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The apple REFPOP—a reference population for genomics-assisted breeding in apple

Michaela Jung 1 Morgane Roth 2, 3 Maria José Aranzana 4 Annemarie Auwerkerken 5 Marco Bink 6, 7 Caroline Denancé 8 Christian Dujak 9 Charles-Eric Durel 8 Carolina Font I Forcada 4 Celia Cantin 4, 10 Walter Guerra 11 Nicholas Howard 12, 13 Beat Keller 1 Mariusz Lewandowski 14 Matthew Ordidge 15 Marijn Rymenants 5, 16 Nadia Sanin 11 Bruno Studer 1 Edward Zurawicz 14 François Laurens 8 Andrea Patocchi 2 Hélène Muranty 8
1 ETH Zürich - Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich]
2 ACW - Agroscope Changins-Wädenswil, Swiss Federal Research Station, Plant Protection Division
3 GAFL - Génétique et Amélioration des Fruits et Légumes
4 IRTA - Institute of Agrifood Research and Technology [Sant Carles de la Ràpita]
5 Better3Fruit N.V.
6 WUR - Wageningen University and Research [Wageningen]
7 Hendrix Genetics Research
8 IRHS - Institut de Recherche en Horticulture et Semences
9 IEEC-CSIC - Institute for Space Studies of Catalonia [Barcelona]
10 ARAID - Fundación Agencia Aragonesa para la Investigación y el Desarrollo
11 Research Centre Laimburg
12 Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
13 Carl Von Ossietzky Universität Oldenburg
14 AI Investments [Skierniewice]
15 UOR - University of Reading
16 KU Leuven - Catholic University of Leuven - Katholieke Universiteit Leuven
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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https://hal.univ-angers.fr/hal-03016720
Contributeur : Hélène Muranty <>
Soumis le : vendredi 20 novembre 2020 - 15:06:00
Dernière modification le : jeudi 27 mai 2021 - 13:54:07

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UNIV-ANGERS | INRAE | UNAM | IRHS

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Michaela Jung, Morgane Roth, Maria José Aranzana, Annemarie Auwerkerken, Marco Bink, et al.. The apple REFPOP—a reference population for genomics-assisted breeding in apple. Horticulture research, Nature Publishing Group, 2020, 7 (1), ⟨10.1038/s41438-020-00408-8⟩. ⟨hal-03016720⟩

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