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A genetic framework underpinning salinity tolerance at reproductive stage was revealed by genome-wide SNP markers and major adaptability genes in synthetic-derived wheats, and trait-associated loci were used to predict phenotypes. Using wild relatives of crops to identify genes related to improved productivity and resilience to climate extremes is a prioritized area of crop genetic improvement. High salinity is a widespread crop production constraint, and development of salt-tolerant cultivars is a sustainable solution. We evaluated a panel of 294 wheat accessions comprising synthetic-derived wheat lines (SYN-DERs) and modern bread wheat advanced lines under control and high salinity conditions at two locations. The GWAS analysis revealed a quantitative genetic framework of more than 200 loci with minor effect underlying salinity tolerance at reproductive stage. The significant trait-associated SNPs were used to predict phenotypes using a GBLUP model, and the prediction accuracy (r

New genomic regions for high accumulation of 10 minerals were identified. The 1B:1R and 2NS translocations enhanced concentrations of four and two minerals, respectively, in addition to disease resistance. Puccinia species, the causal agents of rust diseases of wheat, have the potential to cause total crop failures due their high evolutionary ability to acquire virulence for resistance genes deployed in commercial cultivars. Hence, the discovery of genetically diverse sources of rust resistance is essential. On the other hand, biofortification of wheat for essential nutrients, such as zinc (Zn) and iron (Fe), is also an objective in wheat improvement programs to tackle micronutrient deficiency. The development of rust-resistant and nutrient-concentrated wheat cultivars would be important for sustainable production and the fight against malnutrition. The HarvestPlus association mapping panel (HPAMP) that included nutrient-dense sources from diverse genetic backgrounds was genotyped using a 90 K Infinium SNP array and 13 markers linked with rust resistance genes. The HPAMP was used for genome-wide association mapping to identify genomic regions underpinning rust resistance and mineral accumulation. Twelve QTL for rust resistance and 53 for concentrations of 10 minerals were identified. Comparison of results from this study with the published QTL information revealed the detection of already known and some putatively new genes/QTL underpinning stripe rust and leaf rust resistance in this panel. Thirty-six new QTL for mineral concentration were identified on 17 chromosomes. Accessions carrying the 1B:1R translocation accumulated higher concentrations of Zn, Fe, Copper (Cu) and sulphur (S). The 2NS segment showed enhanced accumulation of grain Fe and Cu. Fifteen rust-resistant and biofortified accessions were identified for use as donor sources in breeding programs.

Warming nights are correlated with declining wheat growth and yield. As a key determinant of plant biomass, respiration consumes O2 as it produces ATP and releases CO2 and is typically reduced under warming to maintain metabolic efficiency. We compared the response of respiratory O2 and CO2 flux to multiple night and day warming treatments in wheat leaves and roots, using one commercial (Mace) and one breeding cultivar grown in controlled environments. We also examined the effect of night warming and a day heatwave on the capacity of the ATP-uncoupled alternative oxidase (AOX) pathway. Under warm nights, plant biomass fell, respiratory CO2 release measured at a common temperature was unchanged (indicating higher rates of CO2 release at prevailing growth temperature), respiratory O2 consumption at a common temperature declined, and AOX pathway capacity increased. The uncoupling of CO2 and O2 exchange and enhanced AOX pathway capacity suggest a reduction in plant energy demand under warm nights (lower O2 consumption), alongside higher rates of CO2 release under prevailing growth temperature (due to a lack of down-regulation of respiratory CO2 release). Less efficient ATP synthesis, teamed with sustained CO2 flux, could thus be driving observed biomass declines under warm nights.

The pathogen Uromyces viciae-fabae causes rust (a fungal disease) on faba bean (Vicia faba). This disease limits faba bean production in Africa, Asia, Europe, and Australia. The development of resistant cultivars to U. viciae-fabae is the optimal solution for sustainable disease management. However, unknown virulence in Australian U. viciae-fabae populations has confounded resistance breeding. This study examined differences in virulence among Australian U. viciae-fabae isolates collected from various locations and established a differential set of faba bean genotypes. Ten rust isolates were collected from the major faba bean growing regions in Australia and single spore cultures produced. These cultures were subsequently used for assessing virulence on 40 diverse faba bean genotypes. Based on the host-pathogen interactions, 12 putative host genotypes were identified as a differential set. A nomenclature system was subsequently developed using the binary pathotype naming system. Based upon host-pathogen interactions, nine virulence patterns were detected, and the isolates were named using the new nomenclature. We report characterization and naming of U. viciae-fabae pathotypes using differential genotypes in Australia. This differential set will help identify and track the evolution of new virulence in pathogen population and will assist pyramiding of rust resistance genes.

