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Ecophysiological and biophysical constraints on domestication in crop plants

Periodic Reporting for period 4 - CONSTRAINTS (Ecophysiological and biophysical constraints on domestication in crop plants)

Reporting period: 2019-12-01 to 2021-05-31

A fundamental question in biology is how constraints drive phenotypic changes and the diversification of life. While domesticated species are extraordinary models for tracking phenotypic changes in response to directional selection, we know little about the role of these constraints on crop domestication, nor how artificial selection can escape them.

Crop yields experienced spectacular growth during the Green Revolution thanks to plant breeding and agronomic development. Yet, crop improvement has not seen comparable advances for increased productivity in the last decades. Artificial selection over preexisting natural variation might have reached a dead end, and the environmental impacts of intensified agronomy are unsustainable in the long term. Thus, plant breeding may have to look for novel strategies to ensure food security and environmental sustainability for a steadily increasing human world population, including the creation of ideotypes adapted to low-input agricultural management. While new biotechnological tools producing ‘super-domesticates’ may offer qualitative advancement in breeding for higher productivity, plant breeding approaches rarely account for ecophysiological and biophysical constraints - linked to resource capture, use and partitioning - that can strongly limit the improvement of the basic functions of plants: growth, reproduction and survival. These constraints arise from trade-offs (i.e. the impossibility to simultaneously optimize two conflicting functions) that take place at different organizational levels: cell, organ, organism and crop (monoculture and mixture). These constraints are considered as obstacles for the improvement of target crop traits by plant breeders but their quantification remains scarce. Interestingly, several generic, cross-species, ecophysiological and biophysical constraints have been identified in theoretical and empirical ecology, with an acceleration in the last two decades with the rising of trait-based ecology. The CONSTRAINTS project highlighted the persistence of these constraints, found across wild species, within and between domesticated species. We have also identified candidate genes associated to these constraints, which represents a possibility to overcome them in future tradeoff-free improvement approaches.
There are three key milestones that the CONSTRAINTS team has accomplished.
First, databasing was pivotal to the CONSTRAINTS project. The team developed the CropTraits database that contains > 8,000 phenotypic data of model and crop species. A website (http://erc-constraints.cefe.cnrs.fr/database-croptraits/) has been created to facilitate interactions with data providers and users. Through the analysis of this database, for the first time, we identified key ecophysiological constraints that shape the phenotypic space of crop species.
Second, the development of the ‘functional rarity’ concept is a major achievement of the CONSTRAINTS project. The general idea was to find a method to test whether and how crop species can be considered as functional outlier (or functionally rare species) compared to wild species. This led to a very general concept that can be applied in many contexts. Two workshops were organized with French and international collaborators to build on the functional rarity project.
Third, we provided robust predictions of plant functional traits (leaf nitrogen content and specific leaf area in particular), plant ecological strategies and plant survival from near-infrared spectrometry using a portable device, which is a promising tool for future plant breeding programmes.
We found clear ecophysiological constraints (unknown up to now) in crop species, which will be very useful for future plant breeding programmes. We considered our findings beyond the state-of-the-art in three disciplines: (i) beyond the trait-by-trait and constraints-blind approach of crop science and plant breeding, (ii) beyond correlative approaches of functional ecology, (iii) beyond the developmental-constraints-as-the-major-constraints-for-trait-evolution paradigm of evolutionary biology. Using model species and genome-wide association studies, we discovered genes coding these constraints, a first step for genetic improvement.
Finally, our development of the functional rarity concept was unexpected at the beginning of the project. Functional ecology has long focused on common trends in trait-trait correlations while ignoring (functional) outliers. Here we developed a comprehensive framework to identify functional outliers among a set of species (or genotypes). These “outliers” can be good candidates to target in future plant breeding programmes. More broadly, our framework has already been used and applied in many contexts, including in biodiversity conservation programmes.
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