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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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Mathur S, Singh D, Ranjan R. Recent advances in plant translational genomics for crop improvement. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:335-382. [PMID: 38448140 DOI: 10.1016/bs.apcsb.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The growing population, climate change, and limited agricultural resources put enormous pressure on agricultural systems. A plateau in crop yields is occurring and extreme weather events and urbanization threaten the livelihood of farmers. It is imperative that immediate attention is paid to addressing the increasing food demand, ensuring resilience against emerging threats, and meeting the demand for more nutritious, safer food. Under uncertain conditions, it is essential to expand genetic diversity and discover novel crop varieties or variations to develop higher and more stable yields. Genomics plays a significant role in developing abundant and nutrient-dense food crops. An alternative to traditional breeding approach, translational genomics is able to improve breeding programs in a more efficient and precise manner by translating genomic concepts into practical tools. Crop breeding based on genomics offers potential solutions to overcome the limitations of conventional breeding methods, including improved crop varieties that provide more nutritional value and are protected from biotic and abiotic stresses. Genetic markers, such as SNPs and ESTs, contribute to the discovery of QTLs controlling agronomic traits and stress tolerance. In order to meet the growing demand for food, there is a need to incorporate QTLs into breeding programs using marker-assisted selection/breeding and transgenic technologies. This chapter primarily focuses on the recent advances that are made in translational genomics for crop improvement and various omics techniques including transcriptomics, metagenomics, pangenomics, single cell omics etc. Numerous genome editing techniques including CRISPR Cas technology and their applications in crop improvement had been discussed.
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Affiliation(s)
- Shivangi Mathur
- Plant Molecular Biology Laboratory, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Agra, India
| | - Deeksha Singh
- Plant Molecular Biology Laboratory, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Agra, India
| | - Rajiv Ranjan
- Plant Molecular Biology Laboratory, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Agra, India.
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Denoyes B, Prohaska A, Petit J, Rothan C. Deciphering the genetic architecture of fruit color in strawberry. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6306-6320. [PMID: 37386925 PMCID: PMC10627153 DOI: 10.1093/jxb/erad245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/28/2023] [Indexed: 07/01/2023]
Abstract
Fruits of Fragaria species usually have an appealing bright red color due to the accumulation of anthocyanins, water-soluble flavonoid pigments. Octoploid cultivated strawberry (Fragaria × ananassa) is a major horticultural crop for which fruit color and associated nutritional value are main breeding targets. Great diversity in fruit color intensity and pattern is observed not only in cultivated strawberry but also in wild relatives such as its octoploid progenitor F. chiloensis or the diploid woodland strawberry F. vesca, a model for fruit species in the Rosaceae. This review examines our understanding of fruit color formation in strawberry and how ongoing developments will advance it. Natural variations of fruit color as well as color changes during fruit development or in response to several cues have been used to explore the anthocyanin biosynthetic pathway and its regulation. So far, the successful identification of causal genetic variants has been largely driven by the availability of high-throughput genotyping tools and high-quality reference genomes of F. vesca and F. × ananassa. The current completion of haplotype-resolved genomes of F. × ananassa combined with QTL mapping will accelerate the exploitation of the untapped genetic diversity of fruit color and help translate the findings into strawberry improvement.
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Affiliation(s)
- Béatrice Denoyes
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Alexandre Prohaska
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
- INVENIO, MIN de Brienne, Bordeaux, France
| | - Johann Petit
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
| | - Christophe Rothan
- INRAE and Univ. of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
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Oh SW, Imran M, Kim EH, Park SY, Lee SG, Park HM, Jung JW, Ryu TH. Approach strategies and application of metabolomics to biotechnology in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1192235. [PMID: 37636096 PMCID: PMC10451086 DOI: 10.3389/fpls.2023.1192235] [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: 03/23/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023]
Abstract
Metabolomics refers to the technology for the comprehensive analysis of metabolites and low-molecular-weight compounds in a biological system, such as cells or tissues. Metabolites play an important role in biological phenomena through their direct involvement in the regulation of physiological mechanisms, such as maintaining cell homeostasis or signal transmission through protein-protein interactions. The current review aims provide a framework for how the integrated analysis of metabolites, their functional actions and inherent biological information can be used to understand biological phenomena related to the regulation of metabolites and how this information can be applied to safety assessments of crops created using biotechnology. Advancement in technology and analytical instrumentation have led new ways to examine the convergence between biology and chemistry, which has yielded a deeper understanding of complex biological phenomena. Metabolomics can be utilized and applied to safety assessments of biotechnology products through a systematic approach using metabolite-level data processing algorithms, statistical techniques, and database development. The integration of metabolomics data with sequencing data is a key step towards improving additional phenotypical evidence to elucidate the degree of environmental affects for variants found in genome associated with metabolic processes. Moreover, information analysis technology such as big data, machine learning, and IT investment must be introduced to establish a system for data extraction, selection, and metabolomic data analysis for the interpretation of biological implications of biotechnology innovations. This review outlines the integrity of metabolomics assessments in determining the consequences of genetic engineering and biotechnology in plants.
