HighlightQTLs and candidate genes for the regulation of budbreak and flowering time reveal new hypotheses on temperature perception in growth resumption at spring time in apple.

Irregular flowering over years is commonly observed in fruit trees. The early prediction of tree behavior is highly desirable in breeding programmes. This study aims at performing such predictions, combining simplified phenotyping and statistics methods. Sequences of vegetative vs. floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families. Sequences were analyzed using Markovian and linear mixed models including year and site effects. Indices of flowering irregularity, periodicity and synchronicity were estimated, at tree and axis scales. They were used to predict tree behavior and detect QTL with a Bayesian pedigree-based analysis, using an integrated genetic map containing 6,849 SNPs. The combination of a Biennial Bearing Index (BBI) with an autoregressive coefficient (γg) efficiently predicted and classified the genotype behaviors, despite few misclassifications. Four QTLs common to BBIs and γg and one for synchronicity were highlighted and revealed the complex genetic architecture of the traits. Irregularity resulted from high AS synchronism, whereas regularity resulted from either asynchronous locally alternating or continual regular AS flowering. A relevant and time-saving method, based on a posteriori sampling of axes and statistical indices is proposed, which is efficient to evaluate the tree breeding values for flowering regularity and could be transferred to other species.

Irregular flowering over years is commonly observed in fruit trees and is assumed to be, at least partly, under genetic control. This study aimed at predicting genotype flowering behaviours and at detecting QTL associated to regularity, in a multi-family apple tree population. Successions of vegetative and floral annual shoots (AS) were observed along axes in trees belonging to five apple related full-sib families, observed at two experimental sites. Sequences were analysed using Markovian and linear mixed models including year and site effects. Indices of flowering regularity, periodicity and synchronicity were estimated, at tree and axis scales. First indices were derived from the Biennial Bearing Index (BBI). A second index was the auto-regressive correlation coefficient between flowering in consecutive years. A third index quantified the synchronicity of meristems within the trees through the measure of differences in the predictability of flowering over years, from a probabilistic viewpoint. These three types of indices were used to predict tree behaviour and to detect QTL with a Bayesian pedigree-based analysis, using an integrated genetic map containing 6,849 SNPs. The combination of the three indices efficiently predicted and classified the genotype behaviours despite few miss-classifications. Four common QTLs for BBIs and auto-regressive coefficient were highlighted (on LG4, 5, 8 and 10) and one for synchronicity (on LG9) in the integrated multi-family map, thus revealing the complex genetic architecture of the considered traits. This study proposes a posteriori sampling of axes within trees as a relevant and time-saving method to estimate tree flowering behaviours. Coupled to appropriate statistical indices, it is efficient to evaluate the tree breeding values for flowering regularity. In apple tree, biennial bearing appeared to result from high AS synchronism in flowering, i.e. with all axes alternatively flowering or not in a given year, whereas regularity resulted from either asynchronous alternating or regular flowering of AS.