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Skytte Af Sätra J, Garkava-Gustavsson L, Ingvarsson PK. Why we thrive beneath a northern sky - genomic signals of selection in apple for adaptation to northern Sweden. Heredity (Edinb) 2024:10.1038/s41437-024-00693-2. [PMID: 38834867 DOI: 10.1038/s41437-024-00693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
Good understanding of the genomic regions underlying adaptation of apple to boreal climates is needed to facilitate efficient breeding of locally adapted apple cultivars. Proper infrastructure for phenotyping and evaluation is essential for identification of traits responsible for adaptation, and dissection of their genetic composition. However, such infrastructure is costly and currently not available for the boreal zone of northern Sweden. Therefore, we used historical pomological data on climate adaptation of 59 apple cultivars and whole genome sequencing to identify genomic regions that have undergone historical selection among apple cultivars recommended for cultivation in northern Sweden. We found the apple collection to be composed of two ancestral groups that are largely concordant with the grouping into 'hardy' and 'not hardy' cultivars based on the pomological literature. Using a number of genome-wide scans for signals of selection, we obtained strong evidence of positive selection at a genomic region around 29 MbHFTH1 of chromosome 1 among apple cultivars in the 'hardy' group. Using phased genotypic data from the 20 K apple Infinium® SNP array, we identified haplotypes associated with the two cultivar groups and traced transmission of these haplotypes through the pedigrees of some apple cultivars. This demonstrates that historical data from pomological literature can be analyzed by population genomic approaches as a step towards revealing the genomic control of a key property for a horticultural niche market. Such knowledge is needed to facilitate efficient breeding strategies for development of locally adapted apple cultivars in the future. The current study illustrates the response to a very strong selective pressure imposed on tree crops by climatic factors, and the importance of genetic research on this topic and feasibility of breeding efforts in the light of the ongoing climate change.
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Affiliation(s)
- J Skytte Af Sätra
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - L Garkava-Gustavsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - P K Ingvarsson
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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2
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Keller B, Jung M, Bühlmann-Schütz S, Hodel M, Studer B, Broggini GAL, Patocchi A. The genetic basis of apple shape and size unraveled by digital phenotyping. G3 (BETHESDA, MD.) 2024; 14:jkae045. [PMID: 38441135 PMCID: PMC11075547 DOI: 10.1093/g3journal/jkae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/22/2024] [Indexed: 05/08/2024]
Abstract
Great diversity of shape, size, and skin color is observed among the fruits of different apple genotypes. These traits are critical for consumers and therefore interesting targets for breeding new apple varieties. However, they are difficult to phenotype and their genetic basis, especially for fruit shape and ground color, is largely unknown. We used the FruitPhenoBox to digitally phenotype 525 genotypes of the apple reference population (apple REFPOP) genotyped for 303,148 single nucleotide polymorphism (SNP) markers. From the apple images, 573 highly heritable features describing fruit shape and size as well as 17 highly heritable features for fruit skin color were extracted to explore genotype-phenotype relationships. Out of these features, seven principal components (PCs) and 16 features with the Pearson's correlation r < 0.75 (selected features) were chosen to carry out genome-wide association studies (GWAS) for fruit shape and size. Four PCs and eight selected features were used in GWAS for fruit skin color. In total, 69 SNPs scattered over all 17 apple chromosomes were significantly associated with round, conical, cylindrical, or symmetric fruit shapes and fruit size. Novel associations with major effect on round or conical fruit shapes and fruit size were identified on chromosomes 1 and 2. Additionally, 16 SNPs associated with PCs and selected features related to red overcolor as well as green and yellow ground color were found on eight chromosomes. The identified associations can be used to advance marker-assisted selection in apple fruit breeding to systematically select for desired fruit appearance.
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Affiliation(s)
- Beat Keller
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Michaela Jung
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Simone Bühlmann-Schütz
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Marius Hodel
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Giovanni A L Broggini
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Andrea Patocchi
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
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3
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Zhang W, Han Y, Liao L. Phenomics and transcriptomic profiling of fruit development in distinct apple varieties. Sci Data 2024; 11:390. [PMID: 38627414 PMCID: PMC11021526 DOI: 10.1038/s41597-024-03220-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
Apple is one of the most economically important and popular temperate fruit trees. The domestication of apple has resulted in substantial phenotypic differences, particularly between wild and cultivated varieties. However, the relationship between gene expression and phenotypic variations in apple remains poorly understood. Here, we present a comprehensive dataset featuring five distinct apple varieties, including two wild varieties and three representative cultivated varieties. The dataset comprises of both phenomics data, encompassing twelve fruit quality-related traits continuously measured over two years, and transcriptomic data obtained at different developmental stages with three biological replicates. We performed basic quality control process, gene expression normalization and differential gene expression analysis to demonstrate the utility and reliability of the dataset. Our findings indicate that gene expression strongly related with phenotypic variations in apple. This dataset serves as a valuable resource, encompassing phenomics and transcriptomic data in multiple formats, thereby facilitating further exploration of the relationships between gene expression and phenotypic traits in apple.
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Affiliation(s)
- Weihan Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yuepeng Han
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Liao Liao
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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4
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Pradas N, Jurado-Ruiz F, Onielfa C, Arús P, Aranzana MJ. PERSEUS: an interactive and intuitive web-based tool for pedigree visualization. Bioinformatics 2024; 40:btae060. [PMID: 38310342 PMCID: PMC10898331 DOI: 10.1093/bioinformatics/btae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 02/05/2024] Open
Abstract
SUMMARY Pedigree-based analyses' prime role is to unravel relationships between individuals in breeding programs and germplasms. This is critical information for decoding the genetics underlying main inherited traits of relevance, and unlocking the genotypic variability of a species to carry out genomic selections and predictions. Despite the great interest, current lineage visualizations become quite limiting in terms of public display, exploration, and tracing of traits up to ancestral donors. PERSEUS is a user-friendly, intuitive, and interactive web-based tool for pedigree visualizations represented as directed graph networks distributed using a force-repulsion method. The visualizations do not only showcase individual relationships among accessions, but also facilitate a seamless search and download of phenotypic traits along the pedigrees. PERSEUS is a promising tool for breeders and scientists, advantageous for evolutionary, genealogy, and diversity analyses among related accessions and species. AVAILABILITY AND IMPLEMENTATION PERSEUS is freely accessible at https://bioinformatics.cragenomica.es/perseus and GitHub code is available at https://github.com/aranzana-lab/PERSEUS.
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Affiliation(s)
- Nicole Pradas
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Federico Jurado-Ruiz
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Carles Onielfa
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, 0814 Barcelona, Spain
| | - Pere Arús
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, 0814 Barcelona, Spain
| | - Maria José Aranzana
- Centre for Research in Agricultural Genomics (CRAG), Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, 0814 Barcelona, Spain
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5
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Švara A, De Storme N, Carpentier S, Keulemans W, De Coninck B. Phenotyping, genetics, and "-omics" approaches to unravel and introgress enhanced resistance against apple scab ( Venturia inaequalis) in apple cultivars ( Malus × domestica). HORTICULTURE RESEARCH 2024; 11:uhae002. [PMID: 38371632 PMCID: PMC10873587 DOI: 10.1093/hr/uhae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 12/27/2023] [Indexed: 02/20/2024]
Abstract
Apple scab disease, caused by the fungus Venturia inaequalis, endangers commercial apple production globally. It is predominantly managed by frequent fungicide sprays that can harm the environment and promote the development of fungicide-resistant strains. Cultivation of scab-resistant cultivars harboring diverse qualitative Rvi resistance loci and quantitative trait loci associated with scab resistance could reduce the chemical footprint. A comprehensive understanding of the host-pathogen interaction is, however, needed to efficiently breed cultivars with enhanced resistance against a variety of pathogenic strains. Breeding efforts should not only encompass pyramiding of Rvi loci and their corresponding resistance alleles that directly or indirectly recognize pathogen effectors, but should also integrate genes that contribute to effective downstream defense mechanisms. This review provides an overview of the phenotypic and genetic aspects of apple scab resistance, and currently known corresponding defense mechanisms. Implementation of recent "-omics" approaches has provided insights into the complex network of physiological, molecular, and signaling processes that occur before and upon scab infection, thereby revealing the importance of both constitutive and induced defense mechanisms. Based on the current knowledge, we outline advances toward more efficient introgression of enhanced scab resistance into novel apple cultivars by conventional breeding or genetic modification techniques. However, additional studies integrating different "-omics" approaches combined with functional studies will be necessary to unravel effective defense mechanisms as well as key regulatory genes underpinning scab resistance in apple. This crucial information will set the stage for successful knowledge-based breeding for enhanced scab resistance.
