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Chen X, Wen K, Zhou X, Zhu M, Liu Y, Jin J, Nellist CF. The devastating oomycete phytopathogen Phytophthora cactorum: Insights into its biology and molecular features. MOLECULAR PLANT PATHOLOGY 2023; 24:1017-1032. [PMID: 37144631 PMCID: PMC10423333 DOI: 10.1111/mpp.13345] [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: 02/24/2023] [Revised: 04/05/2023] [Accepted: 04/05/2023] [Indexed: 05/06/2023]
Abstract
Phytophthora cactorum is one of the most economically important soilborne oomycete pathogens in the world. It infects more than 200 plant species spanning 54 families, most of which are herbaceous and woody species. Although traditionally considered to be a generalist, marked differences of P. cactorum isolates occur in degree of pathogenicity to different hosts. As the impact of crop loss caused by this species has increased recently, there has been a tremendous increase in the development of new tools, resources, and management strategies to study and combat this devastating pathogen. This review aims to integrate recent molecular biology analyses of P. cactorum with the current knowledge of the cellular and genetic basis of its growth, development, and host infection. The goal is to provide a framework for further studies of P. cactorum by highlighting important biological and molecular features, shedding light on the functions of pathogenicity factors, and developing effective control measures. TAXONOMY P. cactorum (Leb. & Cohn) Schröeter: kingdom Chromista; phylum Oomycota; class Oomycetes; order Peronosporales; family Peronosporaceae; genus Phytophthora. HOST RANGE Infects about 200 plant species in 154 genera representing 54 families. Economically important host plants include strawberry, apple, pear, Panax spp., and walnut. DISEASE SYMPTOMS The soilborne pathogen often causes root, stem, collar, crown, and fruit rots, as well as foliar infection, stem canker, and seedling damping off.
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Affiliation(s)
- Xiao‐Ren Chen
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Ke Wen
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Xue Zhou
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Ming‐Yue Zhu
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Yang Liu
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Jing‐Hao Jin
- College of Plant ProtectionYangzhou UniversityYangzhouChina
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Session AM, Rokhsar DS. Transposon signatures of allopolyploid genome evolution. Nat Commun 2023; 14:3180. [PMID: 37263993 DOI: 10.1038/s41467-023-38560-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/08/2023] [Indexed: 06/03/2023] Open
Abstract
Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.
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Affiliation(s)
- Adam M Session
- Department of Molecular and Cell, University of California, Berkeley, CA, 94720, USA.
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Department of Biological Sciences, Binghamton University, Binghamton, NY, 13902, USA.
| | - Daniel S Rokhsar
- Department of Molecular and Cell, University of California, Berkeley, CA, 94720, USA
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Molecular Genetics Unit, Okinawa Institute for Science and Technology Graduate University, Okinawa, Japan
- Chan Zuckerberg BioHub, San Francisco, CA, USA
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Werner CR, Gaynor RC, Sargent DJ, Lillo A, Gorjanc G, Hickey JM. Genomic selection strategies for clonally propagated crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:74. [PMID: 36952013 PMCID: PMC10036424 DOI: 10.1007/s00122-023-04300-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/14/2023] [Indexed: 05/27/2023]
Abstract
For genomic selection in clonally propagated crops with diploid (-like) meiotic behavior to be effective, crossing parents should be selected based on genomic predicted cross-performance unless dominance is negligible. For genomic selection (GS) in clonal breeding programs to be effective, parents should be selected based on genomic predicted cross-performance unless dominance is negligible. Genomic prediction of cross-performance enables efficient exploitation of the additive and dominance value simultaneously. Here, we compared different GS strategies for clonally propagated crops with diploid (-like) meiotic behavior, using strawberry as an example. We used stochastic simulation to evaluate six combinations of three breeding programs and two parent selection methods. The three breeding programs included (1) a breeding program that introduced GS in the first clonal stage, and (2) two variations of a two-part breeding program with one and three crossing cycles per year, respectively. The two parent selection methods were (1) parent selection based on genomic estimated breeding values (GEBVs) and (2) parent selection based on genomic predicted cross-performance (GPCP). Selection of parents based on GPCP produced faster genetic gain than selection of parents based on GEBVs because it reduced inbreeding when the dominance degree increased. The two-part breeding programs with one and three crossing cycles per year using GPCP always produced the most genetic gain unless dominance was negligible. We conclude that (1) in clonal breeding programs with GS, parents should be selected based on GPCP, and (2) a two-part breeding program with parent selection based on GPCP to rapidly drive population improvement has great potential to improve breeding clonally propagated crops.
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Affiliation(s)
- Christian R Werner
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Research Centre, University of Edinburgh, Midlothian, EH25 9RG, UK.
| | - R Chris Gaynor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Research Centre, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Daniel J Sargent
- NIAB EMR, New Road, East Malling, Kent, ME19 6BJ, UK
- East Malling Enterprise Centre, Driscoll's Genetics Ltd, New Road, East Malling, Kent, ME19 6BJ, UK
| | - Alessandra Lillo
- East Malling Enterprise Centre, Driscoll's Genetics Ltd, New Road, East Malling, Kent, ME19 6BJ, UK
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Research Centre, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Research Centre, University of Edinburgh, Midlothian, EH25 9RG, UK
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Pasqualetto G, Palmieri L, Martens S, Bus VGM, Chagné D, Wiedow C, Malnoy MA, Gardiner SE. Molecular characterization of intergeneric hybrids between Malus and Pyrus. HORTICULTURE RESEARCH 2022; 10:uhac239. [PMID: 36643755 PMCID: PMC9832871 DOI: 10.1093/hr/uhac239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/17/2022] [Indexed: 06/17/2023]
Abstract
Apple (Malus) and pear (Pyrus) are economically important fruit crops well known for their unique textures, flavours, and nutritional qualities. Both genera are characterised by a distinct pattern of secondary metabolites, which directly affect not only resistance to certain diseases, but also have significant impacts on the flavour and nutritional value of the fruit. The identical chromosome numbers, similar genome size, and their recent divergence date, together with DNA markers have shown that apple and pear genomes are highly co-linear. This study utilized comparative genomic approaches, including simple sequence repeats, high resolution single nucleotide polymorphism melting analysis, and single nucleotide polymorphism chip analysis to identify genetic differences among hybrids of Malus and Pyrus, and F2 offspring. This research has demonstrated and validated that these three marker types, along with metabolomics analysis are very powerful tools to detect and confirm hybridity of progeny derived from crosses between apple and pear in both cross directions. Furthermore, this work analysed the genus-specific metabolite patterns and the resistance to fire blight (Erwinia amylovora) in progeny. The findings of this work will enhance and accelerate the breeding of novel tree fruit crops that benefit producers and consumers, by enabling marker assisted selection of desired traits introgressed between pear and apple.
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Affiliation(s)
- Giulia Pasqualetto
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, UD 33100, Italy
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - Luisa Palmieri
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
| | - Stefan Martens
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
| | - Vincent G M Bus
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - David Chagné
- PFR, Fitzherbert Science Centre, Palmerston North, New Zealand
| | - Claudia Wiedow
- PFR, Fitzherbert Science Centre, Palmerston North, New Zealand
| | - Mickael A Malnoy
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
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Voorrips RE, Tumino G. PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data. BMC Bioinformatics 2022; 23:442. [PMID: 36274121 PMCID: PMC9590153 DOI: 10.1186/s12859-022-04989-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 10/16/2022] [Indexed: 11/18/2022] Open
Abstract
Background For genetic analyses, multi-allelic markers have an advantage over bi-allelic markers like SNPs (single nucleotide polymorphisms) in that they carry more information about the genetic constitution of individuals. This is especially the case in polyploids, where individuals carry more than two alleles at each locus. Haploblocks are multi-allelic markers that can be derived by phasing sets of closely-linked SNP markers. Phased haploblocks, similarly to other multi-allelic markers, will therefore be advantageous in genetic tasks like linkage mapping, QTL mapping and genome-wide association studies. Results We present a new method to reconstruct haplotypes from SNP dosages derived from genotyping arrays, which is applicable to polyploids. This method is implemented in the software package PolyHaplotyper. In contrast to existing packages for polyploids it makes use of full-sib families among the samples to guide the haplotyping process. We show that in this situation it is much more accurate than other available software, using experimental hexaploid data and simulated tetraploid data. Conclusions Our method and the software package PolyHaplotyper in which it is implemented extend the available tools for haplotyping in polyploids. They perform especially well in situations where one or more full-sib families are present. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04989-0.
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Zurn JD, Hummer KE, Bassil NV. Exploring the diversity and genetic structure of the U.S. National Cultivated Strawberry Collection. HORTICULTURE RESEARCH 2022; 9:uhac125. [PMID: 35928399 PMCID: PMC9343918 DOI: 10.1093/hr/uhac125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
The cultivated strawberry (Fragaria ×ananassa) arose through a hybridization of two wild American octoploid strawberry species in a French garden in the 1750s. Since then, breeders have developed improved cultivars adapted to different growing regions. Diverse germplasm is crucial to meet the challenges strawberry breeders will continue to address. The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon maintains the U.S. strawberry collection. Recent developments in high-throughput genotyping for strawberry can provide new insights about the diversity and structure of the collection, germplasm management, and future breeding strategies. Genotyping was conducted on 539 F. ×ananassa accessions using either the iStraw35 or FanaSNP 50 K Axiom array. Data for markers shared by the two arrays were curated for call quality, missing data, and minor allele frequency resulting in 4033 markers for structure assessment, diversity analysis, pedigree confirmation, core collection development, and the identification of haplotypes associated with desirable traits. The F. ×ananassa collection was equally diverse across the different geographic regions represented. K-means clustering, sNMF, and UPGMA hierarchal clustering revealed seven to nine sub-populations associated with different geographic breeding centers. Two 100 accession core collections were created. Pedigree linkages within the collection were confirmed. Finally, accessions containing disease resistance-associated haplotypes for FaRCa1, FaRCg1, FaRMp1, and FaRPc2 were identified. These new core collections will allow breeders and researchers to more efficiently utilize the F. ×ananassa collection. The core collections and other accessions of interest can be requested for research from the USDA-ARS NCGR via the Germplasm Resources Information Network (https://www.ars-grin.gov/).
