typical climacteric fruit with an attractive aroma after postharvest ripening. Esters are the key volatile compounds determining the typical aroma formation. However, the mechanism of aroma-related ester formation remains largely unknown. In this study, we performed transcriptome and metabolome analyses to reveal the changes of aroma-related compounds during pear ripening in the optimal taste period (OTP). During the pear ripening process, typical fatty acid-derived volatile organic compounds (VOCs) are transformed from aldehydes, alcohols, and ketones to esters, where ethyl hexanoate, hexyl acetate, and ethyl butanoate are the dominant esters in the OTP. Rich aroma-related esters in the OTP are associated with the accumulation of important precursors of aroma volatiles, including linoleic acid, α-linolenic acid, γ-linolenic acid, and oleic acid. Genes encoding key biosynthetic enzymes are associated with the altered levels of aroma-related esters. The candidate genes associated with the high levels of aroma-related esters in 'Nanguo' pears are PuFAD2, PuLOX2, PuLOX5, and PuAAT. Additionally, transcription factor (TF) genes such as PuWRKY24, PuIAA29, and PuTINY may play crucial roles in aroma formation during fruit ripening. Hence, we summarized the TFs that regulate VOC metabolism in different fruit species. The results provided a foundation for further research on aroma-related esters in 'Nanguo' pears and could help to elucidate the mechanisms regulating fruit quality improvement.
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Affiliation(s)
- Xiaojing Li
- Key Laboratory of Fruit Postharvest Biology, Shenyang, 110866, China; Key Laboratory of Protected Horticulture, National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, 110866, China; College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Liyong Qi
- Key Laboratory of Fruit Postharvest Biology, Shenyang, 110866, China; Key Laboratory of Protected Horticulture, National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, 110866, China; College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Nannan Zang
- Key Laboratory of Fruit Postharvest Biology, Shenyang, 110866, China; Key Laboratory of Protected Horticulture, National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, 110866, China; College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Lihong Zhao
- Key Laboratory of Fruit Postharvest Biology, Shenyang, 110866, China; Key Laboratory of Protected Horticulture, National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, 110866, China; College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yiqing Sun
- Key Laboratory of Fruit Postharvest Biology, Shenyang, 110866, China; Key Laboratory of Protected Horticulture, National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, 110866, China; College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xuanting Huang
- Key Laboratory of Fruit Postharvest Biology, Shenyang, 110866, China; Key Laboratory of Protected Horticulture, National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, 110866, China; College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hongyu Wang
- Key Laboratory of Fruit Postharvest Biology, Shenyang, 110866, China; Key Laboratory of Protected Horticulture, National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, 110866, China; College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zepeng Yin
- Key Laboratory of Fruit Postharvest Biology, Shenyang, 110866, China; Key Laboratory of Protected Horticulture, National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, 110866, China; College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Aide Wang
- Key Laboratory of Fruit Postharvest Biology, Shenyang, 110866, China; Key Laboratory of Protected Horticulture, National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology, Shenyang, 110866, China; College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
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Yuan X, Cui H, Jin Y, Zhao W, Liu X, Wang Y, Ding J, Liu L, Wen J, Zhao G. Fatty acid metabolism-related genes are associated with flavor-presenting aldehydes in Chinese local chicken. Front Genet 2022; 13:902180. [PMID: 36035160 PMCID: PMC9412053 DOI: 10.3389/fgene.2022.902180] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Aldehydes are primary volatile organic compounds (VOCs) in local Chinese chicken meat and contribute green grass, fatty, citrus, and bitter almond aromas to chicken meat. To understand the genetic basis of these aldehyde VOC aromas, we used approximately 500 Chinese Jingxing Yellow (JXY) chickens to conduct genome-wide association studies (GWAS) on the flavor traits with the data of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs). In total, 501 association variants (253 SNPs and 248 INDELs) were found to be suggestively (SNPs: p-value < 2.77e-06 and INDELs: p-value < 3.78e-05) associated with total aldehydes (the sum of nine aldehydes), hexanal, heptanal, benzaldehyde, (E,E)-2,4-nonadienal, octanal, (E)-2-decenal, nonanal, decanal, and octadecanal. Of them, six SNPs and 23 INDELs reached a genome-wide significance level (SNPs: p-value < 