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Affiliation(s)
- Anže Švara
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Nico De Storme
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Sebastien Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Genetic resources, Bioversity International, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Wannes Keulemans
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Barbara De Coninck
- Laboratory of Plant Health and Protection, Division of Crop Biotechnics, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
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6
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Dujak C, Coleto-Alcudia V, Aranzana MJ. Genomic analysis of fruit size and shape traits in apple: unveiling candidate genes through GWAS analysis. HORTICULTURE RESEARCH 2024; 11:uhad270. [PMID: 38419968 PMCID: PMC10901474 DOI: 10.1093/hr/uhad270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/05/2023] [Indexed: 03/02/2024]
Abstract
Genomic tools facilitate the efficient selection of improved genetic materials within a breeding program. Here, we focus on two apple fruit quality traits: shape and size. We utilized data from 11 fruit morphology parameters gathered across three years of harvest from 355 genotypes of the apple REFPOP collection, which serves as a representative sample of the genetic variability present in European-cultivated apples. The data were then employed for genome-wide association studies (GWAS) using the FarmCPU and the BLINK models. The analysis identified 59 SNPs associated with fruit size and shape traits (35 with FarmCPU and 45 with BLINK) responsible for 71 QTNs. These QTNs were distributed across all chromosomes except for chromosomes 10 and 15. Thirty-four QTNs, identified by 27 SNPs, were related for size traits, and 37 QTNs, identified by 26 SNPs, were related to shape attributes. The definition of the haploblocks containing the most relevant SNPs served to propose candidate genes, among them the genes of the ovate family protein MdOFP17 and MdOFP4 that were in a 9.7kb haploblock on Chromosome 11. RNA-seq data revealed low or null expression of these genes in the oblong cultivar "Skovfoged" and higher expression in the flat "Grand'mere." The Gene Ontology enrichment analysis support a role of OFPs and hormones in shape regulation. In conclusion, this comprehensive GWAS analysis of the apple REFPOP collection has revealed promising genetic markers and candidate genes associated with apple fruit shape and size attributes, providing valuable insights that could enhance the efficiency of future breeding programs.
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Affiliation(s)
- Christian Dujak
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UABUB, Plant and Animal Genomics, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Veredas Coleto-Alcudia
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UABUB, Plant and Animal Genomics, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Maria José Aranzana
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UABUB, Plant and Animal Genomics, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Genomics and Biotechnology, 08140 Caldes de Montbui, Barcelona, Spain
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7
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Nybom H, Ruan C, Rumpunen K. The Systematics, Reproductive Biology, Biochemistry, and Breeding of Sea Buckthorn-A Review. Genes (Basel) 2023; 14:2120. [PMID: 38136942 PMCID: PMC10743242 DOI: 10.3390/genes14122120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023] Open
Abstract
Both the fruit flesh and seeds of sea buckthorn have multiple uses for medicinal and culinary purposes, including the valuable market for supplementary health foods. Bioactive compounds, such as essential amino acids, vitamins B, C, and E, carotenoids, polyphenols, ursolic acid, unsaturated fatty acids, and other active substances, are now being analyzed in detail for their medicinal properties. Domestication with commercial orchards and processing plants is undertaken in many countries, but there is a large need for improved plant material with high yield, tolerance to environmental stress, diseases, and pests, suitability for efficient harvesting methods, and high contents of compounds that have medicinal and/or culinary values. Applied breeding is based mainly on directed crosses between different subspecies of Hippophae rhamnoides. DNA markers have been applied to analyses of systematics and population genetics as well as for the discrimination of cultivars, but very few DNA markers have as yet been developed for use in selection and breeding. Several key genes in important metabolic pathways have, however, been identified, and four genomes have recently been sequenced.
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Affiliation(s)
- Hilde Nybom
- Department of Plant Breeding–Balsgård, Swedish University of Agricultural Sciences, 29194 Kristianstad, Sweden
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China;
| | - Kimmo Rumpunen
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23053 Alnarp, Sweden;
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8
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Mansfeld BN, Yocca A, Ou S, Harkess A, Burchard E, Gutierrez B, van Nocker S, Gottschalk C. A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:989-1002. [PMID: 37639371 DOI: 10.1111/tpj.16433] [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: 03/22/2023] [Revised: 07/08/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023]
Abstract
SUMMARYThe Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus × domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for the development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca have been hampered by the lack of genomic resources. Here, we present a high‐quality, haplotype‐resolved, chromosome‐scale genome assembly and annotation for M. fusca. The genome was assembled using high‐fidelity long‐reads and scaffolded using genetic maps and high‐throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co‐linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference‐quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA‐informed introgression breeding.
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Affiliation(s)
- Ben N Mansfeld
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Shujun Ou
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Erik Burchard
- USDA ARS, Appalachian Fruit Research Station, Kearneysville, West Virginia, USA
| | | | - Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
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9
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Montanari S, Deng C, Koot E, Bassil NV, Zurn JD, Morrison-Whittle P, Worthington ML, Aryal R, Ashrafi H, Pradelles J, Wellenreuther M, Chagné D. A multiplexed plant-animal SNP array for selective breeding and species conservation applications. G3 (BETHESDA, MD.) 2023; 13:jkad170. [PMID: 37565490 PMCID: PMC10542201 DOI: 10.1093/g3journal/jkad170] [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: 03/02/2023] [Revised: 05/15/2023] [Accepted: 06/30/2023] [Indexed: 08/12/2023]
Abstract
Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programs, and managing wild populations and germplasm collections. Amongst available genotyping tools, single nucleotide polymorphism arrays have been shown to be comparatively easy to use and generate highly accurate genotypic data. Single-species arrays are the most commonly used type so far; however, some multi-species arrays have been developed for closely related species that share single nucleotide polymorphism markers, exploiting inter-species cross-amplification. In this study, the suitability of a multiplexed plant-animal single nucleotide polymorphism array, including both closely and distantly related species, was explored. The performance of the single nucleotide polymorphism array across species for diverse applications, ranging from intra-species diversity assessments to parentage analysis, was assessed. Moreover, the value of genotyping pooled DNA of distantly related species on the single nucleotide polymorphism array as a technique to further reduce costs was evaluated. Single nucleotide polymorphism performance was generally high, and species-specific single nucleotide polymorphisms proved suitable for diverse applications. The multi-species single nucleotide polymorphism array approach reported here could be transferred to other species to achieve cost savings resulting from the increased throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.
