Karine Chenu

Simulating the Yield Impacts of Organ-Level Quantitative Trait Loci Associated With Drought Response in Maize: A “Gene-to-Phenotype” Modeling Approach

Under drought, substantial genotype–environment (G × E) interactions impede breeding progress for yield. Identifying genetic controls associated with yield response is confounded by poor genetic correlations across testing environments. Part of this problem is related to our inability to account for the interplay of genetic controls, physiological traits, and environmental conditions throughout the crop cycle. We propose a modeling approach to bridge this “gene-to-phenotype” gap. For maize under drought, we simulated the impact of quantitative trait loci (QTL) controlling two key processes (leaf and silk elongation) that influence crop growth, water use, and grain yield. Substantial G × E interaction for yield was simulated for hypothetical recombinant inbred lines (RILs) across different seasonal patterns of drought. QTL that accelerated leaf elongation caused an increase in crop leaf area and yield in well-watered or preflowering water deficit conditions, but a reduction in yield under terminal stresses (as such “leafy” genotypes prematurely exhausted the water supply). The QTL impact on yield was substantially enhanced by including pleiotropic effects of these QTL on silk elongation and on consequent grain set. The simulations obtained illustrated the difficulty of interpreting the genetic control of yield for genotypes influenced only by the additive effects of QTL associated with leaf and silk growth. The results highlight the potential of integrative simulation modeling for gene-to-phenotype prediction and for exploiting G × E interactions for complex traits such as drought tolerance.

Environment characterization as an aid to wheat improvement: interpreting genotype–environment interactions by modelling water-deficit patterns in North-Eastern Australia

Genotype-environment interactions (GEI) limit genetic gain for complex traits such as tolerance to drought. Characterization of the crop environment is an important step in understanding GEI. A modelling approach is proposed here to characterize broadly (large geographic area, long-term period) and locally (field experiment) drought-related environmental stresses, which enables breeders to analyse their experimental trials with regard to the broad population of environments that they target. Water-deficit patterns experienced by wheat crops were determined for drought-prone north-eastern Australia, using the APSIM crop model to account for the interactions of crops with their environment (e.g. feedback of plant growth on water depletion). Simulations based on more than 100 years of historical climate data were conducted for representative locations, soils, and management systems, for a check cultivar, Hartog. The three main environment types identified differed in their patterns of simulated water stress around flowering and during grain-filling. Over the entire region, the terminal drought-stress pattern was most common (50% of production environments) followed by a flowering stress (24%), although the frequencies of occurrence of the three types varied greatly across regions, years, and management. This environment classification was applied to 16 trials relevant to late stages testing of a breeding programme. The incorporation of the independently-determined environment types in a statistical analysis assisted interpretation of the GEI for yield among the 18 representative genotypes by reducing the relative effect of GEI compared with genotypic variance, and helped to identify opportunities to improve breeding and germplasm-testing strategies for this region.

Detection and use of QTL for complex traits in multiple environments

QTL mapping methods for complex traits are challenged by new developments in marker technology, phenotyping platforms, and breeding methods. In meeting these challenges, QTL mapping approaches will need to also acknowledge the central roles of QTL by environment interactions (QEI) and QTL by trait interactions in the expression of complex traits like yield. This paper presents an overview of mixed model QTL methodology that is suitable for many types of populations and that allows predictive modeling of QEI, both for environmental and developmental gradients. Attention is also given to multi-trait QTL models which are essential to interpret the genetic basis of trait correlations. Biophysical (crop growth) model simulations are proposed as a complement to statistical QTL mapping for the interpretation of the nature of QEI and to investigate better methods for the dissection of complex traits into component traits and their genetic controls.

