Identification of Haplotypes in Octoploid Strawberry (Fragaria × ananassa) Cultivars using 90K IStraw

Cultivated strawberry (Fragaria x ananassa) is a hybrid octoploid species whose fruit is highly appreciated due to its organoleptic properties and health benefits. Despite its economic importance, the octoploid genome represents a great challenge to study the genome structure and molecular mechanisms related to fruit quality and agronomic traits. The present study centered on utilizing SNP data from genotyping array (IStraw 90K) of 37 cultivars, bred by the company PLANASA, to determine trait-relevant haplotypes in the cultivars. We developed a strategy to extend our F2 genetic linkage map by association of high quality SNPs to the previously mapped ones based on genotype similarity with consistent results. The resultant 33 maps, composed of 2,106 markers, were derived from joining 71 fragments in function of their annotated homeolog group; the highlight is on the 633 markers that were newly incorporated. As genetic distance among cultivars responded to both phenotype and genotype properties, a thorough analysis on those linked by a common feature may shed light on the markers involved with it. Functional annotations of SNPs consisted of prediction of effects on genes, with focus on those variants that disrupted gene transcription; a list of 280 markers with predicted high impact on genes is provided. This work may be continued by performing association analysis when cultivars are fully phenotyped in order to define candidate genes related with traits of economic significance and will generate a small chip for Marker Assisted Selection.