High temperature stress inhibits photosynthesis and threatens wheat production. One measure of photosynthetic heat tolerance is Tcrit – the critical temperature at which incipient damage to photosystem II (PSII) occurs. This trait could be improved in wheat by exploiting genetic variation and genotype-by-environment interactions (GEI). Flag leaf Tcrit of 54 wheat genotypes was evaluated in 12 thermal environments over 3 years in Australia, and analysed using linear mixed models to assess GEI effects. Nine of the 12 environments had significant genetic effects and highly variable broad-sense heritability (H2 ranged from 0.15 to 0.75). Tcrit GEI was variable, with 55.6% of the genetic variance across environments accounted for by the factor analytic model. Mean daily growth temperature in the month preceding anthesis was the most influential environmental driver of Tcrit GEI, suggesting biochemical, physiological and structural adjustments to temperature requiring different durations to manifest. These changes help protect or repair PSII upon exposure to heat stress, and may improve carbon assimilation under high temperature. To support breeding efforts to improve wheat performance under high temperature, we identified genotypes superior to commercial cultivars commonly grown by farmers, and demonstrated potential for developing genotypes with greater photosynthetic heat tolerance.

Cereal rye and its wild forms are important sources of genetic diversity for wheat breeding due to their resistances to biotic and abiotic stresses. Secale strictum subsp. anatolicum (Boiss.) K. Hammer (SSA) is a weedy relative of cultivated rye, S. cereale. Meiotic chromosome pairing in F1 hybrids of SSA and S. cereale reveals strong genomic affinity between the two genomes. A study of the transferability of S. cereale sequence-based markers to SSA and hexaploid triticale demonstrated their applicability for tracing SSA chromatin in wheat. The transferability of the markers was over 80% from homoeologous groups 1, 2, and 3, and greater than 70% from groups 4 to 7. This study focused on the generation and molecular and cytogenetic characterization of wheat–SSA alien derivatives. Twelve were identified using combinations of non-denaturing fluorescence in situ hybridization (ND-FISH), genomic in situ hybridization (GISH), and molecular marker analysis. All SSA chromosomes, except 3Ra and 6Ra, were transferred to wheat either in the form of monosomic additions (MA), mono-telosomic additions (MtA), double-mono-telosomic additions (dMtA), or double-monosomic additions (dMA). The germplasm developed in this study will help to enhance the genetic base of wheat and facilitate molecular breeding of wheat and triticale.

Sequence-based markers have added a new dimension in the efficiency of identifying alien introgressions in wheat. Expressed sequence tag-sequence tagged sites (EST-STS) markers have proved useful in tracing alien chromatin. In this study, we report the development of Thinopyrum bessarabicum- and Secale anatolicum-specific EST-STS markers and their application in tracing respective alien chromatin introgressions in wheat. The parental lines, Chinese Spring (CS), ISR991.1 (CS/Th. bessarabicum amphidiploid), and ISR1049.2 (CS/Secale anatolicum amphidiploid), were used as core experimental materials. Using comparative analysis of RNA-Seq data, 10 903 and 10 660 candidate sequences specific to Th. bessarabicum and S. anatolicum, respectively, were assembled and identified. To validate the genome specificity of these candidate sequences, 68 and 64 EST-STS markers were developed from randomly selected candidate sequences of Th. bessarabicum and S. anatolicum, respectively, and tested on sets of alien addition lines. Fifty-five and 53 markers for Th. bessarabicum and S. anatolicum chromatin, respectively, were assigned to chromosomal location(s), covering all seven chromosomes. Approximately 83% of S. anatolicum-specific markers were transferable to S. cereale. The genome-specific candidate sequences identified and the EST-STS markers developed will be valuable resources for exploitation of Th. bessarabicum and Secale species diversity in wheat and triticale breeding.

