An integrated approach for increasing breeding efficiency in apple and peach in Europe

Abstract

Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders. Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding, development of new, dense SNP arrays in apple and peach, new phenotypic methods for some complex traits, software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis (PBA). This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies (GWAS) on several European genebank collections. FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities. Through FruitBreedomics, significant progresses were made in the field of apple and peach breeding, genetics, genomics and bioinformatics of which advantage will be made by breeders, germplasm curators and scientists. A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public. This review covers the scientific discoveries made in this major endeavour, and perspective in the apple and peach breeding and genomics in Europe and beyond.

High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow

“…To reduce the trimming of pedigrees (as described under ‘Haploblock and haplotype generation’ below), the genotype calls of 18 additional apple individuals genotyped with the 20K SNP array in the FruitBreedomics project [42] or genotyped with the 8K SNP array at KU Leuven, Belgium (Table S1) were added to the data set to complete genotypic data of key ancestors.…”

“…The workflow maximizes the genotypic data obtained from high-throughput genome-scanning tools while minimizing the time needed to identify and remove errors. The workflow resulted from curation needs in the multi state and multi-crop USDA-SCRI project RosBREED [37–39] and the European project FruitBreedomics [40–42]. The workflow is demonstrated for three tree fruit crops, apple, peach, and sweet cherry, using the RosBREED germplasm sets [43].…”

Chromosome-scale de novo diploid assembly of the apple cultivar ‘Gala Galaxy’

“…Given the increasing public demand to reduce fungicide input, disease resistant cultivars are essential for future sustainable apple production. Genotypic information has the potential to speed up the development of resistant cultivars of superior quality (Baumgartner, et al 2016; Laurens, et al 2018; Peace, et al 2019). However, the number of available molecular markers linked to fruit quality traits is low.…”

Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (Pyrus)

“…The Affymetrix IStraw90 Axiom array was developed using the integration of SNP and InDels from one diploid and 19 octoploid accessions of strawberry (Bassil et al ., ). These efforts led by the RosBREED community (Iezzoni et al ., 2016) and FruitBreedomics project (Laurens et al .,), have provided useful array resources to study genome structure and diversity analysis and to perform QTL mapping and GWAS (Urrestarazu et al ., ) for important economic traits in the respective fruit species. In some of these arrays, the limited number of SNPs and germplasm diversity potentially restrict their broader utilization in molecular breeding applications.…”