1
|
Lynn SC, Dunwell JM, Whitehouse AB, Cockerton HM. Genetic loci associated with tissue-specific resistance to powdery mildew in octoploid strawberry ( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2024; 15:1376061. [PMID: 38742212 PMCID: PMC11089197 DOI: 10.3389/fpls.2024.1376061] [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: 01/24/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Powdery mildew is one of the most problematic diseases in strawberry production. To date, few commercial strawberry cultivars are deemed to have complete resistance and as such, an extensive spray programme must be implemented to control the pathogen. Here, a large-scale field experiment was used to determine the powdery mildew resistance status of leaf and fruit tissues across a diverse panel of strawberry genotypes. This phenotypic data was used to identify Quantitative Trait Nucleotides (QTN) associated with tissue-specific powdery mildew resistance. In total, six stable QTN were found to be associated with foliar resistance, with one QTN on chromosome 7D associated with a 61% increase in resistance. In contrast to the foliage results, there were no QTN associated with fruit disease resistance and there was a high level of resistance observed on strawberry fruit, with no genetic correlation observed between fruit and foliar symptoms, indicating a tissue-specific response. Beyond the identification of genetic loci, we also demonstrate that genomic selection can lead to rapid gains in foliar resistance across genotypes, with the potential to capture >50% of the genetic foliage resistance present in the population. To date, breeding of robust powdery mildew resistance in strawberry has been impeded by the quantitative nature of natural resistance and a lack of knowledge relating to the genetic control of the trait. These results address this shortfall, through providing the community with a wealth of information that could be utilized for genomic informed breeding, implementation of which could deliver a natural resistance strategy for combatting powdery mildew.
Collapse
Affiliation(s)
- Samantha C. Lynn
- Genetics, Genomics and Breeding, National Institute of Agricultural Botany (NIAB), Kent, United Kingdom
- Crop Science, University of Reading, Reading, United Kingdom
| | - Jim M. Dunwell
- Crop Science, University of Reading, Reading, United Kingdom
| | - Adam B. Whitehouse
- Genetics, Genomics and Breeding, National Institute of Agricultural Botany (NIAB), Kent, United Kingdom
| | | |
Collapse
|
2
|
Lyzhin AS, Luk'yanchuk IV. Study of a genetic collection of strawberry (Fragaria L.) for resistance to powdery mildew. Vavilovskii Zhurnal Genet Selektsii 2024; 28:166-174. [PMID: 38680188 PMCID: PMC11043506 DOI: 10.18699/vjgb-24-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 05/01/2024] Open
Abstract
Powdery mildew (Sphaerotheca macularis Mag. (syn. Podosphaera aphanis Wallr.)) is a dangerous disease of strawberry (Fragaria L.). The resistance of strawberry to powdery mildew is controlled polygenically. Several genetic loci with a large contribution to disease resistance have been identified in various strawberry varieties. Diagnostic DNA markers have been developed for QTL 08 To-f. They showed a high level of reliable gene detection in mapping populations. The purpose of this study was assessment of a strawberry genetic collection for resistance to powdery mildew and identification of promising strawberry forms for breeding for resistance to S. macularis. The objects of the study were wild species of the genus Fragaria L., varieties and selected seedlings of strawberry (Fragaria × ananassa Duch.) created in the I.V. Michurin Federal Scientific Center, and strawberry varieties introduced from various ecological and geographical regions. To identify QTL 08 To-f, DNA markers IB535110 and IB533828 were used. Locus 08 To-f was detected in 23.2 % of the analyzed strawberry genotypes, including wild species F. moschata and F. orientalis, strawberry varieties of Russian breeding (Bylinnaya and Sudarushka) and foreign breeding (Florence, Korona, Malwina, Ostara, Polka and Red Gauntlet). The correlation between the presence of markers IB535110 and IB533828 and phenotypic resistance (powdery mildew effect on strawberry plants is absent) was 0.649. The determination coefficient (R2 ) showing the contribution of the studied locus to the manifestation of the trait was 0.421, that is, in 42.1 % of cases resistance was explained by the presence of QTL 08 To-f, and in 57.9 % of cases, by other genetic factors. All strawberry genotypes with locus 08 To-f were characterized by high field resistance to S. macularis in the conditions of Michurinsk, Tambov region. Thus, locus 08 To-f is promising for conferring resistance on local powdery mildew races, and markers IB535110 and IB533828 can be used in marker-assisted breeding programs to create powdery mildewresistant strawberry genotypes.
