Data mining for apple S-RNase alleles in resequencing datasets

The sequence of the apple (Malus × domestica Borkh.) genome was obtained from the cultivar ‘Golden Delicious’ and released in 2010; the availability of this draft reference genome opened up the possibility to explore the genetic variation within this species on a genome scale, using high-throughput strategies such as high-density SNP arrays or resequencing of different cultivars. However, while these techniques are immediately effective and highly informative on most genomic loci, the S-locus has some uncommon features, derived from its mechanism of inheritance and evolutionary dynamics, that require different approaches. The extremely high level of allelic polymorphism, the lack of co-linearity between different -haplotypes, the massive presence of transposable elements and the evidence of extensive gene duplication as one of the main forces driving its evolution, are factors that make the Slocus an unsuitable target for common genomic procedures, such as SNP-based high-throughput assays and alignment of resequencing data on the reference genome. The aim of this work was to define a strategy for obtaining information on the S-locus from the high-depth resequencing of 6X apple cultivars. We focused on the S-RNase gene and developed a strategy initially aimed at identifying the S-genotype of resequenced cultivars; the short sequence reads obtained from each cultivar were then used to check and to expand the available sequence data for each identified allele. Our preliminary results suggest that the huge amount of information that derives from resequencing cultivars can be of great help to resolve incomplete, fragmentary or inconsistent data in the current database of apple S-RNase alleles.