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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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Qin J, Wang H, Xu Y, Shi F, Yang S, Huang H, Liu J, Stewart C, Li L, Li F, Han J, Wu W. A simple array integrating machine learning for identification of flavonoids in red wines. RSC Adv 2023; 13:8882-8889. [PMID: 36936820 PMCID: PMC10019168 DOI: 10.1039/d2ra08049d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
Bioactive flavonoids, the major ingredients of red wines, have been proven to prevent atherosclerosis and cardiovascular disease due to their anti-inflammatory and anti-oxidant activity. However, flavonoids have proven challenging to identify, even when multiple approaches are combined. Hereby, a simple array was constructed to detect flavonoids by employing phenylboronic acid modified perylene diimide derivatives (PDIs). Through multiple non-specific interactions (hydrophilic, hydrophobic, charged, aromatic, hydrogen-bonded and reversible covalent interactions) with flavonoids, the fluorescence of PDIs can be modulated, and variations in intensity can be used to create fingerprints of flavonoids. This array successfully discriminated 14 flavonoids of diverse structures and concentrations with 100% accuracy, based on patterns in fluorescence intensity modulation, via optimized machine learning algorithms. As a result, this array demonstrated the parallel detection of 8 different types and origins of red wines with a high accuracy, revealing the excellent potential of the sensor array in food mixtures detection.
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Affiliation(s)
- Jiaojiao Qin
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University 211109 China
| | - Hao Wang
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University 211109 China
| | - Yu Xu
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University 211109 China
| | - Fangfang Shi
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University 211109 China
| | - Shijie Yang
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University 211109 China
| | - Hui Huang
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet Sweden
| | - Jun Liu
- Shandong Yuwang Ecological Food Industry Co., Ltd De Zhou 251200 China
| | - Callum Stewart
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet Sweden
| | - Linxian Li
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet Sweden
| | - Fei Li
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University 211109 China
| | - Jinsong Han
- State Key Laboratory of Natural Medicines and National R&D Center for Chinese Herbal Medicine Processing, Department of Food Quality and Safety, College of Engineering, China Pharmaceutical University 211109 China
| | - Wenwen Wu
- Department of Pharmacy, Children's Hospital of Nanjing Medical University Nanjing Jiangsu Province 211109 China
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Anthony BM, Chaparro JM, Prenni JE, Minas IS. Carbon sufficiency boosts phenylpropanoid biosynthesis early in peach fruit development priming superior fruit quality. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:1019-1031. [PMID: 36898214 DOI: 10.1016/j.plaphy.2023.02.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Manipulating the crop load in peach trees determines carbon supply and optimum balance between fruit yield and quality potentials. The impact of carbon supply on peach fruit quality was assessed in three development stages (S2, S3, S4) on fruit of equal maturity from trees that were carbon (C) starved (unthinned) and sufficient (thinned). Previous studies determined that primary metabolites of peach fruit mesocarp are mainly linked with developmental processes, thus, the secondary metabolite profile was assessed using non-targeted liquid chromatography mass-spectrometry (LC-MS). Carbon sufficient (C-sufficient) fruit demonstrated superior quality attributes as compared to C-starved fruit. Early metabolic shifts in the secondary metabolome appear to prime quality at harvest. Enhanced C-availability facilitated the increased and consistent synthesis of flavonoids, like catechin, epicatechin and eriodyctiol, via the phenylpropanoid pathway, providing a link between the metabolome and fruit quality, and serving as signatures of C-sufficiency during peach fruit development.