Collapse
Affiliation(s)
- A S Lyzhin
- I.V. Michurin Federal Scientific Center, Michurinsk, Russia
| | | |
Collapse
|
3
|
Muñoz P, Castillejo C, Gómez JA, Miranda L, Lesemann S, Olbricht K, Petit A, Chartier P, Haugeneder A, Trinkl J, Mazzoni L, Masny A, Zurawicz E, Ziegler FMR, Usadel B, Schwab W, Denoyes B, Mezzetti B, Osorio S, Sánchez-Sevilla JF, Amaya I. QTL analysis for ascorbic acid content in strawberry fruit reveals a complex genetic architecture and association with GDP-L-galactose phosphorylase. HORTICULTURE RESEARCH 2023; 10:uhad006. [PMID: 36938573 PMCID: PMC10022485 DOI: 10.1093/hr/uhad006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Strawberry (Fragaria × ananassa) fruits are an excellent source of L-ascorbic acid (AsA), a powerful antioxidant for plants and humans. Identifying the genetic components underlying AsA accumulation is crucial for enhancing strawberry nutritional quality. Here, we unravel the genetic architecture of AsA accumulation using an F1 population derived from parental lines 'Candonga' and 'Senga Sengana', adapted to distinct Southern and Northern European areas. To account for environmental effects, the F1 and parental lines were grown and phenotyped in five locations across Europe (France, Germany, Italy, Poland and Spain). Fruit AsA content displayed normal distribution typical of quantitative traits and ranged five-fold, with significant differences among genotypes and environments. AsA content in each country and the average in all of them was used in combination with 6,974 markers for quantitative trait locus (QTL) analysis. Environmentally stable QTLs for AsA content were detected in linkage group (LG) 3A, LG 5A, LG 5B, LG 6B and LG 7C. Candidate genes were identified within stable QTL intervals and expression analysis in lines with contrasting AsA content suggested that GDP-L-Galactose Phosphorylase FaGGP(3A), and the chloroplast-located AsA transporter gene FaPHT4;4(7C) might be the underlying genetic factors for QTLs on LG 3A and 7C, respectively. We show that recessive alleles of FaGGP(3A) inherited from both parental lines increase fruit AsA content. Furthermore, expression of FaGGP(3A) was two-fold higher in lines with high AsA. Markers here identified represent a useful resource for efficient selection of new strawberry cultivars with increased AsA content.
Collapse
Affiliation(s)
- Pilar Muñoz
- Centro IFAPA de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), 29140, Málaga, Spain
- PhD program in Advanced Biotechnology, Universidad de Málaga, 29071, Málaga, Spain
| | - Cristina Castillejo
- Centro IFAPA de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), 29140, Málaga, Spain
| | | | - Luis Miranda
- Finca el Cebollar, Centro IFAPA las Torres, 04745, Huelva, Spain
| | | | | | | | | | - Annika Haugeneder
- Biotechnology of Natural Products, Technische Universität München, 85354, Freising, Germany
| | - Johanna Trinkl
- Biotechnology of Natural Products, Technische Universität München, 85354, Freising, Germany
| | - Luca Mazzoni
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Agnieszka Masny
- Department of Horticultural Crop Breeding, the National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland
| | | | | | - Björn Usadel
- Institute of Bio- and Geosciences, Bioinformatics (IBG-4), Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Wilfried Schwab
- Biotechnology of Natural Products, Technische Universität München, 85354, Freising, Germany
| | - Béatrice Denoyes
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140, France
| | - Bruno Mezzetti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, 60131, Ancona, Italy
| | - Sonia Osorio
- Departamento 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, 29010, Málaga, Spain
| | - José F Sánchez-Sevilla
- Centro IFAPA de Málaga, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), 29140, Málaga, Spain
- Unidad Asociada de I+D+i IFAPA-CSIC Biotecnología y Mejora en Fresa, 29010, Málaga, Spain
| | | |
Collapse
|
4
|
Heaven T, Cockerton HM, Xu X, Goddard M, Armitage AD. A Genomic Resource for the Strawberry Powdery Mildew Pathogen Podosphaera aphanis. PHYTOPATHOLOGY 2023; 113:355-359. [PMID: 36738090 DOI: 10.1094/phyto-03-22-0091-a] [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: 06/18/2023]
Abstract
Powdery mildew is one of the most economically destructive diseases in protected strawberry production. Here we present the first genome assembly for Podosphaera aphanis, the causal agent of powdery mildew on strawberry. This obligate-biotrophic fungal pathogen was sampled from a naturally occurring outbreak on Fragaria × ananassa 'Malling Centenary' plants grown under cover in the United Kingdom. Assembled reads resolved a 55.6 Mb genome, composed of 12,357 contigs whose annotation led to prediction of 17,239 genes encoding 17,328 proteins. The genome is highly-complete, with 97.5% of conserved single-copy Ascomycete genes shown to be present. This annotated P. aphanis genome provides a molecular resource for further investigation into host-pathogen interactions in the strawberry powdery mildew pathosystem.
