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Yu X, Huang Z, Cheng Y, Hu K, Zhou Y, Yao H, Shen J, Huang Y, Zhuang X, Cai Y. Comparative Genomics Screens Identify a Novel Small Secretory Peptide, SlSolP12, which Activates Both Local and Systemic Immune Response in Tomatoes and Exhibits Broad-Spectrum Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18507-18519. [PMID: 39113497 DOI: 10.1021/acs.jafc.4c03633] [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: 08/22/2024]
Abstract
Small secreted peptides (SSPs) are essential for defense mechanisms in plant-microbe interactions, acting as danger-associated molecular patterns (DAMPs). Despite the first discovery of SSPs over three decades ago, only a limited number of SSP families, particularly within Solanaceae plants, have been identified due to inefficient approaches. This study employed comparative genomics screens with Solanaceae proteomes (tomato, tobacco, and pepper) to discover a novel SSP family, SolP. Bioinformatics analysis suggests that SolP may serve as an endogenous signal initiating the plant PTI response. Interestingly, SolP family members from tomato, tobacco, and pepper share an identical sequence (VTSNALALVNRFAD), named SlSolP12 (also referred to as NtSolP15 or CaSolP1). Biochemical and phenotypic analyses revealed that synthetic SlSolP12 peptide triggers multiple defense responses: ROS burst, MAPK activation, callose deposition, stomatal closure, and expression of immune defense genes. Furthermore, SlSolP12 enhances systemic resistance against Botrytis cinerea infection in tomato plants and interferes with classical peptides, flg22 and Systemin, which modulate the immune response. Remarkably, SolP12 activates ROS in diverse plant species, such as Arabidopsis thaliana, soybean, and rice, showing a broad spectrum of biological activities. This study provides valuable approaches for identifying endogenous SSPs and highlights SlSolP12 as a novel DAMP that could serve as a useful target for crop protection.
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Affiliation(s)
- Xiaosong Yu
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Zhongchao Huang
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Yuanyuan Cheng
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Keyi Hu
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Yan Zhou
- Chengdu Lusyno Biotechnology Co., Ltd., Chengdu 610000, Sichuan, China
| | - Huipeng Yao
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 310000, Zhejiang, China
| | - Yan Huang
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
| | - Xiaohong Zhuang
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Yi Cai
- College of Life Sciences, Sichuan Agricultural University, Yaan 625000, Sichuan, China
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Yeon J, Le NT, Heo J, Sim SC. Low-density SNP markers with high prediction accuracy of genomic selection for bacterial wilt resistance in tomato. FRONTIERS IN PLANT SCIENCE 2024; 15:1402693. [PMID: 38872894 PMCID: PMC11169939 DOI: 10.3389/fpls.2024.1402693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/07/2024] [Indexed: 06/15/2024]
Abstract
Bacterial wilt (BW) is a soil-borne disease that leads to severe damage in tomato. Host resistance against BW is considered polygenic and effective in controlling this destructive disease. In this study, genomic selection (GS), which is a promising breeding strategy to improve quantitative traits, was investigated for BW resistance. Two tomato collections, TGC1 (n = 162) and TGC2 (n = 191), were used as training populations. Disease severity was assessed using three seedling assays in each population, and the best linear unbiased prediction (BLUP) values were obtained. The 31,142 SNP data were generated using the 51K Axiom array™ in the training populations. With these data, six GS models were trained to predict genomic estimated breeding values (GEBVs) in three populations (TGC1, TGC2, and combined). The parametric models Bayesian LASSO and RR-BLUP resulted in higher levels of prediction accuracy compared with all the non-parametric models (RKHS, SVM, and random forest) in two training populations. To identify low-density markers, two subsets of 1,557 SNPs were filtered based on marker effects (Bayesian LASSO) and variable importance values (random forest) in the combined population. An additional subset was generated using 1,357 SNPs from a genome-wide association study. These subsets showed prediction accuracies of 0.699 to 0.756 in Bayesian LASSO and 0.670 to 0.682 in random forest, which were higher relative to the 31,142 SNPs (0.625 and 0.614). Moreover, high prediction accuracies (0.743 and 0.702) were found with a common set of 135 SNPs derived from the three subsets. The resulting low-density SNPs will be useful to develop a cost-effective GS strategy for BW resistance in tomato breeding programs.