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Affiliation(s)
- Sara Montanari
- The New Zealand Institute for Plant and Food Research Ltd, Motueka 7198, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant and Food Research Ltd, Auckland 1025, New Zealand
| | - Emily Koot
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North 4410, New Zealand
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Jason D Zurn
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | | | | | - Rishi Aryal
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd, Nelson 7010, New Zealand
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North 4410, New Zealand
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10
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Schaller A, Vanderzande S, Peace C. Deducing genotypes for loci of interest from SNP array data via haplotype sharing, demonstrated for apple and cherry. PLoS One 2023; 18:e0272888. [PMID: 36749762 PMCID: PMC9904487 DOI: 10.1371/journal.pone.0272888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
Breeders, collection curators, and other germplasm users require genetic information, both genome-wide and locus-specific, to effectively manage their genetically diverse plant material. SNP arrays have become the preferred platform to provide genome-wide genetic profiles for elite germplasm and could also provide locus-specific genotypic information. However, genotypic information for loci of interest such as those within PCR-based DNA fingerprinting panels and trait-predictive DNA tests is not readily extracted from SNP array data, thus creating a disconnect between historic and new data sets. This study aimed to establish a method for deducing genotypes at loci of interest from their associated SNP haplotypes, demonstrated for two fruit crops and three locus types: quantitative trait loci Ma and Ma3 for acidity in apple, apple fingerprinting microsatellite marker GD12, and Mendelian trait locus Rf for sweet cherry fruit color. Using phased data from an apple 8K SNP array and sweet cherry 6K SNP array, unique haplotypes spanning each target locus were associated with alleles of important breeding parents. These haplotypes were compared via identity-by-descent (IBD) or identity-by-state (IBS) to haplotypes present in germplasm important to U.S. apple and cherry breeding programs to deduce target locus alleles in this germplasm. While IBD segments were confidently tracked through pedigrees, confidence in allele identity among IBS segments used a shared length threshold. At least one allele per locus was deduced for 64-93% of the 181 individuals. Successful validation compared deduced Rf and GD12 genotypes with reported and newly obtained genotypes. Our approach can efficiently merge and expand genotypic data sets, deducing missing data and identifying errors, and is appropriate for any crop with SNP array data and historic genotypic data sets, especially where linkage disequilibrium is high. Locus-specific genotypic information extracted from genome-wide SNP data is expected to enhance confidence in management of genetic resources.
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Affiliation(s)
- Alexander Schaller
- Department of Horticulture, Washington State University, Pullman, WA, United States of America
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA, United States of America
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA, United States of America
- * E-mail:
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11
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Rong H, Huang B, Han X, Wu K, Xu M, Zhang W, Yang F, Xu LA. Pedigree reconstruction and genetic analysis of major ornamental characters of ornamental crabapple (Malus spp.) based on paternity analysis. Sci Rep 2022; 12:14093. [PMID: 35982151 PMCID: PMC9388634 DOI: 10.1038/s41598-022-18352-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 08/10/2022] [Indexed: 11/09/2022] Open
Abstract
Ornamental crabapple is an important woody ornamental plant in the Northern Hemisphere. Its flowers, fruits, leaves and tree habit are all important ornamental characters. As there has been no research on the selection of superior parents and phenotypic variation, new varieties of ornamental crabapple are mainly selected from open-pollination progeny. In order to explore the transmission rule of ornamental traits between parents and offspring of crabapple, and to provide a basis for the selection of hybrid parents for directional breeding, 14 pairs of SSR markers were used in this study for paternity analysis of 384 offspring from 4 female parents crossed with 91 candidate male parents. And 273 offspring (71.1%) were matched with only the father at a 95% strict confidence level. We reconstructed 7 full-sib families (number of progeny ≥ 10) on the basis of the paternity analysis results. Genetic analysis of characters in the full-sib families revealed that green leaves and white flowers were dominant traits. All the hybrid offspring from the white flower (♀) × non-white flower (♂) cross produced white flowers, while 7.04% produced non-white flowers when both parents had white flowers. The results showed that white flowers might be a dominant qualitative trait in crabapple, while the depth of red was a quantitative trait. The genetic characteristics of green and non-green leaves and the depth of red of the peel were similar to flower color. Compared with the upright and spreading traits, the weeping trait was recessive. Some progeny showed an earlier blooming period, indicating the possibility of breeding for blooming period. Our findings are important for parent screening and improving the breeding efficiency of new varieties in ornamental crabapple hybridization.
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Affiliation(s)
- Hao Rong
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Bin Huang
- Jiangxi Provincial Key Laboratory of Camellia Germplasm Conservation and Utilization, Jiangxi Academy of Forestry, Nanchang, China
| | - Xin Han
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Kai Wu
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Meng Xu
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wangxiang Zhang
- College of Forestry, Nanjing Forestry University, Nanjing, China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Feng Yang
- Qingdao Municipal Supervision Consulting CO., LTD, Qingdao, China
| | - Li-An Xu
- College of Forestry, Nanjing Forestry University, Nanjing, China. .,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
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12
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Nishiyama S, Sato K, Tao R. Integer programming for selecting set of informative markers in paternity inference. BMC Bioinformatics 2022; 23:265. [PMID: 35804290 PMCID: PMC9264695 DOI: 10.1186/s12859-022-04801-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022] Open
Abstract
Background Parentage information is fundamental to various life sciences. Recent advances in sequencing technologies have made it possible to accurately infer parentage even in non-model species. The optimization of sets of genome-wide markers is valuable for cost-effective applications but requires extremely large amounts of computation, which presses for the development of new efficient algorithms. Results Here, for a closed half-sib population, we generalized the process of marker loci selection as a binary integer programming problem. The proposed systematic formulation considered marker localization and the family structure of the potential parental population, resulting in an accurate assignment with a small set of markers. We also proposed an efficient heuristic approach, which effectively improved the number of markers, localization, and tolerance to missing data of the set. Applying this method to the actual genotypes of apple (Malus × domestica) germplasm, we identified a set of 34 SNP markers that distinguished 300 potential parents crossed to a particular cultivar with a greater than 99% accuracy. Conclusions We present a novel approach for selecting informative markers based on binary integer programming. Since the data generated by high-throughput sequencing technology far exceeds the requirement for parentage assignment, a combination of the systematic marker selection with targeted SNP genotyping, such as KASP, allows flexibly enlarging the analysis up to a scale that has been unrealistic in various species. The method developed in this study can be directly applied to unsolved large-scale problems in breeding, reproduction, and ecological research, and is expected to lead to novel knowledge in various biological fields. The implementation is available at https://github.com/SoNishiyama/IP-SIMPAT. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04801-z.
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Affiliation(s)
| | - Kengo Sato
- School of System Design and Technology, Tokyo Denki University, Tokyo, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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13
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Jung M, Keller B, Roth M, Aranzana MJ, Auwerkerken A, Guerra W, Al-Rifaï M, Lewandowski M, Sanin N, Rymenants M, Didelot F, Dujak C, Font i Forcada C, Knauf A, Laurens F, Studer B, Muranty H, Patocchi A. Genetic architecture and genomic predictive ability of apple quantitative traits across environments. HORTICULTURE RESEARCH 2022; 9:uhac028. [PMID: 35184165 PMCID: PMC8976694 DOI: 10.1093/hr/uhac028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/09/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Implementation of genomic tools is desirable to increase the efficiency of apple breeding. Recently, the multi-environment apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic predictive ability, and studying genotype by environment interactions (G × E). So far, only two phenological traits were investigated using the apple REFPOP, although the population may be valuable when dissecting genetic architecture and reporting predictive abilities for additional key traits in apple breeding. Here we show contrasting genetic architecture and genomic predictive abilities for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic predictive abilities of 0.18-0.88 were estimated using main-effect univariate, main-effect multivariate, multi-environment univariate, and multi-environment multivariate models. The G × E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency.