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Affiliation(s)
- Jason D Zurn
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
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Barbey CR, Hogshead MH, Harrison B, Schwartz AE, Verma S, Oh Y, Lee S, Folta KM, Whitaker VM. Genetic Analysis of Methyl Anthranilate, Mesifurane, Linalool, and Other Flavor Compounds in Cultivated Strawberry ( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2021; 12:615749. [PMID: 34093602 PMCID: PMC8170412 DOI: 10.3389/fpls.2021.615749] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/30/2021] [Indexed: 05/27/2023]
Abstract
The cultivated strawberry (Fragaria × ananassa) is an economically important fruit crop that is intensively bred for improved sensory qualities. The diversity of fruit flavors and aromas in strawberry results mainly from the interactions of sugars, acids, and volatile organic compounds (VOCs) that are derived from diverse biochemical pathways influenced by the expression of many genes. This study integrates multiomic analyses to identify QTL and candidate genes for multiple aroma compounds in a complex strawberry breeding population. Novel fruit volatile QTL was discovered for methyl anthranilate, methyl 2-hexenoate, methyl 2-methylbutyrate, mesifurane, and a shared QTL on Chr 3 was found for nine monoterpene and sesquiterpene compounds, including linalool, 3-carene, β-phellandrene, α-limonene, linalool oxide, nerolidol, α-caryophellene, α-farnesene, and β-farnesene. Fruit transcriptomes from a subset of 64 individuals were used to support candidate gene identification. For methyl esters including the grape-like methyl anthranilate, a novel ANTHANILIC ACID METHYL TRANSFERASE-like gene was identified. Two mesifurane QTL correspond with the known biosynthesis gene O-METHYL TRANSFERASE 1 and a novel FURANEOL GLUCOSYLTRANSFERASE. The shared terpene QTL contains multiple fruit-expressed terpenoid pathway-related genes including NEROLIDOL SYNTHASE 1 (FanNES1). The abundance of linalool and other monoterpenes is partially governed by a co-segregating expression-QTL (eQTL) for FanNES1 transcript variation, and there is additional evidence for quantitative effects from other terpenoid-pathway genes in this narrow genomic region. These QTLs present new opportunities in breeding for improved flavor in commercial strawberry.
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Affiliation(s)
- Christopher R. Barbey
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Maxwell H. Hogshead
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Benjamin Harrison
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Anne E. Schwartz
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Sujeet Verma
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Youngjae Oh
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Seonghee Lee
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Kevin M. Folta
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Vance M. Whitaker
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
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Barbey CR, Hogshead MH, Harrison B, Schwartz AE, Verma S, Oh Y, Lee S, Folta KM, Whitaker VM. Genetic Analysis of Methyl Anthranilate, Mesifurane, Linalool, and Other Flavor Compounds in Cultivated Strawberry ( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2021; 12:615749. [PMID: 34093602 DOI: 10.1101/2020.10.07.330001v1.full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/30/2021] [Indexed: 05/27/2023]
Abstract
The cultivated strawberry (Fragaria × ananassa) is an economically important fruit crop that is intensively bred for improved sensory qualities. The diversity of fruit flavors and aromas in strawberry results mainly from the interactions of sugars, acids, and volatile organic compounds (VOCs) that are derived from diverse biochemical pathways influenced by the expression of many genes. This study integrates multiomic analyses to identify QTL and candidate genes for multiple aroma compounds in a complex strawberry breeding population. Novel fruit volatile QTL was discovered for methyl anthranilate, methyl 2-hexenoate, methyl 2-methylbutyrate, mesifurane, and a shared QTL on Chr 3 was found for nine monoterpene and sesquiterpene compounds, including linalool, 3-carene, β-phellandrene, α-limonene, linalool oxide, nerolidol, α-caryophellene, α-farnesene, and β-farnesene. Fruit transcriptomes from a subset of 64 individuals were used to support candidate gene identification. For methyl esters including the grape-like methyl anthranilate, a novel ANTHANILIC ACID METHYL TRANSFERASE-like gene was identified. Two mesifurane QTL correspond with the known biosynthesis gene O-METHYL TRANSFERASE 1 and a novel FURANEOL GLUCOSYLTRANSFERASE. The shared terpene QTL contains multiple fruit-expressed terpenoid pathway-related genes including NEROLIDOL SYNTHASE 1 (FanNES1). The abundance of linalool and other monoterpenes is partially governed by a co-segregating expression-QTL (eQTL) for FanNES1 transcript variation, and there is additional evidence for quantitative effects from other terpenoid-pathway genes in this narrow genomic region. These QTLs present new opportunities in breeding for improved flavor in commercial strawberry.
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Affiliation(s)
- Christopher R Barbey
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Maxwell H Hogshead
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Benjamin Harrison
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Anne E Schwartz
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Sujeet Verma
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Youngjae Oh
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Seonghee Lee
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Kevin M Folta
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Vance M Whitaker
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
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Fan Z, Hasing T, Johnson TS, Garner DM, Schwieterman ML, Barbey CR, Colquhoun TA, Sims CA, Resende MFR, Whitaker VM. Strawberry sweetness and consumer preference are enhanced by specific volatile compounds. HORTICULTURE RESEARCH 2021; 8:66. [PMID: 33790262 PMCID: PMC8012349 DOI: 10.1038/s41438-021-00502-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/16/2020] [Accepted: 02/06/2021] [Indexed: 05/15/2023]
Abstract
Breeding crops for improved flavor is challenging due to the high cost of sensory evaluation and the difficulty of connecting sensory experience to chemical composition. The main goal of this study was to identify the chemical drivers of sweetness and consumer liking for fresh strawberries (Fragaria × ananassa). Fruit of 148 strawberry samples from cultivars and breeding selections were grown and harvested over seven years and were subjected to both sensory and chemical analyses. Each panel consisted of at least 100 consumers, resulting in more than 15,000 sensory data points per descriptor. Three sugars, two acids and 113 volatile compounds were quantified. Consumer liking was highly associated with sweetness intensity, texture liking, and flavor intensity, but not sourness intensity. Partial least square analyses revealed 20 volatile compounds that increased sweetness perception independently of sugars; 18 volatiles that increased liking independently of sugars; and 15 volatile compounds that had positive effects on both. Machine learning-based predictive models including sugars, acids, and volatiles explained at least 25% more variation in sweetness and liking than models accounting for sugars and acids only. Volatile compounds such as γ-dodecalactone; 5-hepten-2-one, 6-methyl; and multiple medium-chain fatty acid esters may serve as targets for breeding or quality control attributes for strawberry products. A genetic association study identified two loci controlling ester production, both on linkage group 6 A. Co-segregating makers in these regions can be used for increasing multiple esters simultaneously. This study demonstrates a paradigm for improvement of fruit sweetness and flavor in which consumers drive the identification of the most important chemical targets, which in turn drives the discovery of genetic targets for marker-assisted breeding.
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Affiliation(s)
- Zhen Fan
- Horticultural Sciences Department, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL, USA
| | | | - Timothy S Johnson
- Department of Environmental Horticulture and Plant Innovation Center, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Drake M Garner
- Department of Environmental Horticulture and Plant Innovation Center, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | | | - Christopher R Barbey
- Horticultural Sciences Department, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL, USA
| | - Thomas A Colquhoun
- Department of Environmental Horticulture and Plant Innovation Center, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Charles A Sims
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL, USA
| | - Marcio F R Resende
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Vance M Whitaker
- Horticultural Sciences Department, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL, USA.
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Nelson JR, Verma S, Bassil NV, Finn CE, Hancock JF, Cole GS, Knapp SJ, Whitaker VM. Discovery of three loci increasing resistance to charcoal rot caused by Macrophomina phaseolina in octoploid strawberry. G3 (BETHESDA, MD.) 2021; 11:jkab037. [PMID: 33565594 PMCID: PMC8022958 DOI: 10.1093/g3journal/jkab037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/25/2021] [Indexed: 11/12/2022]
Abstract
Charcoal rot caused by Macrophomina phaseolinais an increasing economic problem in annualized strawberry production systems around the world. Currently there are no effective postfumigation chemical controls for managing charcoal rot, and no information is available on the genetic architecture of resistance to M. phaseolina in strawberry (Fragaria ×ananassa). In this study, three multiparental discovery populations and two validation populations were inoculated at planting and evaluated for mortality in three consecutive growing seasons. Genome-wide SNP genotyping and pedigree-based analysis with FlexQTL™ software were performed. Two large-effect quantitative trait loci (QTL) increasing charcoal rot resistance were discovered and validated in cultivated germplasm. FaRMp1 was located on linkage group 2A in the interval 20.4to 24.9 cM, while FaRMp2 was located on linkage group 4B in the interval 41.1to 61.2 cM. Together these QTLs explained 27% and 17% of the phenotypic variance in two discovery populations consisting of elite breeding germplasm. For both QTLs, the resistant allele showed some evidence of partial dominance, but no significant interaction was detected between the two loci. As the dosage of resistant alleles increased from 0 to 4 across the two QTLs, mortality decreased regardless of the combination of alleles.A third locus, FaRMp3 on 4D, was discovered in FVC 11-58, a reconstituted F.×ananassa originating from diverse F. virginiana and F. chiloensis accessions. This locus accounted for 44% of phenotypic variation in four segregating crosses. These findings will form the basis for DNA-informed breeding for resistance to charcoal rot in cultivated strawberry.
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Affiliation(s)
- Jonathan R Nelson
- Department of Horticultural Science, University of Florida, IFAS Gulf Coast Research and Education Center, 14625 CR 672 Wimauma, FL 33598, USA
| | - Sujeet Verma
- Department of Horticultural Science, University of Florida, IFAS Gulf Coast Research and Education Center, 14625 CR 672 Wimauma, FL 33598, USA
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Chad E Finn
- USDA-ARS, HCRU, 3420 NW Orchard Avenue, Corvallis, OR 97330, USA (posthumous)
| | - James F Hancock
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Vance M Whitaker
- Department of Horticultural Science, University of Florida, IFAS Gulf Coast Research and Education Center, 14625 CR 672 Wimauma, FL 33598, USA
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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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Cockerton HM, Karlström A, Johnson AW, Li B, Stavridou E, Hopson KJ, Whitehouse AB, Harrison RJ. Genomic Informed Breeding Strategies for Strawberry Yield and Fruit Quality Traits. FRONTIERS IN PLANT SCIENCE 2021; 12:724847. [PMID: 34675948 PMCID: PMC8525896 DOI: 10.3389/fpls.2021.724847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/01/2021] [Indexed: 05/09/2023]
Abstract
Over the last two centuries, breeders have drastically modified the fruit quality of strawberries through artificial selection. However, there remains significant variation in quality across germplasm with scope for further improvements to be made. We reported extensive phenotyping of fruit quality and yield traits in a multi-parental strawberry population to allow genomic prediction and quantitative trait nucleotide (QTN) identification, thereby enabling the description of genetic architecture to inform the efficacy of implementing advanced breeding strategies. A negative relationship (r = -0.21) between total soluble sugar content and class one yield was identified, indicating a trade-off between these two essential traits. This result highlighted an established dilemma for strawberry breeders and a need to uncouple the relationship, particularly under June-bearing, protected production systems comparable to this study. A large effect of quantitative trait nucleotide was associated with perceived acidity and pH whereas multiple loci were associated with firmness. Therefore, we recommended the implementation of both marker assisted selection (MAS) and genomic prediction to capture the observed variation respectively. Furthermore, we identified a large effect locus associated with a 10% increase in the number of class one fruit and a further 10 QTN which, when combined, are associated with a 27% increase in the number of marketable strawberries. Ultimately, our results suggested that the best method to improve strawberry yield is through selecting parental lines based upon the number of marketable fruits produced per plant. Not only were strawberry number metrics less influenced by environmental fluctuations, but they had a larger additive genetic component when compared with mass traits. As such, selecting using "number" traits should lead to faster genetic gain.