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Affiliation(s)
- Jeyun Yeon
- Department of Bioindustry and Bioresource Engineering, Sejong University, Seoul, Republic of Korea
| | - Ngoc Thi Le
- Department of Bioindustry and Bioresource Engineering, Sejong University, Seoul, Republic of Korea
| | - Jaehun Heo
- Department of Bioindustry and Bioresource Engineering, Sejong University, Seoul, Republic of Korea
| | - Sung-Chur Sim
- Department of Bioindustry and Bioresource Engineering, Sejong University, Seoul, Republic of Korea
- Plant Engineering Research Institute, Sejong University, Seoul, Republic of Korea
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Gechev T, Kazakov P, Ivanova A, Ivanova T, Mircheva M, Kolev V, Ganeva D, Tabakova-Komsalova V, Ruseva M, Kantardjieva E, Kazashka VS. Establishment and development of the Center of Plant Systems Biology and Biotechnology in Plovdiv, Bulgaria. OPEN RESEARCH EUROPE 2024; 3:140. [PMID: 38846177 PMCID: PMC11153986 DOI: 10.12688/openreseurope.16514.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/17/2024] [Indexed: 06/09/2024]
Abstract
The Bulgarian research landscape, presented mainly by the research institutes that are part of the Bulgarian Academy of Sciences and the Agricultural Academy, needs diversification to match the research and innovation potential of the other European Union (EU) countries. This article describes the establishment of the Center of Plant Systems Biology and Biotechnology (CPSBB), a new innovative type of independent research organization that is changing the research landscape in Bulgaria. Supported by the EU Commission, Bulgarian Government, and Plovdiv Municipality, CPSBB has quickly become the leading plant science institute in Bulgaria, creating knowledge in diverse fields such as bioinformatics, biotechnology, genetics and genomics, metabolomics, and systems biology. We outline the organizational structure of CPSBB, the development of its infrastructure, and its scientific productivity. Finally, we compare CPSBB with other similar research establishments in Europe and we conclude that such new types of institutes have a bright future in Bulgaria due to their operational flexibility, productivity, and connections with academia and industry.
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Affiliation(s)
- Tsanko Gechev
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Plovdiv Province, Bulgaria
- University of Plovdiv, Plovdiv, 4000, Bulgaria
| | - Petar Kazakov
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Plovdiv Province, Bulgaria
| | - Asia Ivanova
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Plovdiv Province, Bulgaria
| | - Tsvetomira Ivanova
- University of Plovdiv, Plovdiv, 4000, Bulgaria
- Academy of Music, Dance, and Fine Arts, Plovdiv, 4000, Bulgaria
| | - Marina Mircheva
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Plovdiv Province, Bulgaria
| | - Vasil Kolev
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Plovdiv Province, Bulgaria
- Academy of Music, Dance, and Fine Arts, Plovdiv, 4000, Bulgaria
| | - Daniela Ganeva
- Maritsa Vegetable Crops Research Institute, Plovdiv, 4004, Bulgaria
| | | | | | | | - Vesela S. Kazashka
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Plovdiv Province, Bulgaria
- Academy of Music, Dance, and Fine Arts, Plovdiv, 4000, Bulgaria
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Bhattarai A, Nimmakayala P, Davenport B, Natarajan P, Tonapi K, Kadiyala SS, Lopez-Ortiz C, Ibarra-Muñoz L, Chakrabarti M, Benedito V, Adjeroh DA, Balagurusamy N, Reddy UK. Genetic tapestry of Capsicum fruit colors: a comparative analysis of four cultivated species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:130. [PMID: 38744692 DOI: 10.1007/s00122-024-04635-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/17/2024] [Indexed: 05/16/2024]
Abstract
KEY MESSAGE Genome-wide association study of color spaces across the four cultivated Capsicum spp. revealed a shared set of genes influencing fruit color, suggesting mechanisms and pathways across Capsicum species are conserved during the speciation. Notably, Cytochrome P450 of the carotenoid pathway, MYB transcription factor, and pentatricopeptide repeat-containing protein are the major genes responsible for fruit color variation across the Capsicum species. Peppers (Capsicum spp.) rank among the most widely consumed spices globally. Fruit color, serving as a determinant for use in food colorants and cosmeceuticals and an indicator of nutritional contents, significantly influences market quality and price. Cultivated Capsicum species display extensive phenotypic diversity, especially in fruit coloration. Our study leveraged the genetic variance within four Capsicum species (Capsicum baccatum, Capsicum chinense, Capsicum frutescens, and Capsicum annuum) to elucidate the genetic mechanisms driving color variation in peppers and related Solanaceae species. We analyzed color metrics and chromatic attributes (Red, Green, Blue, L*, a*, b*, Luminosity, Hue, and Chroma) on samples cultivated over six years (2015-2021). We resolved genomic regions associated with fruit color diversity through the sets of SNPs obtained from Genotyping by Sequencing (GBS) and genome-wide association study (GWAS) with a Multi-Locus Mixed Linear Model (MLMM). Significant SNPs with FDR correction were identified, within the Cytochrome P450, MYB-related genes, Pentatricopeptide repeat proteins, and ABC transporter family were the most common among the four species, indicating comparative evolution of fruit colors. We further validated the role of a pentatricopeptide repeat-containing protein (Chr01:31,205,460) and a cytochrome P450 enzyme (Chr08:45,351,919) via competitive allele-specific PCR (KASP) genotyping. Our findings advance the understanding of the genetic underpinnings of Capsicum fruit coloration, with developed KASP assays holding potential for applications in crop breeding and aligning with consumer preferences. This study provides a cornerstone for future research into exploiting Capsicum's diverse fruit color variation.
