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Article|01 Nov 2020|OPEN
The apple REFPOP—a reference population for genomics-assisted breeding in apple
Michaela Jung1,2, Morgane Roth2,3, María José Aranzana4,5, Annemarie Auwerkerken6, Marco Bink7,8, Caroline Denancé9, Christian Dujak5, Charles-Eric Durel9, Carolina Font i Forcada4, Celia M. Cantin4,10, Walter Guerra11, Nicholas P. Howard12,13, Beat Keller1,2, Mariusz Lewandowski14, Matthew Ordidge15, Marijn Rymenants6,7,16, Nadia Sanin11, Bruno Studer1, Edward Zurawicz14, François Laurens9, Andrea Patocchi2 & Hélène Muranty9,
1Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
2Breeding Research group, Agroscope 8820 Wädenswil, Switzerland
3Present address: GAFL, INRAE, 84140 Montfavet, France
4IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140 Caldes de Montbui, Barcelona, Spain
5Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Spain
6Better3fruit N.V., 3202 Rillaar, Belgium
7Biometris, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
8Hendrix Genetics Research, Technology and Services B.V., PO Box 1145830AC Boxmeer, The Netherlands
9IRHS, Université d’Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071 Beaucouzé, France
10ARAID (Fundación Aragonesa para la Investigación y el Desarrollo), 50018 Zaragoza, Spain
11Research Centre Laimburg, 39040 Auer, Italy
12Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
13Institute of Biology and Environmental Sciences, University of Oldenburg, 26129 Oldenburg, Germany
14Research Institute of Horticulture, 96-100 Skierniewice, Poland
15School of Agriculture, Policy and Development, University of Reading, Whiteknights RG6 6AR Reading, UK
16Laboratory for Plant Genetics and Crop Improvement, KU Leuven B-3001 Leuven, Belgium

Horticulture Research 7,
Article number: 189 (2020)
doi: 10.1038/hortres.2020.189
Views: 345

Received: 23 Apr 2020
Revised: 25 Aug 2020
Accepted: 06 Sep 2020
Published online: 01 Nov 2020

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.