Large‐scale characterization of drought pattern: a continent‐wide modelling approach applied to the Australian wheatbelt – spatial and temporal trends

Plant response to drought is complex, so that traits adapted to a specific drought type can confer disadvantage in another drought type. Understanding which type(s) of drought to target is of prime importance for crop improvement. Modelling was used to quantify seasonal drought patterns for a check variety across the Australian wheatbelt, using 123 yr of weather data for representative locations and managements. Two other genotypes were used to simulate the impact of maturity on drought pattern. Four major environment types summarized the variability in drought pattern over time and space. Severe stress beginning before flowering was common (44% of occurrences), with (24%) or without (20%) relief during grain filling. High variability occurred from year to year, differing with geographical region. With few exceptions, all four environment types occurred in most seasons, for each location, management system and genotype. Applications of such environment characterization are proposed to assist breeding and research to focus on germplasm, traits and genes of interest for target environments. The method was applied at a continental scale to highly variable environments and could be extended to other crops, to other drought-prone regions around the world, and to quantify potential changes in drought patterns under future climates.

The shifting influence of drought and heat stress for crops in northeast Australia

Characterization of drought environment types (ETs) has proven useful for breeding crops for drought-prone regions. Here, we consider how changes in climate and atmospheric carbon dioxide (CO2 ) concentrations will affect drought ET frequencies in sorghum and wheat systems of northeast Australia. We also modify APSIM (the Agricultural Production Systems Simulator) to incorporate extreme heat effects on grain number and weight, and then evaluate changes in the occurrence of heat-induced yield losses of more than 10%, as well as the co-occurrence of drought and heat. More than six million simulations spanning representative locations, soil types, management systems, and 33 climate projections led to three key findings. First, the projected frequency of drought decreased slightly for most climate projections for both sorghum and wheat, but for different reasons. In sorghum, warming exacerbated drought stresses by raising the atmospheric vapor pressure deficit and reducing transpiration efficiency (TE), but an increase in TE due to elevated CO2 more than offset these effects. In wheat, warming reduced drought stress during spring by hastening development through winter and reducing exposure to terminal drought. Elevated CO2 increased TE but also raised radiation-use efficiency and overall growth rates and water use, thereby offsetting much of the drought reduction from warming. Second, adding explicit effects of heat on grain number and grain size often switched projected yield impacts from positive to negative. Finally, although average yield losses associated with drought will remain generally higher than that for heat stress for the next half century, the relative importance of heat is steadily growing. This trend, as well as the likely high degree of genetic variability in heat tolerance, suggests that more emphasis on heat tolerance is warranted in breeding programs. At the same time, work on drought tolerance should continue with an emphasis on drought that co-occurs with extreme heat.

A multisite managed environment facility for targeted trait and germplasm phenotyping

Field evaluation of germplasm for performance under water and heat stress is challenging. Field environments are variable and unpredictable, and genotype×environment interactions are difficult to interpret if environments are not well characterised. Numerous traits, genes and quantitative trait loci have been proposed for improving performance but few have been used in variety development. This reflects the limited capacity of commercial breeding companies to screen for these traits and the absence of validation in field environments relevant to breeding companies, and because little is known about the economic benefit of selecting one particular trait over another. The value of the proposed traits or genes is commonly not demonstrated in genetic backgrounds of value to breeding companies. To overcome this disconnection between physiological trait breeding and uptake by breeding companies, three field sites representing the main environment types encountered across the Australian wheatbelt were selected to form a set of managed environment facilities (MEFs). Each MEF manages soil moisture stress through irrigation, and the effects of heat stress through variable sowing dates. Field trials are monitored continuously for weather variables and changes in soil water and canopy temperature in selected probe genotypes, which aids in decisions guiding irrigation scheduling and sampling times. Protocols have been standardised for an essential core set of measurements so that phenotyping yield and other traits are consistent across sites and seasons. MEFs enable assessment of a large number of traits across multiple genetic backgrounds in relevant environments, determine relative trait value, and facilitate delivery of promising germplasm and high value traits into commercial breeding programs.

Frost trends and their estimated impact on yield in the Australian wheatbelt

Highlight Over the last decades, the impact of post-heading frost on yield has increased in major parts of the Australian wheatbelt. Despite global warming, frost remains a high priority for breeding.

High-throughput phenotyping of seminal root traits in wheat.