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Affiliation(s)
- Helen M. Cockerton
- Genetics, Genomics and Breeding, NIAB EMR, East Malling, United Kingdom
- University of Kent, Canterbury, United Kingdom
- *Correspondence: Helen M. Cockerton
| | - Amanda Karlström
- Genetics, Genomics and Breeding, NIAB EMR, East Malling, United Kingdom
| | | | - Bo Li
- Genetics, Genomics and Breeding, NIAB EMR, East Malling, United Kingdom
| | | | - Katie J. Hopson
- Genetics, Genomics and Breeding, NIAB EMR, East Malling, United Kingdom
| | | | - Richard J. Harrison
- Genetics, Genomics and Breeding, NIAB EMR, East Malling, United Kingdom
- Cambridge Crop Research, NIAB, Cambridge, United Kingdom
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13
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Li B, Cockerton HM, Johnson AW, Karlström A, Stavridou E, Deakin G, Harrison RJ. Defining strawberry shape uniformity using 3D imaging and genetic mapping. HORTICULTURE RESEARCH 2020; 7:115. [PMID: 32821398 PMCID: PMC7395166 DOI: 10.1038/s41438-020-0337-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/25/2020] [Accepted: 05/17/2020] [Indexed: 05/24/2023]
Abstract
Strawberry shape uniformity is a complex trait, influenced by multiple genetic and environmental components. To complicate matters further, the phenotypic assessment of strawberry uniformity is confounded by the difficulty of quantifying geometric parameters 'by eye' and variation between assessors. An in-depth genetic analysis of strawberry uniformity has not been undertaken to date, due to the lack of accurate and objective data. Nonetheless, uniformity remains one of the most important fruit quality selection criteria for the development of a new variety. In this study, a 3D-imaging approach was developed to characterise berry shape uniformity. We show that circularity of the maximum circumference had the closest predictive relationship with the manual uniformity score. Combining five or six automated metrics provided the best predictive model, indicating that human assessment of uniformity is highly complex. Furthermore, visual assessment of strawberry fruit quality in a multi-parental QTL mapping population has allowed the identification of genetic components controlling uniformity. A "regular shape" QTL was identified and found to be associated with three uniformity metrics. The QTL was present across a wide array of germplasm, indicating a potential candidate for marker-assisted breeding, while the potential to implement genomic selection is explored. A greater understanding of berry uniformity has been achieved through the study of the relative impact of automated metrics on human perceived uniformity. Furthermore, the comprehensive definition of strawberry shape uniformity using 3D imaging tools has allowed precision phenotyping, which has improved the accuracy of trait quantification and unlocked the ability to accurately select for uniform berries.
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Affiliation(s)
- Bo Li
- NIAB EMR, East Malling, Kent, ME19 6BJ UK
- University of the West of England, Bristol, BS16 1QY UK
| | | | | | | | | | | | - Richard J. Harrison
- NIAB EMR, East Malling, Kent, ME19 6BJ UK
- NIAB, Huntingdon Road, Cambridge, CB3 0LE UK
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14
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ddRAD-seq derived genome-wide SNPs, high density linkage map and QTLs for fruit quality traits in strawberry ( Fragaria x ananassa). 3 Biotech 2020; 10:353. [PMID: 32760641 PMCID: PMC7385052 DOI: 10.1007/s13205-020-02291-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 06/07/2020] [Indexed: 12/31/2022] Open
Abstract
Understanding the genetic determinants are essential for improving the fruit quality traits of strawberry. In this study, we focused on mapping the loci for fruit-length (FL), -diameter (FD), -weight (FW) and -soluble solid content (SSC) using the genome-wide single nucleotide polymorphisms (SNPs) identified via ddRAD-sequencing of the F1 population raised from Maehyang (♀) X Festival (♂). A total of 12,698 high quality SNPs were identified of which 1554 SNPs that showed significant Mendelian segregation (p < 0.05) were mapped to 53 linkage groups (LG) spanning a total of 2937.93 cM with an average marker density of 2.14 cM/locus. Six QTLs for FL and four QTLs for each of FD, FW and SSC were identified that explained 24–35%, 21–42%, 24–54% and 23–50% of overall phenotypic variations, respectively. The genes that lie within these QTL regions were extracted and discussed thoroughly. In addition, a high resolution melting marker (MF154) were designed based on the SNP A1723G of the UDP-glucose 4-epimerase GEPI48-like gene FAN_iscf00021287. The marker detected the high vs low sugar containing F1 plants and commercial cultivars with 81.39% and 86.95% detection accuracy, respectively. These SNPs, linkage map, QTLs and candidate genes will be helpful in understanding and improving the fruit quality traits of strawberry.
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15
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Davis TM, Yang Y, Mahoney LL, Frailey DC. A pentaploid-based linkage map of the ancestral octoploid strawberry Fragaria virginiana reveals instances of sporadic hyper-recombination. HORTICULTURE RESEARCH 2020; 7:77. [PMID: 32411378 PMCID: PMC7206004 DOI: 10.1038/s41438-020-0308-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 05/04/2023]
Abstract
The first high-resolution genetic linkage map of the ancestral octoploid (2n = 8x = 56) strawberry species, Fragaria virginiana, was constructed using segregation data obtained from a pentaploid progeny population. This novel mapping population of size 178 was generated by crossing highly heterozygous F. virginiana hybrid "LB48" as a paternal parent with diploid (2n = 2x = 14) Fragaria vesca "Hawaii 4". The LB48 linkage map comprises 6055 markers genotyped on the Axiom® IStraw90 strawberry SNP array. The map consists of 28 linkage groups (LGs) organized into seven homoeology groups of four LGs each, and excludes a small 29th LG of undefined homoeology. One member of each homoeology group was assignable to an "A" subgenome associated with ancestral diploid Fragaria vesca, while no other subgenomes were defined. Despite an intriguing discrepancy within homoeology group VI, synteny comparisons with the previously published Fragaria ×ananassa DA × MO linkage map revealed substantial agreement. Following initial map construction, examination of crossover distributions revealed that six of the total 5162 (=29 chromosomes/individual × 178 individuals) chromosomes making up the data set exhibited abnormally high crossover counts, ranging from 15 to 48 crossovers per chromosome, as compared with the overall mean of 0.66 crossovers per chromosome. Each of these six hyper-recombinant (HypR) chromosomes occurred in a different LG and in a different individual. When calculated upon exclusion of the six HypR chromosomes, the canonical (i.e., broadly representative) LB48 map had 1851 loci distributed over a total map length of 1873 cM, while their inclusion increased the number of loci by 130, and the overall map length by 91 cM. Discovery of these hyper-recombinant chromosomes points to the existence of a sporadically acting mechanism that, if identified and manipulable, could be usefully harnessed for multiple purposes by geneticists and breeders.
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Affiliation(s)
- Thomas M. Davis
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824 USA
| | - Yilong Yang
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824 USA
| | - Lise L. Mahoney
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824 USA
| | - Daniel C. Frailey
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824 USA
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16
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Whitaker VM, Knapp SJ, Hardigan MA, Edger PP, Slovin JP, Bassil NV, Hytönen T, Mackenzie KK, Lee S, Jung S, Main D, Barbey CR, Verma S. A roadmap for research in octoploid strawberry. HORTICULTURE RESEARCH 2020; 7:33. [PMID: 32194969 PMCID: PMC7072068 DOI: 10.1038/s41438-020-0252-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 01/26/2020] [Indexed: 05/02/2023]
Abstract
The cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, originating nearly 300 years ago from wild progenitors from the Americas. Since that time the strawberry has become the most widely cultivated fruit crop in the world, universally appealing due to its sensory qualities and health benefits. The recent publication of the first high-quality chromosome-scale octoploid strawberry genome (cv. Camarosa) is enabling rapid advances in genetics, stimulating scientific debate and provoking new research questions. In this forward-looking review we propose avenues of research toward new biological insights and applications to agriculture. Among these are the origins of the genome, characterization of genetic variants, and big data approaches to breeding. Key areas of research in molecular biology will include the control of flowering, fruit development, fruit quality, and plant-pathogen interactions. In order to realize this potential as a global community, investments in genome resources must be continually augmented.
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Affiliation(s)
- Vance M Whitaker
- 1University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, Florida 33598 USA
| | - Steven J Knapp
- 2Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Michael A Hardigan
- 2Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Patrick P Edger
- 3Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Janet P Slovin
- USDA-ARS Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, MA 20705 USA
| | - Nahla V Bassil
- 5USDA-ARS National Clonal Germplasm Repository, Corvallis, OR 97333 USA
| | - Timo Hytönen
- 6Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00790 Finland
- 7Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00790 Finland
- NIAB EMR, Kent, ME19 6BJ UK
| | - Kathryn K Mackenzie
- 6Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00790 Finland
| | - Seonghee Lee
- 1University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, Florida 33598 USA
| | - Sook Jung
- 9Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Dorrie Main
- 9Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Christopher R Barbey
- 1University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, Florida 33598 USA
| | - Sujeet Verma
- 1University of Florida, Institute of Food and Agricultural Sciences, Gulf Coast Research and Education Center, Wimauma, Florida 33598 USA
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17
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Abstract
Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry’s complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, expression quantitative trait loci (eQTL) analysis and RenSeq analysis in cultivars. Octoploid fruit eQTL were identified for 76 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. ×ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance toward exploiting variation for strawberry cultivar improvement.
