Genome wide association mapping of apple fruit shape

Abstract

Apple shape is an important varietal trait. However, despite such importance, only few QTLs for fruit shape have been identified so far, while candidate genes and the genetic mechanisms underlying this trait are still unknown. Breeders, examination offices and post-registration organizations use standard shape descriptors, based on the visual estimation of the proportion between mid and distal fruit widths, to characterize the fruits. In this work we analyze measures of fruit dimensions obtained with Tomato Analyzer software in scanned fruit sections to define an objective fruit shape index (FSI) as the ration between mid height and mid widht. For this we cut and meassured 1507 apples of 94 accessions randomly sampled from an apple collection of 292 accessions with two replicates each, and genotyped with the Axiom® Apple 480k SNP array. FSI data obtained in the subsample was used in a GWAS analysis using General Linear Model and Mixed Linear Model. The limiting sample size did not allow to find significant SNPs after Bonferroni correction, however this approach has been highly useful to define a phenotyping and GWAS pipeline to study QTLs for apple fruit shape. Our data indicate that FSI is a good descriptor of fruit shape, however other measures and ratios provided by Tomato Analyzer will be also included in further GWAS analysis with the whole 292 apple accessions.