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Lin Q, Chen J, Liu X, Wang B, Zhao Y, Liao L, Allan AC, Sun C, Duan Y, Li X, Grierson D, Verdonk JC, Chen K, Han Y, Bi J. A metabolic perspective of selection for fruit quality related to apple domestication and improvement. Genome Biol 2023; 24:95. [PMID: 37101232 PMCID: PMC10131461 DOI: 10.1186/s13059-023-02945-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Apple is an economically important fruit crop. Changes in metabolism accompanying human-guided evolution can be revealed using a multiomics approach. We perform genome-wide metabolic analysis of apple fruits collected from 292 wild and cultivated accessions representing various consumption types. RESULTS We find decreased amounts of certain metabolites, including tannins, organic acids, phenolic acids, and flavonoids as the wild accessions transition to cultivated apples, while lysolipids increase in the "Golden Delicious" to "Ralls Janet" pedigree, suggesting better storage. We identify a total of 222,877 significant single-nucleotide polymorphisms that are associated with 2205 apple metabolites. Investigation of a region from 2.84 to 5.01 Mb on chromosome 16 containing co-mapping regions for tannins, organic acids, phenolic acids, and flavonoids indicates the importance of these metabolites for fruit quality and nutrition during breeding. The tannin and acidity-related genes Myb9-like and PH4 are mapped closely to fruit weight locus fw1 from 3.41 to 3.76 Mb on chromosome 15, a region under selection during domestication. Lysophosphatidylethanolamine (LPE) 18:1, which is suppressed by fatty acid desaturase-2 (FAD2), is positively correlated to fruit firmness. We find the fruit weight is negatively correlated with salicylic acid and abscisic acid levels. Further functional assays demonstrate regulation of these hormone levels by NAC-like activated by Apetala3/Pistillata (NAP) and ATP binding cassette G25 (ABCG25), respectively. CONCLUSIONS This study provides a metabolic perspective for selection on fruit quality during domestication and improvement, which is a valuable resource for investigating mechanisms controlling apple metabolite content and quality.
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Affiliation(s)
- Qiong Lin
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University, Wageningen, 6708 PD The Netherlands
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 China
| | - Jing Chen
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xuan Liu
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Bin Wang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, 430070 China
| | - Yaoyao Zhao
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Liao Liao
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Andrew C. Allan
- The New Zealand Institute for Plant and Food Research Limited, Auckland Mail Centre, Auckland, 1142 New Zealand
| | - Chongde Sun
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 China
| | - Yuquan Duan
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xuan Li
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Donald Grierson
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 China
- Plant and Science Crop Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Julian C. Verdonk
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University, Wageningen, 6708 PD The Netherlands
| | - Kunsong Chen
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058 China
| | - Yuepeng Han
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Jinfeng Bi
- Key Laboratory of Agro-Products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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Li J, Yan G, Duan X, Zhang K, Zhang X, Zhou Y, Wu C, Zhang X, Tan S, Hua X, Wang J. Research Progress and Trends in Metabolomics of Fruit Trees. FRONTIERS IN PLANT SCIENCE 2022; 13:881856. [PMID: 35574069 PMCID: PMC9106391 DOI: 10.3389/fpls.2022.881856] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Metabolomics is an indispensable part of modern systems biotechnology, applied in the diseases' diagnosis, pharmacological mechanism, and quality monitoring of crops, vegetables, fruits, etc. Metabolomics of fruit trees has developed rapidly in recent years, and many important research results have been achieved in combination with transcriptomics, genomics, proteomics, quantitative trait locus (QTL), and genome-wide association study (GWAS). These research results mainly focus on the mechanism of fruit quality formation, metabolite markers of special quality or physiological period, the mechanism of fruit tree's response to biotic/abiotic stress and environment, and the genetics mechanism of fruit trait. According to different experimental purposes, different metabolomic strategies could be selected, such as targeted metabolomics, non-targeted metabolomics, pseudo-targeted metabolomics, and widely targeted metabolomics. This article presents metabolomics strategies, key techniques in metabolomics, main applications in fruit trees, and prospects for the future. With the improvement of instruments, analysis platforms, and metabolite databases and decrease in the cost of the experiment, metabolomics will prompt the fruit tree research to achieve more breakthrough results.