Fusarium pseudograminearum and Fusarium graminearum commonly cause crown rot (FCR) and head blight (FHB) in wheat, respectively. Disease infection and spread can be reduced by the deployment of resistant cultivars or through management practices that limit inoculum load. Plants deficient in micronutrients, including zinc, tend to be more susceptible to many diseases. On the other hands, and zinc deficiency in cereals is widespread in Australian soils. Zinc deficiency may have particular relevance to crown rot, the most important and damaging Fusarium disease of wheat and barley in Australia. Four wheat genotypes; Batavia, Sunco and two lines from the International Maize and Wheat Improvement Center (CIMMYT) were tested for response to FHB and FCR under differing levels of Zn,1 and 2 g/kg and its correlation with disease severity. Sunco and CIMMYT line 146 were previously rated resistant to crown rot and Zn efficient. Zn application 2 g/kg soil enhanced resistance to FCR of the disease susceptible and Zn in-efficient in Batavia and 48 as its recorded 0.75 and 0.5 respectively compared to Sunco and CIMMYT line 146 as it recorded 0.2 and 0.3 respectively, but did not increase resistance to FHB. However, Zn application did enhance the resistance of Zn efficient genotypes to FHB. Results suggest that higher levels of Zn fertilization could reduce the expression of Fusarium diseases in wheat.

Heat-induced inhibition of photosynthesis is a key factor in declining wheat performance and yield. Variation in wheat heat tolerance can be characterised using the critical temperature (Tcrit) above which incipient damage to the photosynthetic machinery occurs. We investigated intraspecies variation and plasticity of wheat Tcrit under elevated temperature in field and controlled environment experiments. We also assessed whether intraspecies variation in wheat Tcrit mirrors patterns of global interspecies variation in heat tolerance reported for mostly wild, woody plants. In the field, wheat Tcrit varied through the course of a day, peaking at noon and lowest at sunrise, and increased as plants developed from heading to anthesis and grain filling. Under controlled temperature conditions, heat stress (36°C) was associated with a rapid rise in wheat Tcrit (i.e. within two hours of heat stress) that peaked after 3–4 days. These peaks in Tcrit indicate a physiological limitation to photosystem II heat tolerance. Analysis of a global dataset (comprising 183 Triticum and wild wheat (Aegilops) species) generated from the current study and a systematic literature review showed that wheat leaf Tcrit varied by up to 20°C (about two-thirds of reported global plant interspecies variation). However, unlike global patterns of interspecies Tcrit variation which has been linked to latitude of genotype origin, intraspecific variation in wheat Tcrit was unrelated to that. Yet, the observed genotypic variation and plasticity of wheat Tcrit suggests that this trait could be a useful tool for high-throughput phenotyping of wheat photosynthetic heat tolerance.

Stripe rust caused by Puccnina striiformis (Pst) is an economically important disease attacking wheat all over the world. Identifying and deploying new genes for Pst resistance is an economical and long-term strategy for controlling Pst. A genome-wide association study (GWAS) using single nucleotide polymorphisms (SNPs) and functional haplotypes were used to identify loci associated with stripe rust resistance in synthetic-derived (SYN-DER) wheats in four environments. In total, 92 quantitative trait nucleotides (QTNs) distributed over 65 different loci were associated with resistance to Pst at seedling and adult plant stages. Nine additional loci were discovered by the linkage disequilibrium-based haplotype-GWAS approach. The durable rust-resistant gene Lr34/Yr18 provided resistance in all four environments, and against all the five Pst races used in this study. The analysis identified several SYN-DER accessions that carried major genes: either Yr24/Yr26 or Yr32. New loci were also identified on chr2B, chr5B, and chr7D, and 14 QTNs and three haplotypes identified on the D-genome possibly carry new alleles of the known genes contributed by the Ae. tauschii founders. We also evaluated eleven different models for genomic prediction of Pst resistance, and a prediction accuracy up to 0.85 was achieved for an adult plant resistance, however, genomic prediction for seedling resistance remained very low. A meta-analysis based on a large number of existing GWAS would enhance the identification of new genes and loci for stripe rust resistance in wheat. The genetic framework elucidated here for stripe rust resistance in SYN-DER identified the novel loci for resistance to Pst assembled in adapted genetic backgrounds.