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Affiliation(s)
- Brendon M Anthony
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, United States
| | - Jacqueline M Chaparro
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, United States
| | - Jessica E Prenni
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, United States
| | - Ioannis S Minas
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, United States.
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Yang C, Wu P, Cao Y, Yang B, Liu L, Chen J, Zhuo R, Yao X. Overexpression of dihydroflavonol 4-reductase ( CoDFR) boosts flavonoid production involved in the anthracnose resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:1038467. [PMID: 36438122 PMCID: PMC9682034 DOI: 10.3389/fpls.2022.1038467] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
The outbreak of anthracnose caused by Colletotrichum spp. represents a devastating epidemic that severely affects oil tea (Camellia oleifera) production in China. However, the unknown resistance mechanism to anthracnose in C. oleifera has impeded the progress of breeding disease-resistant varieties. In this study, we investigated the physiological responses of resistant and susceptible lines during C. gloeosporioides infection. Our results showed that the accumulation of malondialdehyde (MDA), catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) in both disease-resistant and susceptible lines increased by C. gloeosporioides infection. Also, disease-resistant lines exhibited lower MDA, but higher POD, SOD, and CAT activities compared to susceptible lines. The accumulation of flavonoids in both resistant and susceptible C. oleifera leaves increased following C. gloeosporioides infection, and the increase was greater in resistant lines. Further, we identified and functionally characterized the dihydroflavonol 4-reductase (CoDFR) from the resistant C. oleifera line. We showed that the full-length coding sequence (CDS) of CoDFR is 1044 bp encoding 347 amino acids. The overexpression of CoDFR in tobacco altered the expression of flavonoid biosynthetic genes, resulting in an increased flavonoid content in leaves. CoDFR transgenic tobacco plants exhibited increased anthracnose resistance. Furthermore, the transgenic plants had higher salicylic acid content. These findings offer potential insights into the pivotal role of CoDFR involved in flavonoid-mediated defense mechanisms during anthracnose invasion in resistant C. oleifera.
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Affiliation(s)
| | | | | | | | | | | | | | - Xiaohua Yao
- *Correspondence: Renying Zhuo, ; Xiaohua Yao,
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Li C, Wang S, Wang J, Wu Z, Xu Y, Wu Z. Ozone treatment promotes physicochemical properties and antioxidant capacity of fresh-cut red pitaya based on phenolic metabolism. Front Nutr 2022; 9:1016607. [PMID: 36276831 PMCID: PMC9583149 DOI: 10.3389/fnut.2022.1016607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/08/2022] [Indexed: 12/03/2022] Open
Abstract
Pitaya is an important fresh-cut product in the global fruit market. The health benefits of fresh-cut red pitaya fruit are attributed to its unique phenolic content and other antioxidants, but the fruit is highly susceptible to spoilage which causes a decline in nutritional quality. In this study, we monitored changes in quality and phenolic compounds of pitaya fruit treated with gaseous ozone during storage at 8 ± 2°C for 4 days. Compared with the control group, ozone treatment was an effective strategy for preserving quality by controlling the growth of microorganisms, preventing weight loss and softening, and improving the content of soluble solids and titratable acids. The results showed that ozone induced the accumulation of phenolic compounds while maintaining the quality. The content of phenolic compounds in fresh-cut pitaya was positively correlated with antioxidant activity. Ultra-performance liquid chromatography-electrospray tandem mass spectrometry was used to fingerprint the phenolic metabolites and metabolomic analysis identified 26 phenolic compounds. The majority of these were phenylpropanoids, and the key metabolic pathways were phenylpropane metabolism and flavonoid synthesis. This study illustrated the mechanism by which of ozone prolongs the shelf life of fresh-cut pitaya fruit and validated ozone as a valuable phenolic inducer and regulator of antioxidant activity, positively influencing the potential health benefits of fresh-cut products.