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Affiliation(s)
- Ambika Bhattarai
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Padma Nimmakayala
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA.
| | - Brittany Davenport
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Purushothaman Natarajan
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Krittika Tonapi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Sai Satish Kadiyala
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Carlos Lopez-Ortiz
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
| | - Lizbeth Ibarra-Muñoz
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, 27275, Torreon, Coahuila, Mexico
| | - Manohar Chakrabarti
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Vagner Benedito
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Donald A Adjeroh
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, 26506, USA
| | - Nagamani Balagurusamy
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, 27275, Torreon, Coahuila, Mexico.
| | - Umesh K Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA.
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He S, Dong W, Chen J, Zhang J, Lin W, Yang S, Xu D, Zhou Y, Miao B, Wang W, Chen F. DataColor: unveiling biological data relationships through distinctive color mapping. HORTICULTURE RESEARCH 2024; 11:uhad273. [PMID: 38333729 PMCID: PMC10852383 DOI: 10.1093/hr/uhad273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/06/2023] [Indexed: 02/10/2024]
Abstract
In the era of rapid advancements in high-throughput omics technologies, the visualization of diverse data types with varying orders of magnitude presents a pressing challenge. To bridge this gap, we introduce DataColor, an all-encompassing software solution meticulously crafted to address this challenge. Our aim is to empower users with the ability to handle a wide array of data types through an assortment of tools, while simultaneously streamlining parameter selection for rapid insights and detailed enhancements. DataColor stands as a robust toolkit, encompassing 23 distinct tools coupled with over 600 parameters. The defining characteristic of this toolkit is its adept utilization of the color spectrum, allowing for the representation of data spanning diverse types and magnitudes. Through the integration of advanced algorithms encompassing data clustering, normalization, squarified layouts, and customizable parameters, DataColor unveils an abundance of insights that lay hidden within the intricate relationships embedded in the data. Whether you find yourself navigating the analysis of expansive datasets or embarking on the quest to visualize intricate patterns, DataColor stands as the comprehensive and potent solution. We extend the availability of DataColor to all users at no cost, accessible through the following link: https://github.com/frankgenome/DataColor.
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Affiliation(s)
- Shuang He
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Wei Dong
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou 510055, China
| | - Junhao Chen
- Department of Biology, Saint Louis University, St Louis, MO 63103, USA
| | - Junyu Zhang
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Weiwei Lin
- Merkle Business Information Consultancy (Nanjing) Co., Ltd, Nanjing 210032, China
| | - Shuting Yang
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Dong Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yuhan Zhou
- State Key Laboratory of Rice Biology & Breeding, Zhejiang Provincial Key Laboratory of Crop Germplasm, The Advanced Seed Institute, Zhejiang University, Hangzhou 310058, China
| | - Benben Miao
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Wenquan Wang
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Fei Chen
- Sanya Institute of Breeding and Multiplication, National Key Laboratory for Tropical Crop Breeding, Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
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Lozada DN, Sandhu KS, Bhatta M. Ridge regression and deep learning models for genome-wide selection of complex traits in New Mexican Chile peppers. BMC Genom Data 2023; 24:80. [PMID: 38110866 PMCID: PMC10726521 DOI: 10.1186/s12863-023-01179-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Genomewide prediction estimates the genomic breeding values of selection candidates which can be utilized for population improvement and cultivar development. Ridge regression and deep learning-based selection models were implemented for yield and agronomic traits of 204 chile pepper genotypes evaluated in multi-environment trials in New Mexico, USA. RESULTS Accuracy of prediction differed across different models under ten-fold cross-validations, where high prediction accuracy was observed for highly heritable traits such as plant height and plant width. No model was superior across traits using 14,922 SNP markers for genomewide selection. Bayesian ridge regression had the highest average accuracy for first pod date (0.77) and total yield per plant (0.33). Multilayer perceptron (MLP) was the most superior for flowering time (0.76) and plant height (0.73), whereas the genomic BLUP model had the highest accuracy for plant width (0.62). Using a subset of 7,690 SNP loci resulting from grouping markers based on linkage disequilibrium coefficients resulted in improved accuracy for first pod date, ten pod weight, and total yield per plant, even under a relatively small training population size for MLP and random forest models. Genomic and ridge regression BLUP models were sufficient for optimal prediction accuracies for small training population size. Combining phenotypic selection and genomewide selection resulted in improved selection response for yield-related traits, indicating that integrated approaches can result in improved gains achieved through selection. CONCLUSIONS Accuracy values for ridge regression and deep learning prediction models demonstrate the potential of implementing genomewide selection for genetic improvement in chile pepper breeding programs. Ultimately, a large training data is relevant for improved genomic selection accuracy for the deep learning models.
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Affiliation(s)
- Dennis N Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA.
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Magon G, De Rosa V, Martina M, Falchi R, Acquadro A, Barcaccia G, Portis E, Vannozzi A, De Paoli E. Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1293186. [PMID: 38148866 PMCID: PMC10750425 DOI: 10.3389/fpls.2023.1293186] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes.
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Affiliation(s)
- Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
| | - Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Rachele Falchi
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padova, Agripolis, Viale dell’Università 16, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Via delle Scienze, 206, Udine, Italy
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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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