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Affiliation(s)
- Michaela Jung
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Beat Keller
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Morgane Roth
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- GAFL, INRAE, 84140 Montfavet, France
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140 Caldes de Montbui, Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | | | | | - Mehdi Al-Rifaï
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Mariusz Lewandowski
- The National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | | | - Marijn Rymenants
- Better3fruit N.V., 3202 Rillaar, Belgium
- Laboratory for Plant Genetics and Crop Improvement, KU Leuven, B-3001 Leuven, Belgium
| | | | - Christian Dujak
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Carolina Font i Forcada
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140 Caldes de Montbui, Barcelona, Spain
| | - Andrea Knauf
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - François Laurens
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Hélène Muranty
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Andrea Patocchi
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
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14
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Howard NP, van de Weg E, Luby JJ. A new method to reconstruct the direction of parent-offspring duo relationships using SNP array data and its demonstration on ancient and modern cultivars in the outcrossing species malus × domestica. HORTICULTURE RESEARCH 2022; 9:uhab069. [PMID: 35043196 PMCID: PMC8881379 DOI: 10.1093/hr/uhab069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/17/2021] [Accepted: 10/28/2021] [Indexed: 06/14/2023]
Abstract
Unordered parent-offspring (PO) relationships are an outstanding issue in pedigree reconstruction studies. Resolution of the order of these relationships would expand the results, conclusions, and usefulness of such studies; however, no such PO order resolution (POR) tests currently exist. This study describes two such tests, demonstrated using SNP array data in the outcrossing species apple (Malus × domestica) on a PO relationship of known order ("Keepsake" as a parent of "Honeycrisp") and two PO relationships previously ordered only via provenance information. The first test, POR-1, tests whether some of the extended haplotypes deduced from homozygous SNP calls from one individual in an unordered PO duo are composed of recombinant haplotypes from accurately phased SNP genotypes from the second individual. If so, the first individual would be the offspring of the second individual, otherwise the opposite relationship would be present. The second test, POR-2, does not require phased SNP genotypes and uses similar logic as the POR-1 test, albeit in a different approach. The POR-1 and POR-2 tests determined the correct relationship between "Keepsake" and "Honeycrisp". The POR-2 test confirmed "Reinette Franche" as a parent of "Nonpareil" and "Brabant Bellefleur" as a parent of "Court Pendu Plat". The latter finding conflicted with the recorded provenance information, demonstrating the need for these tests. The successful demonstration of these tests suggests they can add insights to future pedigree reconstruction studies, though caveats, like extreme inbreeding or selfing, would need to be considered where relevant.
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Affiliation(s)
- Nicholas P Howard
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky University, Oldenburg, 26129 Germany
- Department of Horticultural Science, University of Minnesota, St. Paul, 55108 United States of America
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen, 6708 PB The Netherlands
| | - James J Luby
- Department of Horticultural Science, University of Minnesota, St. Paul, 55108 United States of America
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15
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Cazenave X, Petit B, Lateur M, Nybom H, Sedlak J, Tartarini S, Laurens F, Durel CE, Muranty H. Combining genetic resources and elite material populations to improve the accuracy of genomic prediction in apple. G3 (BETHESDA, MD.) 2021; 12:6459174. [PMID: 34893831 PMCID: PMC9210277 DOI: 10.1093/g3journal/jkab420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/29/2021] [Indexed: 11/12/2022]
Abstract
Genomic selection is an attractive strategy for apple breeding that could reduce the length of breeding cycles. A possible limitation to the practical implementation of this approach lies in the creation of a training set large and diverse enough to ensure accurate predictions. In this study, we investigated the potential of combining two available populations, i.e., genetic resources and elite material, in order to obtain a large training set with a high genetic diversity. We compared the predictive ability of genomic predictions within-population, across-population or when combining both populations, and tested a model accounting for population-specific marker effects in this last case. The obtained predictive abilities were moderate to high according to the studied trait and small increases in predictive ability could be obtained for some traits when the two populations were combined into a unique training set. We also investigated the potential of such a training set to predict hybrids resulting from crosses between the two populations, with a focus on the method to design the training set and the best proportion of each population to optimize predictions. The measured predictive abilities were very similar for all the proportions, except for the extreme cases where only one of the two populations was used in the training set, in which case predictive abilities could be lower than when using both populations. Using an optimization algorithm to choose the genotypes in the training set also led to higher predictive abilities than when the genotypes were chosen at random. Our results provide guidelines to initiate breeding programs that use genomic selection when the implementation of the training set is a limitation.
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Affiliation(s)
- Xabi Cazenave
- Univ Angers, INRAE, Institut Agro, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Bernard Petit
- Univ Angers, INRAE, Institut Agro, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Marc Lateur
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Hilde Nybom
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | - Jiri Sedlak
- Výzkumný a Šlechtitelský ústav Ovocnářský Holovousy s.r.o, Holovousy, Czech Republic
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - François Laurens
- Univ Angers, INRAE, Institut Agro, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Charles-Eric Durel
- Univ Angers, INRAE, Institut Agro, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Hélène Muranty
- Univ Angers, INRAE, Institut Agro, IRHS, SFR QuaSaV, F-49000 Angers, France,Corresponding author:
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16
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Barreneche T, Cárcamo de la Concepción M, Blouin-Delmas M, Ordidge M, Nybom H, Lacis G, Feldmane D, Sedlak J, Meland M, Kaldmäe H, Kahu K, Békefi Z, Stanivuković S, Đurić G, Höfer M, Galik M, Schüller E, Spornberger A, Sirbu S, Drogoudi P, Agulheiro-Santos AC, Kodad O, Vokurka A, Lateur M, Fernández Fernández F, Giovannini D, Quero-García J. SSR-Based Analysis of Genetic Diversity and Structure of Sweet Cherry ( Prunus avium L.) from 19 Countries in Europe. PLANTS 2021; 10:plants10101983. [PMID: 34685793 PMCID: PMC8540667 DOI: 10.3390/plants10101983] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022]
Abstract
Sweet cherry (Prunus avium L.) is a temperate fruit species whose production might be highly impacted by climate change in the near future. Diversity of plant material could be an option to mitigate these climate risks by enabling producers to have new cultivars well adapted to new environmental conditions. In this study, subsets of sweet cherry collections of 19 European countries were genotyped using 14 SSR. The objectives of this study were (i) to assess genetic diversity parameters, (ii) to estimate the levels of population structure, and (iii) to identify germplasm redundancies. A total of 314 accessions, including landraces, early selections, and modern cultivars, were monitored, and 220 unique SSR genotypes were identified. All 14 loci were confirmed to be polymorphic, and a total of 137 alleles were detected with a mean of 9.8 alleles per locus. The average number of alleles (N = 9.8), PIC value (0.658), observed heterozygosity (Ho = 0.71), and expected heterozygosity (He = 0.70) were higher in this study compared to values reported so far. Four ancestral populations were detected using STRUCTURE software and confirmed by Principal Coordinate Analysis (PCoA), and two of them (K1 and K4) could be attributed to the geographical origin of the accessions. A N-J tree grouped the 220 sweet cherry accessions within three main clusters and six subgroups. Accessions belonging to the four STRUCTURE populations roughly clustered together. Clustering confirmed known genealogical data for several accessions. The large genetic diversity of the collection was demonstrated, in particular within the landrace pool, justifying the efforts made over decades for their conservation. New sources of diversity will allow producers to face challenges, such as climate change and the need to develop more sustainable production systems.
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Affiliation(s)
- Teresa Barreneche
- INRAE, University of Bordeaux, UMR BFP, 33882 Villenave d’Ornon, France;
| | | | - Marine Blouin-Delmas
- INRAE, Unité Expérimentale Arboricole, Domaine de la Tour de Rance, 47320 Bourran, France;
| | - Matthew Ordidge
- Department of Crop Science, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK;
| | - Hilde Nybom
- Balsgård-Department of Plant Breeding, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, 29194 Kristianstad, Sweden;
| | - Gunars Lacis
- Institute of Horticulture, Graudu 1, LV-3701 Dobele, Latvia; (G.L.); (D.F.)
| | - Daina Feldmane
- Institute of Horticulture, Graudu 1, LV-3701 Dobele, Latvia; (G.L.); (D.F.)
| | - Jiri Sedlak
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, 508 01 Hořice, Czech Republic;
| | - Mekjell Meland
- NIBIO Ullensvang, The Norwegian Institute of Bioeconomy Research, Ullensvangvegen 1005, N-5781 Lofthus, Norway;
| | - Hedi Kaldmäe
- Polli Horticultural Research Centre, Institute of Agricultural and Environmental Sciences, Uus 2, 69108 Polli, Estonia; (H.K.); (K.K.)
| | - Kersti Kahu
- Polli Horticultural Research Centre, Institute of Agricultural and Environmental Sciences, Uus 2, 69108 Polli, Estonia; (H.K.); (K.K.)
