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.
Highlights
Apple (Malus × domestica Borkh.) is one of the most economically valuable fruit crops in temperate regions[1]
Composition of the apple REFPOP The apple REFPOP was built with (i) 269 diploid accessions representing a wide range of genetic diversity in apple, originating from various geographic regions around the globe and (ii) 265 diploid progeny from 27 parental combinations from several European breeding programs (Supplementary Tables 1 and 2)
Since relatedness between training and breeding populations is a crucial factor for successful genomic prediction[13], the European breeding programs can directly profit from the outcomes of the project because their breeding material has been included in the apple REFPOP
Summary
Apple (Malus × domestica Borkh.) is one of the most economically valuable fruit crops in temperate regions[1]. Thousands of cultivars are grown in national and private repositories around the globe. Extensive genetic variation described in the European apple germplasm illustrates the available genetic diversity among cultivars[2,3]. A fraction of the existing apple cultivars is commercially used. Since the advent of genomics, genotyping tools have begun to produce affordable genome-wide marker data. Large datasets are being analyzed to explore genotype–phenotype relationships in genome-wide association studies (GWAS) and to allow genomic prediction. Genomic prediction[5] has revolutionized breeding and more than doubled genetic progress of major livestock such as cattle[6]. The method relies upon models fitted to broad datasets of genotypes and phenotypes from a training population.
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