Development of Applied Genomic Tools for Markers Assisted Breeding in Apple

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. Sucharrays are now commercially available for plant species with complex polyploid genomes.

We developed an Illumina Infinium 20K array in apple, a species with a highly heterozygous genome that has undergone a recent whole genome duplication. SNPs contained on the array were predicted from re-sequencing data derived from 14 apple genotypes and two doubled-haploids. An ad-hoc pipeline for SNP selection was devised avoiding the pitfalls of paralogous sequence variants , to reach the target of 20k SNPs. The performance of the array was assessed using data from mapping populations and germplasm collections. Marker positions based on 23 genetic maps provided valuable information that was used to improve the scaffolding and anchoring of the apple reference genome. Furthermore, the array 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.