1.38e-07 and INDELs: p-value < 1.89e-06). Potential candidate aldehyde genes were functionally annotated for lipid metabolism, especially fatty acid-related pathways and phospholipid-related gene ontology (GO) terms. Moreover, the GWAS analysis of total aldehydes, hexanal, and nonanal generated the most significant signals, and phenotypic content differed between different genotypes at candidate gene-related loci. For total aldehydes and hexanal traits, candidate genes were annotated based on the significant and suggestive variants on chromosomes 3 and 8 with highly polymorphic linkage blocks. The following candidate genes were also identified: GALM, MAP4K3, GPCPD1, RPS6KA2, CRLS1, ASAP1, TRMT6, SDC1, PUM2, ALDH9A1, MGST3, GMEB1, MECR, LDLRAP1, GPAM and ACSL5. We also found that polyunsaturated fatty acids (PUFAs) (C18:2n6c linoleic acid and C18:3n3 linolenic acid) were significantly correlated with total aldehydes and hexanal contents. PUFAs are important aldehyde precursors, and consistently, our results suggested that candidate genes involved in fatty acid pathways and phospholipid GO terms were identified in association loci. This work provides an understanding of the genetic basis of aldehyde formation, which is a key flavor-forming compound.
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Chen X, Quek SY. Free and glycosidically bound aroma compounds in fruit: biosynthesis, transformation, and practical control. Crit Rev Food Sci Nutr 2022; 63:9052-9073. [PMID: 35452325 DOI: 10.1080/10408398.2022.2064422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fruit aroma makes an initial flavor impression and largely determines the consumer preference and acceptance of fruit products. Free volatile organic compounds (FVOCs) directly make up the characteristic aromas of fruits. While glycosidically bound volatile compounds (GBVs) can be hydrolyzed during fruit ripening, postharvest storage, and processing, releasing the attached aglycones as free volatiles that could alter the overall aroma attributes of fruits. GBVs typically exhibit significantly higher concentrations than their free counterparts in fruits such as grapes, cherries, kiwifruits, tomatoes, and tamarillos. This review highlights the biosynthesis of FVOCs and GBVs in fruit and illustrates their biological transformations for various functional purposes such as detoxification, aroma enhancement, plant defense, and pollinator attraction. Practical applications for regulating the levels of aroma compounds emitted or accumulated in fruit are also reviewed, emphasizing the metabolic engineering of free volatile metabolites and hydrolytic technologies on aroma glycosides. Generally, enzymatic hydrolysis using AR2000 is a common strategy to enhance the sensory attributes of fruit juices/wines, while acidic hydrolysis induces the oxidation and rearrangement of aglycones, generating artifacts with off-aromas. This review associates the occurrence of free and glycosidic bound volatiles in fruit and addresses their importance in fruit flavor enhancement and industrial applications.
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Affiliation(s)
- Xiao Chen
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Siew Young Quek
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
- Riddet Institute, Centre of Research Excellence in Food Research, Palmerston North, New Zealand
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20
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Zhang J, Gu X, Yan W, Lou L, Xu X, Chen X. Characterization of Differences in the Composition and Content of Volatile Compounds in Cucumber Fruit. Foods 2022; 11:foods11081101. [PMID: 35454687 PMCID: PMC9027996 DOI: 10.3390/foods11081101] [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: 02/24/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 02/04/2023] Open
Abstract
The cucumber is characterized by the presence of a wide range of volatile organic compounds (VOCs), which are recognized as the main responsible for its unique flavor. However, research on the types and contents of VOCs in different cucumber cultivars remains fragmentary. Here, using an automatic headspace solid-phase microextraction coupled with the gas chromatography-mass spectrometry method, the VOCs were analyzed in three representative cucumber cultivars, including YX, KX, and GX, with the best, middle, and worst flavor quality, respectively, which were selected from 30 cultivars after flavor quality evaluation. Principal component analysis revealed that the six biological replicates were grouped, indicating high reliability of the data. A total of 163 VOCs were detected. There were 28 differential VOCs in YX compared to GX, 33 differential VOCs in YX compared to KX, and 10 differential VOCs in KX compared to GX. Furthermore, K-means clustering analysis showed that 38 of the 43 no-overlapping differential VOCs were represented by the most abundant compounds detected in YX. The prevailing VOCs in YX included: hydrocarbons, aldehydes, and ketones. The data obtained in the present study extend our understanding the impact of cultivars on VOCs in cucumber and will help facilitate targeted breeding.
