Trait-based model development to support breeding programs. A case study for salt tolerance and rice

Abstract

Eco-physiological models are increasingly used to analyze G × E × M interactions to support breeding programs via the design of ideotypes for specific contexts. However, available crop models are only partly suitable for this purpose, since they often lack clear relationships between parameters and traits breeders are working on. Taking salt stress tolerance and rice as a case study, we propose a paradigm shift towards the building of ideotyping-specific models explicitly around traits involved in breeding programs. Salt tolerance is a complex trait relying on different physiological processes that can be alternatively selected to improve the overall crop tolerance. We developed a new model explicitly accounting for these traits and we evaluated its performance using data from growth chamber experiments (e.g., R2 ranged from 0.74 to 0.94 for the biomass of different plant organs). Using the model, we were able to show how an increase in the overall tolerance can derive from completely different physiological mechanisms according to soil/water salinity dynamics. The study demonstrated that a trait-based approach can increase the usefulness of mathematical models for supporting breeding programs.

Analysis and Modeling of Processes Involved with Salt Tolerance and Rice

“…Data from the two experiments validated the model proposed by Paleari et al (2017b), given the strong agreement achieved between measured and simulated data. Agreement metrics indeed confirmed the capability of the model to correctly reproduce the impact of salt stress on crop growth, especially the salt-induced decrease in AGB and panicle biomass.…”

“…The salinity model proposed by Paleari et al (2017b) was used, coupled with the World Food Studies (WOFOST) crop model (Van Diepen et al, 1989). In particular, we used the version of WOFOST proposed by Stella et al (2014), available at http:// www.cassandralab.com/components/1.…”

“…A quantitative understanding of the different mechanisms involved with salt stress would represent a solution for increasing food production (Reddy et al, 2017), given that it would allow developing cultivars improved for the specific traits that guarantee the largest benefits for the salinity dynamics affecting a given rice district (Paleari et al, 2017b). However, progress in dedicated breeding programs has been limited by (i) gaps in knowledge of the genetic basis of tolerance, (ii) the involvement of different complex tolerance mechanisms, (iii) inadequate screening techniques, and (iv) low selection efficiency (Yeo and Flowers, 1986;Reddy et al, 2014).…”

“…A new model for the simulation of the ionic component of salt stress was recently proposed by Paleari et al (2017b). The model focuses on the key mechanisms that regulate Na + uptake, Na + sequestration into different organs, and the related impacts on photosynthesis, leaf senescence, and spikelet sterility.…”

“…This study was aimed at (i) collecting specific datasets (from growth chamber experiments) to investigate the effects of the ionic component of salt stress at the plant organ level, and (ii) parameterizing and evaluating the salinity model developed by Paleari et al (2017b) for three cultivars differing in salt tolerance.…”