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18
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Cockerton HM, Li B, Vickerstaff RJ, Eyre CA, Sargent DJ, Armitage AD, Marina-Montes C, Garcia-Cruz A, Passey AJ, Simpson DW, Harrison RJ. Identifying Verticillium dahliae Resistance in Strawberry Through Disease Screening of Multiple Populations and Image Based Phenotyping. FRONTIERS IN PLANT SCIENCE 2019; 10:924. [PMID: 31379904 PMCID: PMC6657532 DOI: 10.3389/fpls.2019.00924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 07/01/2019] [Indexed: 05/06/2023]
Abstract
Verticillium dahliae is a highly detrimental pathogen of soil cultivated strawberry (Fragaria x ananassa). Breeding of Verticillium wilt resistance into commercially viable strawberry cultivars can help mitigate the impact of the disease. In this study we describe novel sources of resistance identified in multiple strawberry populations, creating a wealth of data for breeders to exploit. Pathogen-informed experiments have allowed the differentiation of subclade-specific resistance responses, through studying V. dahliae subclade II-1 specific resistance in the cultivar "Redgauntlet" and subclade II-2 specific resistance in "Fenella" and "Chandler." A large-scale low-cost phenotyping platform was developed utilizing automated unmanned vehicles and near infrared imaging cameras to assess field-based disease trials. The images were used to calculate disease susceptibility for infected plants through the normalized difference vegetation index score. The automated disease scores showed a strong correlation with the manual scores. A co-dominant resistant QTL; FaRVd3D, present in both "Redgauntlet" and "Hapil" cultivars exhibited a major effect of 18.3% when the two resistance alleles were combined. Another allele, FaRVd5D, identified in the "Emily" cultivar was associated with an increase in Verticillium wilt susceptibility of 17.2%, though whether this allele truly represents a susceptibility factor requires further research, due to the nature of the F1 mapping population. Markers identified in populations were validated across a set of 92 accessions to determine whether they remained closely linked to resistance genes in the wider germplasm. The resistant markers FaRVd2B from "Redgauntlet" and FaRVd6D from "Chandler" were associated with resistance across the wider germplasm. Furthermore, comparison of imaging versus manual phenotyping revealed the automated platform could identify three out of four disease resistance markers. As such, this automated wilt disease phenotyping platform is considered to be a good, time saving, substitute for manual assessment.
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Affiliation(s)
| | - Bo Li
- NIAB EMR, East Malling, United Kingdom
| | | | - Catherine A. Eyre
- Driscoll’s Genetics Ltd., East Malling Enterprise Centre, East Malling, United Kingdom
| | - Daniel J. Sargent
- Driscoll’s Genetics Ltd., East Malling Enterprise Centre, East Malling, United Kingdom
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Salinas N, Verma S, Peres N, Whitaker VM. FaRCa1: a major subgenome-specific locus conferring resistance to Colletotrichum acutatum in strawberry. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1109-1120. [PMID: 30564908 PMCID: PMC6449309 DOI: 10.1007/s00122-018-3263-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/07/2018] [Indexed: 05/18/2023]
Abstract
Optimal strategies for genetic improvement in crops depend on accurate assessments of the genetic architecture of traits. The overall objective of the present study was to determine the genetic architecture of anthracnose fruit rot (AFR) resistance caused by the fungus Colletotrichum acutatum in the University of Florida strawberry (Fragaria × ananassa) breeding germplasm. In 2016-2017, 33 full-sib families resulting from crosses between parents with varying levels of AFR resistance were tested. In 2017-2018, six full-sib families resulting from putative heterozygous resistant parents and homozygous susceptible parents were tested. Additionally, a validation population consisting of 77 advanced selections and ten cultivars was tested in the second season. Inoculation was performed using a mixture of three local isolates of the C. acutatum species complex. Phenotypes were scored weekly, and genotyping was performed using the IStraw35 Affymetrix Axiom® SNP array. A pedigree-based QTL analysis was performed using FlexQTL™ software. A major resistance locus, which we name FaRCa1, was detected in both seasons with a peak located at 55-56 cM on LG 6B and explaining at least 50% of the phenotypic variation across trials and seasons. The resistant allele exhibited partial dominance in all trials. The FaRCa1 locus is distinct from the previously discovered Rca2 locus, which mapped to LG 7B. While Rca2 is effective against European isolates from pathogenicity group 2, FaRCa1 appears to confer resistance to isolates of pathogenicity group 1.
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Affiliation(s)
- Natalia Salinas
- Department of Horticultural Sciences, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL, 33598, USA
| | - Sujeet Verma
- Department of Horticultural Sciences, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL, 33598, USA
| | - Natalia Peres
- Department of Plant Pathology, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL, 33598, USA
| | - Vance M Whitaker
- Department of Horticultural Sciences, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, FL, 33598, USA.
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20
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Sharma S, Kaur R, Solanke AKU, Dubey H, Tiwari S, Kumar K. Transcriptome sequencing of Himalayan Raspberry ( Rubus ellipticus) and development of simple sequence repeat markers. 3 Biotech 2019; 9:161. [PMID: 30944808 DOI: 10.1007/s13205-019-1685-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 03/19/2019] [Indexed: 12/11/2022] Open
Abstract
KEY MESSAGE Rubus ellipticus is a wild crop having less number of EST-SSR markers. First attempt was made towards the transcriptomics data analysis and generation of EST-SSR markers which were used in genetic diversity and transferability studies. ABSTRACT Rubus ellipticus is a raspberry with yellow fruits, native to tropical and subtropical India and Asia. Leaves of Rubus ellipticus 'Kumarhatti' collection were utilized for cDNA library construction. More than 15 million sequencing reads were generated using NextSeq 500 Illumina RNA-seq technology. The DNASTAR software was used for de novo assembly from which 7777 unigenes with an average length of 500 bp was obtained. These unigenes were annotated using public databases, including NCBI non-redundant and gene ontology. De novo assembly of R. ellipticus unigenes found the highest similarity to apple than to other members of Rosaceae. This is the first attempt to use the Illumina platform of RNA sequencing and de novo assembly for R. ellipticus without a reference genome. In this study, unigenes were used for SSR marker development. ESTs containing SSR motifs were extracted using an online Microsatellite Identification Tool (MISA). SSR primers were designed from the SSR containing 704 EST sequences using the Websat software. Total 304 EST-SSRs primers were successfully designed, out of which 68 randomly selected primer pairs were custom synthesized and used for validation. Real-time PCR was also performed to analyze the relationship of transcriptional factors with fruit ripening. Out of 68 primer pairs, 61 were found to be informative in R. ellipticus, whereas 65 primer pairs were informative in the five tested genera of Rosaceae, i.e., pear, peach, apple, rose, and strawberry with 95.3% and 93.5% polymorphism, leading to the conclusion that these marker systems are very efficient to carryout diversity and cross transferability study in Rosaceae genera.
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21
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High density linkage map construction and QTL mapping for runner production in allo-octoploid strawberry Fragaria × ananassa based on ddRAD-seq derived SNPs. Sci Rep 2019; 9:3275. [PMID: 30824841 PMCID: PMC6397268 DOI: 10.1038/s41598-019-39808-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/29/2019] [Indexed: 11/08/2022] Open
Abstract
Recent advances in high-throughput genome sequencing technologies are now making the genetic dissection of the complex genome of cultivated strawberry easier. We sequenced Maehyang (short-day cultivar) × Albion (day-neutral cultivar) crossing populations using double digest restriction-associated DNA (ddRAD) sequencing technique that yielded 978,968 reads, 80.2% of which were aligned to strawberry genome allowing the identification of 13,181 high quality single nucleotide polymorphisms (SNPs). Total 3051 SNPs showed Mendelian segregation in F1, of which 1268 were successfully mapped to 46 linkage groups (LG) spanning a total of 2581.57 cM with an average interval genetic distance of 2.22 cM. The LGs were assigned to the 28 chromosomes of Fragaria × ananassa as determined by positioning the sequence tags on F. vesca genome. In addition, seven QTLs namely, qRU-5D, qRU-3D1, qRU-1D2, qRU-4D, qRU-4C, qRU-5C and qRU-2D2 were identified for runner production with LOD value ranging from 3.5–7.24 that explained 22–38% of phenotypic variation. The key candidate genes having putative roles in meristem differentiation for runnering and flowering within these QTL regions were identified. These will enhance our understanding of the vegetative vs sexual reproductive behavior in strawberry and will aid in setting breeding targets for developing perpetual flowering and profuse runnering cultivar.
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Hardigan MA, Feldmann MJ, Lorant A, Bird KA, Famula R, Acharya C, Cole G, Edger PP, Knapp SJ. Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution. FRONTIERS IN PLANT SCIENCE 2019; 10:1789. [PMID: 32158449 PMCID: PMC7020885 DOI: 10.3389/fpls.2019.01789] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/20/2019] [Indexed: 05/18/2023]
Abstract
Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we show that octoploid Fragaria species harbor millions of subgenome-specific DNA variants. Their diversity was sufficient to distinguish duplicated (homoeologous and paralogous) DNA sequences and develop 50K and 850K SNP genotyping arrays populated with co-dominant, disomic SNP markers distributed throughout the octoploid genome. Whole-genome shotgun genotyping of an interspecific segregating population yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks spanning 3,394 cM in F. chiloensis subsp. lucida, and 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning 2,017 cM in F. × ananassa. These studies provide a dense genomic framework of subgenome-specific DNA markers for seamlessly cross-referencing genetic and physical mapping information and unifying existing chromosome nomenclatures. Using comparative genomics, we show that geographically diverse wild octoploids are effectively diploidized, nearly completely collinear, and retain strong macro-synteny with diploid progenitor species. The preservation of genome structure among allo-octoploid taxa is a critical factor in the unique history of garden strawberry, where unimpeded gene flow supported its origin and domestication through repeated cycles of interspecific hybridization.
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Affiliation(s)
- Michael A. Hardigan
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Mitchell J. Feldmann
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Anne Lorant
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Kevin A. Bird
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Randi Famula
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Charlotte Acharya
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Glenn Cole
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Patrick P. Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Steven J. Knapp
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- *Correspondence: Steven J. Knapp,
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23
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Anciro A, Mangandi J, Verma S, Peres N, Whitaker VM, Lee S. FaRCg1: a quantitative trait locus conferring resistance to Colletotrichum crown rot caused by Colletotrichum gloeosporioides in octoploid strawberry. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2167-2177. [PMID: 30032317 DOI: 10.1007/s00122-018-3145-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/14/2018] [Indexed: 05/18/2023]
Abstract
Colletotrichum crown rot (CCR) is an important disease of strawberry (Fragaria ×ananassa) throughout the Southeastern US and in subtropical climates around the world, where hot and humid conditions facilitate rapid disease development. Yet no resistance loci have been described to date, as genetic studies have been historically difficult in allo-octoploid (2n = 8x = 56) strawberry. In the present study, we investigate the genetic architecture of resistance to CCR. Four population sets from the University of Florida were inoculated in four different seasons from 2013-2014 to 2016-2017. Two large, multiparental discovery population sets were used for QTL discovery, and two validation sets of cultivars and advanced selections representing the parent pool of the breeding program were also assessed. Subgenome-specific single-nucleotide polymorphism (SNP) markers were mapped, and FlexQTL™ software was utilized to perform a Bayesian, pedigree-based QTL analysis. A quantitative trait locus on linkage group 6B, which we name FaRCg1, accounts for most of the genetic variation for resistance in the discovery sets (26.8-29.8% in 2013-2014 and 17% in 2015-2016). High-throughput marker assays were developed for the most significant SNPs which correlated with the mode of the QTL region. The discovery and characterization of the FaRCg1 locus and the molecular tools developed from it will be utilized to achieve increased genetic gains for resistance.