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Affiliation(s)
- Jie Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.Z.); (X.G.); (W.Y.); (X.C.)
| | - Xiuchao Gu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.Z.); (X.G.); (W.Y.); (X.C.)
| | - Wenjing Yan
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.Z.); (X.G.); (W.Y.); (X.C.)
| | - Lina Lou
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Xuewen Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.Z.); (X.G.); (W.Y.); (X.C.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
- Correspondence:
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.Z.); (X.G.); (W.Y.); (X.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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21
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Jin Z, Wang J, Cao X, Wei C, Kuang J, Chen K, Zhang B. Peach fruit PpNAC1 activates PpFAD3-1 transcription to provide ω-3 fatty acids for the synthesis of short-chain flavor volatiles. HORTICULTURE RESEARCH 2022; 9:uhac085. [PMID: 35685221 PMCID: PMC9172071 DOI: 10.1093/hr/uhac085] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/27/2022] [Indexed: 06/15/2023]
Abstract
Volatile organic compounds (VOCs) derived from fatty acids are major contributors to fruit flavor and affect human preferences. The ω-3 fatty acid linolenic acid 3 (18:3) serves as an important precursor for synthesis of (E)-2-hexenal and (Z)-3-hexenol. These short-chain C6 VOCs provide unique fresh notes in multiple fruit species. Metabolic engineering to improve fruit aroma requires knowledge of the regulation of fatty acid-derived VOCs. Here, we determined that ripe fruit-specific expression of PpFAD3-1 contributes to 18:3 synthesis in peach fruit. However, no significant increases in (E)-2-hexenal and (Z)-3-hexenol were detected after overexpressing PpFAD3-1. Interestingly, overexpressing the PpNAC1 transcription factor increased the content of 18:3 and enhanced the production of its derived volatiles. Moreover, induced expression of genes responsible for downstream VOC synthesis was observed for transgenic tomato fruit overexpressing PpNAC1, but not for transgenic fruit overexpressing PpFAD3-1. Electrophoretic mobility shift and ChIP-Seq assays showed that PpNAC1 activated PpFAD3-1 expression via binding to its promoter. Therefore, PpNAC1 plays an important role in modulating fatty acid flux to produce fruit flavor-related VOCs. In addition to PpNAC1, PpFAD3-1 expression was also associated with epigenetic modifications during peach fruit ripening. Taken together, our results provide new insights into the molecular mechanisms regulating biosynthesis of fatty acid and short-chain VOCs in fruit.
