Genome wide scan with the IPSC peach SNP array for the identification of QTLs controlling fruit quality, phenological and tree architecture traits.

A BC1 progeny (PxF) obtained crossing two peach accessions, the selection IF7310828 used as female recurrent parent and the oriental accession Ferganensis (formerly P. ferganensis) used as male donor parent was genotyped with the IPSC 9K SNP array. Out of 8144 SNPs available on the chip 3326 (40.8%) resulted polymorphic. We mapped 1660 SNPs and 15 SSR loci, all informative for the F1 parent and segregating in a 1:1 ratio in the PxF population, using JoinMap 4.1 and the Maximum Likelihood mapping algorithm. Grouping was performed at a LOD higher than 10. After grouping, identical loci were eliminated , with the exception of SSRs that were always retained. The final map consisted of 242 loci distributed in 8 groups, covering 607 Haldane cM. This map was used to scan the genome for QTLs using MapQTL6. Interval mapping and MQM mapping were used, both with the mixture Model Algorithm. Traits related to plant structure (internode length, plant height, trunk perimeter), plant physiology (blooming and maturity date),fruit quality (fruit weight, fruit juice pH, titratable acidity, soluble solid content , fruit red overcolor ) were analyzed for at least two years. Several QTLs were identified, the major ones for blooming and maturity date, soluble solid content, fruit red overcolor.