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Affiliation(s)
- Ashlee Anciro
- Department of Horticultural Science, Institute of Food and Agricultural Services, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, USA
| | - Jozer Mangandi
- Department of Horticultural Science, Institute of Food and Agricultural Services, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, USA
| | - Sujeet Verma
- Department of Horticultural Science, Institute of Food and Agricultural Services, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, USA
| | - Natalia Peres
- Department of Plant Pathology, Institute of Food and Agricultural Services, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, USA
| | - Vance M Whitaker
- Department of Horticultural Science, Institute of Food and Agricultural Services, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, USA
| | - Seonghee Lee
- Department of Horticultural Science, Institute of Food and Agricultural Services, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, 33598, USA.
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24
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Yang S, Zhong Q, Tian J, Wang L, Zhao M, Li L, Sun X. Characterization and development of EST-SSR markers to study the genetic diversity and populations analysis of Jerusalem artichoke (Helianthus tuberosus L.). Genes Genomics 2018; 40:1023-1032. [PMID: 29956221 DOI: 10.1007/s13258-018-0708-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/29/2018] [Indexed: 10/28/2022]
Abstract
In recent years, Jerusalem artichoke has received widespread attention as a novel source of sugar, biofuel, and animal feed. Currently, only few gDNA-SSRs derived from sunflower were verified in the Jerusalem artichoke; therefore, it is particularly important to develop SSR primer markers that belonged to Jerusalem artichoke resources. Using EST data to develop EST-SSR markers is simple and effective. In order to understand the general characteristics of SSR markers in Jerusalem artichoke EST sequences and accelerate the use of SSR markers in Jerusalem artichoke research. This study used 40,370 sequenced unigene fragments and MISA software to identify SSR loci. The 48 pairs of EST-SSR primers assessed for the identification of 45 varieties of Jerusalem artichoke. Cluster, genetic diversity parameters and AMOVA analysis was conducted using the genetic similarity coefficient, revealing genetic differences between 48 genetic material. A total of 1204 SSR loci were identified with 13 different types of repeats, distributed among 1020 EST sequences, of which trinucleotide repeats were the most common, accounting for 38.21% of the total SSR loci. Among the 44 repeat motifs, AG/CT, AAG/CTT, and ATC/ATG motifs had the highest frequencies, accounting for 22.45, 14.71, and 7.84% of all motifs, respectively. From these sequences, 48 pairs of EST-SSR primers were designed, and 22 primer pairs for loci with high polymorphism were selected to analyze the genetic diversity of 45 Jerusalem artichoke germplasm sources. The results indicated that the variation range of the effective number of alleles for 22 primers ranged between 1.7502 and 4.5660. The Shannon's information index ranged between 0.6200 and 1.6423. The variation range of PIC ranged between 0.3121 and 0.6662 with an average of 0.5184. Cluster analysis was conducted using the genetic similarity coefficient, revealing significant genetic differences between Asian and European genetic material. Cluster analysis revealed a relationship between the genotypes and geographic origins of the Jerusalem artichoke. The results of AMOVA as well as the genetic identity and genetic distance in the Jerusalem artichoke population showed that there presented certain genetic heterogeneity in Jerusalem artichoke genetic structure of 45 samples from seven different geographic populations. The Jerusalem artichoke EST-SSR marker system established in this study provides an effective molecular marker system for future research focused on Jerusalem artichoke genetic diversity and the breeding of new varieties.
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Affiliation(s)
- Shipeng Yang
- Qinghai Vegetable Genetics and Physiology Laboratory, Xining, 810016, People's Republic of China.,Agriculture and Forestry Sciences Institute of Qinghai University, Xining, 810016, People's Republic of China
| | - Qiwen Zhong
- Qinghai Vegetable Genetics and Physiology Laboratory, Xining, 810016, People's Republic of China.,Agriculture and Forestry Sciences Institute of Qinghai University, Xining, 810016, People's Republic of China.,The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Jie Tian
- Qinghai Vegetable Genetics and Physiology Laboratory, Xining, 810016, People's Republic of China.,Agriculture and Forestry Sciences Institute of Qinghai University, Xining, 810016, People's Republic of China.,The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Lihui Wang
- Qinghai Vegetable Genetics and Physiology Laboratory, Xining, 810016, People's Republic of China.,Agriculture and Forestry Sciences Institute of Qinghai University, Xining, 810016, People's Republic of China
| | - Mengliang Zhao
- Qinghai Vegetable Genetics and Physiology Laboratory, Xining, 810016, People's Republic of China.,Agriculture and Forestry Sciences Institute of Qinghai University, Xining, 810016, People's Republic of China
| | - Li Li
- Qinghai Vegetable Genetics and Physiology Laboratory, Xining, 810016, People's Republic of China.,Agriculture and Forestry Sciences Institute of Qinghai University, Xining, 810016, People's Republic of China.,The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Xuemei Sun
- Qinghai Vegetable Genetics and Physiology Laboratory, Xining, 810016, People's Republic of China. .,Agriculture and Forestry Sciences Institute of Qinghai University, Xining, 810016, People's Republic of China. .,The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China.
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25
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Genome-Wide Association Mapping Uncovers Fw1, a Dominant Gene Conferring Resistance to Fusarium Wilt in Strawberry. G3-GENES GENOMES GENETICS 2018; 8:1817-1828. [PMID: 29602808 PMCID: PMC5940171 DOI: 10.1534/g3.118.200129] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fusarium wilt, a soil-borne disease caused by the fungal pathogen Fusarium oxysporum f. sp. fragariae, threatens strawberry (Fragaria × ananassa) production worldwide. The spread of the pathogen, coupled with disruptive changes in soil fumigation practices, have greatly increased disease pressure and the importance of developing resistant cultivars. While resistant and susceptible cultivars have been reported, a limited number of germplasm accessions have been analyzed, and contradictory conclusions have been reached in earlier studies to elucidate the underlying genetic basis of resistance. Here, we report the discovery of Fw1, a dominant gene conferring resistance to Fusarium wilt in strawberry. The Fw1 locus was uncovered in a genome-wide association study of 565 historically and commercially important strawberry accessions genotyped with 14,408 SNP markers. Fourteen SNPs in linkage disequilibrium with Fw1 physically mapped to a 2.3 Mb segment on chromosome 2 in a diploid F. vesca reference genome. Fw1 and 11 tightly linked GWAS-significant SNPs mapped to linkage group 2C in octoploid segregating populations. The most significant SNP explained 85% of the phenotypic variability and predicted resistance in 97% of the accessions tested-broad-sense heritability was 0.96. Several disease resistance and defense-related gene homologs, including a small cluster of genes encoding nucleotide-binding leucine-rich-repeat proteins, were identified in the 0.7 Mb genomic segment predicted to harbor Fw1 DNA variants and candidate genes identified in the present study should facilitate the development of high-throughput genotyping assays for accurately predicting Fusarium wilt phenotypes and applying marker-assisted selection.
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26
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Pikunova AV, Sedov EN, Tokmakov SV, Suprun II, Gorbatchova NG, Dolzhikova MA, Yanchuk TV, Serova ZM. Microsatellite Loci Polymorphism of Apple (Malus domestica Borkh.) Genotypes with Different Ploidy Level. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418040129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Vining KJ, Salinas N, Tennessen JA, Zurn JD, Sargent DJ, Hancock J, Bassil NV. Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families. PeerJ 2017; 5:e3731. [PMID: 28875078 PMCID: PMC5581533 DOI: 10.7717/peerj.3731] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/03/2017] [Indexed: 12/30/2022] Open
Abstract
Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria × ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. × ananassa chromosomal regions derived from diploid ancestor F. vesca.
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Affiliation(s)
- Kelly J Vining
- Department of Horticulture, Oregon State University, Corvallis, OR, United States of America
| | - Natalia Salinas
- Department of Horticulture, University of Florida, Wimauma, FL, United States of America
| | - Jacob A Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States of America
| | - Jason D Zurn
- National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR, United States of America
| | - Daniel James Sargent
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,East Malling Enterprise Centre, Driscoll's Genetics Limited, East Malling, United Kingdom
| | - James Hancock
- Department of Horticulture, Michigan State University, East Lansing, MI, United States of America
| | - Nahla V Bassil
- Department of Horticulture, Oregon State University, Corvallis, OR, United States of America.,National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR, United States of America
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28
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Mangandi J, Verma S, Osorio L, Peres NA, van de Weg E, Whitaker VM. Pedigree-Based Analysis in a Multiparental Population of Octoploid Strawberry Reveals QTL Alleles Conferring Resistance to Phytophthora cactorum. G3 (BETHESDA, MD.) 2017; 7:1707-1719. [PMID: 28592652 PMCID: PMC5473751 DOI: 10.1534/g3.117.042119] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/03/2017] [Indexed: 02/03/2023]
Abstract
Understanding the genetic architecture of traits in breeding programs can be critical for making genetic progress. Important factors include the number of loci controlling a trait, allele frequencies at those loci, and allele effects in breeding germplasm. To this end, multiparental populations offer many advantages for quantitative trait locus (QTL) analyses compared to biparental populations. These include increased power for QTL detection, the ability to sample a larger number of segregating loci and alleles, and estimation of allele effects across diverse genetic backgrounds. Here, we investigate the genetic architecture of resistance to crown rot disease caused by Phytophthora cactorum in strawberry (Fragaria × ananassa), using connected full-sib families from a breeding population. Clonal replicates of > 1100 seedlings from 139 full-sib families arising from 61 parents were control-inoculated during two consecutive seasons. Subgenome-specific single nucleotide polymorphism (SNP) loci were mapped in allo-octoploid strawberry (2n = 8 × = 56), and FlexQTL software was utilized to perform a Bayesian, pedigree-based QTL analysis. A major locus on linkage group (LG) 7D, which we name FaRPc2, accounts for most of the genetic variation for resistance. Four predominant SNP haplotypes were detected in the FaRPc2 region, two of which are strongly associated with two different levels of resistance, suggesting the presence of multiple resistance alleles. The phenotypic effects of FaRPc2 alleles across trials and across numerous genetic backgrounds make this locus a highly desirable target for genetic improvement of resistance in cultivated strawberry.