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Affiliation(s)
- Zhengnan Jin
- Laboratory of Fruit Quality Biology, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Jiaojiao Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang Campus, Shanghai 200240, China
| | - Xiangmei Cao
- Laboratory of Fruit Quality Biology, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Chunyan Wei
- Laboratory of Fruit Quality Biology, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Jianfei Kuang
- Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou 510642, China
| | - Kunsong Chen
- Laboratory of Fruit Quality Biology, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Bo Zhang
- Laboratory of Fruit Quality Biology, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
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22
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Fiesel PD, Parks HM, Last RL, Barry CS. Fruity, sticky, stinky, spicy, bitter, addictive, and deadly: evolutionary signatures of metabolic complexity in the Solanaceae. Nat Prod Rep 2022; 39:1438-1464. [PMID: 35332352 DOI: 10.1039/d2np00003b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: 2000-2022Plants collectively synthesize a huge repertoire of metabolites. General metabolites, also referred to as primary metabolites, are conserved across the plant kingdom and are required for processes essential to growth and development. These include amino acids, sugars, lipids, and organic acids. In contrast, specialized metabolites, historically termed secondary metabolites, are structurally diverse, exhibit lineage-specific distribution and provide selective advantage to host species to facilitate reproduction and environmental adaptation. Due to their potent bioactivities, plant specialized metabolites attract considerable attention for use as flavorings, fragrances, pharmaceuticals, and bio-pesticides. The Solanaceae (Nightshade family) consists of approximately 2700 species and includes crops of significant economic, cultural, and scientific importance: these include potato, tomato, pepper, eggplant, tobacco, and petunia. The Solanaceae has emerged as a model family for studying the biochemical evolution of plant specialized metabolism and multiple examples exist of lineage-specific metabolites that influence the senses and physiology of commensal and harmful organisms, including humans. These include, alcohols, phenylpropanoids, and carotenoids that contribute to fruit aroma and color in tomato (fruity), glandular trichome-derived terpenoids and acylsugars that contribute to plant defense (stinky & sticky, respectively), capsaicinoids in chilli-peppers that influence seed dispersal (spicy), and steroidal glycoalkaloids (bitter) from Solanum, nicotine (addictive) from tobacco, as well as tropane alkaloids (deadly) from Deadly Nightshade that deter herbivory. Advances in genomics and metabolomics, coupled with the adoption of comparative phylogenetic approaches, resulted in deeper knowledge of the biosynthesis and evolution of these metabolites. This review highlights recent progress in this area and outlines opportunities for - and challenges of-developing a more comprehensive understanding of Solanaceae metabolism.
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Affiliation(s)
- Paul D Fiesel
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Hannah M Parks
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert L Last
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
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23
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Massa S, Pagliarello R, Cemmi A, Di Sarcina I, Bombarely A, Demurtas OC, Diretto G, Paolini F, Petzold HE, Bliek M, Bennici E, Del Fiore A, De Rossi P, Spelt C, Koes R, Quattrocchio F, Benvenuto E. Modifying Anthocyanins Biosynthesis in Tomato Hairy Roots: A Test Bed for Plant Resistance to Ionizing Radiation and Antioxidant Properties in Space. FRONTIERS IN PLANT SCIENCE 2022; 13:830931. [PMID: 35283922 PMCID: PMC8909381 DOI: 10.3389/fpls.2022.830931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Gene expression manipulation of specific metabolic pathways can be used to obtain bioaccumulation of valuable molecules and desired quality traits in plants. A single-gene approach to impact different traits would be greatly desirable in agrospace applications, where several aspects of plant physiology can be affected, influencing growth. In this work, MicroTom hairy root cultures expressing a MYB-like transcription factor that regulates the biosynthesis of anthocyanins in Petunia hybrida (PhAN4), were considered as a testbed for bio-fortified tomato whole plants aimed at agrospace applications. Ectopic expression of PhAN4 promoted biosynthesis of anthocyanins, allowing to profile 5 major derivatives of delphinidin and petunidin together with pelargonidin and malvidin-based anthocyanins, unusual in tomato. Consistent with PhAN4 features, transcriptomic profiling indicated upregulation of genes correlated to anthocyanin biosynthesis. Interestingly, a transcriptome reprogramming oriented to positive regulation of cell response to biotic, abiotic, and redox stimuli was evidenced. PhAN4 hairy root cultures showed the significant capability to counteract reactive oxygen species (ROS) accumulation and protein misfolding upon high-dose gamma irradiation, which is among the most potent pro-oxidant stress that can be encountered in space. These results may have significance in the engineering of whole tomato plants that can benefit space agriculture.