| | - Zsuzsanna Békefi
- National Agricultural Research and Innovation Centre Gödöllő, H-1223 Budapest, Hungary;
| | - Sanda Stanivuković
- Institute for Genetic Resources, University of Banja Luka, Bulevar vojvode Petra Bojovica 1A, 78000 Banja Luka, Bosnia and Herzegovina; (S.S.); (G.Đ.)
| | - Gordana Đurić
- Institute for Genetic Resources, University of Banja Luka, Bulevar vojvode Petra Bojovica 1A, 78000 Banja Luka, Bosnia and Herzegovina; (S.S.); (G.Đ.)
| | - Monika Höfer
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Julius Kühn Institute, Pillnitzer Platz 3a, 01326 Dresden, Germany;
| | - Martin Galik
- NPPC, Výskumný ústav Rastlinnej Výroby–VÚRV, Research Institute of Plant Production–RIPP, Bratislavská 122, 921 68 Piešťany, Slovakia;
| | - Elisabeth Schüller
- Division of Viticulture and Pomology, University of Natural Resources and Life Sciences, Vienna Gregor-Mendel-Strasse 33, 1180 Vienna, Austria; (E.S.); (A.S.)
| | - Andreas Spornberger
- Division of Viticulture and Pomology, University of Natural Resources and Life Sciences, Vienna Gregor-Mendel-Strasse 33, 1180 Vienna, Austria; (E.S.); (A.S.)
| | - Sorina Sirbu
- Research Station for Fruit Growing, 175 Voinesti, RO707305 Iasi, Romania;
| | - Pavlina Drogoudi
- Hellenic Agricultural Organization ‘DEMETER’, Department of Deciduous Fruit Trees, Institute of Plant Breeding and Genetic Resources, 38 RR Station, 59200 Naoussa, Greece;
| | - Ana Cristina Agulheiro-Santos
- Mediterranean Institute for Agriculture, Environment and Development & Departamento de Fitotecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - Ossama Kodad
- Département Arboriculture Arboriculture Fruitière Viticulture Ecole Nationale d’Agriculture de Meknès, B.P. S/40, Meknès 50000, Morocco;
| | - Aleš Vokurka
- Department for Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Svetošimunska 25, HR-10000 Zagreb, Croatia;
| | - Marc Lateur
- CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4-5030 Gembloux, Belgium;
| | | | - Daniela Giovannini
- CREA-Research Centre for Olive, Fruit and Citrus Crops, via la Canapona 1 bis, 47121 Forlì, Italy;
| | - José Quero-García
- INRAE, University of Bordeaux, UMR BFP, 33882 Villenave d’Ornon, France;
- Correspondence:
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17
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Howard NP, Peace C, Silverstein KAT, Poets A, Luby JJ, Vanderzande S, Durel CE, Muranty H, Denancé C, van de Weg E. The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry. HORTICULTURE RESEARCH 2021; 8:202. [PMID: 34465774 PMCID: PMC8408172 DOI: 10.1038/s41438-021-00637-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/05/2021] [Accepted: 07/17/2021] [Indexed: 05/29/2023]
Abstract
Pedigree information is of fundamental importance in breeding programs and related genetics efforts. However, many individuals have unknown pedigrees. While methods to identify and confirm direct parent-offspring relationships are routine, those for other types of close relationships have yet to be effectively and widely implemented with plants, due to complications such as asexual propagation and extensive inbreeding. The objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes (referred to in this study as "summed potential lengths of shared haplotypes", SPLoSH). A custom Python script, HapShared, was developed to generate SPLoSH data in apple and sweet cherry. HapShared was used to establish empirical distributions of SPLoSH data for known relationships in these crops. These distributions were then used to estimate previously unknown relationships. Case studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH data. For cherry, a full-sib relationship was deduced for 'Emperor Francis, and 'Schmidt', a half-sib relationship for 'Van' and 'Windsor', and the paternal grandparents of 'Stella' were confirmed. For apple, 29 cultivars were found to share an unknown parent, the pedigree of the unknown parent of 'Cox's Pomona' was reconstructed, and 'Fameuse' was deduced to be a likely grandparent of 'McIntosh'. Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets, integrated genetic maps, and previously identified pedigree relationships. Crops with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.
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Affiliation(s)
- Nicholas P Howard
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky University, Oldenburg, Germany.
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, USA.
| | - Cameron Peace
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, WA, USA.
| | | | - Ana Poets
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - James J Luby
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, USA
| | - Stijn Vanderzande
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, WA, USA
| | - Charles-Eric Durel
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207, QuaSaV, Beaucouzé, France
| | - Hélène Muranty
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207, QuaSaV, Beaucouzé, France
| | - Caroline Denancé
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207, QuaSaV, Beaucouzé, France
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
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18
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Pincot DDA, Ledda M, Feldmann MJ, Hardigan MA, Poorten TJ, Runcie DE, Heffelfinger C, Dellaporta SL, Cole GS, Knapp SJ. Social network analysis of the genealogy of strawberry: retracing the wild roots of heirloom and modern cultivars. G3-GENES GENOMES GENETICS 2021; 11:6117203. [PMID: 33772307 PMCID: PMC8022721 DOI: 10.1093/g3journal/jkab015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/12/2020] [Indexed: 01/22/2023]
Abstract
The widely recounted story of the origin of cultivated strawberry (Fragaria × ananassa) oversimplifies the complex interspecific hybrid ancestry of the highly admixed populations from which heirloom and modern cultivars have emerged. To develop deeper insights into the three-century-long domestication history of strawberry, we reconstructed the genealogy as deeply as possible—pedigree records were assembled for 8,851 individuals, including 2,656 cultivars developed since 1775. The parents of individuals with unverified or missing pedigree records were accurately identified by applying an exclusion analysis to array-genotyped single-nucleotide polymorphisms. We identified 187 wild octoploid and 1,171 F. × ananassa founders in the genealogy, from the earliest hybrids to modern cultivars. The pedigree networks for cultivated strawberry are exceedingly complex labyrinths of ancestral interconnections formed by diverse hybrid ancestry, directional selection, migration, admixture, bottlenecks, overlapping generations, and recurrent hybridization with common ancestors that have unequally contributed allelic diversity to heirloom and modern cultivars. Fifteen to 333 ancestors were predicted to have transmitted 90% of the alleles found in country-, region-, and continent-specific populations. Using parent–offspring edges in the global pedigree network, we found that selection cycle lengths over the past 200 years of breeding have been extraordinarily long (16.0-16.9 years/generation), but decreased to a present-day range of 6.0-10.0 years/generation. Our analyses uncovered conspicuous differences in the ancestry and structure of North American and European populations, and shed light on forces that have shaped phenotypic diversity in F. × ananassa.
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Affiliation(s)
- Dominique D A Pincot
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mirko Ledda
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Thomas J Poorten
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Daniel E Runcie
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Stephen L Dellaporta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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19
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Ordidge M, Litthauer S, Venison E, Blouin-Delmas M, Fernandez-Fernandez F, Höfer M, Kägi C, Kellerhals M, Marchese A, Mariette S, Nybom H, Giovannini D. Towards a Joint International Database: Alignment of SSR Marker Data for European Collections of Cherry Germplasm. PLANTS (BASEL, SWITZERLAND) 2021; 10:1243. [PMID: 34207415 PMCID: PMC8235247 DOI: 10.3390/plants10061243] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022]
Abstract
The objective of our study was the alignment of microsatellite or simple sequence repeat (SSR) marker data across germplasm collections of cherry within Europe. Through the European Cooperative program for Plant Genetic Resources ECPGR, a number of European germplasm collections had previously been analysed using standard sets of SSR loci. However, until now these datasets remained unaligned. We used a combination of standard reference genotypes and ad-hoc selections to compile a central dataset representing as many alleles as possible from national datasets produced in France, Great Britain, Germany, Italy, Sweden and Switzerland. Through the comparison of alleles called in data from replicated samples we were able to create a series of alignment factors, supported across 448 different allele calls, that allowed us to align a dataset of 2241 SSR profiles from six countries. The proportion of allele comparisons that were either in agreement with the alignment factor or confounded by null alleles ranged from 67% to 100% and this was further improved by the inclusion of a series of allele-specific adjustments. The aligned dataset allowed us to identify groups of previously unknown matching accessions and to identify and resolve a number of errors in the prior datasets. The combined and aligned dataset represents a significant step forward in the co-ordinated management of field collections of cherry in Europe.