Collapse
Affiliation(s)
- Thomas Heaven
- NIAB, New Road, East Malling, Kent, ME19 6BJ, U.K
- School of Life Sciences, University of Lincoln, Lincoln, Lincolnshire, LN6 7DL, U.K
| | - Helen M Cockerton
- NIAB, New Road, East Malling, Kent, ME19 6BJ, U.K
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NZ, U.K
| | - Xiangming Xu
- NIAB, New Road, East Malling, Kent, ME19 6BJ, U.K
| | - Matthew Goddard
- School of Life Sciences, University of Lincoln, Lincoln, Lincolnshire, LN6 7DL, U.K
| | - Andrew D Armitage
- National Resources Institute, University of Greenwich, Kent, ME4 4TB, U.K
| |
Collapse
|
5
|
Tapia R, Abd-Elrahman A, Osorio L, Whitaker VM, Lee S. Combining canopy reflectance spectrometry and genome-wide prediction to increase response to selection for powdery mildew resistance in cultivated strawberry. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5322-5335. [PMID: 35383379 DOI: 10.1093/jxb/erac136] [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: 12/14/2021] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
High-throughput phenotyping is an emerging approach in plant science, but thus far only a few applications have been made in horticultural crop breeding. Remote sensing of leaf or canopy spectral reflectance can help breeders rapidly measure traits, increase selection accuracy, and thereby improve response to selection. In the present study, we evaluated the integration of spectral analysis of canopy reflectance and genomic information for the prediction of strawberry (Fragaria × ananassa) powdery mildew disease. Two multi-parental breeding populations of strawberry comprising a total of 340 and 464 pedigree-connected seedlings were evaluated in two separate seasons. A single-trait Bayesian prediction method using 1001 spectral wavebands in the ultraviolet-visible-near infrared region (350-1350 nm wavelength) combined with 8552 single nucleotide polymorphism markers showed up to 2-fold increase in predictive ability over models using markers alone. The integration of high-throughput phenotyping was further validated independently across years/trials with improved response to selection of up to 90%. We also conducted Bayesian multi-trait analysis using the estimated vegetative indices as secondary traits. Three vegetative indices (Datt3, REP_Li, and Vogelmann2) had high genetic correlations (rA) with powdery mildew visual ratings with average rA values of 0.76, 0.71, and 0.71, respectively. Increasing training population sizes by incorporating individuals with only vegetative index information yielded substantial increases in predictive ability. These results strongly indicate the use of vegetative indices as secondary traits for indirect selection. Overall, combining spectrometry and genome-wide prediction improved selection accuracy and response to selection for powdery mildew resistance, demonstrating the power of an integrated phenomics-genomics approach in strawberry breeding.
Collapse
Affiliation(s)
- Ronald Tapia
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, 14625 County Road 672, Wimauma, FL 33598, USA
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Amr Abd-Elrahman
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, 14625 County Road 672, Wimauma, FL 33598, USA
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32603, USA
| | - Luis Osorio
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, 14625 County Road 672, Wimauma, FL 33598, USA
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Vance M Whitaker
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, 14625 County Road 672, Wimauma, FL 33598, USA
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Seonghee Lee
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, 14625 County Road 672, Wimauma, FL 33598, USA
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA
| |
Collapse
|
6
|
Sangiorgio D, Cellini A, Donati I, Ferrari E, Tanunchai B, Fareed Mohamed Wahdan S, Sadubsarn D, Farneti B, Checcucci A, Buscot F, Spinelli F, Purahong W. Taxonomical and functional composition of strawberry microbiome is genotype-dependent. J Adv Res 2022; 42:189-204. [PMID: 36513413 PMCID: PMC9788945 DOI: 10.1016/j.jare.2022.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/01/2022] [Accepted: 02/17/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Specific microbial communities are associated to host plants, influencing their phenotype and fitness.Despite the rising interest in plant microbiome, the role of microbial communities associated with perennial fruit plants remains overlooked. OBJECTIVES This work provides the first comprehensive descriptionof the taxonomical and functional bacterial and fungal microbiota of below- and above-ground organsof three commercially important strawberry genotypes under cultural conditions. METHODS Strawberry-associatedfungal and bacterial microbiomes were characterised by Next-Generation Sequencing and the potential functions expressed by the bacterial microbiome were analysed by both in silico and in vitro characterisation of plant growth-promoting abilities of native bacteria. Additionally, the association between the strawberry microbiome, plant disease tolerance, plant mineral nutrient content, and fruit quality was investigated. RESULTS Results showed that thestrawberry core microbiome included 24 bacteria and 15 fungal operational taxonomicunits (OTUs).However, plant organ and genotype had a significant role in determining the taxonomical and functional composition of microbial communities. Interestingly, the cultivar with the highesttolerance against powdery mildew and leaf spot and the highest fruit productivity was the only one able to ubiquitously recruit the beneficial bacterium, Pseudomonasfluorescens, and to establish a mutualistic symbiosis with the arbuscular mycorrhizaRhizophagus irregularis. CONCLUSION This work sheds light on the interaction of cultivated strawberry genotypes with a variety of microbes and highlights the importance of their applications to increase the sustainability of fruit crop production.
