Character integration, breeding goals compatibility and selection indexes using genome wide breeding values: a study case

Breeding in apple is characterized by a high number of characters concerned, related to several biological processes. The main characters are fruit quality, disease resistance and yield. In addition, the will to reduce the use of chemical products in agriculture and the changing climatic context causes the need to breed for new complex characters such as yield regularity and adaptation to temperature increase. This work is a study case of trait integration for fruit quality, yield level and regularity, and bud phenology related traits. Compatibility of breeding objectives, according to one fixed ideotype, were analysed and a strategy for the introduction of new characters in breeding schemes using molecular markers, breeding values estimation, and selection indexes was proposed. Two unrelated families were phenotyped, QTL analyses were run with the Bayesian software FlexQTLTM and the individual genetic breeding values were computed trait by trait by adding the genetic effect of loci estimated during the QTL mapping process. An ideotype integrating all traits was fixed and principal component analyses were realized in order to study the breeding goals compatibility. Traits were integrated in two selection indexes computed with breeding values. Synergistic correlations between fruit size and yield regularity was identified and antagonistic correlation was observed between fruit size and yield level, and yield regularity and level and partially explained by colocalization of QTLs with high opposite effects according to the ideotype. In case of antagonistic correlation between important traits, a genetic ideotype could be a tool to monitor precisely the choice of genitors and identification of progenies compatible with the ideotype. Principal component analyses and selection indexes values revealed a differential genetic potential of the two families depending on traits and their correlations, and interesting individuals could be identified in both families even if selection indexes values were in favor of one of the families. In conclusion, the use of molecular markers, genetic effects estimation in a genomic selection approach, combined with a selection index strategy would be an efficient way to introduce simultaneously new complex characters in breeding schemes.