Team Sweet cherry adaptation to climate change - A3C

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Team leader: Benedicte Wenden (benedicte.wenden@inrae.fr)

Presentation and research aims :

The A3C (sweet Cherry Adaptation to Climate Change) group is part of the Biology and Plant Breeding research department (BAP). The group collaborates with many partners not only in France but also worldwide, from academic world as well as industry. Our international network has even grown broader as A3C coordinates a COST action, financed by the European Union (Action FA1104, https://www.bordeaux.inra.fr/cherry), with cherry specialists from more than 30 countries.

Our main partner for field experimentation is the Tree Experimental Station (UEA) in INRA Bordeaux Aquitaine, based on two sites, Domaine des Jarres in Toulenne (Gironde) and Domaine de la Tour de Rance in Bourran (Lot et Garonne).

Research led by the A3C group aims to understand sweet cherry adaptive responses to climate change, through several scientific questions:

• What are the most pertinent phenotypic traits for measuring chill requirement, dormancy release, and fruit cracking in sweet cherry?
• Which genetic and molecular cues are involved in traits variability related to sweet cherry response to environmental constraints?
• In order to develop ideotypes adapted to future climatic conditions, which mechanisms should we take into account?

Our project focuses on the analysis of phenology and fruit quality traits. Marker assisted selection (MAS) will be developed to help selecting plant material that will be adapted to upcoming climatic conditions while producing high quality fruits. Our economic and public challenge is to help maintaining, and even expanding, cherry production in regions where it is traditionally grown and prospection in new regions that might become favorable to its production.

In addition, the A3C group leads its research with the assistance of the Bordeaux Functional Genomics Center (CGFB) and the INRA’s Prunus Genetic Resources Centre.

Our research :

1 - Sweet cherry phenology in the context of climate change

In fruit trees/species, productivity and fruit quality highly depend on an optimal timing of flowering. This key event directly depends on dormancy, which is a period of arrested plant growth triggered by low temperature in Rosaceae, and its release in response to endogenous and environmental conditions, including chill and heat requirements. New dormancy markers (biochemical, molecular and epigenetic) are being investigated, including high throughput and non-destructive phenotyping technics.

Candidate genes (CGs) involved in chill requirements and flowering time are investigated using two complementary approaches: 1) Functional CGs search in the sweet cherry gene atlas obtained from high throughput sequencing (454) from various tissues of ‘Regina’ cultivar (1.175.000 sequences of 330 bases) developed by the A3C group, 2) expressional CGs search based on differential Gene Expression (DGE) using RNA-Seq and comparing gene expression levels between cDNA banks from buds at 3 stages (before, during and after dormancy release) of two varieties characterized as early (Garnet) and late (Regina) flowering.
These CGs are then mapped and selected, based on their co-localization with QTLs, for validation using quantitative RT-PCR and association genetics.

Our project is part of a cherry breeding strategy mainly focused on developing cultivars that will be well adapted to future climatic conditions. However, the principal difficulty to this approach is our inability to test the trees under putative environmental conditions. We propose to develop a model that will predict a phenotype for a given genotype under expected climatic conditions. A preliminary predictive model is currently being built based on a wide set of flowering data obtained from various experimental sites in France and in Europe. Phenomic and genomic approaches allow us to better understand and identify key signaling pathways, which will be integrated in the phenology model. Thus the descriptive and predictive model will be based on more precise mechanisms involved in the developmental response of cherry tree to environmental conditions.

2 - Cherry quality: tolerance to fruit cracking

In addition to an increase in temperature, climate change is predicted to also lead to an evolution of rain falls, including an increase of rainstorms during spring and summer. In the last years, heavy rain falls have already been observed during springtime, which led to more than 80% yield loss caused by fruit cracking. We will then focus particularly on tolerance to rain-induced fruit cracking that currently represents the major agriculture issue in sweet cherry.

Study of the genetic determinism of tolerance to cracking is on-going using classic methods of mapping and QTL detection. Phenotyping is based on tedious visual observations, as they request a large amount of cherries per genotype in order to discriminate the different types of cracking (see figure below). Fine phenotypic studies are being investigated, which would allow correlating the tolerance to cracking to cell wall components and cherry fruit metabolites, characterized by high throughput metabolomics approaches. Subsequently, CGs, selected from signaling pathways that are potentially involved in the tolerance to cracking, will be further analyzed and co-localization between CGs and QTLs will be searched.

As a further step, multi-sites assays and experiments under controlled conditions will allow us to carry out finer studies on interaction between tolerance to cracking and climatic conditions.

Finally, modeling approaches will be developed in order to predict the cracking behavior of different genotypes, thus leading to ideotypes development.

A Breeding program

In addition to research, the A3C group leads a breeding program and conducts DUS (‘Distinction, Uniformity and Stability’) studies under the supervision of GEVES :

Breeding methodology :

The breeding program led on cherry focuses on a methodology of selection. Developing a marker assisted selection (MAS) should allow linking results on genetic determinism for the most important production traits in cherry to the breeding program. Molecular information will be transferred in order to select the most promising hybrids at very early stages using genotyping. Cherry trees are characterized by a long juvenile phase (4-5 years between hybrid seeds sowing and first fruits) hence this early selection approach is very interesting. The principal targeted traits are flowering and maturity dates, weight, fruit firmness and tolerance to fruit cracking. In the future, genomic selection strategies will also be explored.

This breeding program is led in close collaboration with CEP Innovation, our private partner, co-financing part of the program since 2011 and also co-breeder for future commercial cultivars.

DUS :

The A3C group conducts DUS (‘Distinction, Uniformity and Stability’) studies under the supervision of GEVES for cherry trees and their rootstocks. DUS studies consist in observing on several years new varieties according to well established descriptors. This leads to the confirmation that the request for the inscription into the official catalogue is acceptable. Therefore, following our DUS activity, the Plant Breeder’s Rights (In French, COV - Certificat d’Obtention Végétale) or the registration to the official varieties catalogue are granted.