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Affiliation(s)
- Jozer Mangandi
- Department of Horticultural Science, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | - Sujeet Verma
- Department of Horticultural Science, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | - Luis Osorio
- Department of Horticultural Science, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | - Natalia A Peres
- Department of Plant Pathology, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, Florida 33598
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, 6708 PB, The Netherlands
| | - Vance M Whitaker
- Department of Horticultural Science, University of Florida, IFAS Gulf Coast Research and Education Center, Wimauma, Florida 33598
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29
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Gezan SA, Osorio LF, Verma S, Whitaker VM. An experimental validation of genomic selection in octoploid strawberry. HORTICULTURE RESEARCH 2017; 4:16070. [PMID: 28090334 PMCID: PMC5225750 DOI: 10.1038/hortres.2016.70] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/06/2016] [Accepted: 12/08/2016] [Indexed: 05/03/2023]
Abstract
The primary goal of genomic selection is to increase genetic gains for complex traits by predicting performance of individuals for which phenotypic data are not available. The objective of this study was to experimentally evaluate the potential of genomic selection in strawberry breeding and to define a strategy for its implementation. Four clonally replicated field trials, two in each of 2 years comprised of a total of 1628 individuals, were established in 2013-2014 and 2014-2015. Five complex yield and fruit quality traits with moderate to low heritability were assessed in each trial. High-density genotyping was performed with the Affymetrix Axiom IStraw90 single-nucleotide polymorphism array, and 17 479 polymorphic markers were chosen for analysis. Several methods were compared, including Genomic BLUP, Bayes B, Bayes C, Bayesian LASSO Regression, Bayesian Ridge Regression and Reproducing Kernel Hilbert Spaces. Cross-validation within training populations resulted in higher values than for true validations across trials. For true validations, Bayes B gave the highest predictive abilities on average and also the highest selection efficiencies, particularly for yield traits that were the lowest heritability traits. Selection efficiencies using Bayes B for parent selection ranged from 74% for average fruit weight to 34% for early marketable yield. A breeding strategy is proposed in which advanced selection trials are utilized as training populations and in which genomic selection can reduce the breeding cycle from 3 to 2 years for a subset of untested parents based on their predicted genomic breeding values.
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Affiliation(s)
- Salvador A Gezan
- School of Forest Resources and Conservation, University of Florida, 363 Newins-Ziegler Hall, PO Box 110410, Gainesville, FL 32611-0410, USA
| | - Luis F Osorio
- Gulf Coast Research and Education Center, University of Florida, 14625 CR 672, Wimauma, FL 33598, USA
| | - Sujeet Verma
- Gulf Coast Research and Education Center, University of Florida, 14625 CR 672, Wimauma, FL 33598, USA
| | - Vance M Whitaker
- Gulf Coast Research and Education Center, University of Florida, 14625 CR 672, Wimauma, FL 33598, USA
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30
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Verma S, Zurn JD, Salinas N, Mathey MM, Denoyes B, Hancock JF, Finn CE, Bassil NV, Whitaker VM. Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry ( Fragaria× ananassa) breeding populations using pedigree-based QTL analysis. HORTICULTURE RESEARCH 2017; 4:17062. [PMID: 29138689 PMCID: PMC5676184 DOI: 10.1038/hortres.2017.62] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/02/2017] [Accepted: 10/05/2017] [Indexed: 05/08/2023]
Abstract
The cultivated strawberry (Fragaria×ananassa) is consumed worldwide for its flavor and nutritional benefits. Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species. Although several quantitative trait loci (QTL) have been previously detected for fruit quality and flowering traits using low-density genetic maps, clarity on the sub-genomic locations of these QTLs was missing. Recent discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism (SNP) array, enabling high-density genetic maps and finer resolution QTL analysis. In this study, breeder-specified traits were evaluated in the Eastern (Michigan) and Western (Oregon) United States for a common set of breeding populations during 2 years. Several QTLs were validated for soluble solids content (SSC), fruit weight (FWT), pH and titratable acidity (TA) using a pedigree-based QTL analysis approach. For fruit quality, a QTL for SSC on linkage group (LG) 6A, a QTL for FWT on LG 2BII, a QTL for pH on LG 4CII and two QTLs for TA on LGs 2A and 5B were detected. In addition, a large-effect QTL for flowering was detected at the distal end of LG 4A, coinciding with the FaPFRU locus. Marker haplotype analysis in the FaPFRU region indicated that the homozygous recessive genotype was highly predictive of seasonal flowering. SNP probes in the FaPFRU region may help facilitate marker-assisted selection for this trait.
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Affiliation(s)
- Sujeet Verma
- IFAS/Department of Horticulture, University of Florida, Gulf Coast Research and Education Center, 14625 CR 672, Wimauma, FL 33598, USA
| | - Jason D Zurn
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333, USA
| | - Natalia Salinas
- IFAS/Department of Horticulture, University of Florida, Gulf Coast Research and Education Center, 14625 CR 672, Wimauma, FL 33598, USA
| | - Megan M Mathey
- Department of Horticulture, Oregon State University, 4017 Agriculture and Life Sciences Building, Corvallis, OR 97331, USA
| | - Beatrice Denoyes
- Department of Horticulture, UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d’Ornon F-33140, France
| | | | - Chad E Finn
- USDA-ARS, HCRU, 3420 NW Orchard Avenue, Corvallis, OR 97330, USA
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333, USA
- ()
| | - Vance M Whitaker
- IFAS/Department of Horticulture, University of Florida, Gulf Coast Research and Education Center, 14625 CR 672, Wimauma, FL 33598, USA
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31
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Peace CP. DNA-informed breeding of rosaceous crops: promises, progress and prospects. HORTICULTURE RESEARCH 2017; 4:17006. [PMID: 28326185 PMCID: PMC5350264 DOI: 10.1038/hortres.2017.6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/02/2017] [Accepted: 02/03/2017] [Indexed: 05/18/2023]
Abstract
Crops of the Rosaceae family provide valuable contributions to rural economies and human health and enjoyment. Sustained solutions to production challenges and market demands can be met with genetically improved new cultivars. Traditional rosaceous crop breeding is expensive and time-consuming and would benefit from improvements in efficiency and accuracy. Use of DNA information is becoming conventional in rosaceous crop breeding, contributing to many decisions and operations, but only after past decades of solved challenges and generation of sufficient resources. Successes in deployment of DNA-based knowledge and tools have arisen when the 'chasm' between genomics discoveries and practical application is bridged systematically. Key steps are establishing breeder desire for use of DNA information, adapting tools to local breeding utility, identifying efficient application schemes, accessing effective services in DNA-based diagnostics and gaining experience in integrating DNA information into breeding operations and decisions. DNA-informed germplasm characterization for revealing identity and relatedness has benefitted many programs and provides a compelling entry point to reaping benefits of genomics research. DNA-informed germplasm evaluation for predicting trait performance has enabled effective reallocation of breeding resources when applied in pioneering programs. DNA-based diagnostics is now expanding from specific loci to genome-wide considerations. Realizing the full potential of this expansion will require improved accuracy of predictions, multi-trait DNA profiling capabilities, streamlined breeding information management systems, strategies that overcome plant-based features that limit breeding progress and widespread training of current and future breeding personnel and allied scientists.
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Affiliation(s)
- Cameron P Peace
- Department of Horticulture, Washington State University, PO Box 646414, Pullman, WA 99164-6414, USA
- ()
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32
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Perrotte J, Gaston A, Potier A, Petit A, Rothan C, Denoyes B. Narrowing down the single homoeologous FaPFRU locus controlling flowering in cultivated octoploid strawberry using a selective mapping strategy. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2176-2189. [PMID: 27168086 PMCID: PMC5095798 DOI: 10.1111/pbi.12574] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 04/23/2016] [Accepted: 05/02/2016] [Indexed: 05/04/2023]
Abstract
Extending the period of fruit production is a way to substantially increase crop yield in many fruit or ornamental species. In the cultivated octoploid strawberry (Fragaria × ananassa), the most consumed small fruit worldwide, fruit production season can be extended by selecting the perpetual flowering (PF) cultivars. This trait is of considerable interest to growers and to the food industry. Four homoeologous loci controlling a single trait can be expected in such a complex octoploid species. However, we recently showed that the PF trait is under the control of the single dominant FaPFRU locus (J. Exp. Bot., 2013, 64, 1837), making it potentially amenable to marker-assisted selection (MAS). Here, we report the successful use of a strategy, based on a selective mapping using a reduced sample of individuals, to identify nine markers in close linkage to the FaPFRU allelic variant. Thus, this strategy can be used to fine map the target homoeologous loci in other complex polyploid crop species. Recombinant analysis further enabled us to reduce the locus to a region flanked by two markers, Bx083_206 and Bx215_131, corresponding to a 1.1 Mb region in the diploid F. vesca reference genome. This region comprises 234 genes, including 15 flowering associated genes. Among these, the FLOWERING LOCUS T (FT) is known to be a key activator of flowering. The close association between the PF trait and the FaPFRU flanking markers was validated using an additional segregating population and genetic resources. This study lays the foundation for effective and rapid breeding of PF strawberry cultivars by MAS.
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Affiliation(s)
- Justine Perrotte
- INRA, UMR 1332 BFP, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1332 BFP, Villenave d'Ornon, France
- Ciref Création Variétale Fraises Fruits Rouges, Douville, France
| | - Amèlia Gaston
- INRA, UMR 1332 BFP, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1332 BFP, Villenave d'Ornon, France
| | - Aline Potier
- INRA, UMR 1332 BFP, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1332 BFP, Villenave d'Ornon, France
| | - Aurélie Petit
- Ciref Création Variétale Fraises Fruits Rouges, Douville, France
| | - Christophe Rothan
- INRA, UMR 1332 BFP, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1332 BFP, Villenave d'Ornon, France
| | - Béatrice Denoyes
- INRA, UMR 1332 BFP, Villenave d'Ornon, France.
- Université de Bordeaux, UMR 1332 BFP, Villenave d'Ornon, France.
