Discovery of a QTL for cherry leaf spot resistance and validation in tetraploid sour cherry of QTLs for bloom time and fruit quality traits from diploid Prunus species

With heterozygous polyploid species, detecting quantitative trait loci (QTL) can be an arduous process, especially in segmental allopolyploids like sour cherry (2n=4x=32) where non-homologous pairing is common. In our sour cherry breeding and genetics program at Michigan State University, we have taken a QTL validation approach for identifying relevant QTLs, whereby QTLs more easily discovered in related diploid species are tested for their association in sour cherry. SNP markers on the Illumina 6K Infinium II array were used for genotyping sour cherry plant materials included in the USDA-SCRI funded RosBREED project (www.rosbreed.org). GenomeStudio polyploidy functionalities were used to score SNP genotypes, including dosage. Previously identified QTLs/candidate genes for several horticulturally important traits (fruit size, fruit flesh color, fruit acidity, fruit firmness and bloom time) were identified from the peach (P. persica), almond (P. dulcis) and sweet cherry (P. avium) literature. SNP markers spanning the target QTL intervals were identified based on synteny with the peach genome sequence, and marker linkage phase was determined based on sour cherry progeny segregation. The different haplotypes identified for these targeted regions were then tested for haplotype trait association. Haplotypes with significant effect on phenotype were identified for marker-assisted breeding. In certain cases, the SNP haplotype was converted to an SSR marker to facilitate future genotyping. Not all regions found to be significant in diploid relatives were significant in sour cherry, indicating either they are absent, fixed or cannot be detected due to complexity of dosage and more allelic variants compared to diploid species. This approach has been successful for QTLs with fairly large effects, which are good targets for marker-assisted breeding. Since no QTL studies have been done previously with cherry leaf spot (CLS) resistance, we utilized the Bayesian approach, implemented in FlexQTL™ software which allowed us to follow important genotypic regions from multiple populations through generations by including pedigreed parents and grandparents in the analysis. By studying two populations, one with P. canescens derived CLS resistance, and one without, we were able to locate a QTL on the top of linkage group (G)4 between SNP markers ss490552303 and ss490552492 (between 2.9-13.4 cM). When individuals with and without the P. canescens haplotype at this region were compared, it was found the P. canescens haplotype was significantly associated with disease resistance. The same was found in sour cherry, where all individuals that were resistant to CLS had P. canescens haplotypes at this region. In both sweet and sour cherry, however, individuals with the P. canescens segment were found that were also susceptible, indicating that this is not the only region important for conferring CLS disease resistance.