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Affiliation(s)
- Chen Li
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Shan Wang
- College of Light Industry, Liaoning University, Shenyang, China
| | - Jiayi Wang
- College of Life Science & Technology, Xinjiang University, Xinjiang, China
| | - Zhaohui Wu
- Institute of Food and Processing, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yaping Xu
- Chaoyang Engineering Technical School, Chaoyang, China
| | - Zhaoxia Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, China,*Correspondence: Zhaoxia Wu,
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10
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Advances in Metabolomics-Driven Diagnostic Breeding and Crop Improvement. Metabolites 2022; 12:metabo12060511. [PMID: 35736444 PMCID: PMC9228725 DOI: 10.3390/metabo12060511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 02/04/2023] Open
Abstract
Climate change continues to threaten global crop output by reducing annual productivity. As a result, global food security is now considered as one of the most important challenges facing humanity. To address this challenge, modern crop breeding approaches are required to create plants that can cope with increased abiotic/biotic stress. Metabolomics is rapidly gaining traction in plant breeding by predicting the metabolic marker for plant performance under a stressful environment and has emerged as a powerful tool for guiding crop improvement. The advent of more sensitive, automated, and high-throughput analytical tools combined with advanced bioinformatics and other omics techniques has laid the foundation to broadly characterize the genetic traits for crop improvement. Progress in metabolomics allows scientists to rapidly map specific metabolites to the genes that encode their metabolic pathways and offer plant scientists an excellent opportunity to fully explore and rationally harness the wealth of metabolites that plants biosynthesize. Here, we outline the current application of advanced metabolomics tools integrated with other OMICS techniques that can be used to: dissect the details of plant genotype–metabolite–phenotype interactions facilitating metabolomics-assisted plant breeding for probing the stress-responsive metabolic markers, explore the hidden metabolic networks associated with abiotic/biotic stress resistance, facilitate screening and selection of climate-smart crops at the metabolite level, and enable accurate risk-assessment and characterization of gene edited/transgenic plants to assist the regulatory process. The basic concept behind metabolic editing is to identify specific genes that govern the crucial metabolic pathways followed by the editing of one or more genes associated with those pathways. Thus, metabolomics provides a superb platform for not only rapid assessment and commercialization of future genome-edited crops, but also for accelerated metabolomics-assisted plant breeding. Furthermore, metabolomics can be a useful tool to expedite the crop research if integrated with speed breeding in future.
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11
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Wang P, Schumacher AM, Shiu SH. Computational prediction of plant metabolic pathways. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102171. [PMID: 35078130 DOI: 10.1016/j.pbi.2021.102171] [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: 11/02/2021] [Revised: 12/07/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Uncovering genes encoding enzymes responsible for the biosynthesis of diverse plant metabolites is essential for metabolic engineering and production of plant metabolite-derived medicine. With the availability of multi-omics data for an ever-increasing number of plant species and the development of computational approaches, the metabolic pathways of many important plant compounds can be predicted, complementing a more traditional genetic and/or biochemical approach. Here, we summarize recent progress in predicting plant metabolic pathways using genome, transcriptome, proteome, interactome, and/or metabolome data, and the utility of integrating these data with machine learning to further improve metabolic pathway predictions.
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Affiliation(s)
- Peipei Wang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
| | - Ally M Schumacher
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, 48824, USA.
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Labadie M, Vallin G, Potier A, Petit A, Ring L, Hoffmann T, Gaston A, Munoz-Blanco J, Caballero JL, Schwab W, Rothan C, Denoyes B. High Resolution Quantitative Trait Locus Mapping and Whole Genome Sequencing Enable the Design of an Anthocyanidin Reductase-Specific Homoeo-Allelic Marker for Fruit Colour Improvement in Octoploid Strawberry ( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2022; 13:869655. [PMID: 35371183 PMCID: PMC8972132 DOI: 10.3389/fpls.2022.869655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 02/24/2022] [Indexed: 05/02/2023]
Abstract
Fruit colour is central to the sensorial and nutritional quality of strawberry fruit and is therefore a major target in breeding programmes of the octoploid cultivated strawberry (Fragaria × ananassa). The red colour of the fruit is caused by the accumulation of anthocyanins, which are water-soluble flavonoids. To facilitate molecular breeding, here we have mapped with high resolution fruit colour quantitative trait loci (QTLs) (COLOUR, scored visually as in selection programmes) and associated flavonoid metabolic QTLs (5 anthocyanins compounds together with 8 flavonols and flavan-3-ols) to specific subgenomes of cultivated strawberry. Two main colour-related QTLs were located on the LG3A linkage group (Fragaria vesca subgenome). Genetic mapping, transcriptome analysis and whole genome sequencing enabled the detection of a homoeo-allelic variant of ANTHOCYANIDIN REDUCTASE (ANR) underlying the major male M3A COLOUR and pelargonidin-3-glucoside (PgGs) QTLs (up to ∼20% of explained variance). Consistent with previously published functional studies, ANR transcript abundance was inversely related with PgGs content in contrasted progeny individuals. Genetic segregation analyses further indicated that a molecular marker designed using an 18 bp deletion found in the 5'UTR of the candidate ANR homoeo-allelic variant is effective in identifying genotypes with intense red fruit colour. Our study provides insights into the genetic and molecular control of colour-related traits in strawberry and further defines a genetic marker for marker-assisted selection of new strawberry varieties with improved colour. The QTLs detected and the underlying candidate genes are different from those described to date, emphasising the importance of screening a wide diversity of genetic resources in strawberry.
