Genetic mechanisms underlying alternate cropping in apple (Malus x domestica) – AlternApp

These objectives are carried out in three WP aiming to study:
(1) the genetic determinism; this WP includes phenotyping, statistical analyses, genetic map construction and QTL detection, selection of candidate genes
(2) the physiological processes associated with candidate genes, including histological analyses, hormonal and carbohydrate analyses, microclimate and architectural analyses
(3) gene expressions, including transcriptomic analyses, search for expressional candidate genes and allelic variations

Three annual meetings have been carried out to present our respective results, adjust protocols, meet non-permanent persons recruited by each partners (PhD in Germany and post-doc in France). All partners also met in June 2017 at the 1st ISHS International symposium on Fruit Set and Alternate Bearing in Palermo, Italy where a presentation of the global project was performed by Pr J. Wunsche and more specific results by H. Flachowski, B. Pallas and E. Costes (see table).
The most significant results are (i) the construction of GD x R genetic map, with a good quality with respect to the number of markers and the robustness of their order; (2) the shared protocol for phenotyping; (3) the shared protocol for histology with the model for data analyses; (4) the definition of orthologs for flowering genes and the list of 48 positional and functional candidate genes, (4) the analysis of the local variation in FI related to within-tree variation of source-sink relationships, (5) sequencing of 700 flowering candidate genes in 384 Malus accessions.

In WP1, we will finish the statistical analyses on flowering behaviour in the GD x R population, in two steps: in the last months of 2017 we will analyse the shoot sequences. At spring 2018, we will analyse the total number of flowers per tree and then will perform the QTL detection.
In WP2, the experiments with defoliation and de-fruiting treatments are now achieved and under analysis. A first publication will be submitted during the next year and will include results on the non-structural carbohydrate (NSC) and photosynthesis. Analyses on gibberellin contents are ongoing with a repetition of the comparison of ON and OFF trees in 2017 and an extension of those analyses to shoots in the different parts of the defoliated or defructified trees. These contents will be analyzed with respect to the observed floral induction rate in the different parts of the trees.
The leaves and shoots sampled in summer 2017 under different light conditions will be analyzed for their carbohydrates and nitrogen contents, increasing the ecophysiological dataset. A publication will be initiated by the end of 2017, for a submission early 2018. Moreover, the carbohydrate dataset will be compared to those acquired on the defoliation/de-fruiting experiment, in order link local variation in light conditions or in source-sink ratio with carbohydrate content and FI.
In WP3, gene expression using both qPCR and Fluidigm technologies are currently performed as well as the exploration of allelic variation of flowering genes selected for target enrichment sequencing at INRA-Mtp. Target capture is analysed for the set of genotypes selected in France and on the accessions of wild species within Malus genius from the JKI collection.
For all WP, we plan to finish analysing the data over the last year of the project, in 2018. We plan to prepare scientific publications and submit them to journals with high impact factors.
A last consortium meeting is planned at JKI, Dresden (Germany) in May 2018.

1. Guitton B., Kelner J.J., J.M. Celton, X. Sabau, J.P. Renou, Chagné D., Costes E. 2016. Analysis of transcripts differentially expressed between fruited and deflowered ‘Gala’ adult trees: a contribution to biennial bearing understanding in apple. BMC Plant Biology. 16:55; DOI: 10.1186/s12870-016-0739-y;
2. J-B Durand, A Allard, B Guitton, E van de Weg, M Bink, E Costes Predicting flowering behavior and exploring its genetic determinism in an apple multi-family population based on statistical indices and simplified phenotyping. Under revision at Frontiers in Plant Science.
Oral and posters presented during conferences:
1. Guitton, B. ,Kelner J.J., J.M. Celton, X. Sabau, J.P. Renou, Chagné D., Costes E. 2016. Transcriptomic comparison between fruited and deflowered trees: toward the understanding of biennial bearing understanding in apple.
Oral presentation at the RGC8 Conference, Angers 21-23 June, 2016.
2. B. Pallas, JJ Kelner, D. Chen, S. Martinez, E.Costes. 2017. Investigating the impact of source/sink manipulations on within tree variations of floral induction and fruit weight.
Oral presentation at the ISHS symposium on Flowering, Fruit Set and Alternate Bearing, Palermo June 19-23, 2017.
3. J-B Durand, A Allard, B Guitton, E van de Weg, M Bink, E Costes. 2017. Genetic determinism of flowering regularity over years in an apple multi-family population.
Oral presentation at the ISHS symposium on Flowering, Fruit Set and Alternate Bearing, Palermo June 19-23, 2017.
4. F. Belhassine, B. Pallas, D. Fumey, E. Costes. 2017. How to understand the alternate production in apple tree ? A modeling approach of carbon and hormones fluxes.
Poster presentation at the ISHS symposium on Flowering, Fruit Set and Alternate Bearing, Palermo June 19-23, 2017.