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Affiliation(s)
- Matthew Ordidge
- Department of Crop Science, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK;
| | - Suzanne Litthauer
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, UK; (S.L.); (F.F.-F.)
| | - Edward Venison
- Department of Crop Science, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK;
| | - Marine Blouin-Delmas
- INRAE-Unité Expérimentale Arboricole, Domaine de la Tour de Rance, 47320 Bourran, France;
| | | | - Monika Höfer
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Julius Kühn Institute, Pillnitzer Platz 3a, 01326 Dresden, Germany;
| | - Christina Kägi
- Federal Office for Agriculture, Genetic Resources and Technologies, Schwarzenburgstrasse 165, 3003 Bern, Switzerland;
| | - Markus Kellerhals
- Agroscope, Strategic Research Division Plant Breeding, Müller-Thurgau-Str. 29, 8820 Wädenswil, Switzerland;
| | - Annalisa Marchese
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze-Ed. 4, 90128 Palermo, Italy;
| | - Stephanie Mariette
- BIOGECO, INRAE, University of Bordeaux, Route d’Arcachon 69, 33612 Cestas, France;
| | - Hilde Nybom
- Balsgård-Department of Plant Breeding, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, 29194 Kristianstad, Sweden;
| | - Daniela Giovannini
- CREA-Research Centre for Olive, Fruit and Citrus Crops, via la Canapona 1 bis, 47121 Forlì, Italy;
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20
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Evaluation of Scab and Mildew Resistance in the Gene Bank Collection of Apples in Dresden-Pillnitz. PLANTS 2021; 10:plants10061227. [PMID: 34208651 PMCID: PMC8234245 DOI: 10.3390/plants10061227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/09/2021] [Accepted: 06/12/2021] [Indexed: 11/18/2022]
Abstract
A set of 680 apple cultivars from the Fruit Gene bank in Dresden Pillnitz was evaluated for the incidence of powdery mildew and scab in two consecutive years. The incidence of both scab and powdery mildew increased significantly in the second year. Sixty and 43 cultivars with very low incidence in both years of scab and powdery mildew, respectively, were analysed with molecular markers linked to known resistance genes. Thirty-five cultivars were identified to express alleles or combinations of alleles linked to Rvi2, Rvi4, Rvi6, Rvi13, Rvi14, or Rvi17. Twenty of them, modern as well as a few traditional cultivars known before the introduction or Rvi6 from Malus floribunda 821, amplified the 159 bp fragment of marker CH_Vf1 that is linked to Rvi6. Alleles linked to Pl1, Pld, or Plm were expressed from five cultivars resistant to powdery mildew. Eleven cultivars were identified to have very low susceptibility to both powdery mildew and scab. The information on resistance/susceptibility of fruit genetic resources towards economically important diseases is important for breeding and for replanting traditional cultivars. Furthermore, our work provides a well-defined basis for the discovery of undescribed, new scab, and powdery mildew resistance.
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21
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Howard NP, Troggio M, Durel CE, Muranty H, Denancé C, Bianco L, Tillman J, van de Weg E. Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls. BMC Genomics 2021; 22:246. [PMID: 33827434 PMCID: PMC8028180 DOI: 10.1186/s12864-021-07565-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/30/2021] [Indexed: 11/23/2022] Open
Abstract
Background Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel data, a need to integrate data from different arrays and array platforms has arisen. This study was undertaken in view of our need for an integrated high-quality dataset of Illumina Infinium® 20 K and Affymetrix Axiom® 480 K SNP array data in apple (Malus × domestica). In this study, we qualify and quantify the compatibility of SNP calling, defined as SNP calls that are both accurate and concordant, across both arrays by two approaches. First, the concordance of SNP calls was evaluated using a set of 417 duplicate individuals genotyped on both arrays starting from a set of 10,295 robust SNPs on the Infinium array. Next, the accuracy of the SNP calls was evaluated on additional germplasm (n = 3141) from both arrays using Mendelian inconsistent and consistent errors across thousands of pedigree links. While performing this work, we took the opportunity to evaluate reasons for probe failure and observed discordant SNP calls. Results Concordance among the duplicate individuals was on average of 97.1% across 10,295 SNPs. Of these SNPs, 35% had discordant call(s) that were further curated, leading to a final set of 8412 (81.7%) SNPs that were deemed compatible. Compatibility was highly influenced by the presence of alternate probe binding locations and secondary polymorphisms. The impact of the latter was highly influenced by their number and proximity to the 3′ end of the probe. Conclusions The Infinium and Axiom SNP array data were mostly compatible. However, data integration required intense data filtering and curation. This work resulted in a workflow and information that may be of use in other data integration efforts. Such an in-depth analysis of array concordance and accuracy as ours has not been previously described in the literature and will be useful in future work on SNP array data integration and interpretation, and in probe/platform development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07565-7.
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Affiliation(s)
- Nicholas P Howard
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Univ., Oldenburg, Germany.,Department of Horticultural Science, Univ. of Minnesota, St Paul, USA
| | | | - Charles-Eric Durel
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, Beaucouzé, France
| | - Hélène Muranty
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, Beaucouzé, France
| | - Caroline Denancé
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, Beaucouzé, France
| | - Luca Bianco
- Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - John Tillman
- Department of Horticultural Science, Univ. of Minnesota, St Paul, USA
| | - Eric van de Weg
- Department of Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
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22
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Wedger MJ, Schumann AC, Gross BL. Candidate genes and signatures of directional selection on fruit quality traits during apple domestication. AMERICAN JOURNAL OF BOTANY 2021; 108:616-627. [PMID: 33837962 DOI: 10.1002/ajb2.1636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
PREMISE During plant domestication, traits can be subject to a variety of types of selection, ranging from strong directional selection for traits such as seed or fruit size to diversifying selection for traits like color or flavor. These types of selection interact with other evolutionary processes including genetic bottlenecks and interspecific gene flow to generate different levels of genetic diversity across the genome and at target genes in domesticated lineages, but little is known about the impacts of these processes in perennial fruit crops. METHODS We used sequence capture by hybridization to examine patterns of diversity at a suite of candidate domestication and anonymous background genes in domesticated apple (Malus ×domestica) in comparison to its wild relatives Malus sieversii and Malus orientalis. RESULTS We found no change in average diversity at these candidate domestication genes across the three species. However, a subset of the genes did exhibit patterns of very high or very low diversity in M. ×domestica compared to its progenitor, M. sieversii. Of the genes with characterized function, the low-diversity genes mainly contributed to fruit quality traits like color and flavor, predicted to be under conscious, directional selection relatively late in the domestication process, while the high-diversity genes included a variety of functions. CONCLUSIONS Overall, these results are consistent with predictions based on the likely timing and nature of selection during domestication and open new avenues for understanding genes with high diversity in a perennial crop compared to its wild relatives.
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Affiliation(s)
- Marshall J Wedger
- Department of Biology, Washington University, Campus Box 1137, St. Louis, MO, 63130, USA
| | - Abby C Schumann
- Minnesota Poultry Testing Laboratory, P.O. Box 126, 622 Bus. Hwy 71 NE, Wilmar, MN, 56201, USA
| | - Briana L Gross
- Department of Biology, University of Minnesota Duluth, 207 Swenson Science Building, 1035 Kirby Drive, Duluth, MN, 55812, USA
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23
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Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops. PLANTS 2021; 10:plants10020415. [PMID: 33672381 PMCID: PMC7926561 DOI: 10.3390/plants10020415] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.