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Hancock JF, Sooriyapathirana SS, Bassil NV, Stegmeir T, Cai L, Finn CE, Van de Weg E, Weebadde CK. Public Availability of a Genotyped Segregating Population May Foster Marker Assisted Breeding (MAB) and Quantitative Trait Loci (QTL) Discovery: An Example Using Strawberry. FRONTIERS IN PLANT SCIENCE 2016; 7:619. [PMID: 27242825 PMCID: PMC4860510 DOI: 10.3389/fpls.2016.00619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/22/2016] [Indexed: 05/30/2023]
Abstract
Much of the cost associated with marker discovery for marker assisted breeding (MAB) can be eliminated if a diverse, segregating population is generated, genotyped, and made available to the global breeding community. Herein, we present an example of a hybrid, wild-derived family of the octoploid strawberry that can be used by other breeding programs to economically find and tag useful genes for MAB. A pseudo test cross population between two wild species of Fragaria virginiana and F. chiloensis (FVC 11) was generated and evaluated for a set of phenotypic traits. A total of 106 individuals in the FVC 11 were genotyped for 29,251 single nucleotide polymorphisms (SNPs) utilizing a commercially available, genome-wide scanning platform (Affymetrix Axiom IStraw90(TW)). The marker trait associations were deduced using TASSEL software. The FVC 11 population segregating for daughters per mother, inflorescence number, inflorescence height, crown production, flower number, fruit size, yield, internal color, soluble solids, fruit firmness, and plant vigor. Coefficients of variations ranged from 10% for fruit firmness to 68% for daughters per mother, indicating an underlying quantitative inheritance for each trait. A total of 2,474 SNPs were found to be polymorphic in FVC 11 and strong marker trait associations were observed for vigor, daughters per mother, yield and fruit weight. These data indicate that FVC 11 can be used as a reference population for quantitative trait loci detection and subsequent MAB across different breeding programs and geographical locations.
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Affiliation(s)
- James F. Hancock
- Department of Horticulture, Michigan State University, East Lansing, MIUSA
| | - Suneth S. Sooriyapathirana
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, PeradeniyaSri Lanka
| | - Nahla V. Bassil
- United States Department of Agriculture – Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, ORUSA
| | | | - Lichun Cai
- Department of Horticulture, Michigan State University, East Lansing, MIUSA
| | - Chad E. Finn
- United States Department of Agriculture – Agricultural Research Service, Horticultural Crops Research Unit, Corvallis, ORUSA
| | | | - Cholani K. Weebadde
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MIUSA
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Sargent DJ, Yang Y, Šurbanovski N, Bianco L, Buti M, Velasco R, Giongo L, Davis TM. HaploSNP affinities and linkage map positions illuminate subgenome composition in the octoploid, cultivated strawberry (Fragaria×ananassa). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:140-150. [PMID: 26566832 DOI: 10.1016/j.plantsci.2015.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/05/2015] [Accepted: 07/06/2015] [Indexed: 05/18/2023]
Abstract
The cultivated strawberry, Fragaria×ananassa possesses a genetically complex allo-octoploid genome. Advances in genomics research in Fragaria, including the release of a genome sequence for F. vesca, have permitted the development of a high throughput whole genome genotyping array for strawberry, which promises to facilitate genetics and genomics research. In this investigation, we used the Axiom® IStraw90®)array for linkage map development, and produced a linkage map containing 8,407 SNP markers spanning 1,820cM. Whilst the linkage map provides good coverage of the genome of both parental genotypes, the map of 'Monterey' contained significantly fewer mapped markers than did that of 'Darselect'. The array contains a novel marker class known as haploSNPs, which exploit homoeologous sequence variants as probe destabilization sites to effectively reduce marker ploidy. We examined these sites as potential indicators of subgenomic identities by using comparisons to allele states in two ancestral diploids. On this basis, haploSNP loci could be inferred to be derived from F. vesca, F. iinumae, or from an unknown source. When the identity classifications of haploSNPs were considered in conjunction with their respective linkage map positions, it was possible to define two discrete subgenomes, while the remaining homoeologues of each chromosome could not be partitioned into two discrete subgenomic groupings. These findings suggested a novel hypothesis regarding octoploid strawberry subgenome structure and evolutionary origins.
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Affiliation(s)
- D J Sargent
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige 38010, TN, Italy
| | - Y Yang
- Department of Biological Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - N Šurbanovski
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige 38010, TN, Italy
| | - L Bianco
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige 38010, TN, Italy
| | - M Buti
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige 38010, TN, Italy
| | - R Velasco
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige 38010, TN, Italy
| | - L Giongo
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige 38010, TN, Italy
| | - T M Davis
- Department of Biological Sciences, University of New Hampshire, Durham, NH, 03824, USA
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Sánchez-Sevilla JF, Horvath A, Botella MA, Gaston A, Folta K, Kilian A, Denoyes B, Amaya I. Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa). PLoS One 2015; 10:e0144960. [PMID: 26675207 PMCID: PMC4682937 DOI: 10.1371/journal.pone.0144960] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 11/25/2015] [Indexed: 12/21/2022] Open
Abstract
Cultivated strawberry (Fragaria × ananassa) is a genetically complex allo-octoploid crop with 28 pairs of chromosomes (2n = 8x = 56) for which a genome sequence is not yet available. The diploid Fragaria vesca is considered the donor species of one of the octoploid sub-genomes and its available genome sequence can be used as a reference for genomic studies. A wide number of strawberry cultivars are stored in ex situ germplasm collections world-wide but a number of previous studies have addressed the genetic diversity present within a limited number of these collections. Here, we report the development and application of two platforms based on the implementation of Diversity Array Technology (DArT) markers for high-throughput genotyping in strawberry. The first DArT microarray was used to evaluate the genetic diversity of 62 strawberry cultivars that represent a wide range of variation based on phenotype, geographical and temporal origin and pedigrees. A total of 603 DArT markers were used to evaluate the diversity and structure of the population and their cluster analyses revealed that these markers were highly efficient in classifying the accessions in groups based on historical, geographical and pedigree-based cues. The second DArTseq platform took benefit of the complexity reduction method optimized for strawberry and the development of next generation sequencing technologies. The strawberry DArTseq was used to generate a total of 9,386 SNP markers in the previously developed ‘232’ × ‘1392’ mapping population, of which, 4,242 high quality markers were further selected to saturate this map after several filtering steps. The high-throughput platforms here developed for genotyping strawberry will facilitate genome-wide characterizations of large accessions sets and complement other available options.
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Affiliation(s)
- José F. Sánchez-Sevilla
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140, Málaga, Spain
| | - Aniko Horvath
- INRA, UMR 1332 BFP, F-33140 Villenave d’Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d’Ornon, France
| | - Miguel A. Botella
- Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC),
Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, 29071, Málaga, Spain
| | - Amèlia Gaston
- INRA, UMR 1332 BFP, F-33140 Villenave d’Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d’Ornon, France
| | - Kevin Folta
- University of Florida, Horticultural Sciences Department, Gainesville, Florida, 32611, United States of America
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, Building 3, University of Canberra, Bruce, ACT 2617, Australia
| | - Beatrice Denoyes
- INRA, UMR 1332 BFP, F-33140 Villenave d’Ornon, France, Université de Bordeaux, UMR 1332 NFP, F-33140, Villenave d’Ornon, France
| | - Iraida Amaya
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA) Centro de Churriana, Cortijo de la Cruz, 29140, Málaga, Spain
- University of Florida, Horticultural Sciences Department, Gainesville, Florida, 32611, United States of America
- * E-mail:
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Bushakra JM, Lewers KS, Staton ME, Zhebentyayeva T, Saski CA. Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.). BMC PLANT BIOLOGY 2015; 15:258. [PMID: 26499487 PMCID: PMC4620654 DOI: 10.1186/s12870-015-0629-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 09/28/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed sequence tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders. METHODS Leaf and meristem tissue from 'Heritage' red raspberry (Rubus idaeus) and 'Bristol' black raspberry (R. occidentalis) were utilized for RNA extraction. After conversion to cDNA and library construction, ESTs were sequenced, quality verified, assembled and scanned for SSRs. Primers flanking the SSRs were designed and a subset tested for amplification, polymorphism and transferability across species. ESTs containing SSRs were functionally annotated using the GenBank non-redundant (nr) database and further classified using the gene ontology database. RESULTS To accelerate development of EST-SSRs in the genus Rubus (Rosaceae), 1149 and 2358 cDNA sequences were generated from red raspberry and black raspberry, respectively. The cDNA sequences were screened using rigorous filtering criteria which resulted in the identification of 121 and 257 SSR loci for red and black raspberry, respectively. Primers were designed from the surrounding sequences resulting in 131 and 288 primer pairs, respectively, as some sequences contained more than one SSR locus. Sequence analysis revealed that the SSR-containing genes span a diversity of functions and share more sequence identity with strawberry genes than with other Rosaceous species. CONCLUSION This resource of Rubus-specific, gene-derived markers will facilitate the construction of linkage maps composed of transferable markers for studying and manipulating important traits in this economically important genus.
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Affiliation(s)
- Jill M Bushakra
- USDA-ARS, National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR, 97333-2521, USA.
| | - Kim S Lewers
- USDA-ARS, Beltsville Agricultural Research Center, Genetic Improvement of Fruits and Vegetables Lab, Bldg. 010A, BARC-West, 10300 Baltimore Ave., Beltsville, MD, 20705-2350, USA.
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, University of Tennessee, 2505 EJ Chapman Drive, 370 PBB, Knoxville, TN, 37996, USA.
| | - Tetyana Zhebentyayeva
- Genomics & Computational Biology Laboratory, Biosystems Research Complex, Clemson University, 51 New Cherry St., 304, Clemson, SC, 29634, USA.
| | - Christopher A Saski
- Genomics & Computational Biology Laboratory, Biosystems Research Complex, Clemson University, 51 New Cherry St., 304, Clemson, SC, 29634, USA.
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Davik J, Sargent DJ, Brurberg MB, Lien S, Kent M, Alsheikh M. A ddRAD Based Linkage Map of the Cultivated Strawberry, Fragaria xananassa. PLoS One 2015; 10:e0137746. [PMID: 26398886 PMCID: PMC4580419 DOI: 10.1371/journal.pone.0137746] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/21/2015] [Indexed: 01/27/2023] Open
Abstract
The cultivated strawberry (Fragaria ×ananassa Duch.) is an allo-octoploid considered difficult to disentangle genetically due to its four relatively similar sub-genomic chromosome sets. This has been alleviated by the recent release of the strawberry IStraw90 whole genome genotyping array. However, array resolution relies on the genotypes used in the array construction and may be of limited general use. SNP detection based on reduced genomic sequencing approaches has the potential of providing better coverage in cases where the studied genotypes are only distantly related from the SNP array’s construction foundation. Here we have used double digest restriction-associated DNA sequencing (ddRAD) to identify SNPs in a 145 seedling F1 hybrid population raised from the cross between the cultivars Sonata (♀) and Babette (♂). A linkage map containing 907 markers which spanned 1,581.5 cM across 31 linkage groups representing the 28 chromosomes of the species. Comparing the physical span of the SNP markers with the F. vesca genome sequence, the linkage groups resolved covered 79% of the estimated 830 Mb of the F. ×ananassa genome. Here, we have developed the first linkage map for F. ×ananassa using ddRAD and show that this technique and other related techniques are useful tools for linkage map development and downstream genetic studies in the octoploid strawberry.