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Affiliation(s)
- Marc Labadie
- Université de Bordeaux, INRAE, UMR BFP, Villenave d’Ornon, France
| | - Guillaume Vallin
- Université de Bordeaux, INRAE, UMR BFP, Villenave d’Ornon, France
| | - Aline Potier
- Université de Bordeaux, INRAE, UMR BFP, Villenave d’Ornon, France
| | | | - Ludwig Ring
- Biotechnology of Natural Products, Technical University of Munich, Freising, Germany
| | - Thomas Hoffmann
- Biotechnology of Natural Products, Technical University of Munich, Freising, Germany
| | - Amèlia Gaston
- Université de Bordeaux, INRAE, UMR BFP, Villenave d’Ornon, France
| | - Juan Munoz-Blanco
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
| | - José L. Caballero
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Córdoba, Spain
| | - Wilfried Schwab
- Biotechnology of Natural Products, Technical University of Munich, Freising, Germany
| | - Christophe Rothan
- Université de Bordeaux, INRAE, UMR BFP, Villenave d’Ornon, France
- Christophe Rothan, , orcid.org/0000-0002-6831-2823
| | - Béatrice Denoyes
- Université de Bordeaux, INRAE, UMR BFP, Villenave d’Ornon, France
- *Correspondence: Béatrice Denoyes, , orcid.org/0000-0002-0369-9609
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13
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Manivannan A, Han K, Lee SY, Lee HE, Hong JP, Kim J, Lee YR, Lee ES, Kim DS. Genome-Wide Analysis of MYB10 Transcription Factor in Fragaria and Identification of QTLs Associated with Fruit Color in Octoploid Strawberry. Int J Mol Sci 2021; 22:ijms222212587. [PMID: 34830464 PMCID: PMC8620777 DOI: 10.3390/ijms222212587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/24/2022] Open
Abstract
The genus Fragaria encompass fruits with diverse colors influenced by the distribution and accumulation of anthocyanin. Particularly, the fruit colors of strawberries with different ploidy levels are determined by expression and natural variations in the vital structural and regulatory genes involved in the anthocyanin pathway. Among the regulatory genes, MYB10 transcription factor is crucial for the expression of structural genes in the anthocyanin pathway. In the present study, we performed a genome wide investigation of MYB10 in the diploid and octoploid Fragaria species. Further, we identified seven quantitative trait loci (QTLs) associated with fruit color in octoploid strawberry. In addition, we predicted 20 candidate genes primarily influencing the fruit color based on the QTL results and transcriptome analysis of fruit skin and flesh tissues of light pink, red, and dark red strawberries. Moreover, the computational and transcriptome analysis of MYB10 in octoploid strawberry suggests that the difference in fruit colors could be predominantly influenced by the expression of MYB10 from the F. iinumae subgenome. The outcomes of the present endeavor will provide a platform for the understanding and tailoring of anthocyanin pathway in strawberry for the production of fruits with aesthetic colors.
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14
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Evolutionary history and pan-genome dynamics of strawberry ( Fragaria spp.). Proc Natl Acad Sci U S A 2021; 118:2105431118. [PMID: 34697247 PMCID: PMC8609306 DOI: 10.1073/pnas.2105431118] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2021] [Indexed: 01/29/2023] Open
Abstract
Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y. Here, we report chromosome-scale reference genomes for five strawberry species, including three newly sequenced species' genomes, and genome resequencing data for 128 additional accessions to estimate the genetic diversity, structure, and demographic history of key Fragaria species. Our analyses obtained fully resolved and strongly supported phylogenies and divergence times for most diploid strawberry species. These analyses also uncovered a new diploid species (Fragaria emeiensis Jia J. Lei). Finally, we constructed a pan-genome for Fragaria and examined the evolutionary dynamics of gene families. Notably, we identified multiple independent single base mutations of the MYB10 gene associated with white pigmented fruit shared by different strawberry species. These reference genomes and datasets, combined with our phylogenetic estimates, should serve as a powerful comparative genomic platform and resource for future studies in strawberry.