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Affiliation(s)
- Silvia Massa
- Department for Sustainability, Biotechnology and Agro-Industry Division - Biotec Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Riccardo Pagliarello
- Department for Sustainability, Biotechnology and Agro-Industry Division - Biotec Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Alessia Cemmi
- Fusion and Nuclear Safety Technologies Department, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Ilaria Di Sarcina
- Fusion and Nuclear Safety Technologies Department, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | | | - Olivia Costantina Demurtas
- Department for Sustainability, Biotechnology and Agro-Industry Division - Biotec Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Gianfranco Diretto
- Department for Sustainability, Biotechnology and Agro-Industry Division - Biotec Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Francesca Paolini
- 'Regina Elena' National Cancer Institute, HPV-UNIT, Department of Research, Advanced Diagnostic and Technological Innovation, Translational Research Functional Departmental Area, Rome, Italy
| | - H Earl Petzold
- School of Plants and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Mattijs Bliek
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Elisabetta Bennici
- Department for Sustainability, Biotechnology and Agro-Industry Division - Biotec Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Antonella Del Fiore
- Department for Sustainability, Biotechnology and Agro-Industry Division - Agrifood Sustainability, Quality, and Safety Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Patrizia De Rossi
- Energy Efficiency Unit Department - Northern Area Regions Laboratory, Casaccia Research Center, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Cornelis Spelt
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Ronald Koes
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Francesca Quattrocchio
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Eugenio Benvenuto
- Department for Sustainability, Biotechnology and Agro-Industry Division - Biotec Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
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24
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Li X, Wang X, Zhang Y, Zhang A, You CX. Regulation of fleshy fruit ripening: From transcription factors to epigenetic modifications. HORTICULTURE RESEARCH 2022; 9:uhac013. [PMID: 35147185 PMCID: PMC9035223 DOI: 10.1093/hr/uhac013] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/01/2021] [Indexed: 05/24/2023]
Abstract
Fleshy fruits undergo a complex ripening process, developing organoleptic fruit traits that attract herbivores and maximize seed dispersal. Ripening is the terminal stage of fruit development and involves a series of physiological and biochemical changes. In fleshy fruits, ripening always involves a drastic color change triggered by the accumulation of pigments and degradation of chlorophyll, softening caused by cell wall remodeling, and flavor formation as acids and sugars accumulate alongside volatile compounds. The mechanisms underlying fruit ripening rely on the orchestration of ripening-related transcription factors, plant hormones, and epigenetic modifications. In this review, we discuss current knowledge of the transcription factors that regulate ripening in conjunction with ethylene and environmental signals (light and temperature) in the model plant tomato (Solanum lycopersicum) and other fleshy fruits. We emphasize the critical roles of epigenetic regulation, including DNA methylation and histone modification as well as RNA m6A modification, which has been studied intensively. This detailed review was compiled to provide a comprehensive description of the regulatory mechanisms of fruit ripening and guide new strategies for its effective manipulation.
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Affiliation(s)
- Xiuming Li
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Xuemei Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yi Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai-An, 271018, China
| | - Aihong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai-An, 271018, China
| | - Chun-Xiang You
- National Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
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25
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Shen G, Sun W, Chen Z, Shi L, Hong J, Shi J. Plant GDSL Esterases/Lipases: Evolutionary, Physiological and Molecular Functions in Plant Development. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040468. [PMID: 35214802 PMCID: PMC8880598 DOI: 10.3390/plants11040468] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/02/2022] [Accepted: 02/04/2022] [Indexed: 05/14/2023]
Abstract
GDSL esterases/lipases (GELPs), present throughout all living organisms, have been a very attractive research subject in plant science due mainly to constantly emerging properties and functions in plant growth and development under both normal and stressful conditions. This review summarizes the advances in research on plant GELPs in several model plants and crops, including Arabidopsis, rice, maize and tomato, while focusing on the roles of GELPs in regulating plant development and plant-environment interactions. In addition, the possible regulatory network and mechanisms of GELPs have been discussed.
