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

Abstract

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.

Two QTL characterized for soft scald and soggy breakdown in apple (Malus × domestica) through pedigree-based analysis of a large population of interconnected families

“…A total of 3419 SNPs were used in the QTL analyses. The genetic map used in this study is described in Howard et al (2017). The marker data for seedling individuals evaluated in this study can be found in Table S2.…”

“…The origin of the HDI haplotypes in 'Honeycrisp' were traced to 'Northern Spy' through parent 'Keepsake,' and 'Grimes Golden' through parent MN1627 (Howard et al 2017) (Table S4). Multiple parents of families evaluated in this study share one copy of the HDI haplotype by descent (Table S4).…”

“…Genome-wide phased marker data for parents that did not have SNP-confirmed pedigrees were compared to founder genotypes that had the same haplotype at QTL of interest to determine whether it is likely that important haplotypes may also be IBD via distant, but still unidentified genetic relationships. Haplotypes that were identical by state (IBS) between these parents and founders were considered likely to be IBD if they shared multiple extended IBS haplotypes of more than 10 cM that together totaled more than 10% of the SNP genome from the linkage map used in this study, which is more than 234.4 cM (= 10% × 1172 cM (Howard et al 2017) × 2 parental haplotypes for diploids). These postulated relationships also had to be temporally and geographically consistent with available historical information about the listed pedigree for the parent under consideration.…”

“…Suspected false or questionable recombinations were evaluated, and genotype scores were changed or recoded as missing data if it was evident that an individual had a genotype score that could not have been inherited or passed on to offspring given information from the connected pedigree. All pedigree relationships used in this study have been validated through SNP data using a process similar to that used in Howard et al (2017) to confirm ancestors of 'Honeycrisp.' A total of 3419 SNPs were used in the QTL analyses.…”

“…The DNA extraction methods used were as in Clark et al (2014b). Genotype data for the four large full-sib families came from a previous study on the creation of an integrated genetic map (Howard et al 2017). SNP alleles for the remaining germplasm were called together using automated allele calling in GenomeStudio™.…”