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Affiliation(s)
- Jahn Davik
- Norwegian Institute for Bioeconomy Research, Ås, Norway
- * E-mail:
| | - Daniel James Sargent
- Fondazione Edmund Mach, Centre for Research and Innovation, San Michele all'Adige, Italy
| | | | - Sigbjørn Lien
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew Kent
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Muath Alsheikh
- Graminor Breeding Ltd., Ridabu, Norway; Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
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Govindarajulu R, Parks M, Tennessen JA, Liston A, Ashman TL. Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species. AMERICAN JOURNAL OF BOTANY 2015; 102:544-554. [PMID: 25878088 DOI: 10.3732/ajb.1500026] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/05/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Molecular phylogenies derived from all three plant genomes can provide insight into the evolutionary history of plant groups influenced by reticulation. We sought to reconstruct mitochondrial exome, chloroplast, and nuclear genome phylogenies for octoploid Fragaria and their diploid ancestors and to document patterns of incongruence between and within the cytoplasmic genomes and interpret these in the context of evolutionary origin of the octoploid strawberries. METHODS Using a genome-skimming approach, we assembled chloroplast genomes and mitochondrial exomes, and we used the POLiMAPS method to assemble nuclear sequence for octoploid species and constructed phylogenies from all three genomes. We assessed incongruence between and within cytoplasmic genomes using topology-based phylogenetic incongruence tests. KEY RESULTS The incongruent cytoplasmic genome phylogeny with respect to the placement of octoploids suggests potential breakage in linkage disequilibrium of cytoplasmic genomes during allopolyploid origin of the octoploids. Furthermore, a single mitochondrial chimeric gene with a putative role in cytoplasmic male sterility yields a phylogeny that is inconsistent with the rest of the mitochondrial genome but consistent with the chloroplast phylogeny, suggesting intracellular gene transfer between heteroplasmic mitochondria, possibly driven by selection to overcome the effects of mito-nuclear incompatibility in octoploid origins. CONCLUSIONS This work expands on the current understanding of evolutionary history of the octoploid ancestors of cultivated strawberry. It demonstrates phylogenetic incongruence between cytoplasmic genomes in octoploids with respect to diploid ancestors, indicating breakage in linkage disequilibrium of cytoplasmic genomes. We discuss potential organism-level processes that may have contributed to the observed incongruence in Fragaria.
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Affiliation(s)
| | - Matthew Parks
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Jacob A Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 USA
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Bassil NV, Davis TM, Zhang H, Ficklin S, Mittmann M, Webster T, Mahoney L, Wood D, Alperin ES, Rosyara UR, Koehorst-Vanc Putten H, Monfort A, Sargent DJ, Amaya I, Denoyes B, Bianco L, van Dijk T, Pirani A, Iezzoni A, Main D, Peace C, Yang Y, Whitaker V, Verma S, Bellon L, Brew F, Herrera R, van de Weg E. Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa. BMC Genomics 2015; 16:155. [PMID: 25886969 PMCID: PMC4374422 DOI: 10.1186/s12864-015-1310-1] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 02/02/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca 'Hawaii 4' reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array. RESULTS About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing "haploSNPs" (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative "codon-based" SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix's "SNPolisher" R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family 'Holiday' × 'Korona' with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM. CONCLUSIONS The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array's high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.
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Affiliation(s)
| | | | | | | | | | | | | | - David Wood
- University of New Hampshire, Durham, NH, USA.
| | | | | | | | - Amparo Monfort
- IRTA-Center for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain.
| | - Daniel J Sargent
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, 38010, TN, Italy.
| | | | | | - Luca Bianco
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, 38010, TN, Italy.
| | - Thijs van Dijk
- Wageningen-UR Plant Breeding, Wageningen, The Netherlands.
| | | | - Amy Iezzoni
- Michigan State University, East Lansing, MI, USA.
| | - Dorrie Main
- Washington State University, Pullman, WA, USA.
| | | | - Yilong Yang
- University of New Hampshire, Durham, NH, USA.
| | | | | | | | - Fiona Brew
- Affymetrix UK Ltd, Wooburn Green, High Wycombe, UK.
| | - Raul Herrera
- Instituto Ciencias Biologicas, Universidad de Talca, Talca, Chile.
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40
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Bassil NV, Davis TM, Zhang H, Ficklin S, Mittmann M, Webster T, Mahoney L, Wood D, Alperin ES, Rosyara UR, Koehorst-Vanc Putten H, Monfort A, Sargent DJ, Amaya I, Denoyes B, Bianco L, van Dijk T, Pirani A, Iezzoni A, Main D, Peace C, Yang Y, Whitaker V, Verma S, Bellon L, Brew F, Herrera R, van de Weg E. Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa. BMC Genomics 2015. [PMID: 25886969 DOI: 10.1186/s12864-12015-11310-12861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
BACKGROUND A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca 'Hawaii 4' reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array. RESULTS About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing "haploSNPs" (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative "codon-based" SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix's "SNPolisher" R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family 'Holiday' × 'Korona' with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM. CONCLUSIONS The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array's high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.
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Affiliation(s)
| | | | | | | | | | | | | | - David Wood
- University of New Hampshire, Durham, NH, USA.
| | | | | | | | - Amparo Monfort
- IRTA-Center for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain.
| | - Daniel J Sargent
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, 38010, TN, Italy.
| | | | | | - Luca Bianco
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, 38010, TN, Italy.
| | - Thijs van Dijk
- Wageningen-UR Plant Breeding, Wageningen, The Netherlands.
| | | | - Amy Iezzoni
- Michigan State University, East Lansing, MI, USA.
| | - Dorrie Main
- Washington State University, Pullman, WA, USA.
| | | | - Yilong Yang
- University of New Hampshire, Durham, NH, USA.
| | | | | | | | - Fiona Brew
- Affymetrix UK Ltd, Wooburn Green, High Wycombe, UK.
| | - Raul Herrera
- Instituto Ciencias Biologicas, Universidad de Talca, Talca, Chile.
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Antanaviciute L, Šurbanovski N, Harrison N, McLeary KJ, Simpson DW, Wilson F, Sargent DJ, Harrison RJ. Mapping QTL associated with Verticillium dahliae resistance in the cultivated strawberry (Fragaria × ananassa). HORTICULTURE RESEARCH 2015; 2:15009. [PMID: 26504565 PMCID: PMC4595976 DOI: 10.1038/hortres.2015.9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/02/2015] [Accepted: 02/05/2015] [Indexed: 05/04/2023]
Abstract
A biparental cross of octoploid strawberry segregating for resistance to Verticillium dahliae, the causative agent of Verticillium wilt, was screened under field conditions for three seasons. Average wilt scores were significantly associated with multiple QTL, which were mostly significant across all years. Markers significantly associated with the traits were used to screen material with known wilt resistance and susceptibility phenotypes. A clear and statistically significant relationship was observed between resistant, tolerant and susceptible material and the total number of markers present in the different resistance classes. In field situations resistance QTL appear to behave in an additive manner. These markers are abundant in the cultivated strawberry germplasm indicating that, despite the large number of markers, clear genetic gain is possible through marker-assisted breeding.
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Affiliation(s)
- L Antanaviciute
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK
| | - N Šurbanovski
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige (TN), Italy
| | - N Harrison
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK
| | - K J McLeary
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK
| | - D W Simpson
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK
| | - F Wilson
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK
| | - D J Sargent
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige (TN), Italy
| | - R J Harrison
- East Malling Research, New Road, East Malling, Kent ME19 6BJ, UK
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42
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Tennessen JA, Govindarajulu R, Ashman TL, Liston A. Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps. Genome Biol Evol 2014; 6:3295-313. [PMID: 25477420 PMCID: PMC4986458 DOI: 10.1093/gbe/evu261] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the challenge of distinguishing homologous sequences from each other. Here, we use dense linkage maps generated with targeted sequence capture to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the subgenomes of the wild octoploid progenitors of cultivated strawberry, Fragaria virginiana and Fragaria chiloensis. Our novel approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), leverages sequence reads to associate informative interhomeolog phylogenetic markers with linkage groups and reference genome positions. In contrast to a widely accepted model, we find that one of the four subgenomes originates with the diploid cytoplasm donor F. vesca, one with the diploid Fragaria iinumae, and two with an unknown ancestor close to F. iinumae. Extensive unidirectional introgression has converted F. iinumae-like subgenomes to be more F. vesca-like, but never the reverse, due either to homoploid hybridization in the F. iinumae-like diploid ancestors or else strong selection spreading F. vesca-like sequence among subgenomes through homeologous exchange. In addition, divergence between homeologous chromosomes has been substantially augmented by interchromosomal rearrangements. Our phylogenetic approach reveals novel aspects of the complicated web of genetic exchanges that occur during polyploid evolution and suggests a path forward for unraveling other agriculturally and ecologically important polyploid genomes.
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Affiliation(s)
| | | | | | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University
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Liston A, Cronn R, Ashman TL. Fragaria: a genus with deep historical roots and ripe for evolutionary and ecological insights. AMERICAN JOURNAL OF BOTANY 2014; 101:1686-99. [PMID: 25326614 DOI: 10.3732/ajb.1400140] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The cultivated strawberry, Fragaria ×ananassa, is one of the youngest domesticated plants. Its 18th century origin via hybridization in Europe between the North American F. virginiana and the South American F. chiloensis was documented by the botanist Antoine Nicolas Duchesne. His 1766 "Natural History of Strawberries" is an extraordinary work that integrates fundamental discoveries on the biology, ecology, and phylogeny of Fragaria with applied information on cultivation and ethnobotanical uses, serving as an inspiration for current research in the genus. Fragaria species exhibit the full range of sexual systems in the gynodioecy pathway from hermaphroditism to dioecy (and back again), as well as variation in self-compatibility, and evidence of sex chromosomes with female heterogamety. The genus is also characterized by interspecific hybridization and polyploidy, with a natural range of ploidy levels from diploids to decaploids. This biological diversity, combined with the availability of genomic resources and the ease of growing and experimenting with the plants, makes Fragaria a very attractive system for ecological and evolutionary genomics. The goal of this review is to introduce Fragaria as a model genus and to provide a roadmap for future integrative research. These research directions will deepen our understanding of the ecological and evolutionary context that shaped the ancestors of the cultivated strawberry, not only providing information that can be applied to efforts to shape the future of this important fruit crop but also our understanding of key transitions in plant evolution.
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Affiliation(s)
- Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon 97331 USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 USA
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