Adapting APSIM to model the physiology and genetics of complex adaptive traits in field crops

Abstract

Progress in molecular plant breeding is limited by the ability to predict plant phenotype based on its genotype, especially for complex adaptive traits. Suitably constructed crop growth and development models have the potential to bridge this predictability gap. A generic cereal crop growth and development model is outlined here. It is designed to exhibit reliable predictive skill at the crop level while also introducing sufficient physiological rigour for complex phenotypic responses to become emergent properties of the model dynamics. The approach quantifies capture and use of radiation, water, and nitrogen within a framework that predicts the realized growth of major organs based on their potential and whether the supply of carbohydrate and nitrogen can satisfy that potential. The model builds on existing approaches within the APSIM software platform. Experiments on diverse genotypes of sorghum that underpin the development and testing of the adapted crop model are detailed. Genotypes differing in height were found to differ in biomass partitioning among organs and a tall hybrid had significantly increased radiation use efficiency: a novel finding in sorghum. Introducing these genetic effects associated with plant height into the model generated emergent simulated phenotypic differences in green leaf area retention during grain filling via effects associated with nitrogen dynamics. The relevance to plant breeding of this capability in complex trait dissection and simulation is discussed.

Genotypic variation in soil water use and root distribution and their implications for drought tolerance in chickpea

“…In summary, when water is not limited plants prefer to utilise water more from surface soil layers (Ludlow and Muchow 1990). Plants are forced to mine deeper soil layers only when water is limited (Serraj et al 2004;Pinheiro et al 2005;Yu et al 2007;Manschadi et al 2010;Hammer et al 2009Hammer et al , 2010Wasson et al 2012;Comas et al 2013;Krishnamurthy et al 2013;Lynch 2013;Steele et al 2013). For example, in modelling exercises of soil water utilisation the root system had been considered to extract 40% of the total transpiration from the top quarter of root zone, even if the top layer is desiccated by evapotranspiration (Molz and Remson 1970) that was also confirmed to occur in chickpea (Krishnamurthy et al 1999(Krishnamurthy et al , 2010Serraj et al 2004;Kashiwagi et al 2015).…”

Water: the most important ‘molecular’ component of water stress tolerance research

“…Crop models can serve to 'integrate' complex behavioural/developmental processes of plants that are all related through water need/use. Not all models are suitable for this purpose, and those that are suitable must be designed such that the algorithms that are part of the model structure reflect observable and quantifiable biological observations (Sinclair and Seligman 2000;Hammer et al 2010).…”

Multiple cropping systems as drivers for providing multiple ecosystem services: from concepts to design

“…The combination of targeted functional traits can be based on current knowledge of the relationship between traits and functions (Lavorel and Garnier 2002;Suding et al 2008) or from a mechanistic model (Hammer et al 2010;Lynch 2013). If a trait value/state (or a combination of trait values) is not found in an available variety/breeding line, a breeding strategy is required specifically for multiple cropping systems.…”