A High Resolution SNP Linkage Map of a ‘Honeycrisp' Apple (Malus x domestica) Progeny

The apple cultivar Honeycrisp has outstanding flavor and texture traits that are maintained through several months of storage, contributing to its emerging importance in the North American apple industry.  'Honeycrisp' has also been shown to exhibit resistance to foliar apple scab infection, a major disease of apple worldwide.  The use of 'Honeycrisp' as a parent offers the genetic background for superb fruit quality and disease resistance traits.  A high-resolution consensus linkage map was constructed using a ‘Honeycrisp’ x MN1764 progeny population (n = 119).   The whole-genome array (International RosBREED SNP Consortium (IRSC) apple 8K SNP array v1) provided 1,952 (24.8%) high quality, polymorphic SNP markers which were assigned to the 17 known Malus linkage groups.  Total map length was ~1329 cM with an average density of ~0.64 cM/marker.  The largest marker gap in the linkage map was ~21.9 cM.  Four other regions had gaps larger than 10 cM.  The development of a 'Honeycrisp' linkage map based on the IRSC SNP array will facilitate detection and validation of QTL in pedigree-based analysis of breeding populations using FlexQTL (www.flexqtl.nl) and in bi-parental mapping populations for apple scab and fruit quality traits.  A high quality linkage map may also help resolve issues in the apple physical map including improvement of the primary genome sequence assembly hosted in the Genome Database for Rosaceae (GDR).