BackgroundWater availability is a major limiting factor for wheat (Triticum aestivum L.) production in rain-fed agricultural systems worldwide. Root system architecture has important functional implications for the timing and extent of soil water extraction, yet selection for root architectural traits in breeding programs has been limited by a lack of suitable phenotyping methods. The aim of this research was to develop low-cost high-throughput phenotyping methods to facilitate selection for desirable root architectural traits. Here, we report two methods, one using clear pots and the other using growth pouches, to assess the angle and the number of seminal roots in wheat seedlings– two proxy traits associated with the root architecture of mature wheat plants.ResultsBoth methods revealed genetic variation for seminal root angle and number in the panel of 24 wheat cultivars. The clear pot method provided higher heritability and higher genetic correlations across experiments compared to the growth pouch method. In addition, the clear pot method was more efficient – requiring less time, space, and labour compared to the growth pouch method. Therefore the clear pot method was considered the most suitable for large-scale and high-throughput screening of seedling root characteristics in crop improvement programs.ConclusionsThe clear-pot method could be easily integrated in breeding programs targeting drought tolerance to rapidly enrich breeding populations with desirable alleles. For instance, selection for narrow root angle and high number of seminal roots could lead to deeper root systems with higher branching at depth. Such root characteristics are highly desirable in wheat to cope with anticipated future climate conditions, particularly where crops rely heavily on stored soil moisture at depth, including some Australian, Indian, South American, and African cropping regions.

Integrated responses of rosette organogenesis, morphogenesis and architecture to reduced incident light in Arabidopsis thaliana results in higher efficiency of light interception

Plants have a high phenotypic plasticity in response to light. We investigated changes in plant architecture in response to decreased incident light levels in Arabidopsis thaliana (L.) Heynh, focusing on organogenesis and morphogenesis, and on consequences for the efficiency of light interception of the rosette. A. thaliana ecotype Columbia plants were grown under various levels of incident photosynthetically active radiation (PAR), with blue light (BL) intensity proportional to incident PAR intensity and with a high and stable red to far-red light ratio. We estimated the PAR absorbed by the plant, using data from precise characterisation of the light environment and 3-dimensional simulations of virtual plants generated with AMAPsim software. Decreases in incident PAR modified rosette architecture; leaf area decreased, leaf blades tended to be more circular and petioles were longer and thinner. However, the efficiency of light interception by the rosette was slightly higher in plants subjected to lower PAR intensities, despite the reduction in leaf area. Decreased incident PAR delayed leaf initiation and slowed down relative leaf expansion rate, but increased the duration of leaf expansion. The leaf initiation rate and the relative expansion rate during the first third of leaf development were related to the amount of PAR absorbed. The duration of leaf expansion was related to PAR intensity. The relationships identified could be used to analyse the phenotypic plasticity of various genotypes of Arabidopsis. Overall, decreases in incident PAR result in an increase in the efficiency of light interception.

Using a 3-D virtual sunflower to simulate light capture at organ, plant and plot levels : Contribution of organ interception, impact of heliotropism and analysis of genotypic differences

BACKGROUND AND AIMS Light interception is a critical factor in the production of biomass. The study presented here describes a method used to take account of architectural changes over time in sunflower and to estimate absorbed light at the organ level. METHODS The amount of photosynthetically active radiation absorbed by a plant is estimated on a daily or hourly basis through precise characterization of the light environment and three-dimensional virtual plants built using AMAP software. Several treatments are performed over four experiments and on two genotypes to test the model, quantify the contribution of different organs to light interception and evaluate the impact of heliotropism. KEY RESULTS This approach is used to simulate the amount of light absorbed at organ and plant scales from crop emergence to maturity. Blades and capitula were the major contributors to light interception, whereas that by petioles and stem was negligible. Light regimen simulations showed that heliotropism decreased the cumulated light intercepted at the plant scale by close to 2.2% over one day. CONCLUSIONS The approach is useful in characterizing the light environment of organs and the whole plant, especially for studies on heterogeneous canopies or for quantifying genotypic or environmental impacts on plant architecture, where conventional approaches are ineffective. This model paves the way to analyses of genotype-environment interactions and could help establish new selection criteria based on architectural improvement, enhancing plant light interception.