A multi-environment genomic prediction model incorporating environmental covariates increased the prediction accuracy of wheat grain protein content. The advantage of the haplotype-based model was dependent upon the trait of interest. The inclusion of environment covariates (EC) in genomic prediction models has the potential to precisely model environmental effects and genotype-by-environment interactions. Together with EC, a haplotype-based genomic prediction approach, which is capable of accommodating the interaction between local epistasis and environment, may increase the prediction accuracy. The main objectives of our study were to evaluate the potential of EC to portray the relationship between environments and the relevance of local epistasis modelled by haplotype-based approaches in multi-environment prediction. The results showed that among five traits: grain yield (GY), plant height, protein content, screenings percentage (SP) and thousand kernel weight, protein content exhibited a 2.1% increase in prediction accuracy when EC was used to model the environmental relationship compared to treatment of the environment as a regular random effect without a variance-covariance structure. The approach used a Gaussian kernel to characterise the relationship among environments that displayed no advantage in contrast to the use of a genomic relationship matrix. The prediction accuracies of haplotype-based approaches for SP were consistently higher than the genotype-based model when the numbers of single-nucleotide polymorphisms (SNP) in a haplotype were from three to ten. In contrast, for GY, haplotype-based models outperformed genotype-based methods when two to four SNPs were used to construct the haplotype.

Tomato is a mild season crop and high temperature stress impacts productivity negatively. However, the development of cultivars with improved heat tolerance is possible as genetic variability has been consistently reported. This study aimed to identify candidate genes that impact various traits under heat stress. Genome-wide association studies (GWAS) were conducted on a diverse set of 144 tomato genotypes collected from various germplasm centers and breeding programs. The genotypes were grown under control and heat stress in poly tunnels having mean temperatures of 30°C and 45°C for two seasons and phenotypic data were collected on seven agro-physiological traits. All individuals were genotyped withthe80K DArTseq platform using 31237 SNP markers. Data were analysed using a mixed model based on restricted maximum likelihood (REML). Pattern analysis of the phenotypic data showed five primary clusters each with genotypes from multiple origins. Based on the genotypic data, three wild tomato genotypes showed a degree of un-relatedness with the other materials as they were distantly located from the rest of the genotypes in the scatter plot. Control treatment data were used to ascertain markers that are exclusively important under high temperature stress. A large number of markers were significantly associated with various traits under heat stress. These included strong marker associations for number of inflorescence/plant (IPP), number of flowers/inflorescence (FPI), fresh fruit weight (FFrW), and electrolyte leakage (EL). High association with EL was found due to two SNPs 7858523|F|0-25:G>A-25:G>A and 4705224|F|0-60:C>G-60:C>G located on Chr 6. Other less pronounced marker-trait associations were observed for plant dry weight (PDW), and number of fruit/plant (FrPP).

Crop-wild introgressions have long been exploited without knowing the favorable recombination points. Synthetic hexaploid wheats are one of the most exploited genetic resources for bread wheat improvement. However, despite some QTL with major effects, much less is known about genome-wide patterns of introgressions and their effects on phenotypes. We used two genome-wide association approaches: SNP-GWAS and haplotype-GWAS to identify SNPs and haplotypes associated with productivity under water-limited conditions in a synthetic-derived wheat (SYN-DER) population. Haplotype-GWAS further enriched and identified 20 more genomic regions associated with drought adaptability that did not overlap with SNP-GWAS. Since GWAS is biased to the phenotypes in the study and may fail to detect important genetic diversity during breeding, we used five complementary analytical approaches (t-test, Tajima’s D, nucleotide diversity (π), Fst, and EigenGWAS) to identify divergent selections in SYN-DER compared to modern bread wheat. These approaches consistently pinpointed 89 ‘selective sweeps’, out of which 30 selection loci were identified on D-genome. These key selections co-localized with important functional genes of adaptive traits such as TaElf3-D1 (1D) for earliness per se (Eps), TaCKX-D1 (3D), TaGS1a (6D) and TaGS-D1 (7D) for grain size, weight and morphology, TaCwi-D1 (5D) influencing drought tolerance, and Vrn-D3 (7D) for vernalization. Furthermore, 55 SNPs and 23 haplotypes of agronomic and physiological importance such as grain yield, relative water content and thousand grain weight in SYN-DER, were among the top 5% of divergent selections contributed by synthetic hexaploid wheats. These divergent selections associated with improved agronomic performance carry new alleles that have been introduced to wheat. Our results demonstrated that GWAS and selection sweep analyses are powerful approaches for investigating favorable introgressions under strong selection pressure and the use of crop-wild hybridization to assist the improvement of wheat yield and productivity under moisture limiting environments.

