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Vallarino JG, Jun H, Wang S, Wang X, Sade N, Orf I, Zhang D, Shi J, Shen S, Cuadros-Inostroza Á, Xu Q, Luo J, Fernie AR, Brotman Y. Limitations and advantages of using metabolite-based genome-wide association studies: focus on fruit quality traits. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 333:111748. [PMID: 37230189 DOI: 10.1016/j.plantsci.2023.111748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 05/27/2023]
Abstract
In the last decades, linkage mapping has help in the location of metabolite quantitative trait loci (QTL) in many species; however, this approach shows some limitations. Recently, thanks to the most recent advanced in high-throughput genotyping technologies like next-generation sequencing, metabolite genome-wide association study (mGWAS) has been proposed a powerful tool to identify the genetic variants in polygenic agrinomic traits. Fruit flavor is a complex interaction of aroma volatiles and taste being sugar and acid ratio key parameter for flavor acceptance. Here, we review recent progress of mGWAS in pinpoint gene polymorphisms related to flavor-related metabolites in fruits. Despite clear successes in discovering novel genes or regions associated with metabolite accumulation affecting sensory attributes in fruits, GWAS incurs in several limitations summarized in this review. In addition, in our own work, we performed mGWAS on 194 Citrus grandis accessions to investigate the genetic control of individual primary and lipid metabolites in ripe fruit. We have identified a total of 667 associations for 14 primary metabolites including amino acids, sugars, and organic acids, and 768 associations corresponding to 47 lipids. Furthermore, candidate genes related to important metabolites related to fruit quality such as sugars, organic acids and lipids were discovered.
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Affiliation(s)
- José G Vallarino
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Campus de Teatinos, 29071 Málaga, Spain
| | - Hong Jun
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | | | - Xia Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Isabel Orf
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
| | - Dabing Zhang
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Waite Research Institute, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Jianxin Shi
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangqian Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | | | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Jie Luo
- College of Tropical Crops, Hainan University, Haikou, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Alisdair R Fernie
- Department of Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, 1 Am Mühlenberg, Golm, Potsdam 14476, Germany; Department of Plant Metabolomics, Center for Plant Systems Biology and Biotechnology, 139 Ruski Blvd., Plovdiv 4000, Bulgaria.
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel.
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Liu R, Deng Y, Liu Y, Wang Z, Yu S, Nie Y, Zhu W, Zhou Z, Diao J. Combined Analysis of Transcriptome and Metabolome Reveals the Potential Mechanism of the Enantioselective Effect of Chiral Penthiopyrad on Tomato Fruit Flavor Quality. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10872-10885. [PMID: 36006413 DOI: 10.1021/acs.jafc.2c03870] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study investigated the enantioselective effects of S-, R-, and rac-penthiopyrad (PEN) on the flavor quality of tomato fruit through the levels of sugars, acids, volatiles, and nutrients and explored the potential mechanism by combined analysis of the transcriptome and metabolome. The results revealed that the S-enantiomer increased the content of soluble sugars while decreasing the content of organic acids, thereby increasing the taste of tomato fruit. Furthermore, S-(+)-PEN promoted the accumulation of volatile compounds and nutrients (total phenols, flavonoids, and vitamin C). Transcriptome and metabolome data showed that the S-enantiomer improved fruit flavor and quality by influencing metabolites and genes in glycolysis, starch and sucrose metabolism, the citrate cycle, and amino acid biosynthesis pathways. However, R-(-)-PEN had a negative effect on tomato flavor. The effect of the racemate on fruit flavor quality was between a pair of enantiomers. The comprehensive data of PEN enantiomers will provide theoretical support for the application of PEN in tomatoes. Thus, developing enantiopure S-(+)-PEN products might be more conducive to the flavor and quality of the tomato fruit.
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Affiliation(s)
- Rui Liu
- Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, China
| | - Yue Deng
- Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, China
| | - Yuping Liu
- Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, China
| | - Zikang Wang
- Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, China
| | - Simin Yu
- Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, China
| | - Yufan Nie
- Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, China
| | - Wentao Zhu
- Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, China
| | - Zhiqiang Zhou
- Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, China
| | - Jinling Diao
- Department of Applied Chemistry, China Agricultural University, Yuanmingyuan west road 2, Beijing 100193, China
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