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15
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Durán-Soria S, Pott DM, Will F, Mesa-Marín J, Lewandowski M, Celejewska K, Masny A, Żurawicz E, Jennings N, Sønsteby A, Krüger E, Osorio S. Exploring Genotype-by-Environment Interactions of Chemical Composition of Raspberry by Using a Metabolomics Approach. Metabolites 2021; 11:metabo11080490. [PMID: 34436431 PMCID: PMC8398420 DOI: 10.3390/metabo11080490] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022] Open
Abstract
Promoting the consumption of fruits is a key objective of nutrition policy campaigns due to their associated health benefits. Raspberries are well appreciated for their remarkable flavor and nutritional value attributable to their antioxidant properties. Consequently, one of the objectives of present-day raspberry breeding programs is to improve the fruit’s sensory and nutritive characteristics. However, developing new genotypes with enhanced quality traits is a complex task due to the intricate impacts genetic and environmental factors have on these attributes, and the difficulty to phenotype them. We used a multi-platform metabolomic approach to compare flavor- and nutritional-related metabolite profiles of four raspberry cultivars (‘Glen Ample’, ‘Schönemann’, ‘Tulameen’ and ‘Veten’) grown in different European climates. Although the cultivars appear to be better adapted to high latitudes, for their content in soluble solids and acidity, multivariate statistical analyses allowed us to underscore important genotypic differences based on the profiles of important metabolites. ‘Schönemann’ and ‘Veten’ were characterized by high levels of anthocyanins and ellagitannins, respectively, ‘Tulameen’ by its acidity, and ‘Glen Ample’ for its content of sucrose and β-ionone, two main flavor contributors. Our results confirmed the value of metabolomic-driven approaches, which may foster the development of cultivars with enhanced health properties and flavor.
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Affiliation(s)
- Sara Durán-Soria
- Departamento de Biología Molecular y Bioquímica, Campus de Teatinos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071 Málaga, Spain; (S.D.-S.); (D.M.P.); (J.M.-M.)
| | - Delphine M. Pott
- Departamento de Biología Molecular y Bioquímica, Campus de Teatinos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071 Málaga, Spain; (S.D.-S.); (D.M.P.); (J.M.-M.)
| | - Frank Will
- Institute of Beverage Research, Hochschule Geisenheim University, 65366 Geisenheim, Germany;
| | - Jennifer Mesa-Marín
- Departamento de Biología Molecular y Bioquímica, Campus de Teatinos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071 Málaga, Spain; (S.D.-S.); (D.M.P.); (J.M.-M.)
| | - Mariusz Lewandowski
- The National Institute of Horticultural Research (INHORT), Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland; (M.L.); (K.C.); (A.M.)
| | - Karolina Celejewska
- The National Institute of Horticultural Research (INHORT), Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland; (M.L.); (K.C.); (A.M.)
| | - Agnieszka Masny
- The National Institute of Horticultural Research (INHORT), Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland; (M.L.); (K.C.); (A.M.)
| | - Edward Żurawicz
- The National Institute of Horticultural Research (INHORT), Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland; (M.L.); (K.C.); (A.M.)
| | - Nikki Jennings
- Department of Genetics, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK;
| | - Anita Sønsteby
- NIBIO, Norwegian Institute of Bioeconomy Research, 1431 Ås, Norway;
| | - Erika Krüger
- Institute of Pomology, Hochschule Geisenheim University, 65366 Geisenheim, Germany;
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica, Campus de Teatinos, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071 Málaga, Spain; (S.D.-S.); (D.M.P.); (J.M.-M.)