The leaf features like trichome density, gradient grooves, and leaf wettability determine the efficiency to capture air moisture for self-irrigation in the wheat plant. Plants in water-scarce environments evolved to capture air moisture for their water needs either directly or indirectly. Structural features like cones, hairs, and grooves assist water capture. The morphology of crops such as wheat can promote self-irrigation under drought. To examine this further, 34 wheat genotypes were characterized for leaf traits in near optimal conditions in the field using a randomized complete block design with 3 replications. An association was found between morphological and physiological traits and yield using simple correlation plots. A core set of nine genotypes was subsequently evaluated for moisture harvesting ability and leaf wettability. Results showed that variation among genotypes exists for fog harvesting ability attributed to structural leaf features. Physiological traits, especially photosynthesis and water use efficiency, were positively associated with yield, negatively correlated with soil moisture at booting, and positively correlated with soil moisture at anthesis. The genotypes with deep to medium leaf grooves and dense hairs on the edges and adaxial surfaces (genotypes 7 and 18) captured the most moisture. This was a function of higher water drop rolling efficiency resulting from lower contact angle hysteresis. These results can be exploited to develop more heat and drought-tolerant crops.

Increasing the number of environments for phenotyping of crop lines in earlier stages of breeding programs can improve selection accuracy. However, this is often not feasible due to cost. In our study, we investigated a partial phenotyping strategy that does not test all entries in all environments, but instead capitalizes on genomic prediction to predict missing phenotypes in additional environments without extra phenotyping expenditure. The breeders’ main interest – response to selection – was directly simulated to evaluate the effectiveness of the partial genomic phenotyping strategy in a wheat dataset. Whether the partial phenotyping strategy resulted in more selection response depended on the correlations of phenotypes between environments. The partial phenotyping strategy consistently showed statistically significant higher simulated responses to selection, compared to complete phenotyping, when the majority of completely phenotyped environments were negatively correlated and any extension environment was highly positively correlated with any of the completely phenotyped environments. Our results indicate that genomics-based partial phenotyping can improve selection response at middle stages of crop breeding programs.

Heat stress tolerance in plants is a complex trait controlled by multiple genes of minor effect which are influenced by the environment and this makes breeding and selection complicated. Emmer wheat (Triticum dicoccon Schrank) carries valuable diversity that can be used to improve the heat tolerance of modern bread wheat. A diverse set of emmer-based genotypes was developed by crossing emmer wheat with hexaploid wheat. These materials, along with their hexaploid recurrent parents and commercial cultivars, were evaluated at optimum (E1) and heat stressed (E2) sowing times in the field for three consecutive years (2014-2016). The material was genotyped using the Infinium iSelect SNP 90K SNP Assay. The phenotypic data were combined across years within each sowing time and best linear unbiased estimators calculated for each genotype in each environment. These estimates were used for GWAS analysis. Significant phenotypic and genotypic variation was observed for all traits. A total of 125 and 142 marker-trait associations (MTAs) were identified in E1 and E2, respectively. The highest number of MTAs were observed on the A genome (106), followed by the B (105) and D (56) genomes. MTAs with pleiotropic effects within and across the environments were observed. Many of the MTAs found were reported previously for various traits, and a few significant MTAs under heat stress were new and linked to emmer genome. Genomic regions identified on chromosomes 2B and 3A had a significant positive impact on grain yield under stress with a 7% allelic effect. Genomic regions on chromosomes 1A and 4B contributed 11% and 9% of the variation for thousand kernel weight (TKW) under heat stress respectively. Following fine mapping, these regions could be used for marker-assisted selection to improve heat tolerance in wheat. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-021-01222-3.