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26
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Zhu F, Wen W, Cheng Y, Fernie AR. The metabolic changes that effect fruit quality during tomato fruit ripening. MOLECULAR HORTICULTURE 2022; 2:2. [PMID: 37789428 PMCID: PMC10515270 DOI: 10.1186/s43897-022-00024-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/12/2022] [Indexed: 10/05/2023]
Abstract
As the most valuable organ of tomato plants, fruit has attracted considerable attention which most focus on its quality formation during the ripening process. A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators. In recent years, with the development of the next generation sequencing, molecular and genetic analysis methods, lots of genes which are involved in the chlorophyll, carotenoid, cell wall, central and secondary metabolism have been identified and confirmed to regulate pigment contents, fruit softening and other aspects of fruit flavor quality. Here, both research concerning the dissection of fruit quality related metabolic changes, the transcriptional and post-translational regulation of these metabolic pathways are reviewed. Furthermore, a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis, fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.
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Affiliation(s)
- Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany
| | - Weiwei Wen
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunjiang Cheng
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany.
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27
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Feng X, Li X, Zhang C, Kong X, Chen Y, Hua Y. Formation Mechanism of Hexanal and ( E)-2-Hexenal during Soybean [ Glycine max (L.) Merr] Processing Based on the Subcellular and Molecular Levels. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:289-300. [PMID: 34965722 DOI: 10.1021/acs.jafc.1c06732] [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] [Indexed: 06/14/2023]
Abstract
Hexanal and (E)-2-hexenal in soymilk mainly form during the soaking and grinding of soybeans. In this study, freshly dehulled soybeans were soaked or ground in the presence or absence of different enzyme inhibitors. The results showed that (1) 1-palmitoyl-2-linoleoyl-sn-3-phosphatidylcholine, 1-stearoyl-2-linoleoyl-sn-3-phosphatidylcholine, 1-palmitoyl-2-linolenoyl-sn-3-phosphatidylcholine, and 1-stearoyl-2-linolenoyl-sn-3-phosphatidylcholine were preferentially acted upon by lipoxygenases (LOXs) and made predominant contributions to hexanal/(E)-2-hexenal formation. Phospholipase A2 (PLA2) is one of the key enzymes for hexanal/(E)-2-hexenal formation. (2) The ratio of net increase in hexanal/(E)-2-hexenal and net decrease in linoleic acid/linolenic acid was close to 100% during soaking, but it was only 60% during grinding. Only 13-hydroperoxy octadecad(tr)ienoic acid (13-HPOD/T) was formed for the membrane LOX, but both 13- and 9-hydroperoxy octadecad(tr)ienoic acid (9-HPOD/T) were produced for the cytoplasm LOX. Thus, only the membrane LOX was involved during soaking, while both membrane- and cytoplasm-bound LOXs worked during grinding. (3) Hydroperoxides and hexanal/(E)-2-hexenal during soybean grinding were studied. PC hydroperoxides formed almost instantly and reached a maximum in 10 s, while fatty acid hydroperoxides and hexanal/(E)-2-hexenal formed relatively slowly and reached a maximum in 50 s. The experimental data were fitted to the integrated form of the Michaelis-Menten equation, and Km, Vmax, and kcat for the LOX, PLA2, and hydroperoxide lyase were obtained, respectively.
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Affiliation(s)
- Xiaoxiao Feng
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, P. R. China
| | - Xingfei Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, P. R. China
| | - Caimeng Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, P. R. China
| | - Xiangzhen Kong
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, P. R. China
| | - Yeming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, P. R. China
| | - Yufei Hua
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, 214122 Wuxi, P. R. China
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Wang T, Zhang C, Zhang H, Zhu H. CRISPR/Cas9-Mediated Gene Editing Revolutionizes the Improvement of Horticulture Food Crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13260-13269. [PMID: 33734711 DOI: 10.1021/acs.jafc.1c00104] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Horticultural food crops are important sources of nutrients for humans. With the increase of the global population, enhanced horticulture food crop production has become a new challenge, and enriching their nutritional content has also been required. Gene editing systems, such as zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9), have accelerated crop improvement through the modification of targeted genomes precisely. Here, we review the development of various gene editors and compare their advantages and shortcomings, especially the newly emerging CRISPR/Cas systems, such as base editing and prime editing. We also summarize their practical applications in crop trait improvement, including yield, nutritional quality, and other consumer traits.