- Correspondence: ; Tel.: +34-952-132-394
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16
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Li D, Wang D, Fang Y, Li L, Lin X, Xu Y, Chen H, Zhu M, Luo Z. A novel phase change coolant promoted quality attributes and glutamate accumulation in postharvest shiitake mushrooms involved in energy metabolism. Food Chem 2021; 351:129227. [PMID: 33647695 DOI: 10.1016/j.foodchem.2021.129227] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 12/17/2022]
Abstract
Cold chain transportation is an important link in postharvest logistics of agricultural products. In current study, we developed a novel water-based phase change coolant (PCC), which showed longer effectiveness in maintaining low temperature condition compared with ice, and applied in preserving the postharvest mushrooms. The results showed that the novel PCC effectively inhibited water loss, as well as maintained quality attributes including firmness, color, phenolics, flavonoids, and thus prolonged the shelf-life of mushrooms. Low temperature condition created by the novel PCC treatment maintained high level of energy charge by activating the activities of SDH, CCO, H+-ATPase and Ca2+-ATPase, resulting in the delay of postharvest senescence. In addition, sufficient energy supply decreased the consumption of glutamate as carbon skeleton by inhibiting GDH activity, improved glutamate accumulation, and therefore maintained sensory properties as a result. Thus, the novel PCC might be an excellent substitute for ice in cold chain transportation of mushrooms.
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Affiliation(s)
- Dong Li
- Zhejiang University, College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Hangzhou 310058, People's Republic of China
| | - Di Wang
- Zhejiang University, College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Hangzhou 310058, People's Republic of China
| | - Yida Fang
- Zhejiang University, College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Hangzhou 310058, People's Republic of China
| | - Li Li
- Zhejiang University, College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Hangzhou 310058, People's Republic of China
| | - Xingyu Lin
- Zhejiang University, College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Hangzhou 310058, People's Republic of China
| | - Yanqun Xu
- Zhejiang University, College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Hangzhou 310058, People's Republic of China; Zhejiang University, Ningbo Research Institute, Ningbo 315100, People's Republic of China.
| | - Hangjun Chen
- Zhejiang Academy of Agricultural Science, Institute of Food Science, Hangzhou 310058, People's Republic of China
| | - Ming Zhu
- Ministry of Agriculture and Rural Affairs, Academy of Agricultural Planning and Engineering, Beijing 100125, People's Republic of China
| | - Zisheng Luo
- Zhejiang University, College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Hangzhou 310058, People's Republic of China; Zhejiang University, Ningbo Research Institute, Ningbo 315100, People's Republic of China; Fuli Institute of Food Science, Hangzhou 310058, People's Republic of China.
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17
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Warner R, Wu BS, MacPherson S, Lefsrud M. A Review of Strawberry Photobiology and Fruit Flavonoids in Controlled Environments. FRONTIERS IN PLANT SCIENCE 2021; 12:611893. [PMID: 33633764 PMCID: PMC7902047 DOI: 10.3389/fpls.2021.611893] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/06/2021] [Indexed: 05/03/2023]
Abstract
Rapid technology development in controlled environment (CE) plant production has been applied to a large variety of plants. In recent years, strawberries have become a popular fruit for CE production because of their high economic and nutritional values. With the widespread use of light-emitting diode (LED) technology in the produce industry, growers can manipulate strawberry growth and development by providing specific light spectra. Manipulating light intensity and spectral composition can modify strawberry secondary metabolism and highly impact fruit quality and antioxidant properties. While the impact of visible light on secondary metabolite profiles for other greenhouse crops is well documented, more insight into the impact of different light spectra, from UV radiation to the visible light spectrum, on strawberry plants is required. This will allow growers to maximize yield and rapidly adapt to consumer preferences. In this review, a compilation of studies investigating the effect of light properties on strawberry fruit flavonoids is provided, and a comparative analysis of how light spectra influences strawberry's photobiology and secondary metabolism is presented. The effects of pre-harvest and post-harvest light treatments with UV radiation and visible light are considered. Future studies and implications for LED lighting configurations in strawberry fruit production for researchers and growers are discussed.