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Affiliation(s)
- Jing Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Guohua Yan
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Xuwei Duan
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Kaichun Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Xiaoming Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Yu Zhou
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Chuanbao Wu
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Xin Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Shengnan Tan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
- Analysis and Test Center, Northeast Forestry University, Harbin, China
| | - Xin Hua
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Jing Wang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
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McClure KA, Gong Y, Song J, Vinqvist-Tymchuk M, Campbell Palmer L, Fan L, Burgher-MacLellan K, Zhang Z, Celton JM, Forney CF, Migicovsky Z, Myles S. Genome-wide association studies in apple reveal loci of large effect controlling apple polyphenols. HORTICULTURE RESEARCH 2019; 6:107. [PMID: 31645962 PMCID: PMC6804656 DOI: 10.1038/s41438-019-0190-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 05/03/2023]
Abstract
Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing, primarily as dietary antioxidants. Although numerous pre- and post-harvest factors can affect the composition of polyphenols in apples, genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple cultivars. Here we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography (HPLC) data with ~100,000 single nucleotide polymorphisms (SNPs) from two diverse apple populations. We found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars, and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic loci. Using GWAS, we identified candidate genes for the production of quercitrin, epicatechin, catechin, chlorogenic acid, 4-O-caffeoylquinic acid and procyanidins B1, B2, and C1. Our observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through marker-assisted breeding or gene editing.
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Affiliation(s)
- Kendra A. McClure
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - YuiHui Gong
- College of Horticulture, South China Agriculture University, Guangzhou, 510642 China
| | - Jun Song
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Melinda Vinqvist-Tymchuk
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Leslie Campbell Palmer
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Lihua Fan
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Karen Burgher-MacLellan
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - ZhaoQi Zhang
- College of Horticulture, South China Agriculture University, Guangzhou, 510642 China
| | - Jean-Marc Celton
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Charles F. Forney
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Zoë Migicovsky
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
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Igarashi M, Hatsuyama Y, Harada T, Fukasawa-Akada T. Biotechnology and apple breeding in Japan. BREEDING SCIENCE 2016; 66:18-33. [PMID: 27069388 PMCID: PMC4780799 DOI: 10.1270/jsbbs.66.18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/23/2015] [Indexed: 05/11/2023]
Abstract
Apple is a fruit crop of significant economic importance, and breeders world wide continue to develop novel cultivars with improved characteristics. The lengthy juvenile period and the large field space required to grow apple populations have imposed major limitations on breeding. Various molecular biological techniques have been employed to make apple breeding easier. Transgenic technology has facilitated the development of apples with resistance to fungal or bacterial diseases, improved fruit quality, or root stocks with better rooting or dwarfing ability. DNA markers for disease resistance (scab, powdery mildew, fire-blight, Alternaria blotch) and fruit skin color have also been developed, and marker-assisted selection (MAS) has been employed in breeding programs. In the last decade, genomic sequences and chromosome maps of various cultivars have become available, allowing the development of large SNP arrays, enabling efficient QTL mapping and genomic selection (GS). In recent years, new technologies for genetic improvement, such as trans-grafting, virus vectors, and genome-editing, have emerged. Using these techniques, no foreign genes are present in the final product, and some of them show considerable promise for application to apple breeding.