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Affiliation(s)
- Tian Wang
- College of Life Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China
| | - Hongyan Zhang
- College of Life Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
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Pereira L, Sapkota M, Alonge M, Zheng Y, Zhang Y, Razifard H, Taitano NK, Schatz MC, Fernie AR, Wang Y, Fei Z, Caicedo AL, Tieman DM, van der Knaap E. Natural Genetic Diversity in Tomato Flavor Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:642828. [PMID: 34149747 PMCID: PMC8212054 DOI: 10.3389/fpls.2021.642828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/23/2021] [Indexed: 05/22/2023]
Abstract
Fruit flavor is defined as the perception of the food by the olfactory and gustatory systems, and is one of the main determinants of fruit quality. Tomato flavor is largely determined by the balance of sugars, acids and volatile compounds. Several genes controlling the levels of these metabolites in tomato fruit have been cloned, including LIN5, ALMT9, AAT1, CXE1, and LoxC. The aim of this study was to identify any association of these genes with trait variation and to describe the genetic diversity at these loci in the red-fruited tomato clade comprised of the wild ancestor Solanum pimpinellifolium, the semi-domesticated species Solanum lycopersicum cerasiforme and early domesticated Solanum lycopersicum. High genetic diversity was observed at these five loci, including novel haplotypes that could be incorporated into breeding programs to improve fruit quality of modern tomatoes. Using newly available high-quality genome assemblies, we assayed each gene for potential functional causative polymorphisms and resolved a duplication at the LoxC locus found in several wild and semi-domesticated accessions which caused lower accumulation of lipid derived volatiles. In addition, we explored gene expression of the five genes in nine phylogenetically diverse tomato accessions. In general, the expression patterns of these genes increased during fruit ripening but diverged between accessions without clear relationship between expression and metabolite levels.
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Affiliation(s)
- Lara Pereira
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Manoj Sapkota
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Michael Alonge
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States
| | - Yi Zheng
- Boyce Thompson Institute, Ithaca, NY, United States
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Hamid Razifard
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Nathan K. Taitano
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, United States
- U.S. Department of Agriculture, Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Ana L. Caicedo
- Biology Department, University of Massachusetts Amherst, Amherst, MA, United States
| | - Denise M. Tieman
- Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Horticulture, University of Georgia, Athens, GA, United States
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30
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Xia Z, Huang D, Zhang S, Wang W, Ma F, Wu B, Xu Y, Xu B, Chen D, Zou M, Xu H, Zhou X, Zhan R, Song S. Chromosome-scale genome assembly provides insights into the evolution and flavor synthesis of passion fruit (Passiflora edulis Sims). HORTICULTURE RESEARCH 2021; 8:14. [PMID: 33419990 PMCID: PMC7794574 DOI: 10.1038/s41438-020-00455-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 05/04/2023]
Abstract
Passion fruit (Passiflora edulis Sims) is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world. Here, we report an ~1341.7 Mb chromosome-scale genome assembly of passion fruit, with 98.91% (~1327.18 Mb) of the assembly assigned to nine pseudochromosomes. The genome includes 23,171 protein-coding genes, and most of the assembled sequences are repetitive sequences, with long-terminal repeats (LTRs) being the most abundant. Phylogenetic analysis revealed that passion fruit diverged after Brassicaceae and before Euphorbiaceae. Ks analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA, which may have contributed to its large genome size. An integrated analysis of genomic, transcriptomic, and metabolomic data showed that 'alpha-linolenic acid metabolism', 'metabolic pathways', and 'secondary metabolic pathways' were the main pathways involved in the synthesis of important volatile organic compounds (VOCs) in passion fruit, and this analysis identified some candidate genes, including GDP-fucose Transporter 1-like, Tetratricopeptide repeat protein 33, protein NETWORKED 4B isoform X1, and Golgin Subfamily A member 6-like protein 22. In addition, we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene pathways. Gene family analysis showed that the ACX, ADH, ALDH, and HPL gene families, especially ACX13/14/15/20, ADH13/26/33, ALDH1/4/21, and HPL4/6, were the key genes for ester synthesis, while the TPS gene family, especially PeTPS2/3/4/24, was the key gene family for terpene synthesis. This work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.
