Potential abiotic stress targets for modern genetic manipulation

Research into crop yield and resilience has underpinned global food security, evident in yields tripling in the past 5 decades. The challenges that global agriculture now faces are not just to feed 10+ billion people within a generation, but to do so under a harsher, more variable, and less predictable climate, and in many cases with less water, more expensive inputs, and declining soil quality. The challenges of climate change are not simply to breed for a "hotter drier climate," but to enable resilience to floods and droughts and frosts and heat waves, possibly even within a single growing season. How well we prepare for the coming decades of climate variability will depend on our ability to modify current practices, innovate with novel breeding methods, and communicate and work with farming communities to ensure viability and profitability. Here we define how future climates will impact farming systems and growing seasons, thereby identifying the traits and practices needed and including exemplars being implemented and developed. Critically, this review will also consider societal perspectives and public engagement about emerging technologies for climate resilience, with participatory approaches presented as the best approach.

Seedling and field assessment of wheat (Triticum aestivum L.) dwarfing genes and their influence on root traits in multiple genetic backgrounds

Deployment of the Rht-B1b and Rht-D1b dwarfing genes helped facilitate the Green Revolution to increase wheat yields globally. Much is known of the influence of these genes on plant height and agronomic performance, but not of their effects on root architecture. We assessed 29 near-isogenic lines (NILs) representing 11 Green Revolution and alternative dwarfing genes across multiple genetic backgrounds for root architecture characteristics in controlled and field environments. Genetic background did not influence plant height, but had a small and significant (P<0.05) effect on root architecture. All dwarfing gene NILs were significantly (P<0.01) shorter compared with tall controls. The Green Revolution Rht-B1b and Rht-D1b sometimes had longer seedling roots but were not different from their respective tall controls for root depth in the field. The Rht8, Rht12, and Rht18 dwarfing gene NILs produced long seminal roots in seedling pouches, and a greater maximum rooting depth (MRD) and root penetration rate (RPR) in the field. Genotypic increases in MRD and RPR were strongly correlated with increased harvest index and grain yield, particularly in dry environments. Careful root phenotyping highlights the potential of novel dwarfing genes for wheat genetic improvement under water-limited conditions.

Genotypic variation and covariation in wheat seedling seminal root architecture and grain yield under field conditions

Greater embryo size in a large and carefully phenotyped mapping population was genetically associated with a greater number of longer seminal roots to increase grain yield in droughted field environments. Breeding modification of root architecture is challenging in field environments owing to genetic and phenotypic complexity, and poor repeatability with root sampling. Seeds from a large mapping population varying in embryo size were harvested from a common glasshouse and standardised to a common size before assessing in rolled germination paper at 12 and 20 °C for seedling growth. Differences in genotype means were large and heritabilities high (h² = 0.55-0.93) indicating strong and repeatable genotypic differences for most root traits. Seminal roots 1 to 3 were produced on all seedlings, whereas growth of seminal roots 4, 5 and 6 was associated with differences in embryo size. Increases in seminal root number from 4 to 6 per plant were strongly, genetically correlated with increases in total seminal length (r_g = 0.84, < 0.01). Multivariate analysis confirmed initiation and growth of seminal roots 1, 2 and 3, and of roots 4, 5 and 6 behaved as genetically independent (r_Pg = 0.15 ns) cohorts. Tails representing extremes in seedling root length and number were associated with significant differences in grain yield of up to 35% in droughted field environments but were not different in irrigated environments. Increases in grain yield were linked to greater lengths of seminal roots 4, 5 and 6 and were largely independent of plant height or development. This is the first report on the genetic relationship of seedling root architecture and embryo size, and potential in selection of seminal root size for accessing deep-soil moisture in droughted environments.

Selection for early shoot vigour in wheat increases root hair length but reduces epidermal cell size of roots and leaves

Six cycles of recurrent selection for early shoot vigour in wheat resulted in significant increases in leaf width and shoot biomass. Here, in replicated controlled-environment studies, the effect of early shoot vigour on root biomass, rhizosheath size, root hair length, and cell size in the roots and leaves was examined across different cycles of selection. Increased shoot vigour was associated with greater root biomass, larger rhizosheath size, and longer root hairs. Our findings demonstrate that rhizosheath size was a reliable surrogate for root hair length in this germplasm. Examination of the root epidermis revealed that the 'cell body' of the trichoblasts (hair-forming cells) and the atrichoblasts (non-hair-forming cells) decreased in size as shoot vigour increased. Therefore, in higher vigour germplasm, longer root hairs emerged from smaller trichoblasts so that total trichoblast volume (root hair plus cell body) was generally similar regardless of shoot vigour. Similarly, the sizes of the four main cell types on the leaf epidermis became progressively smaller as shoot vigour increased, which also increased stomatal density. The relationship between shoot vigour and root traits is considered, and the potential contribution of below-ground root traits to performance and competitiveness of high vigour germplasm is discussed.

Impact of Varying Light and Dew on Ground Cover Estimates from Active NDVI, RGB, and LiDAR

Canopy ground cover (GC) is an important agronomic measure for evaluating crop establishment and early growth. This study evaluates the reliability of GC estimates, in the presence of varying light and dew on leaves, from three different ground-based sensors: (1) normalized difference vegetation index (NDVI) from the commercially available GreenSeeker®; (2) RGB images from a digital camera, where GC was determined as the portion of pixels from each image meeting a greenness criterion (i.e., (Green - Red)/(Green + Red) > 0); and (3) LiDAR using two separate approaches: (a) GC from LiDAR red reflectance (whereby red reflectance less than five was classified as vegetation) and (b) GC from LiDAR height (whereby height greater than 10 cm was classified as vegetation). Hourly measurements were made early in the season at two different growth stages (tillering and stem elongation), among wheat genotypes highly diverse for canopy characteristics. The active NDVI showed the least variation through time and was particularly stable, regardless of the available light or the presence of dew. In addition, between-sample-time Pearson correlations for NDVI were consistently high and significant (P < 0.0001), ranging from 0.89 to 0.98. In comparison, GC from LiDAR and RGB showed greater variation across sampling times, and LiDAR red reflectance was strongly influenced by the presence of dew. Excluding times when the light was exceedingly low, correlations between GC from RGB and NDVI were consistently high (ranging from 0.79 to 0.92). The high reliability of the active NDVI sensor potentially affords a high degree of flexibility for users by enabling sampling across a broad range of acceptable light conditions.

A reduced-tillering trait shows small but important yield gains in dryland wheat production

Reducing the number of tillers per plant using a tiller inhibition (tin) gene has been considered as an important trait for wheat production in dryland environments. We used a spatial analysis approach with a daily time-step coupled radiation and transpiration efficiency model to simulate the impact of the reduced-tillering trait on wheat yield under different climate change scenarios across Australia's arable land. Our results show a small but consistent yield advantage of the reduced-tillering trait in the most water-limited environments both under current and likely future conditions. Our climate scenarios show that whilst elevated [CO₂ ] (e[CO₂ ]) alone might limit the area where the reduced-tillering trait is advantageous, the most likely climate scenario of e[CO₂ ] combined with increased temperature and reduced rainfall consistently increased the area where restricted tillering has an advantage. Whilst long-term average yield advantages were small (ranged from 31 to 51 kg ha^-1  year^-1 ), across large dryland areas the value is large (potential cost-benefits ranged from Australian dollar 23 to 60 MIL/year). It seems therefore worthwhile to further explore this reduced-tillering trait in relation to a range of different environments and climates, because its benefits are likely to grow in future dry environments where wheat is grown around the world.

Ground-Based LiDAR Improves Phenotypic Repeatability of Above-Ground Biomass and Crop Growth Rate in Wheat

Highly repeatable, nondestructive, and high-throughput measures of above-ground biomass (AGB) and crop growth rate (CGR) are important for wheat improvement programs. This study evaluates the repeatability of destructive AGB and CGR measurements in comparison to two previously described methods for the estimation of AGB from LiDAR: 3D voxel index (3DVI) and 3D profile index (3DPI). Across three field experiments, contrasting in available water supply and comprising up to 98 wheat genotypes varying for canopy architecture, several concurrent measurements of LiDAR and AGB were made from jointing to anthesis. Phenotypic correlations at discrete events between AGB and the LiDAR-derived biomass indices were significant, ranging from 0.31 (P < 0.05) to 0.86 (P < 0.0001), providing confidence in the LiDAR indices as effective surrogates for AGB. The repeatability of the LiDAR biomass indices at discrete events was at least similar to and often higher than AGB, particularly under water limitation. The correlations between calculated CGR for AGB and the LiDAR indices were moderate to high and varied between experiments. However, across all experiments, the repeatabilities of the CGR derived from the LiDAR indices were appreciably greater than those for AGB, except for the 3DPI in the water-limited environment. In our experiments, the repeatability of either LiDAR index was consistently higher than that of AGB, both at discrete time points and when CGR was calculated. These findings provide promising support for the reliable use of ground-based LiDAR, as a surrogate measure of AGB and CGR, for screening germplasm in research and wheat breeding.

Wheat drought tolerance in the field is predicted by amino acid responses to glasshouse-imposed drought

Water limits crop productivity, so selecting for a minimal yield gap in drier environments is critical to mitigate against climate change and land-use pressure. We investigated the responses of relative water content (RWC), stomatal conductance, chlorophyll content, and metabolites in flag leaves of commercial wheat (Triticum aestivum L.) cultivars to three drought treatments in the glasshouse and in field environments. We observed strong genetic associations between glasshouse-based RWC, metabolites, and yield gap-based drought tolerance (YDT; the ratio of yield in water-limited versus well-watered conditions) across 18 field environments spanning sites and seasons. Critically, RWC response to glasshouse drought was strongly associated with both YDT (r2=0.85, P<8E-6) and RWC under field drought (r2=0.77, P<0.05). Moreover, multiple regression analyses revealed that 98% of genetic YDT variance was explained by drought responses of four metabolites: serine, asparagine, methionine, and lysine (R2=0.98; P<0.01). Fitted coefficients suggested that, for given levels of serine and asparagine, stronger methionine and lysine accumulation was associated with higher YDT. Collectively, our results demonstrate that high-throughput, targeted metabolic phenotyping of glasshouse-grown plants may be an effective tool for selection of wheat cultivars with high field-derived YDT.

Deeper roots associated with cooler canopies, higher normalized difference vegetation index, and greater yield in three wheat populations grown on stored soil water

Simple and repeatable methods are needed to select for deep roots under field conditions. A large-scale field experiment was conducted to assess the association between canopy temperature (CT) measured by airborne thermography and rooting depth determined by the core-break method. Three wheat populations, C306×Westonia (CW), Hartog×Drysdale (HD), and Sundor×Songlen (SS), were grown on stored soil water in NSW Australia in 2017 (n=196-252). Cool and warm CT extremes ('tails') were cored after harvest (13-32% of each population). Rooting depth was significantly correlated with CT at late flowering (r= -0.25, -0.52, and -0.23 for CW, HD, and SS, respectively, P<0.05 hereafter), with normalized difference vegetation index (NDVI) at early grain filling (r=0.30-0.39), and with canopy height (r=0.23-0.48). The cool tails showed significantly deeper roots than the respective warm tails by 8.1 cm and 6.2 cm in CW and HD, and correspondingly, greater yields by an average 19% and 7%, respectively. This study highlighted that CT measured rapidly by airborne thermography or NDVI at early grain filling could be used to guide selection of lines with deeper roots to increase wheat yields. The remote measurement methods in this study were repeatable and high throughput, making them well suited to use in breeding programmes.

Evaluation of the Phenotypic Repeatability of Canopy Temperature in Wheat Using Continuous-Terrestrial and Airborne Measurements

Infrared canopy temperature (CT) is a well-established surrogate measure of stomatal conductance. There is ample evidence showing that genotypic variation in stomatal conductance is associated with grain yield in wheat. Our goal was to determine when CT repeatability is greatest (throughout the season and within the day) to guide CT deployment for research and wheat breeding. CT was measured continuously with ArduCrop wireless infrared thermometers from post-tillering to physiological maturity, and with airborne thermography on cloudless days from manned helicopter at multiple times before and after flowering. Our experiments in wheat, across two years contrasting for water availability, showed that repeatability for CT was greatest later in the season, during grain-filling, and usually in the afternoon. This was supported by the observation that repeatability for ArduCrop, and more so for airborne CT, was significantly associated (P < 0.0001) with calculated clear-sky solar radiation and to a lesser degree, vapor pressure deficit. Adding vapor pressure deficit to a model comprising either clear-sky solar radiation or its determinants, day-of-year and hour-of-day, made little to no improvement to the coefficient of determination. Phenotypic correlations for airborne CT afternoon sampling events were consistently high between events in the same year, more so for the year when soil water was plentiful (r = 0.7 to 0.9) than the year where soil water was limiting (r = 0.4 to 0.9). Phenotypic correlations for afternoon airborne CT were moderate between years contrasting in soil water availability (r = 0.1 to 0.5) and notably greater on two separate days following irrigation or rain in the drier year, ranging from r = 0.39 to 0.53 (P < 0.0001) for the midday events. For ArduCrop CT the pattern of phenotypic correlations, within a given year, was similar for both years: phenotypic correlations were higher during the grain-filling months of October and November and for hours-of-day from 11 onwards. The lowest correlations comprised events from hours-of-day 8 and 9 across all months. The capacity for the airborne method to instantaneously sample CT on hundreds of plots is more suited to large field experiments than the static ArduCrop sensors which measure CT continuously on a single experimental plot at any given time. Our findings provide promising support for the reliable deployment of CT phenotyping for research and wheat breeding, whereby the high repeatability and high phenotypic correlations between afternoon sampling events during grain-filling could enable reliable screening of germplasm from only one or two sampling events.

Review: High-throughput phenotyping to enhance the use of crop genetic resources

Improved genetic, genomic and statistical technologies have increased the capacity to enrich breeding populations for key alleles underpinning adaptation and continued genetic gain. In turn, directed genomic selection together with increased heritability will reduce genetic variance to narrow the genetic base in many crop breeding programs. Diverse genetic resources (GR), including wild and weedy relatives, landraces and reconstituted synthetics, have potential to contribute novel alleles for key traits. Targeted trait identification may also identify genetic diversity in addressing new challenges including the need for modified root architecture, greater nutrient-use efficiency, and adaptation to warmer air and soil temperatures forecast with climate change. Yet while core collections and other GR sources have historically been invaluable for major gene control of disease and subsoil constraints, the mining of genetically (and phenotypically) complex traits in GR remains a significant challenge owing to reduced fertility, limited seed quantities and poor adaptation through linkage drag with undesirable alleles. High-throughput field phenomics (HTFP) offers the opportunity to capture phenotypically complex variation underpinning adaptation in traditional phenotypic selection or statistics-based breeding programs. Targeted HTFP will permit the reliable phenotyping of greater numbers of GR-derived breeding lines using smaller plot sizes and at earlier stages of population development to reduce the duration of breeding cycles and the loss of potentially important alleles with linkage drag. Two key opportunities are highlighted for use of HTFP in selection among GR-derived wheat breeding lines for greater biomass and stomatal conductance through canopy temperature.

Modelling impact of early vigour on wheat yield in dryland regions

Early vigour, or faster early leaf area development, has been considered an important trait for rainfed wheat in dryland regions such as Australia. However, early vigour is a genetically complex trait, and results from field experiments have been highly variable. Whether early vigour can lead to improved water use efficiency and crop yields is strongly dependent on climate and management conditions across the entire growing season. Here, we present a modelling framework for simulating the impact of early vigour on wheat growth and yield at eight sites representing the major climate types in Australia. On a typical soil with plant available water capacity (PAWC) of 147 mm, simulated yield increase with early vigour associated with larger seed size was on average 4% higher compared with normal vigour wheat. Early vigour through selection of doubled early leaf sizes could increase yield by 16%. Increase in yield was mainly from increase in biomass and grain number, and was reduced at sites with seasonal rainfall plus initial soil water <300 mm. Opportunities exists for development of early vigour wheat varieties for wetter sites. Soil PAWC could play a significant role in delivering the benefit of early vigour and would require particular attention.

Improving process-based crop models to better capture genotype×environment×management interactions

In spite of the increasing expectation for process-based crop modelling to capture genotype (G) by environment (E) by management (M) interactions to support breeding selections, it remains a challenge to use current crop models to accurately predict phenotypes from genotypes or from candidate genes. We use wheat as a target crop and the APSIM farming systems model (Holzworth et al., 2014) as an example to analyse the current status of process-based crop models with a major focus on need to improve simulation of specific eco-physiological processes and their linkage to underlying genetic controls. For challenging production environments in Australia, we examine the potential opportunities to capture physiological traits, and to integrate genetic and molecular approaches for future model development and applications. Model improvement will require both reducing the uncertainty in simulating key physiological processes and enhancing the capture of key observable traits and underlying genetic control of key physiological responses to environment. An approach consisting of three interactive stages is outlined to (i) improve modelling of crop physiology, (ii) develop linkage from model parameter to genotypes and further to loci or alleles, and (iii) further link to gene expression pathways. This helps to facilitate the integration of modelling, phenotyping, and functional gene detection and to effectively advance modelling of G×E×M interactions. While gene-based modelling is not always needed to simulate G×E×M, including well-understood gene effects can improve the estimation of genotype effects and prediction of phenotypes. Specific examples are given for enhanced modelling of wheat in the APSIM framework.

Accounting for Genotype-by-Environment Interactions and Residual Genetic Variation in Genomic Selection for Water-Soluble Carbohydrate Concentration in Wheat

Abiotic stress tolerance traits are often complex and recalcitrant targets for conventional breeding improvement in many crop species. This study evaluated the potential of genomic selection to predict water-soluble carbohydrate concentration (WSCC), an important drought tolerance trait, in wheat under field conditions. A panel of 358 varieties and breeding lines constrained for maturity was evaluated under rainfed and irrigated treatments across two locations and two years. Whole-genome marker profiles and factor analytic mixed models were used to generate genomic estimated breeding values (GEBVs) for specific environments and environment groups. Additive genetic variance was smaller than residual genetic variance for WSCC, such that genotypic values were dominated by residual genetic effects rather than additive breeding values. As a result, GEBVs were not accurate predictors of genotypic values of the extant lines, but GEBVs should be reliable selection criteria to choose parents for intermating to produce new populations. The accuracy of GEBVs for untested lines was sufficient to increase predicted genetic gain from genomic selection per unit time compared to phenotypic selection if the breeding cycle is reduced by half by the use of GEBVs in off-season generations. Further, genomic prediction accuracy depended on having phenotypic data from environments with strong correlations with target production environments to build prediction models. By combining high-density marker genotypes, stress-managed field evaluations, and mixed models that model simultaneously covariances among genotypes and covariances of complex trait performance between pairs of environments, we were able to train models with good accuracy to facilitate genetic gain from genomic selection.

High Throughput Determination of Plant Height, Ground Cover, and Above-Ground Biomass in Wheat with LiDAR

Crop improvement efforts are targeting increased above-ground biomass and radiation-use efficiency as drivers for greater yield. Early ground cover and canopy height contribute to biomass production, but manual measurements of these traits, and in particular above-ground biomass, are slow and labor-intensive, more so when made at multiple developmental stages. These constraints limit the ability to capture these data in a temporal fashion, hampering insights that could be gained from multi-dimensional data. Here we demonstrate the capacity of Light Detection and Ranging (LiDAR), mounted on a lightweight, mobile, ground-based platform, for rapid multi-temporal and non-destructive estimation of canopy height, ground cover and above-ground biomass. Field validation of LiDAR measurements is presented. For canopy height, strong relationships with LiDAR (r2 of 0.99 and root mean square error of 0.017 m) were obtained. Ground cover was estimated from LiDAR using two methodologies: red reflectance image and canopy height. In contrast to NDVI, LiDAR was not affected by saturation at high ground cover, and the comparison of both LiDAR methodologies showed strong association (r2 = 0.92 and slope = 1.02) at ground cover above 0.8. For above-ground biomass, a dedicated field experiment was performed with destructive biomass sampled eight times across different developmental stages. Two methodologies are presented for the estimation of biomass from LiDAR: 3D voxel index (3DVI) and 3D profile index (3DPI). The parameters involved in the calculation of 3DVI and 3DPI were optimized for each sample event from tillering to maturity, as well as generalized for any developmental stage. Individual sample point predictions were strong while predictions across all eight sample events, provided the strongest association with biomass (r2 = 0.93 and r2 = 0.92) for 3DPI and 3DVI, respectively. Given these results, we believe that application of this system will provide new opportunities to deliver improved genotypes and agronomic interventions via more efficient and reliable phenotyping of these important traits in large experiments.

Selection for water-soluble carbohydrate accumulation and investigation of genetic × environment interactions in an elite wheat breeding population

Water-soluble carbohydrate accumulation can be selected in wheat breeding programs with consideration of genetic × environmental interactions and relationships with other important characteristics such as relative maturity and nitrogen concentration, although the correlation between WSC traits and grain yield is low and inconsistent. The potential to increase the genetic capacity for water-soluble carbohydrate (WSC) accumulation is an opportunity to improve the drought tolerance capability of rainfed wheat varieties, particularly in environments where terminal drought is a significant constraint to wheat production. A population of elite breeding germplasm was characterized to investigate the potential for selection of improved WSC concentration and total amount in water deficit and well-watered environments. Accumulation of WSC involves complex interactions with other traits and the environment. For both WSC concentration (WSCC) and total WSC per area (WSCA), strong genotype × environment interactions were reflected in the clear grouping of experiments into well-watered and water deficit environment clusters. Genetic correlations between experiments were high within clusters. Heritability for WSCC was larger than for WSCA, and significant associations were observed in both well-watered and water deficit experiment clusters between the WSC traits and nitrogen concentration, tillering, grains per m², and grain size. However, correlations between grain yield and WSCC or WSCA were weak and variable, suggesting that selection for these traits is not a better strategy for improving yield under drought than direct selection for yield.

Genome-Wide Associations for Water-Soluble Carbohydrate Concentration and Relative Maturity in Wheat Using SNP and DArT Marker Arrays

Improving water-use efficiency by incorporating drought avoidance traits into new wheat varieties is an important objective for wheat breeding in water-limited environments. This study uses genome wide association studies (GWAS) to identify candidate loci for water-soluble carbohydrate accumulation-an important drought-avoidance characteristic in wheat. Phenotypes from a multi-environment trial with experiments differing in water availability and separate single nucleotide polymorphism (SNP) and diversity arrays technology (DArT) marker sets were used to perform the analyses. Significant associations for water-soluble carbohydrate accumulation were identified on chromosomes 1A, 1B, 1D, 2D, and 4A. Notably, these loci did not collocate with the major loci identified for relative maturity. Loci on chromosome 1D collocated with markers previously associated with the high molecular weight glutenin Glu-D1 locus. Genetic × environmental interactions impacted the results strongly, with significant associations for carbohydrate accumulation identified only in the water-deficit experiments. The markers associated with carbohydrate accumulation may be useful for marker-assisted selection of drought tolerance in wheat.

Methodology for High-Throughput Field Phenotyping of Canopy Temperature Using Airborne Thermography

Lower canopy temperature (CT), resulting from increased stomatal conductance, has been associated with increased yield in wheat. Historically, CT has been measured with hand-held infrared thermometers. Using the hand-held CT method on large field trials is problematic, mostly because measurements are confounded by temporal weather changes during the time required to measure all plots. The hand-held CT method is laborious and yet the resulting heritability low, thereby reducing confidence in selection in large scale breeding endeavors. We have developed a reliable and scalable crop phenotyping method for assessing CT in large field experiments. The method involves airborne thermography from a manned helicopter using a radiometrically-calibrated thermal camera. Thermal image data is acquired from large experiments in the order of seconds, thereby enabling simultaneous measurement of CT on potentially 1000s of plots. Effects of temporal weather variation when phenotyping large experiments using hand-held infrared thermometers are therefore reduced. The method is designed for cost-effective and large-scale use by the non-technical user and includes custom-developed software for data processing to obtain CT data on a single-plot basis for analysis. Broad-sense heritability was routinely >0.50, and as high as 0.79, for airborne thermography CT measured near anthesis on a wheat experiment comprising 768 plots of size 2 × 6 m. Image analysis based on the frequency distribution of temperature pixels to remove the possible influence of background soil did not improve broad-sense heritability. Total image acquisition and processing time was ca. 25 min and required only one person (excluding the helicopter pilot). The results indicate the potential to phenotype CT on large populations in genetics studies or for selection within a plant breeding program.

Do wheat breeders have suitable genetic variation to overcome short coleoptiles and poor establishment in the warmer soils of future climates?

Increases in air and soil temperatures will impact cereal growth and reduce crop yields. Little is known about how increasing temperatures will impact seedling growth and crop establishment. Climate forecast models predict that by 2060, mean and maximum air temperatures in the Australian wheatbelt will increase by 2-4°C during the March-June sowing period, and particularly at lower latitudes. Concomitant increases in soil temperature will shorten coleoptile length to reduce crop establishment, particularly where deep sowing to access sub-surface moisture. Mean coleoptile length was reduced in commercial wheat (Triticum aestivum L.) germplasm with increasing soil temperature (106mm and 51mm at 15°C and 31°C, respectively). Coleoptile lengths of modern semidwarf varieties were significantly (P<0.01) shorter than those of older tall wheats at 15°C (95mm and 135mm) and 31°C (46mm and 70mm). A 12-parent diallel indicated large additive and small non-maternal genetic effects for coleoptile length at 15°C and 27°C. Large genotype rank changes for coleoptile length across temperatures (rs=0.37, P<0.05) contributed to smaller entry-mean heritabilities (0.41-0.67) to reduce confidence in selection for long-coleoptile genotypes across contrasting temperatures. General combining ability effects were strongly correlated across temperatures (rp=0.81, P < 0.01), indicating the potential of some donors in identification of progeny with consistently longer coleoptiles. Warmer soils in future will contribute to poor establishment and crop failure, particularly with deep-sown semidwarf wheat. Breeding long-coleoptile genotypes with improved performance will require targeted selection at warmer temperatures in populations incorporating novel sources of reduced height and greater coleoptile length.

Dynamic quantification of canopy structure to characterize early plant vigour in wheat genotypes

Early vigour is an important physiological trait to improve establishment, water-use efficiency, and grain yield for wheat. Phenotyping large numbers of lines is challenging due to the fast growth and development of wheat seedlings. Here we developed a new photo-based workflow to monitor dynamically the growth and development of the wheat canopy of two wheat lines with a contrasting early vigour trait. Multiview images were taken using a 'vegetation stress' camera at 2 d intervals from emergence to the sixth leaf stage. Point clouds were extracted using the Multi-View Stereo and Structure From Motion (MVS-SFM) algorithm, and segmented into individual organs using the Octree method, with leaf midribs fitted using local polynomial function. Finally, phenotypic parameters were calculated from the reconstructed point cloud including: tiller and leaf number, plant height, Haun index, phyllochron, leaf length, angle, and leaf elongation rate. There was good agreement between the observed and estimated leaf length (RMSE=8.6mm, R (2)=0.98, n=322) across both lines. Significant contrasts of phenotyping parameters were observed between the two lines and were consistent with manual observations. The early vigour line had fewer tillers (2.4±0.6) and larger leaves (308.0±38.4mm and 17.1±2.7mm for leaf length and width, respectively). While the phyllochron of both lines was quite similar, the non-vigorous line had a greater Haun index (more leaves on the main stem) on any date, as the vigorous line had slower development of its first two leaves. The workflow presented in this study provides an efficient method to phenotype individual plants using a low-cost camera (an RGB camera is also suitable) and could be applied in phenotyping for applications in both simulation modelling and breeding. The rapidity and accuracy of this novel method can characterize the results of specific selection criteria (e.g. width of leaf three, number of tillers, rate of leaf appearance) that have been or can now be utilized to breed for early leaf growth and tillering in wheat.

Awns reduce grain number to increase grain size and harvestable yield in irrigated and rainfed spring wheat

Genotypic variation in ear morphology is linked to differences in photosynthetic potential to influence grain yield in winter cereals. Awns contribute to photosynthesis, particularly under water-limited conditions when canopy assimilation is restricted. We assessed performance of up to 45 backcross-derived, awned-awnletted NILs representing four diverse genetic backgrounds in 25 irrigated or rainfed, and droughted environments in Australia and Mexico. Mean environment grain yields were wide-ranging (1.38-7.93 t ha(-1)) with vegetative and maturity biomass, plant height, anthesis date, spike number, and harvest index all similar (P >0.05) for awned and awnletted NILs. Overall, grain yields of awned-awnletted sister-NILs were equivalent, irrespective of yield potential and genetic background. Awnletted wheats produced significantly more grains per unit area (+4%) and per spike (+5%) reflecting more fertile spikelets and grains in tertiary florets. Increases in grain number were compensated for by significant reductions in grain size (-5%) and increased frequency (+0.8%) of small, shrivelled grains ('screenings') to reduce seed-lot quality of awnletted NILs. Post-anthesis canopies of awnletted NILs were marginally warmer over all environments (+0.27 °C) but were not different and were sometimes cooler than awned NILs at cooler air temperatures. Awns develop early and represented up to 40% of total spikelet biomass prior to ear emergence. We hypothesize that the allocation of assimilate to large and rapidly developing awns decreases spikelet number and floret fertility to reduce grain number, particularly in distal florets. Individual grain size is increased to reduce screenings and to increase test weight and milling quality, particularly in droughted environments. Despite the average reduction in grain size, awnless lines could be identified that combined higher grain yield with larger grain size, increased grain protein concentration, and reduced screenings.

A tillering inhibition gene influences root-shoot carbon partitioning and pattern of water use to improve wheat productivity in rainfed environments

Genetic modification of shoot and root morphology has potential to improve water and nutrient uptake of wheat crops in rainfed environments. Near-isogenic lines (NILs) varying for a tillering inhibition (tin) gene and representing multiple genetic backgrounds were phenotyped in contrasting, controlled environments for shoot and root growth. Leaf area, shoot and root biomass were similar until tillering, whereupon reduced tillering in tin-containing NILs produced reductions of up to 60% in total leaf area and biomass, and increases in total root length of up to 120% and root biomass to 145%. Together, the root-to-shoot ratio increased two-fold with the tin gene. The influence of tin on shoot and root growth was greatest in the cv. Banks genetic background, particularly in the biculm-selected NIL, and was typically strongest in cooler environments. A separate de-tillering study confirmed greater root-to-shoot ratios with regular tiller removal in non-tin-containing genotypes. In validating these observations in a rainfed field study, the tin allele had a negligible effect on seedling growth but was associated with significantly (P<0.05) reduced tiller number (-37%), leaf area index (-26%), and spike number (-35%) to reduce plant biomass (-19%) at anthesis. Root biomass, root-to-shoot ratio at early stem elongation, and root depth at maturity were all increased in tin-containing NILs. Soil water use was slowed in tin-containing NILs, resulting in greater water availability, greater stomatal conductance, cooler canopy temperatures, and maintenance of green leaf area during grain-filling. Together these effects contributed to increases in harvest index and grain yield. In both the controlled and field environments, the tin gene was commonly associated with increased root length and biomass, but the significant influence of genetic background and environment suggests careful assessment of tin-containing progeny in selection for genotypic increases in root growth.

Of growing importance: combining greater early vigour and transpiration efficiency for wheat in variable rainfed environments

Increasing climate variability, particularly variability in the timing and amount of soil water, means that breeding wheat (Triticum aestivum L.) varieties with stable high grain yields is increasingly more challenging. Changing environmental conditions in water-limited rainfed environments will alter genotype ranking to reduce confidence in the identification of consistently higher yielding performers. Greater early vigour (EV) and transpiration efficiency (TE) are two physiological traits that have demonstrated benefits as breeding targets for efficient water-use in Mediterranean in-season water and monsoonal stored water environments, respectively. This Perspective discusses the hypothesis that combining higher TE and greater EV will broaden the adaptation and increase grain yields for wheats grown across most rainfed environments. We examine the physiology underpinning adaptation with greater EV and higher TE, as well as the challenges and potential benefits of deploying these traits in combination. We then discuss how these two traits interact with different environments and, in particular, the different wheat-growing regions of Australia. We conclude that the combination of these two traits is genetically and physiologically feasible, as well theoretically beneficial to average yield in most rainfed environments. Hence, we suggest a strategy for reliably managing the complex genetics underpinning EV and TE when phenotyping and selecting both traits in commercial wheat breeding programs.

Recurrent selection for wider seedling leaves increases early biomass and leaf area in wheat (Triticum aestivum L.)

The breeding of wheat with greater early vigour has potential to increase water- and nutrient-use efficiency, as well as to improve weed competitiveness to raise crop yields profitably. Given that wheat is inherently conservative in its early growth, a sustained breeding effort was initiated to increase genetically seedling leaf area in developing novel high vigour germplasm. A recurrent selection programme was initiated by intercrossing a genetically diverse set of 28 vigorous wheat lines identified globally. These were intercrossed at random and S1:2 progeny with the largest leaf 1 and 2 widths were intermated to develop new populations for assessment of early growth. This procedure was repeated for up to 60 segregating families per cycle across six cycles over 15 years. Thirty random S1:2 progeny were retained from each cycle and seed-increased together to produce seed for early vigour assessment in multiple sowings. The most vigorous wheat seedlings were identified in later cycles, with some lines producing more than double the leaf area and biomass of elite commercial wheat varieties. Phenotypic selection for greater leaf width was associated with a realized significant (P<0.01) linear increase per seedling of 0.41 mm per cycle (+7.1%) for mean leaf width, and correlated linear increases in total leaf area and biomass of 4.48 cm(2) per cycle (+10.3%) and 10.8 mg per cycle (+5.3%), respectively. Genetic gains in widths of leaves 2 (+8.4%) and 3 (+11.5%) were significantly (P<0.01) greater than for leaf 1 (+5.3%). Selection for greater leaf width was associated with linear increases in coleoptile tiller leaf area, small curvilinear increases in leaf 1 length, and reductions in numbers of leaves and mainstem tillers. Genetic variances were large and heritabilities high for leaf width and total leaf area in each cycle, but reduced linearly in size with selection across cycles. Coupling diverse germplasm with a simple, inexpensive, and repeatable selection process has confirmed the value of recurrent selection in developing uniquely vigorous wheat germplasm for use as parents in commercial breeding.

Soil coring at multiple field environments can directly quantify variation in deep root traits to select wheat genotypes for breeding

We aim to incorporate deep root traits into future wheat varieties to increase access to stored soil water during grain development, which is twice as valuable for yield as water captured at younger stages. Most root phenotyping efforts have been indirect studies in the laboratory, at young plant stages, or using indirect shoot measures. Here, soil coring to 2 m depth was used across three field environments to directly phenotype deep root traits on grain development (depth, descent rate, density, length, and distribution). Shoot phenotypes at coring included canopy temperature depression, chlorophyll reflectance, and green leaf scoring, with developmental stage, biomass, and yield. Current varieties, and genotypes with breeding histories and plant architectures expected to promote deep roots, were used to maximize identification of variation due to genetics. Variation was observed for deep root traits (e.g. 111.4-178.5cm (60%) for depth; 0.09-0.22cm/°C day (144%) for descent rate) using soil coring in the field environments. There was significant variation for root traits between sites, and variation in the relative performance of genotypes between sites. However, genotypes were identified that performed consistently well or poorly at both sites. Furthermore, high-performing genotypes were statistically superior in root traits than low-performing genotypes or commercial varieties. There was a weak but significant negative correlation between green leaf score (-0.5), CTD (0.45), and rooting depth and a positive correlation for chlorophyll reflectance (0.32). Shoot phenotypes did not predict other root traits. This study suggests that field coring can directly identify variation in deep root traits to speed up selection of genotypes for breeding programmes.

Integration of phenotyping and genetic platforms for a better understanding of wheat performance under drought

Identifying markers for physiological traits of proven value in breeding, especially ones that are consistent across environments with different patterns of stress, strengthens the toolkit to increase confidence in the value and delivery from physiological breeding. To identify markers relevant to drought adaptation, this review will highlight the importance of development and implementation of robust and repeatable phenotyping that is relevant to the different target drought types, and practical examples of managed environment facilities in Australia and Mexico are given. These facilities can be used as models to: (i) improve reliability and consistency of environments and genetic responses to the environment at a global scale; (ii) improve the capacity to deliver quantitative trait loci (QTLs) as user-friendly markers for enriching populations; and (iii) illustrate the use of populations with a narrow range of variation for phenology allowing the identification of QTLs for drought-adaptive traits. However, the importance of further optimizing phenology and plant height at a global scale is highlighted. Finally, the impact of physiological trait-based crossing is demonstrated and supports the need for urgent development of robust genetic markers.

Use of a large multiparent wheat mapping population in genomic dissection of coleoptile and seedling growth

Identification of alleles towards the selection for improved seedling vigour is a key objective of many wheat breeding programmes. A multiparent advanced generation intercross (MAGIC) population developed from four commercial spring wheat cultivars (cvv. Baxter, Chara, Westonia and Yitpi) and containing ca. 1000 F(2) -derived, F(6:7) RILs was assessed at two contrasting soil temperatures (12 and 20 °C) for shoot length and coleoptile characteristics length and thickness. Narrow-sense heritabilities were high for coleoptile and shoot length (h(2) = 0.68-0.70), indicating a strong genetic basis for the differences among progeny. Genotypic variation was large, and distributions of genotype means were approximately Gaussian with evidence for transgressive segregation for all traits. A number of significant QTL were identified for all early growth traits, and these were commonly repeatable across the different soil temperatures. The largest negative effects on coleoptile lengths were associated with Rht-B1b (-8.2%) and Rht-D1b (-10.9%) dwarfing genes varying in the population. Reduction in coleoptile length with either gene was particularly large at the warmer soil temperature. Other large QTL for coleoptile length were identified on chromosomes 1A, 2B, 4A, 5A and 6B, but these were relatively smaller than allelic effects at the Rht-B1 and Rht-D1 loci. A large coleoptile length effect allele (a = 5.3 mm at 12 °C) was identified on chromosome 1AS despite the relatively shorter coleoptile length of the donor Yitpi. Strong, positive genetic correlations for coleoptile and shoot lengths (r(g) = 0.85-0.90) support the co-location of QTL for these traits and suggest a common physiological basis for both. The multiparent population has enabled the identification of promising shoot and coleoptile QTL despite the potential for the confounding of large effect dwarfing gene alleles present in the commercial parents. The incidence of these alleles in commercial wheat breeding programmes should facilitate their ready implementation in selection of varieties with improved establishment and early growth.

Plot size matters: interference from intergenotypic competition in plant phenotyping studies

Genetic and physiological studies often comprise genotypes diverse in vigour, size and flowering time. This can make the phenotyping of complex traits challenging, particularly those associated with canopy development, biomass and yield, as the environment of one genotype can be influenced by a neighbouring genotype. Limited seed and space may encourage field assessment in single, spaced rows or in small, unbordered plots, whereas the convenience of a controlled environment or greenhouse makes pot studies tempting. However, the relevance of such growing conditions to commercial field-grown crops is unclear and often doubtful. Competition for water, light and nutrients necessary for canopy growth will be variable where immediate neighbours are genetically different, particularly under stress conditions, where competition for resources and influence on productivity is greatest. Small hills and rod-rows maximise the potential for intergenotypic competition that is not relevant to a crop's performance in monocultures. Response to resource availability will typically vary among diverse genotypes to alter genotype ranking and reduce heritability for all growth-related traits, with the possible exception of harvest index. Validation of pot experiments to performance in canopies in the field is essential, whereas the planting of multirow plots and the simple exclusion of plot borders at harvest will increase experimental precision and confidence in genotype performance in target environments.

Evaluation of reduced-tillering (tin) wheat lines in managed, terminal water deficit environments

Small or shrivelled wheat kernels (screenings) that reduce crop value are commonly produced in terminal drought environments. The aim of this study was to establish whether the incorporation of the tiller inhibition (tin) gene would contribute to maintenance of kernel weight and reductions in screenings under terminal water deficit. Five Silverstar near-isogenic lines contrasting in high and low tiller potential and their recurrent Silverstar parent were established at two plant densities under managed terminal water deficit (mild and severe) and irrigated conditions. With irrigation (grain yield of 5.6 t ha(-1)), kernels of all lines weighed ~31 mg, with restricted-tillering (R-tin) lines producing an average 15% lower grain yield. Under both mild and severe terminal water deficit (4.1 t ha(-1) and 2.8 t ha(-1)), free-tillering lines had relatively high screenings ranging from 11.9% to 16.2%. Compared with free-tillering lines, R-tin lines maintained large kernel weight (~29 mg kernel(-1)) and had 29% and 51% fewer screenings under the two stresses, and a significantly greater (+11%) grain yield under mild stress. Higher kernel weights in tin lines were realized even with the greater kernel number per spike. The higher kernel weight of the R-tin lines under stress conditions was associated with greater anthesis biomass and increased stem water-soluble carbohydrates, ensuring more assimilate for later translocation to filling grain. The incorporation of the tin gene into genetic material adapted to the target environments provides scope for improvement in both grain yield and kernel weight, and a reduction in screenings in terminal water deficit environments.

A rapid, controlled-environment seedling root screen for wheat correlates well with rooting depths at vegetative, but not reproductive, stages at two field sites

BACKGROUND AND AIMS

Root length and depth determine capture of water and nutrients by plants, and are targets for crop improvement. Here we assess a controlled-environment wheat seedling screen to determine speed, repeatability and relatedness to performance of young and adult plants in the field.

METHODS

Recombinant inbred lines (RILs) and diverse genotypes were grown in rolled, moist germination paper in growth cabinets, and primary root number and length were measured when leaf 1 or 2 were fully expanded. For comparison, plants were grown in the field and root systems were harvested at the two-leaf stage with either a shovel or a soil core. From about the four-leaf stage, roots were extracted with a steel coring tube only, placed directly over the plant and pushed to the required depth with a hydraulic ram attached to a tractor.

KEY RESULTS

In growth cabinets, repeatability was greatest (r = 0.8, P < 0.01) when the paper was maintained moist and seed weight, pathogens and germination times were controlled. Scanned total root length (slow) was strongly correlated (r = 0.7, P < 0.01) with length of the two longest seminal axile roots measured with a ruler (fast), such that 100-200 genotypes were measured per day. Correlation to field-grown roots at two sites at two leaves was positive and significant within the RILs and cultivars (r = 0.6, P = 0.01), and at one of the two sites at the five-leaf stage within the RILs (r = 0.8, P = 0.05). Measurements made in the field with a shovel or extracted soil cores were fast (5 min per core) and had significant positive correlations to scanner measurements after root washing and cleaning (>2 h per core). Field measurements at two- and five-leaf stages did not correlate with root depth at flowering.

CONCLUSIONS

The seedling screen was fast, repeatable and reliable for selecting lines with greater total root length in the young vegetative phase in the field. Lack of significant correlation with reproductive stage root system depth at the field sites used in this study reflected factors not captured in the screen such as time, soil properties, climate variation and plant phenology.

Analysis of leaf and stripe rust severities reveals pathotype changes and multiple minor QTLs associated with resistance in an Avocet × Pastor wheat population

Leaf rust and stripe rust are important diseases of wheat world-wide and deployment of cultivars with genetic resistance is an effective and environmentally sound control method. The use of minor, additive genes conferring adult plant resistance (APR) has been shown to provide resistance that is durable. The wheat cultivar 'Pastor' originated from the CIMMYT breeding program that focuses on minor gene-based APR to both diseases by selecting and advancing generations alternately under leaf rust and stripe rust pressures. As a consequence, Pastor has good resistance to both rusts and was used as the resistant parent to develop a mapping population by crossing with the susceptible 'Avocet'. All 148 F(5) recombinant inbred lines were evaluated under artificially inoculated epidemic environments for leaf rust (3 environments) and stripe rust (4 environments, 2 of which represent two evaluation dates in final year due to the late build-up of a new race virulent to Yr31) in Mexico. Map construction and QTL analysis were completed with 223 polymorphic markers on 84 randomly selected lines in the population. Pastor contributed Yr31, a moderately effective race-specific gene for stripe rust resistance, which was overcome during this study, and this was clearly shown in the statistical analysis. Linked or pleiotropic chromosomal regions contributing to resistance against both pathogens included Lr46/Yr29 on 1BL, the Yr31 region on 2BS, and additional minor genes on 5A, 6B and 7BL. Other minor genes for leaf rust resistance were located on 1B, 2A and 2D and for stripe rust on 1AL, 1B, 3A, 3B, 4D, 6A, 7AS and 7AL. The 1AL, 1BS and 7AL QTLs are in regions that were not identified previously as having QTLs for stripe rust resistance. The development of uniform and severe epidemics facilitated excellent phenotyping, and when combined with multi-environment analysis, resulted in the relatively large number of QTLs identified in this study.

Traits and selection strategies to improve root systems and water uptake in water-limited wheat crops

Wheat yields globally will depend increasingly on good management to conserve rainfall and new varieties that use water efficiently for grain production. Here we propose an approach for developing new varieties to make better use of deep stored water. We focus on water-limited wheat production in the summer-dominant rainfall regions of India and Australia, but the approach is generally applicable to other environments and root-based constraints. Use of stored deep water is valuable because it is more predictable than variable in-season rainfall and can be measured prior to sowing. Further, this moisture is converted into grain with twice the efficiently of in-season rainfall since it is taken up later in crop growth during the grain-filling period when the roots reach deeper layers. We propose that wheat varieties with a deeper root system, a redistribution of branch root density from the surface to depth, and with greater radial hydraulic conductivity at depth would have higher yields in rainfed systems where crops rely on deep water for grain fill. Developing selection systems for mature root system traits is challenging as there are limited high-throughput phenotyping methods for roots in the field, and there is a risk that traits selected in the lab on young plants will not translate into mature root system traits in the field. We give an example of a breeding programme that combines laboratory and field phenotyping with proof of concept evaluation of the trait at the beginning of the selection programme. This would greatly enhance confidence in a high-throughput laboratory or field screen, and avoid investment in screens without yield value. This approach requires careful selection of field sites and years that allow expression of deep roots and increased yield. It also requires careful selection and crossing of germplasm to allow comparison of root expression among genotypes that are similar for other traits, especially flowering time and disease and toxicity resistances. Such a programme with field and laboratory evaluation at the outset will speed up delivery of varieties with improved root systems for higher yield.

Genomic regions for canopy temperature and their genetic association with stomatal conductance and grain yield in wheat

Stomata are the site of CO2 exchange for water in a leaf. Variation in stomatal control offers promise in genetic improvement of transpiration and photosynthetic rates to improve wheat performance. However, techniques for estimating stomatal conductance (SC) are slow, limiting potential for efficient measurement and genetic modification of this trait. Genotypic variation in canopy temperature (CT) and leaf porosity (LP), as surrogates for SC, were assessed in three wheat mapping populations grown under well-watered conditions. The range and resulting genetic variance were large but not always repeatable across days and years for CT and LP alike. Leaf-to-leaf variation was large for LP, reducing heritability to near zero on a single-leaf basis. Replication across dates and years increased line-mean heritability to ~75% for both CT and LP. Across sampling dates and populations, CT showed a large, additive genetic correlation with LP (rg=-0.67 to -0.83) as expected. Genetic increases in pre-flowering CT were associated with reduced final plant height and both increased harvest index and grain yield but were uncorrelated with aerial biomass. In contrast, post-flowering, cooler canopies were associated with greater aerial biomass and increased grain number and yield. A multi-environment QTL analysis identified up to 16 and 15 genomic regions for CT and LP, respectively, across all three populations. Several of the LP and CT QTL co-located with known QTL for plant height and phenological development and intervals for many of the CT and LP quantitative trait loci (QTL) overlapped, supporting a common genetic basis for the two traits. Notably, both Rht-B1b and Rht-D1b dwarfing alleles were paradoxically positive for LP and CT (i.e. semi-dwarfs had higher stomatal conductance but warmer canopies) highlighting the issue of translation from leaf to canopy in screening for greater transpiration. The strong requirement for repeated assessment of SC suggests the more rapid CT assessment may be of greater value for indirect screening of high or low SC among large numbers of early-generation breeding lines. However, account must be taken of variation in development and canopy architecture when interpreting performance and selecting breeding lines on the basis of CT.

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.

Genetic control of duration of pre-anthesis phases in wheat (Triticum aestivum L.) and relationships to leaf appearance, tillering, and dry matter accumulation

The duration of pre-anthesis developmental phases is of interest in breeding for improved adaptation and yield potential in temperate cereals. Yet despite numerous studies on the genetic control of anthesis (flowering) time and floral initiation, little is known about the genetic control of other pre-anthesis phases. Furthermore, little is known about the effect that changes in the duration of pre-anthesis phases could have on traits related to leaf appearance and tillering, or dry matter accumulation before terminal spikelet initiation (TS). The genetic control of the leaf and spikelet initiation phase (LS; from sowing to TS), the stem elongation phase (SE; from TS to anthesis), and, within the latter, from TS to flag leaf appearance and from then to anthesis, was studied in two doubled-haploid, mapping bread wheat populations, Cranbrook × Halberd and CD87 × Katepwa, in two field experiments (ACT and NSW, Australia). The lengths of phases were estimated from measurements of both TS and the onset of stem elongation. Dry weight per plant before TS, rate of leaf appearance, tillering rate, maximum number of tillers and number of leaves, and dry weight per plant at TS were also estimated in the Cranbrook × Halberd population. More genomic regions were identified for the length of the different pre-anthesis phases than for total time to anthesis. Although overall genetic correlations between LS and SE were significant and positive, independent genetic variability between LS and SE, and several quantitative trait loci (QTLs) with different effects on both phases were found in the two populations. Several of these QTLs (which did not seem to coincide with reported major genes) could be of interest for breeding purposes since they were only significant for either LS or SE. There was no relationship between LS and the rate of leaf appearance. LS was strongly and positively correlated with dry weight at TS but only slightly negatively correlated with early vigour (dry weight before TS). Despite significant genetic correlations between LS and some tillering traits, shortening LS so as to lengthen SE without modifying total time to anthesis would not necessarily reduce tillering capacity, as QTLs for tillering traits did not coincide with those QTLs significant only for LS or SE. Therefore, the study of different pre-anthesis phases is relevant for a better understanding of genetic factors regulating developmental time and may offer new tools for fine-tuning it in breeding for both adaptability and yield potential.

Large root systems: are they useful in adapting wheat to dry environments?

There is little consensus on whether having a large root system is the best strategy in adapting wheat (Triticum aestivum L.) to water-limited environments. We explore the reasons for the lack of consensus and aim to answer the question of whether a large root system is useful in adapting wheat to dry environments. We used unpublished data from glasshouse and field experiments examining the relationship between root system size and their functional implication for water capture. Individual root traits for water uptake do not describe a root system as being large or small. However, the recent invigoration of the root system in wheat by indirect selection for increased leaf vigour has enlarged the root system through increases in root biomass and length and root length density. This large root system contributes to increasing the capture of water and nitrogen early in the season, and facilitates the capture of additional water for grain filling. The usefulness of a vigorous root system in increasing wheat yields under water-limited conditions maybe greater in environments where crops rely largely on seasonal rainfall, such as the Mediterranean-type environments. In environments where crops are reliant on stored soil water, a vigorous root system increases the risk of depleting soil water before completion of grain filling.

Simultaneous selection of major and minor genes: use of QTL to increase selection efficiency of coleoptile length of wheat (Triticum aestivum L.)

Plant breeders simultaneously select for qualitative traits controlled by one or a small number of major genes, as well as for polygenic traits controlled by multiple genes that may be detected as quantitative trait loci (QTL). In this study, we applied computer simulation to investigate simultaneous selection for alleles at both major and minor gene (as QTL) loci in breeding populations of two wheat parental lines, HM14BS and Sunstate. Loci targeted for selection included six major genes affecting plant height, disease resistance, and grain quality, plus 6 known and 11 "unidentified" QTL affecting coleoptile length (CL). Parental line HM14BS contributed the target alleles at two of the major gene loci, while parental line Sunstate contributed target alleles at four loci. The parents have similar plant height, but HM14BS has a longer coleoptile, a desirable attribute for deep sowing in rainfed environments. Including the wild-type allele at the major reduced-height locus Rht-D1, HM14BS was assumed to have 13 QTL for increased CL, and Sunstate four; these assumptions being derived from mapping studies and empirical data from an actual HM14BS/Sunstate population. Simulation indicated that compared to backcross populations, a single biparental F(1) cross produced the highest frequency of target genotypes (six desired alleles at major genes plus desired QTL alleles for long CL). From 1,000 simulation runs, an average of 2.4 individuals with the target genotype were present in unselected F(1)-derived doubled haploid (DH) or recombinant inbred line (RIL) populations of size 200. A selection scheme for the six major genes increased the number of target individuals to 19.1, and additional marker-assisted selection (MAS) for CL increased the number to 23.0. Phenotypic selection (PS) of CL outperformed MAS in this study due to the high heritability of CL, incompletely linked markers for known QTL, and the existence of unidentified QTL. However, a selection scheme combining MAS and PS was equally as efficient as PS and would result in net savings in production and time to delivery of long coleoptile wheats containing the six favorable alleles.

Quantitative trait loci for carbon isotope discrimination are repeatable across environments and wheat mapping populations

Wheat productivity is commonly limited by a lack of water essential for growth. Carbon isotope discrimination (Delta), through its negative relationship with transpiration efficiency, has been used in selection of higher wheat yields in breeding for rainfed environments. The potential also exists for selection of increased Delta for improved adaptation to irrigated and high rainfall environments. Selection efficiency of Delta would be enhanced with a better understanding of its genetic control. Three wheat mapping populations (Cranbrook/Halberd, Sunco/Tasman and CD87/Katepwa) containing between 161 and 190 F(1)-derived, doubled-haploid progeny were phenotyped for Delta and agronomic traits in 3-5 well-watered environments. The range for Delta was large among progeny (c. 1.2-2.3 per thousand), contributing to moderate-to-high single environment (h (2) = 0.37-0.91) and line-mean (0.63-0.86) heritabilities. Transgressive segregation was large and genetic control complex with between 9 and 13 Delta quantitative trait loci (QTL) identified in each cross. The Delta QTL effects were commonly small, accounting for a modest 1-10% of the total additive genetic variance, while a number of chromosomal regions appeared in two or more populations (e.g. 1BL, 2BS, 3BS, 4AS, 4BS, 5AS, 7AS and 7BS). Some of the Delta genomic regions were associated with variation in heading date (e.g. 2DS, 4AS and 7AL) and/or plant height (e.g. 1BL, 4BS and 4DS) to confound genotypic associations between Delta and grain yield. As a group, high Delta progeny were significantly (P < 0.10-0.01) taller and flowered earlier but produced more biomass and grain yield in favorable environments. After removing the effect of height and heading date, strong genotypic correlations were observed for Delta and both yield and biomass across populations (r (g) = 0.29-0.57, P < 0.05) as might be expected for the favorable experimental conditions. Thus selection for Delta appears beneficial in increasing grain yield and biomass in favorable environments. However, care must be taken to avoid confounding genotypic differences in Delta with stature and development time when selecting for improved biomass and yield especially in environments experiencing terminal droughts. Polygenic control and small size of individual QTL for Delta may reduce the potential for QTL in marker-assisted selection for improved yield of wheat.

Quantitative trait loci for slow-rusting resistance in wheat to leaf rust and stripe rust identified with multi-environment analysis

Rust diseases are a major cause of yield loss in wheat worldwide, and are often controlled through the incorporation of resistance genes using conventional phenotypic selection methods. Slow-rusting resistance genes are expressed quantitatively and are typically small in genetic effect thereby requiring multiple genes to provide adequate protection against pathogens. These effects are valuable and are generally considered to confer durable resistance. Therefore an understanding of the chromosomal locations of such genes and their biological effects are important in order to ensure they are suitably deployed in elite germplasm. Attila is an important wheat grown throughout the world and is used as a slow-rusting donor in international spring wheat breeding programs. This study identified chromosomal regions associated with leaf rust and stripe rust resistances in a cross between Attila and a susceptible parent, Avocet-S, evaluated over 3 years in the field. Genotypic variation for both rusts was large and repeatable with line-mean heritabilities of 94% for leaf rust resistance and 87% for stripe rust. Three loci, including Lr46/Yr29 on chromosome 1BL, were shown to provide resistance to leaf rust whereas six loci with small effects conferred stripe rust resistance, with a seventh locus having an effect only by epistasis. Disease scoring over three different years enabled inferences to be made relating to stripe rust pathogen strains that predominated in different years.

Molecular mapping of genes for Coleoptile growth in bread wheat (Triticum aestivum L.)

Successful plant establishment is critical to the development of high-yielding crops. Short coleoptiles can reduce seedling emergence particularly when seed is sown deep as occurs when moisture necessary for germination is deep in the subsoil. Detailed molecular maps for a range of wheat doubled-haploid populations (Cranbrook/Halberd, Sunco/Tasman, CD87/Katepwa and Kukri/Janz) were used to identify genomic regions affecting coleoptile characteristics length, cross-sectional area and degree of spiralling across contrasting soil temperatures. Genotypic variation was large and distributions of genotype means were approximately normal with evidence for transgressive segregation. Narrow-sense heritabilities were high for coleoptile length and cross-sectional area indicating a strong genetic basis for differences among progeny. In contrast, heritabilities for coleoptile spiralling were small. Molecular marker analyses identified a number of significant quantitative trait loci (QTL) for coleoptile growth. Many of the coleoptile growth QTL mapped directly to the Rht-B1 or Rht-D1 dwarfing gene loci conferring reduced cell size through insensitivity to endogenous gibberellins. Other QTL for coleoptile growth were identified throughout the genome. Epistatic interactions were small or non-existent, and there was little evidence for any QTL x temperature interaction. Gene effects at significant QTL were approximately one-half to one-quarter the size of effects at the Rht-B1 and Rht-D1 regions. However, selection at these QTL could together alter coleoptile length by up to 50 mm. In addition to Rht-B1b and Rht-D1b, genomic regions on chromosomes 2B, 2D, 4A, 5D and 6B were repeatable across two or more populations suggesting their potential value for use in breeding and marker-aided selection for greater coleoptile length and improved establishment.

Genotypic variation in water-soluble carbohydrate accumulation in wheat

The water-soluble carbohydrate (WSC) that accumulates in the stems of wheat during growth can be an important contributor to grain filling, particularly under conditions when assimilation is limited, such as during end-of-season drought. WSC concentration was measured at anthesis across a diverse set of wheat genotypes over multiple environments. Environmental differences in WSC concentration were large (means for the set ranging between 108 and 203 mg g^-1 dry weight), and there were significant and repeatable differences in WSC accumulation among genotypes (means ranging from 112 to 213 mg g^-1 dry weight averaged across environments), associated with large broad-sense heritability (H = 0.90 ± 0.12). These results suggest that breeding for high WSC should be possible in wheat. The composition of the WSC, examined in selected genotypes, indicated that the variation in total WSC was attributed mainly to variation in the fructan component, with the other major soluble carbohydrates, sucrose and hexose, varying less. The degree of polymerisation (DP) of fructo-oligosaccharides was up to ~13 in samples where higher levels of WSC were accumulated, owing either to genotype or environment, but the higher DP components (DP > 6) were decreased in samples of lower total WSC. The results are consistent with fructan biosynthesis occurring via a sequential mechanism that is dependent on the availability of sucrose, and differences in WSC contents of genotypes are unlikely to be due to major mechanistic differences.

Molecular mapping of gibberellin-responsive dwarfing genes in bread wheat

Opportunities exist for replacing reduced height (Rht) genes Rht-B1b and Rht-D1b with alternative dwarfing genes for bread wheat improvement. In this study, the chromosomal locations of several height-reducing genes were determined by screening populations of recombinant inbred lines or doubled haploid lines varying for plant height with microsatellite markers. Linked markers were found for Rht5 (on chromosome 3BS), Rht12 (5AL) and Rht13 (7BS), which accounted for most of the phenotypic variance in height in the respective populations. Large height differences between genotypes (up to 43 cm) indicated linkage to major height-reducing genes. Rht4 was associated with molecular markers on chromosome 2BL, accounting for up to 30% of the variance in height. Confirming previous studies, Rht8 was linked to markers on chromosome 2DS, whereas a population varying for Rht9 revealed a region with a small but significant height effect on chromosome 5AL. The height-reducing effect of these dwarfing genes was repeatable across a range of environments. The molecular markers developed in this study will be useful for marker-assisted selection of alternative height-reducing genes, and to better understand the effects of different Rht genes on wheat growth and agronomic performance.

Breeding for high water-use efficiency

There is a pressing need to improve the water-use efficiency of rain-fed and irrigated crop production. Breeding crop varieties with higher water-use efficiency is seen as providing part of the solution. Three key processes can be exploited in breeding for high water-use efficiency: (i) moving more of the available water through the crop rather than it being wasted as evaporation from the soil surface or drainage beyond the root zone or being left behind in the root zone at harvest; (ii) acquiring more carbon (biomass) in exchange for the water transpired by the crop, i.e. improving crop transpiration efficiency; (iii) partitioning more of the achieved biomass into the harvested product. The relative importance of any one of these processes will vary depending on how water availability varies during the crop cycle. However, these three processes are not independent. Targeting specific traits to improve one process may have detrimental effects on the other two, but there may also be positive interactions. Progress in breeding for improved water-use efficiency of rain-fed wheat is reviewed to illustrate the nature of some of these interactions and to highlight opportunities that may be exploited in other crops as well as potential pitfalls. For C3 species, measuring carbon isotope discrimination provides a powerful means of improving water-use efficiency of leaf gas exchange, but experience has shown that improvements in leaf-level water-use efficiency may not always translate into higher crop water-use efficiency or yield. In fact, the reverse has frequently been observed. Reasons for this are explored in some detail. Crop simulation modelling can be used to assess the likely impact on water-use efficiency and yield of changing the expression of traits of interest. Results of such simulations indicate that greater progress may be achieved by pyramiding traits so that potential negative effects of individual traits are neutralized. DNA-based selection techniques may assist in such a strategy.

The effect of different height reducing genes on the early growth of wheat

Genes that reduce height without compromising seedling vigour or coleoptile length have great potential for wheat improvement. We therefore investigated the effects of various reduced height (Rht) genes on the early stages of plant development, using a combination of near isogenic, recombinant, mutant and wild type comparisons. Gibberellin (GA) insensitivity caused by Rht-B1b or Rht-D1b was associated with reduced leaf elongation rate and coleoptile length. Similar results were found for two other sources of dwarfing, Rht11 and Rht17. We found one class of Rht genes (e.g. Rht8) which had no effect on coleoptile length, leaf elongation rate or responsiveness to GA, indicating that these dwarfing genes may act later in wheat development to reduce height and increase harvest index, without affecting early growth. A third class of Rht genes was found in three durum backgrounds. These had reduced coleoptile lengths and leaf elongation rates, but had a greater response to GA than the corresponding tall varieties. We discuss these results in relation to the possible mechanisms underlying the reduction in height and the suitability of the different Rht genes for wheat improvement.