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Affiliation(s)
- Megumi Igarashi
- Hirosaki Industrial Research Institute, Aomori Prefectural Industrial Technology Research Center,
Ogimachi 1-1-8, Hirosaki, Aomori 036-8104,
Japan
| | - Yoshimichi Hatsuyama
- Apple Research Institute, Aomori Prefectural Industrial Technology Research Center,
Fukutami 24, Botandaira, Kuroishi, Aomori 036-0332,
Japan
| | - Takeo Harada
- Department of Agriculture and Life Science, Hirosaki University,
Bunkyouchou 3, Hirosaki, Aomori 036-8563,
Japan
| | - Tomoko Fukasawa-Akada
- Hirosaki Industrial Research Institute, Aomori Prefectural Industrial Technology Research Center,
Ogimachi 1-1-8, Hirosaki, Aomori 036-8104,
Japan
- Corresponding author (e-mail: )
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Leforestier D, Ravon E, Muranty H, Cornille A, Lemaire C, Giraud T, Durel CE, Branca A. Genomic basis of the differences between cider and dessert apple varieties. Evol Appl 2015; 8:650-61. [PMID: 26240603 PMCID: PMC4516418 DOI: 10.1111/eva.12270] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 04/15/2015] [Indexed: 12/26/2022] Open
Abstract
Unraveling the genomic processes at play during variety diversification is of fundamental interest for understanding evolution, but also of applied interest in crop science. It can indeed provide knowledge on the genetic bases of traits for crop improvement and germplasm diversity management. Apple is one of the most important fruit crops in temperate regions, having both great economic and cultural values. Sweet dessert apples are used for direct consumption, while bitter cider apples are used to produce cider. Several important traits are known to differentiate the two variety types, in particular fruit size, biennial versus annual fruit bearing, and bitterness, caused by a higher content in polyphenols. Here, we used an Illumina 8k SNP chip on two core collections, of 48 dessert and 48 cider apples, respectively, for identifying genomic regions responsible for the differences between cider and dessert apples. The genome-wide level of genetic differentiation between cider and dessert apples was low, although 17 candidate regions showed signatures of divergent selection, displaying either outlier FST values or significant association with phenotypic traits (bitter versus sweet fruits). These candidate regions encompassed 420 genes involved in a variety of functions and metabolic pathways, including several colocalizations with QTLs for polyphenol compounds.
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Affiliation(s)
- Diane Leforestier
- UMR 1345 Institut de Recherche en Horticulture et Semences, Université d'Angers Angers, France
| | - Elisa Ravon
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Hélène Muranty
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Amandine Cornille
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
| | - Christophe Lemaire
- UMR 1345 Institut de Recherche en Horticulture et Semences, Université d'Angers Angers, France
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
| | - Charles-Eric Durel
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Antoine Branca
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
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Gesell A, Yoshida K, Tran LT, Constabel CP. Characterization of an apple TT2-type R2R3 MYB transcription factor functionally similar to the poplar proanthocyanidin regulator PtMYB134. PLANTA 2014; 240:497-511. [PMID: 24923676 DOI: 10.1007/s00425-014-2098-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 05/19/2014] [Indexed: 05/06/2023]
Abstract
The apple MdMYB9 gene encodes a positive regulator of proanthocyanidin synthesis that activates anthocyanidin reductase promoters from apple and poplar via interaction with basic helix-loop-helix proteins. The regulation of proanthocyanidins (PAs, condensed tannins) is of great importance in food plants due to the many benefits of PAs in the human diet. Two candidate flavonoid MYB regulators, MdMYB9 and MdMYB11, were cloned from apple (Malus × domestica) based on their similarity to known MYB PA regulators. Transcript accumulation of both MdMYB9 and MdMYB11 was induced by high light and wounding, similar to the poplar (Populus spp) PA regulator PtMYB134. In transient activation assays with various basic helix-loop-helix (bHLH) co-regulators, MdMYB9 activated apple and poplar anthocyanidin reductase (ANR) promoters, while MdMYB11 showed no activity. Potential transcription factor binding elements were found within several ANR promoters, and the importance of the bHLH binding site (E-box) on ANR promoter activation was demonstrated via mutational analysis. The ability of MdMYB9 and PtMYB134 to reciprocally activate ANR promoters from both apple and poplar and to partner with heterologous bHLH co-factors from these plants confirms the high degree of conservation of PA regulatory complexes across species. The similarity in apple and poplar PA regulation suggests that regulatory genes from poplar could be effectively employed for metabolic engineering of the PA pathway in apple.
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Affiliation(s)
- Andreas Gesell
- Department of Biology & Centre for Forest Biology, University of Victoria, Station CSC, Box 3020, Victoria, BC, V8W 3N5, Canada
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