The apple REFPOP—a reference population for genomics-assisted breeding in apple
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Author
Jung, Michaela
Roth, Morgane
Aranzana, Maria José
Auwerkerken, Annemarie
Bink, Marco
Denancé, Caroline
Dujak, Christian
Durel, Charles-Eric
Cantin, Celia M.
Guerra, Walter
Howard, Nicholas P.
Keller, Beat
Lewandowski, Mariusz
Ordidge, Matthew
Rymenants, Marijn
Sanin, Nadia
Studer, Bruno
Zurawicz, Edward
Laurens, François
Patocchi, Andrea
Muranty, Hélène
Publication date
2020-11-01ISSN
2052-7276
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.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
633 - Field crops and their production
Pages
16
Publisher
Springer Nature
Is part of
Horticulture Research
Citation
Jung, Michaela, Morgane Roth, Maria José Aranzana, Annemarie Auwerkerken, Marco Bink, Caroline Denancé, and Christian Dujak et al. 2020. "The Apple REFPOP—A Reference Population For Genomics-Assisted Breeding In Apple". Horticulture Research 7 (1). doi:10.1038/s41438-020-00408-8.
Grant agreement number
MINECO/Programa Estatal de fomento de la investigación científica y técnica de excelencia/SEV-2015-0533/ES/ /
EC/FP7/265582/EU/Integrated approach for increasing breeding efficiency in fruit tree crops/FRUIT BREEDOMICS
FEDER/ / /EU/ /
Program
Genòmica i Biotecnologia
Fructicultura
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2542]
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Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/