Use Of Genotyping-By-Sequencing For QTL Mapping Of Chilling Requirement and Bloom Date In Peach

Bloom date (BD) and chilling requirement (CR) are economically important traits for breeding fruit and nut tree species adapted to local climate conditions. We have developed a peach F₂ mapping population with 57 genotypes from a selfed F₁ progeny of a cross between ‘Hakuho’ (high CR) and ‘UFGold’ (low CR). We scored BD in seven years; CR was evaluated over two winter seasons by scoring bud break of forced cuttings. Initial marker screening identified 37 polymorphic simple sequence repeat (SSR) markers distributed across all linkage groups (G). To saturate our genetic map with markers, we tested a genotyping-by-sequencing (GBS) approach to discover single nucleotide polymorphisms (SNP) present in the population. Genomic DNA was ApeKI restricted, ligated to barcoded adaptors, and pooled and amplified for multiplex sequencing on the Illumina HiSeq 2000 platform. Approximately 160 million sequence reads were processed using TASSEL 3.0. TASSEL output was manually filtered to 4283 SNPs which were distributed across the twelve largest scaffolds of the peach v1.0 genome assembly at between 1.0 and 2.6 per 100 kbp. SNPs in common with previously published data sets on unrelated germplasm were found. 648 SNPs were combined with the 37 SSRs to construct a linkage map with a total distance of 686 cM. Twenty quantitative trait loci (QTL) were detected for BD and CR on G1, G4 and G7. GBS provided a rapid and relatively low cost method to produce a SNP-based map in a novel progeny.