Application of the 8K Illumina Infinium apple SNP-chip to estimate linkage disequilibrium and population structure in an apple germplasm collection

Discovering genetic variations that cause the observed variations for important plant traits, is one of the key challenges for plant researchers. For apple, the International RosBREED SNP Consortium developed an 8K SNP-chip on the Illumina Infinium platform that can be used for such association and genotyping studies. This SNP-chip was used to genotype our Malus x domestica germplasm collection consisting of both commercial and old cultivars as well as some genotypes from a Telamon x Braeburn progeny.
We used the SNP data obtained from this SNP-array to estimate the linkage disequilibrium (LD) between adjacent SNPs as well as the LD decay across larger regions because this determines the number of markers necessary for association studies. In addition, association analyses can be biased by the population structure present in the collection used for these studies. Therefore we determined the population structure of our germplasm collection using the software STRUCTURE.
Evanno’s criterium indicated that the most likely numbers of subpopulations present in our collection were two and three subpopulations with two being the most likely. The first subpopulation was a group with the Telamon x Braeburn progeny and other Braeburn-related cultivars. The other subpopulation contained all other commercial and old cultivars. Thislatter group split into a group of commercial cultivarsand a group of old cultivars when increasing the number of subpopulations to three while the first group remained unchanged.
The estimated LD between adjacent SNPs using the r2 parameter was 0.23 and decayed quickly below 0.18 after about35kb.