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18
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Lee HE, Manivannan A, Lee SY, Han K, Yeum JG, Jo J, Kim J, Rho IR, Lee YR, Lee ES, Kang BC, Kim DS. Chromosome Level Assembly of Homozygous Inbred Line 'Wongyo 3115' Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry ( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2021; 12:696229. [PMID: 34335662 PMCID: PMC8317996 DOI: 10.3389/fpls.2021.696229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/08/2021] [Indexed: 05/02/2023]
Abstract
Strawberry is an allo-octoploid crop with high genome heterozygosity and complexity, which hinders the sequencing and the assembly of the genome. However, in the present study, we have generated a chromosome level assembly of octoploid strawberry sourced from a highly homozygous inbred line 'Wongyo 3115', using long- and short-read sequencing technologies. The assembly of 'Wongyo 3115' produced 805.6 Mb of the genome with 323 contigs scaffolded into 208 scaffolds with an N50 of 27.3 Mb after further gap filling. The whole genome annotation resulted in 151,892 genes with a gene density of 188.52 (genes/Mb) and validation of a genome, using BUSCO analysis resulted in 94.10% complete BUSCOs. Firmness is one of the vital traits in strawberry, which facilitate the postharvest shelf-life qualities. The molecular and genetic mechanisms that contribute the firmness in strawberry remain unclear. We have constructed a high-density genetic map based on the 'Wongyo 3115' reference genome to identify loci associated with firmness in the present study. For the quantitative trait locus (QTL) identification, the 'BS F2' populations developed from two inbred lines were genotyped, using an Axiom 35K strawberry chip, and marker positions were analyzed based on the 'Wongyo 3115' genome. Genetic maps were constructed with 1,049 bin markers, spanning the 3,861 cM. Using firmness data of 'BS F2' obtained from 2 consecutive years, five QTLs were identified on chromosomes 3-3, 5-1, 6-1, and 6-4. Furthermore, we predicted the candidate genes associated with firmness in strawberries by utilizing transcriptome data and QTL information. Overall, we present the chromosome-level assembly and annotation of a homozygous octoploid strawberry inbred line and a linkage map constructed to identify QTLs associated with fruit firmness.
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Affiliation(s)
- Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Abinaya Manivannan
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Sun Yi Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Jun-Geol Yeum
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jinkwan Jo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jinhee Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Il Rae Rho
- Department of Agronomy, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Ye-Rin Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Eun Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- *Correspondence: Byoung-Cheorl Kang
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
- Do-Sun Kim
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19
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Pott DM, Vallarino JG, Cruz-Rus E, Willmitzer L, Sánchez-Sevilla JF, Amaya I, Osorio S. Genetic analysis of phenylpropanoids and antioxidant capacity in strawberry fruit reveals mQTL hotspots and candidate genes. Sci Rep 2020; 10:20197. [PMID: 33214566 PMCID: PMC7677386 DOI: 10.1038/s41598-020-76946-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/04/2020] [Indexed: 12/19/2022] Open
Abstract
Phenylpropanoids are a large class of plant secondary metabolites, which play essential roles in human health mainly associated with their antioxidant activity. Strawberry (Fragaria × ananassa) is a rich source of phytonutrients, including phenylpropanoids, which have been shown to have beneficial effects on human health. In this study, using the F. × ananassa '232' × '1392' F1 segregating population, we analyzed the genetic control of individual phenylpropanoid metabolites, total polyphenol content (TPC) and antioxidant capacity (TEAC) in strawberry fruit over two seasons. We have identified a total of 7, 9, and 309 quantitative trait loci (QTL) for TPC, TEAC and for 77 polar secondary metabolites, respectively. Hotspots of stable QTL for health-related antioxidant compounds were detected on linkage groups LG IV-3, LG V-2 and V-4, and LG VI-1 and VI-2, where associated markers represent useful targets for marker-assisted selection of new varieties with increased levels of antioxidant secondary compounds. Moreover, differential expression of candidate genes for major and stable mQTLs was studied in fruits of contrasting lines in important flavonoids. Our results indicate that higher expression of FaF3'H, which encodes the flavonoid 3'-hydroxylase, is associated with increased content of these important flavonoids.
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Affiliation(s)
- Delphine M Pott
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071, Málaga, Spain.,Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain
| | - José G Vallarino
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071, Málaga, Spain.,Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain
| | - Eduardo Cruz-Rus
- Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain.,Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Centro IFAPA de Málaga, 29140, Málaga, Spain
| | - Lothar Willmitzer
- Max-Planck-Institut Für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
| | - José F Sánchez-Sevilla
- Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain.,Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Centro IFAPA de Málaga, 29140, Málaga, Spain
| | - Iraida Amaya
- Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain. .,Laboratorio de Genómica y Biotecnología, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Centro IFAPA de Málaga, 29140, Málaga, Spain.
| | - Sonia Osorio
- Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071, Málaga, Spain. .,Unidad Asociada de I + D + i IFAPA-CSIC Biotecnología y Mejora en Fresa, Málaga, Spain.
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