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24
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Cmejlova J, Rejlova M, Paprstein F, Cmejla R. A new one-tube reaction kit for the SSR genotyping of apple (Malus × domestica Borkh.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110768. [PMID: 33487353 DOI: 10.1016/j.plantsci.2020.110768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Though apple genotyping is mainly used for scientific and breeding purposes, it can also be adopted by national authorities to control the authenticity of apple cultivars. To facilitate the introduction of routine apple genotyping into practice, a new apple simple sequence repeat (SSR) genotyping kit was developed (called the Ap17 in. SSR Genotyping Kit). The kit combines 17 SSR markers including those recommended by the Working Group of the European Cooperative Programme for Plant Genetic Resources (ECPGR), covering all apple linkage groups in a one-tube reaction format, using a fragment analysis method to simplify the genotyping procedure. The kit was successfully tested using 880 unique diploid apple germplasm accessions; the kit can also readily discriminate triploid and tetraploid samples. The total probability of identity for the kit and the sample collection used was calculated to be 1.73 × 10-22. Tables for converting results to enable genotype comparisons between currently-used genotyping systems and the Ap17 in. kit are provided. The kit is ideally suited for validation in laboratories genotyping a large number of apple samples, saving time, costs, and labor, while minimizing technical and human errors.
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Affiliation(s)
- Jana Cmejlova
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 508 01 Horice, Czech Republic
| | - Martina Rejlova
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 508 01 Horice, Czech Republic
| | - Frantisek Paprstein
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 508 01 Horice, Czech Republic
| | - Radek Cmejla
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 508 01 Horice, Czech Republic.
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25
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Migicovsky Z, Gardner KM, Richards C, Thomas Chao C, Schwaninger HR, Fazio G, Zhong GY, Myles S. Genomic consequences of apple improvement. HORTICULTURE RESEARCH 2021; 8:9. [PMID: 33384408 PMCID: PMC7775473 DOI: 10.1038/s41438-020-00441-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/09/2020] [Indexed: 05/10/2023]
Abstract
The apple (Malus domestica) is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years. Here, we genetically characterise over 1000 apple accessions from the United States Department of Agriculture (USDA) germplasm collection using over 30,000 single-nucleotide polymorphisms (SNPs). We confirm the close genetic relationship between modern apple cultivars and their primary progenitor species, Malus sieversii from Central Asia, and find that cider apples derive more of their ancestry from the European crabapple, Malus sylvestris, than do dessert apples. We determine that most of the USDA collection is a large complex pedigree: over half of the collection is interconnected by a series of first-degree relationships. In addition, 15% of the accessions have a first-degree relationship with one of the top 8 cultivars produced in the USA. With the exception of 'Honeycrisp', the top 8 cultivars are interconnected to each other via pedigree relationships. The cultivars 'Golden Delicious' and 'Red Delicious' were found to have over 60 first-degree relatives, consistent with their repeated use by apple breeders. We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased firmness. Our results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will benefit from increased exploitation of its tremendous natural genetic diversity.
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Affiliation(s)
- Zoë Migicovsky
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Kyle M Gardner
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, Fredericton, NB, Canada
| | | | - C Thomas Chao
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, USA
| | | | - Gennaro Fazio
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, USA
| | - Gan-Yuan Zhong
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, USA.
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.
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26
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Pérez de Los Cobos F, Martínez-García PJ, Romero A, Miarnau X, Eduardo I, Howad W, Mnejja M, Dicenta F, Socias I Company R, Rubio-Cabetas MJ, Gradziel TM, Wirthensohn M, Duval H, Holland D, Arús P, Vargas FJ, Batlle I. Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars. HORTICULTURE RESEARCH 2021; 8:11. [PMID: 33384415 PMCID: PMC7775440 DOI: 10.1038/s41438-020-00444-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/04/2020] [Accepted: 11/13/2020] [Indexed: 05/16/2023]
Abstract
Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. However, in almond, little is known about the genetic variability in current breeding stocks, although several cases of inbreeding depression have been reported. To gain insights into the genetic structure in modern breeding programs worldwide, marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed. Inbreeding coefficients, pairwise relatedness, and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars: "Tuono", "Cristomorto", and "Nonpareil". Descendants from "Tuono" or "Cristomorto" number 76 (sharing 34 descendants), while "Nonpareil" has 71 descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.041, with 14 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from France, the USA, and Spain showed inbreeding coefficients of 0.075, 0.070, and 0.037, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain, and Australia trace back to a maximum of six main founding genotypes. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.125, with "Tuono" as the main founding genotype (24.7% of total genetic contribution). The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide. Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.
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Affiliation(s)
- Felipe Pérez de Los Cobos
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8, 43120, Constantí, Tarragona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Pedro J Martínez-García
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), P.O. Box 164, 30100, Espinardo, Murcia, Spain
| | - Agustí Romero
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8, 43120, Constantí, Tarragona, Spain
| | - Xavier Miarnau
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Fruitcentre, PCiTAL, Gardeny Park, Fruitcentre Building, 25003, Lleida, Spain
| | - Iban Eduardo
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Werner Howad
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Mourad Mnejja
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Federico Dicenta
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), P.O. Box 164, 30100, Espinardo, Murcia, Spain
| | - Rafel Socias I Company
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059, Zaragoza, Instituto Agroalimentario de Aragón IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Maria J Rubio-Cabetas
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059, Zaragoza, Instituto Agroalimentario de Aragón IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | | | - Michelle Wirthensohn
- University of Adelaide, Waite Research, School of Agriculture, Food and Wine, PMB 1, Glen Osmond, Adelaide, SA, 5064, Australia
| | - Henri Duval
- Institut National de la Recherche Agronomique (INRA), Domain St. Maurice CS 60094, 84143, Montfavet Cedex, France
| | - Doron Holland
- Agricultural Research Organization, Newe-Ya'ar Research Center, P.O. Box 1021, Ramat Yishad, 30095, Israel
| | - Pere Arús
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB. Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Francisco J Vargas
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8, 43120, Constantí, Tarragona, Spain
| | - Ignasi Batlle
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Mas Bové, Ctra. Reus-El Morell Km 3,8, 43120, Constantí, Tarragona, Spain.
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27
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Christodoulou MD, Culham A. Apples before the fall: Does shape stability coincide with maturity? QUANTITATIVE PLANT BIOLOGY 2021; 2:e5. [PMID: 37077215 PMCID: PMC10095885 DOI: 10.1017/qpb.2021.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 05/03/2023]
Abstract
Fruit shape is the result of the interaction between genetic, epigenetic, environmental factors and stochastic processes. As a core biological descriptor both for taxonomy and horticulture, the point at which shape stability is reached becomes paramount in apple cultivar identification, and authentication in commerce. Twelve apple cultivars were sampled at regular intervals from anthesis to harvest over two growing seasons. Linear and geometric morphometrics were analysed to establish if and when shape stabilised and whether fruit asymmetry influenced this. Shape stability was detected in seven cultivars, four asymmetric and three symmetric. The remaining five did not stabilise. Shape stability, as defined here, is cultivar-dependent, and when it occurs, it is late in the growing season. Geometric morphometrics detected stability more readily than linear, especially in symmetric cultivars. Key shape features are important in apple marketing, giving the distinctness and apparent uniformity between cultivars expected at point of sale.
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Affiliation(s)
- Maria D. Christodoulou
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- University of Reading Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom
- Authors for correspondence: M. D. Christodoulou, E-mail: ; and Alastair Culham, E-mail:
| | - Alastair Culham
- University of Reading Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom
- Authors for correspondence: M. D. Christodoulou, E-mail: ; and Alastair Culham, E-mail:
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28
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Winfield M, Burridge A, Ordidge M, Harper H, Wilkinson P, Thorogood D, Copas L, Edwards K, Barker G. Development of a minimal KASP marker panel for distinguishing genotypes in apple collections. PLoS One 2020; 15:e0242940. [PMID: 33253289 PMCID: PMC7703965 DOI: 10.1371/journal.pone.0242940] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/11/2020] [Indexed: 11/23/2022] Open
Abstract
Accurate identification of named accessions in germplasm collections is extremely important, especially for vegetatively propagated crops which are expensive to maintain. Thus, an inexpensive, reliable, and rapid genotyping method is essential because it avoids the need for laborious and time-consuming morphological comparisons. Single Nucleotide Polymorphism (SNP) marker panels containing large numbers of SNPs have been developed for many crop species, but such panels are much too large for basic cultivar identification. Here, we have identified a minimum set of SNP markers sufficient to distinguish apple cultivars held in the English and Welsh national collections providing a cheaper and automatable alternative to the markers currently used by the community. We show that SNP genotyping with a small set of well selected markers is equally efficient as microsatellites for the identification of apple cultivars and has the added advantage of automation and reduced cost when screening large numbers of samples.