Collapse
Affiliation(s)
- Daniela Sangiorgio
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - University of Bologna, viale Fanin 46, 40127 Bologna, Italy
| | - Antonio Cellini
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - University of Bologna, viale Fanin 46, 40127 Bologna, Italy
| | | | - Erika Ferrari
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy
| | - Benjawan Tanunchai
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany
| | - Sara Fareed Mohamed Wahdan
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany,Department of Botany, Faculty of Science, Suez Canal University, 41522 Ismailia, Egypt
| | - Dolaya Sadubsarn
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany
| | - Brian Farneti
- Fondazione Edmund Mach, Research and Innovation Centre, Via E. Mach 1, 38010, S. Michele all’Adige, TN, Italy
| | - Alice Checcucci
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - University of Bologna, viale Fanin 46, 40127 Bologna, Italy
| | - François Buscot
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - Francesco Spinelli
- Department of Agricultural and Food Sciences (DISTAL), Alma Mater Studiorum - University of Bologna, viale Fanin 46, 40127 Bologna, Italy,Corresponding authors.
| | - Witoon Purahong
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany,Corresponding authors.
| |
Collapse
|
7
|
Rey-Serra P, Mnejja M, Monfort A. Shape, firmness and fruit quality QTLs shared in two non-related strawberry populations. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 311:111010. [PMID: 34482914 DOI: 10.1016/j.plantsci.2021.111010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 05/24/2023]
Abstract
The cultivated strawberry (Fragaria x ananassa) is an octoploid species (2n = 8x = 56), appreciated widely for its fruit. There have been very few studies on fruit quality traits, which are known to be mostly polygenic and environmentally dependent. To identify higher genetic variability, two non-related populations were genotyped: an F1 population cross between 'FC50' and 'FD54' and an F2 population cross between 'Camarosa' and 'Dover', hybridizing both with IStraw35k and IStraw90k SNP arrays, respectively. The F1 genetic map was constructed with 14595 SNPs and the F2 map with 7977 SNPs. High collinearity was observed when comparing one genetic map with the other and on comparing both with the octoploid genome. To assess fruit variability, both populations were phenotyped for shape, firmness, taste and other fruit traits over the 2016-2019 period. With QTL analyses, 33 stable QTLs were mapped in the 'FC50xFD54' population, and three hotspot regions were found for shape traits in LG3A, LG4D and LG6D. In the '21AF' population, only eight stable QTLs were detected. Despite that, two major and stable QTLs were mapped in the same interval of confidence for both populations. A shared fruit shape ratio QTL which explained around 25 % of trait variance was mapped in LG3A, and a shared firmness QTL explaining 26.9 % of trait variance in LG7C. For the first time, two QTLs were discovered in LG3A and LG4A for a phenotype neck without achenes. When analysing two different mapping populations, in addition to finding specific QTL regions for the studied traits, a narrowing down of the interval of confidence for the shared QTLs is achieved. As a result of this study, a new set of SNPs for fruit firmness and shape is now available for use in MAS in strawberry breeding programs.
Collapse
Affiliation(s)
- Pol Rey-Serra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona, Spain; Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| | - Mourad Mnejja
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona, Spain; Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| | - Amparo Monfort
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona, Spain; Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain.
| |
Collapse
|