The apple REFPOP-a reference population for genomics-assisted breeding in apple
Jung, Michaela (Breeding Research group (Switzerland))
Roth, Morgane (Breeding Research group (Switzerland))
Aranzana, Maria José (Centre de Recerca en Agrigenòmica)
Auwerkerken, Annemarie (Better3fruit N.V.)
Bink, Marco (Hendrix Genetics Research, Technology & Services (The Netherlands))
Denancé, Caroline (Université d'Angers)
Dujak, Christian (Centre de Recerca en Agrigenòmica)
Durel, Charles-Eric (Université d'Angers)
Font i Forcada, Carolina (Institut de Recerca i Tecnologia Agroalimentàries)
Cantin, Celia M. (Institut de Recerca i Tecnologia Agroalimentàries)
Guerra, Walter (Research Centre Laimburg (Italy))
Howard, Nicholas P. (University of Oldenburg)
Keller, Beat (Breeding Research group (Switzerland))
Lewandowski, Mariusz (Research Institute of Horticulture (Poland))
Ordidge, Matthew (University of Reading)
Rymenants, Marijn (Laboratory for Plant Genetics and Crop Improvement (Belgium))
Sanin, Nadia (Research Centre Laimburg (Italy))
Studer, Bruno (Institute of Agricultural Sciences (Switzerland))
Zurawicz, Edward (Research Institute of Horticulture (Poland))
Laurens, François (Université d'Angers)
Patocchi, Andrea (Breeding Research group (Switzerland))
Muranty, Hélène (Université d'Angers)

Date:	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.
Grants:	Ministerio de Economía y Competitividad SEV-20150533 European Commission 265582
Note:	Altres ajuts: CERCA Programme/Generalitat de Catalunya, Project RIS3CAT (COTPAFRUIT3CAT) financed by the European Regional Development Fund through the FEDER frame of Catalonia 2014-2020
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Plant breeding ; Genome-wide association studies
Published in:	Horticulture research, Vol. 7 (November 2020) , art. 189, ISSN 2052-7276

DOI: 10.1038/s41438-020-00408-8
PMID: 33328447

16 p, 1.3 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles