Genotype-by-environment and QTL-by-environment interactions in sweet cherry (Prunus avium L.) for flowering date

Abstract

In sweet cherry (Prunus avium L.), flowering date is strongly dependent on the environment conditions and, therefore, is a trait of major interest for adaptation to climate change. Such trait can be influenced by genotype-by-environment interaction (G×E), that refers to differences in the response of genotypes to different environments. If not taken into account, G×E can reduce selection accuracy and overall genetic gain. However, little is known about G×E in fruit tree species. Flowering date is a highly heritable and polygenic trait for which many quantitative trait loci (QTLs) have been identified. As for the overall genetic performance, differential expression of QTLs in response to environment (QTL-by-environment interaction, QTL×E) can occur. The present study is based on the analysis of a multi-environment trial (MET) suitable for the study of G×E and QTL×E in sweet cherry. It consists of a sweet cherry F1 full-sib family (n = 121) derived from the cross between cultivars ‘Regina’ and ‘Lapins’ and planted in two copies in five locations across four European countries (France, Italy, Slovenia and Spain) covering a large range of climatic conditions. The aim of this work was to study the effect of the environment on flowering date and estimate G×E, to carry QTL detection in different environments in order to study the QTL stability across environments and to estimate QTL×E. A strong effect of the environment on flowering date and its genetic control was highlighted. Two large-effect and environment-specific QTLs with significant QTL×E were identified on linkage groups (LGs) 1 and 4. This work gives new insights into the effect of the environment on a trait of main importance in one of the most economically important fruit crops in temperate regions. Moreover, molecular markers were developed for flowering date and a strategy consisting in using specific markers for warm or cold regions was proposed to optimize marker-assisted selection (MAS) in sweet cherry breeding programs.

Strawberry phenotypic plasticity in flowering time is driven by interaction between genetic loci and temperature

“…We showed here that in strawberry, the G×E variance for flowering time represents a high proportion of the total variance. This result indicates that, when flowering time is considered, strawberry is a very plastic species, more so than suggested for sorghum and cherry (Li et al, 2018; Branchereau et al, 2023). Among the models used for studying G×E, the factorial regression models describe a genetically controlled differential sensitivity to explicit environmental factors (Malosetti et al, 2013).…”

“…The genetic architecture of the plasticity, i.e. the ability of a plant to change its phenotype according to environments, has been investigated in a limited number of crop species (e.g., sorghum, Li et al, 2018; tomato, Diouf et al, 2020; maize, Jin et al, 2023; cherry, Branchereau et al, 2023). To date, no similar effort has been devoted to strawberry.…”

Genome-wide association analysis of flowering date in a collection of cultivated olive tree

“…Another perspective of the present work would be to deepen the comprehension of the year effects and their interaction with genotypic effects on the FFD. Indeed, as previously found, flowering date is a highly heritable trait but also strongly depends on environmental conditions (Branchereau et al, 2023). Winter temperatures are particularly known to influence chilling fulfillment, which impacts FFD (Atkinson et al, 2013).…”

Climate change impacts on temperate fruit and nut production: a systematic review

“…For instance, because chilling requirements are becoming a limiting factor for cultivar adaptation in warming environments, scientists are working on identifying genes associated with bud dormancy and flowering time in temperate crops to elucidate the genetic control of these processes and develop new cultivars adapted to different climatic conditions ( Castede et al., 2014 ; Romeu et al., 2014 ; Allard et al., 2016 ; Prudencio et al., 2018 ; Cantin et al., 2020 ; Prudencio et al., 2021 ; Zhang et al., 2022 ). New technologies have also enabled the identification of the genetic regions controlling traits such as flowering time ( Ruiz et al., 2019 ; Branchereau et al., 2023 ) and bud dormancy ( Allard et al., 2016 ; Prudencio et al., 2018 , Prudencio et al., 2021 ), as well as traits related to temperature requirements for endodormancy release ( Romeu et al., 2014 ). The identification of regions harboring genes related with the response of trees to environmental cues has facilitated the efficient use of molecular markers to reliably select genotypes that are better suited to particular climatic conditions.…”