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Affiliation(s)
- Mark Winfield
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
- * E-mail:
| | - Amanda Burridge
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Helen Harper
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Paul Wilkinson
- Department of Functional and Comparative Genomics, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Danny Thorogood
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Liz Copas
- Lullingstone, Fore Street, Winsham, Somerset, United Kingdom
| | - Keith Edwards
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Gary Barker
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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29
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Wang X, Shen F, Gao Y, Wang K, Chen R, Luo J, Yang L, Zhang X, Qiu C, Li W, Wu T, Xu X, Wang Y, Cong P, Han Z, Zhang X. Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus accessions. BMC PLANT BIOLOGY 2020; 20:540. [PMID: 33256591 PMCID: PMC7708918 DOI: 10.1186/s12870-020-02744-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Apple (Malus ssp.), one of the most important temperate fruit crops, has a long cultivation history and is economically important. To identify the genetic relationships among the apple germplasm accessions, whole-genome structural variants identified between M. domestica cultivars 'Jonathan' and 'Golden Delicious' were used. RESULTS A total of 25,924 insertions and deletions (InDels) were obtained, from which 102 InDel markers were developed. Using the InDel markers, we found that 942 (75.3%) of the 1251 Malus accessions from 35 species exhibited a unique identity signature due to their distinct genotype combinations. The 102 InDel markers could distinguish 16.7-71.4% of the 331 bud sports derived from 'Fuji', 'Red Delicious', 'Gala', 'Golden Delicious', and other cultivars. Five distinct genetic patterns were found in 1002 diploid accessions based on 78 bi-allele InDel markers. Genetic structure analysis indicated that M. domestica showed higher genetic diversity than the other species. Malus underwent a relatively high level of wild-to-crop or crop-to-wild gene flow. M. sieversii was closely related to both M. domestica and cultivated Chinese cultivars. CONCLUSIONS The identity signatures of Malus accessions can be used to determine distinctness, uniformity, and stability. The results of this study may also provide better insight into the genetic relationships among Malus species.
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Affiliation(s)
- Xuan Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yuan Gao
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Kun Wang
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Ruiting Chen
- College of Horticulture, China Agricultural University, Beijing, China
- Present Address: Shaanxi Haisheng Fruit Industry Development Co., Ltd., Shaanxi, Xian, China
| | - Jun Luo
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Lili Yang
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Xi Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Changpeng Qiu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Wei Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Peihua Cong
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China.
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Jung M, Roth M, Aranzana MJ, Auwerkerken A, Bink M, Denancé C, Dujak C, Durel CE, Font I Forcada C, Cantin CM, Guerra W, Howard NP, Keller B, Lewandowski M, Ordidge M, Rymenants M, Sanin N, Studer B, Zurawicz E, Laurens F, Patocchi A, Muranty H. The apple REFPOP-a reference population for genomics-assisted breeding in apple. HORTICULTURE RESEARCH 2020; 7:189. [PMID: 33328447 PMCID: PMC7603508 DOI: 10.1038/s41438-020-00408-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/25/2020] [Accepted: 09/06/2020] [Indexed: 05/16/2023]
Abstract
Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates. Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs, and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions. Here we present an apple reference population: the apple REFPOP, a large collection formed of 534 genotypes planted in six European countries, as a unique tool to accelerate apple breeding. The population consisted of 269 accessions and 265 progeny from 27 parental combinations, representing the diversity in cultivated apple and current European breeding material, respectively. A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95. Based on the genotypic data, linkage disequilibrium was low and population structure was weak. Two well-studied phenological traits of horticultural importance were measured. We found marker-trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date, respectively. With decreasing SNP density, the detection of significant marker-trait associations varied depending on trait architecture. Regardless of the trait, 10,000 SNPs sufficed to maximize genomic prediction ability. We confirm the suitability of the apple REFPOP design for genomics-assisted breeding, especially for breeding programs using related germplasm, and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.
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Affiliation(s)
- Michaela Jung
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | - Morgane Roth
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
- GAFL, INRAE, 84140, Montfavet, France
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | | | - Marco Bink
- Biometris, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Hendrix Genetics Research, Technology and Services B.V., PO Box 114, 5830AC, Boxmeer, The Netherlands
| | - Caroline Denancé
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Christian Dujak
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Charles-Eric Durel
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Carolina Font I Forcada
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Celia M Cantin
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
- ARAID (Fundación Aragonesa para la Investigación y el Desarrollo), 50018, Zaragoza, Spain
| | | | - Nicholas P Howard
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA
- Institute of Biology and Environmental Sciences, University of Oldenburg, 26129, Oldenburg, Germany
| | - Beat Keller
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | | | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, RG6 6AR, Reading, UK
| | - Marijn Rymenants
- Better3fruit N.V., 3202, Rillaar, Belgium
- Biometris, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Laboratory for Plant Genetics and Crop Improvement, KU Leuven, B-3001, Leuven, Belgium
| | - Nadia Sanin
- Research Centre Laimburg, 39040, Auer, Italy
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Edward Zurawicz
- Research Institute of Horticulture, 96-100, Skierniewice, Poland
| | - François Laurens
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Andrea Patocchi
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | - Hélène Muranty
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France.
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Reconstruction of the Largest Pedigree Network for Pear Cultivars and Evaluation of the Genetic Diversity of the USDA-ARS National Pyrus Collection. G3-GENES GENOMES GENETICS 2020; 10:3285-3297. [PMID: 32675069 PMCID: PMC7466967 DOI: 10.1534/g3.120.401327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, maintains one of the world's largest and most diverse living Pyrus collection. A thorough genetic characterization of this germplasm will provide relevant information to optimize the conservation strategy of pear biodiversity, support the use of this germplasm in breeding, and increase our knowledge of Pyrus taxonomy, evolution, and domestication. In the last two decades simple sequence repeat (SSR) markers have been used at the NCGR for cultivar identification and small population structure analysis. However, the recent development of the Applied Biosystems Axiom Pear 70K Genotyping Array has allowed high-density single nucleotide polymorphism (SNP)-based genotyping of almost the entire collection. In this study, we have analyzed this rich dataset to discover new synonyms and mutants, identify putative labeling errors in the collection, reconstruct the largest pear cultivar pedigree and further elucidate the genetic diversity of Pyrus.
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32
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Gross BL. How the apple escaped cultivation in North America. Mol Ecol 2020; 29:1761-1763. [PMID: 32338794 DOI: 10.1111/mec.15456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/13/2020] [Accepted: 04/16/2020] [Indexed: 11/29/2022]
Abstract
Domesticated plants have been transported around the globe through their association with humans and have undergone changes in response to their new environments. In many regions, farmers and, later, plant breeders have developed local landraces to deal with the new conditions or to satisfy the culinary needs of consumers, showing the versatility of these plants and the ingenuity of plant breeders, both ancient and modern. However, in some cases, plants leave behind their human associations and become feral in either the crop fields or natural landscape of the new region. The evolution of ferality has been studied in some crop systems, with many advances made in our understanding of annual crop ferality (e.g., Burger, Lee, & Ellstrand, 2006; Hegde et al., 2006). In contrast, very little is known about the genetics of feral perennial crops, and the study by Cronin, Kron, and Husband (2020) in this issue of Molecular Ecology sheds new light on this type of evolution, revealing the remarkable ability of domesticated apple (Malus domestica) to thrive and reproduce in North America without genetic input from local species.
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Affiliation(s)
- Briana L Gross
- Biology Department, University of Minnesota Duluth, Duluth, MN, USA
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