DNA-informed breeding of rosaceous crops: promises, progress and prospects

Crops of the Rosaceae family provide valuable contributions to rural economies and human health and enjoyment.Sustained solutions to production challenges and market demands can be met with genetically improved new cultivars.Traditional rosaceous crop breeding is expensive and time-consuming and would benefit from improvements in efficiency and accuracy.Use of DNA information is becoming conventional in rosaceous crop breeding,contributing to many decisions and operations,but only after past decades of solved challenges and generation of sufficient resources.Successes in deployment of DNA-based knowledge and tools have arisen when the‘chasm’between genomics discoveries and practical application is bridged systematically.Key steps are establishing breeder desire for use of DNA information,adapting tools to local breeding utility,identifying efficient application schemes,accessing effective services in DNA-based diagnostics and gaining experience in integrating DNA information into breeding operations and decisions.DNA-informed germplasm characterization for revealing identity and relatedness has benefitted many programs and provides a compelling entry point to reaping benefits of genomics research.DNA-informed germplasm evaluation for predicting trait performance has enabled effective reallocation of breeding resources when applied in pioneering programs.DNA-based diagnostics is now expanding from specific loci to genome-wide considerations.Realizing the full potential of this expansion will require improved accuracy of predictions,multi-trait DNA profiling capabilities,streamlined breeding information management systems,strategies that overcome plant-based features that limit breeding progress and widespread training of current and future breeding personnel and allied scientists.

Elucidation of the ‘Honeycrisp’ pedigree through haplotype analysis with a multi-family integrated SNP linkage map and a large apple (Malus×domestica) pedigree-connected SNP data set

The apple(Malus×domestica)cultivar Honeycrisp has become important economically and as a breeding parent.An earlier study with SSR markers indicated the original recorded pedigree of‘Honeycrisp’was incorrect and‘Keepsake’was identified as one putative parent,the other being unknown.The objective of this study was to verify‘Keepsake’as a parent and identify and genetically describe the unknown parent and its grandparents.A multi-family based dense and high-quality integrated SNP map was created using the apple 8 K Illumina Infinium SNP array.This map was used alongside a large pedigree-connected data set from the RosBREED project to build extended SNP haplotypes and to identify pedigree relationships.‘Keepsake’was verified as one parent of‘Honeycrisp’and‘Duchess of Oldenburg’and‘Golden Delicious’were identified as grandparents through the unknown parent.Following this finding,siblings of‘Honeycrisp’were identified using the SNP data.Breeding records from several of these siblings suggested that the previously unreported parent is a University of Minnesota selection,MN1627.This selection is no longer available,but now is genetically described through imputed SNP haplotypes.We also present the mosaic grandparental composition of‘Honeycrisp’for each of its 17 chromosome pairs.This new pedigree and genetic information will be useful in future pedigree-based genetic studies to connect‘Honeycrisp’with other cultivars used widely in apple breeding programs.The created SNP linkage map will benefit future research using the data from the Illumina apple 8 and 20 K and Affymetrix 480 K SNP arrays.