Enabling Marker-assisted Breeding in Heterozygous Polyploid Species: The Strategy Used in Sour Cherry (Prunus cerasus)

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.