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Affiliation(s)
- Zhiqiang Xia
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, 571101, Haikou, Hainan, P. R. China
- Hainan University, 571101, Haikou, Hainan, P. R. China
| | - Dongmei Huang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, 571101, Haikou, Hainan, P. R. China
| | - Shengkui Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), 250353, Jinan, Shandong, P. R. China
| | - Wenquan Wang
- Hainan University, 571101, Haikou, Hainan, P. R. China
- The Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, Hainan, P. R. China
| | - Funing Ma
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, 571101, Haikou, Hainan, P. R. China
| | - Bin Wu
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, 571101, Haikou, Hainan, P. R. China
| | - Yi Xu
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, 571101, Haikou, Hainan, P. R. China
| | - Bingqiang Xu
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, 571101, Haikou, Hainan, P. R. China
| | - Di Chen
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, 571101, Haikou, Hainan, P. R. China
| | - Meiling Zou
- Hainan University, 571101, Haikou, Hainan, P. R. China
- The Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, Hainan, P. R. China
| | - Huanyu Xu
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, 571101, Haikou, Hainan, P. R. China
| | - Xincheng Zhou
- The Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, 571101, Haikou, Hainan, P. R. China
| | - Rulin Zhan
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, 571101, Haikou, Hainan, P. R. China.
| | - Shun Song
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, 571101, Haikou, Hainan, P. R. China.
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Fenn MA, Giovannoni JJ. Phytohormones in fruit development and maturation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:446-458. [PMID: 33274492 DOI: 10.1111/tpj.15112] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 05/21/2023]
Abstract
Phytohormones are integral to the regulation of fruit development and maturation. This review expands upon current understanding of the relationship between hormone signaling and fruit development, emphasizing fleshy fruit and highlighting recent work in the model crop tomato (Solanum lycopersicum) and additional species. Fruit development comprises fruit set initiation, growth, and maturation and ripening. Fruit set transpires after fertilization and is associated with auxin and gibberellic acid (GA) signaling. Interaction between auxin and GAs, as well as other phytohormones, is mediated by auxin-responsive Aux/IAA and ARF proteins. Fruit growth consists of cell division and expansion, the former shown to be influenced by auxin signaling. While regulation of cell expansion is less thoroughly understood, evidence indicates synergistic regulation via both auxin and GAs, with input from additional hormones. Fruit maturation, a transitional phase that precipitates ripening, occurs when auxin and GA levels subside with a concurrent rise in abscisic acid (ABA) and ethylene. During fruit ripening, ethylene plays a clear role in climacteric fruits, whereas non-climacteric ripening is generally associated with ABA. Recent evidence indicates varying requirements for both hormones within both ripening physiologies, suggesting rebalancing and specification of roles for common regulators rather than reliance upon one. Numerous recent discoveries pertaining to the molecular basis of hormonal activity and crosstalk are discussed, while we also note that many questions remain such as the molecular basis of additional hormonal activities, the role of epigenome changes, and how prior discoveries translate to the plethora of angiosperm species.
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Affiliation(s)
- Matthew A Fenn
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - James J Giovannoni
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
- United States Department of Agriculture - Agricultural Research Service and Boyce Thompson Institute for Plant Research, Cornell University campus, Ithaca, NY, 14853, USA
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