Advances in DNA markers in cherry: from the S-locus to a genome wide array

The availability of genetic linkage maps and new sequencing technologies have revolutionized genetic discovery yielding important breeding applications. The DNA markers initially used to construct cherry linkage maps were simple sequence repeat (SSR) markers, many of which were also used in other Prunus species. Subsequently, a set of Rosaceae Conserved Orthologous Set (RosCOS) markers used for comparative mapping among apple, peach and diploid strawberry, were extended for use in sweet cherry. A total of 282 genome-wide RosCOS were identified that were polymorphic among a set of six diverse cultivars, the majority of which were single nucleotide polymorphisms (SNPs). Most recently, a 6K medium density Illumina Infinium^® II system SNP array was developed by a RosBREED led effort (www.rosbreed.org) for use with both diploid sweet cherry and allotetraploid sour cherry. A total of 1825 polymorphic SNPs were verified in sweet cherry and 2085 polymorphic SNPs, for which dosage could be resolved, were verified for sour cherry. In a separate project, a total of 335 genomic regions polymorphic in two sweet cherry cultivars were identified with SNP markers. These publicly available genomic resources represent a significant advance in the genome scanning capability in cherry that will enable the discovery of the genetic bases of trait variation in this diploid-tetraploid crop set.