New insights in apple genomics

Next generation sequencing has significantly reduced sequencing costs and has permitted de-novo assembly of complex genomes, and re-sequencing of multiple genotypes within a species. The availability of plant reference genomes has accelerated genetics and genomics research, providing tools to identify functional elements, leading to the efficient development of improved varieties. Understanding the links between phenotypic variation and DNA variation the major challenge for plant geneticists. High-density SNP arrays for genome-wide assessment of allelic variation, have made high resolution genetic characterization of crop germplasm feasible. Such arrays are now commercially available for plant species with complex polyploid genomes.
Here we present an Illumina Infinium 20K array in apple that will be implemented in Genome Wide Association Studies as well as Pedigree Based Analyses. In both cases it will be employed to dissect the genetic mechanism controlling important fruit quality traits, towards the identification of valuable markers suitable for the assisted selection activity in apple breeding programs.. SNPs contained on the array were predicted from re-sequencing data derived from 14 apple genotypes and two doubled-haploids of Golden Delicious. An customised pipeline for SNP selection was devised avoiding the pitfalls of paralogous sequence variants. The performance of the array was assessed using data from mapping 23 populations from controlled crosses and germplasm collections. Marker positions based on the 23 genetic maps provided new insights on the apple genome, which will be presented and which were used to improve the scaffolding and anchoring of the apple reference genome, now available in the 3.0 new assembly.