International audience; Processes based on homogeneous catalysts are the most widely used for industrial production of fatty acid derivatives, despite catalyst loss in aqueous effluents during the wet-purification stage. In this work, dry-purification of the crude bioproducts; ethyl biodiesel and biolubricants, derived from Indian mustard was conducted using various natural mineral (clay) and organic (plant issue) adsorbents to evaluate operating conditions including temperature, contact time and number of treatment cycles and to define the optimal procedure. Adsorbent characterization was determined by average particle size assessed using laser granulometry, morphology and elemental chemical composition measured by scanning electron spectroscopy with microanalysis using energy dispersive X-ray spectroscopy, chemical structure determination based on Fourier Transform InfraRed spectroscopy and porosity and specific area assessed using carbon dioxide or nitrogen adsorption. The quality of the biofuel and biolubricants, before and after dry-purification on the above adsorbents, was evaluated using different methods including Karl Fischer titration, gas chromatography with a flame ionization detector and inductively coupled plasma-atomic emission spectroscopy. Montmorillonite clay and finely ground Indian mustard stems (particle size of 100–710 μm) without further pyrolysis or carbonization treatment were found to be the best adsorbents. Combined with the selected dry-purification procedure (35–45 °C, 20 min, single treatment cycle), most impurities including residual glycerides, free glycerin, water, catalysts and metals were removed from the resultant ethyl biodiesel thus meeting the basic biofuel specifications of acid value, color, density, viscosity, flash point, pour point, cloud point, cold filter plugging point, higher heating value, and oxidation stability. Further purification of biolubricants was required using bubble-washing with citric acid and vacuum distillation to obtain a product with acceptable density, viscosity and color. This work highlights the potential of a biorefinery system focused on Indian mustard contributing to a green circular economy, that would benefit both farmers and consumers in the respect of environment; farmers would gain in energy security and flexibility by biofuel, biolubricant and other bioproducts on-farm production, while ensuring healthy food security and offering job opportunities, the whole with reduced chemical and energy inputs and minimized waste effluents.

Wheat is a major food crop, with around 765 million tonnes produced globally. The largest wheat producers include the European Union, China, India, Russia, United States, Canada, Pakistan, Australia, Ukraine and Argentina. Cultivation of wheat across such diverse global environments with variation in climate, biotic and abiotic stresses, requires cultivars adapted to a range of growing conditions. One intrinsic way that wheat achieves adaptation is through variation in phenology (seasonal timing of the lifecycle) and related traits (e.g., those affecting plant architecture). It is important to understand the genes that underlie this variation, and how they interact with each other, other traits and the growing environment. This review summarises the current understanding of phenology and developmental traits that adapt wheat to different environments. Examples are provided to illustrate how different combinations of alleles can facilitate breeding of wheat varieties with optimal crop performance for different growing regions or farming systems.

The leaf features like trichome density, gradient grooves, and leaf wettability determine the efficiency to capture air moisture for self-irrigation in the wheat plant. Plants in water-scarce environments evolved to capture air moisture for their water needs either directly or indirectly. Structural features like cones, hairs, and grooves assist water capture. The morphology of crops such as wheat can promote self-irrigation under drought. To examine this further, 34 wheat genotypes were characterized for leaf traits in near optimal conditions in the field using a randomized complete block design with 3 replications. An association was found between morphological and physiological traits and yield using simple correlation plots. A core set of nine genotypes was subsequently evaluated for moisture harvesting ability and leaf wettability. Results showed that variation among genotypes exists for fog harvesting ability attributed to structural leaf features. Physiological traits, especially photosynthesis and water use efficiency, were positively associated with yield, negatively correlated with soil moisture at booting, and positively correlated with soil moisture at anthesis. The genotypes with deep to medium leaf grooves and dense hairs on the edges and adaxial surfaces (genotypes 7 and 18) captured the most moisture. This was a function of higher water drop rolling efficiency resulting from lower contact angle hysteresis. These results can be exploited to develop more heat and drought-tolerant crops.

Climate change and future warming will significantly affect crop yield. The capacity of crops to dynamically adjust physiological processes (i.e. acclimate) to warming might improve overall performance. Understanding and quantifying the degree of acclimation in field crops could ensure better parameterization of crop and Earth System models and predictions of crop performance. We hypothesized that for field-grown wheat, when measured at a common temperature (25°C), crops grown under warmer conditions would exhibit acclimation, leading to enhanced crop performance and yield. Acclimation was defined as: (i) decreased rates of net photosynthesis at 25°C (A25) coupled with lower maximum carboxylation capacity (Vcmax25); (ii) reduced leaf dark respiration at 25°C (both in terms of O2 consumption, Rdark_O225; and CO2 efflux, Rdark_CO225); and (iii) lower Rdark_CO225:Vcmax25. Field experiments were conducted over two seasons with 20 wheat genotypes, sown at three different planting dates, to test these hypotheses. Leaf-level CO2 based traits (A25, Rdark_CO225, and Vcmax25) did not show the classic acclimation responses that we hypothesized; by contrast, the hypothesized changes in Rdark_O2 were observed. These findings have implications for predictive crop models that assume similar temperature response among these physiological processes, and for predictions of crop performance in a future warmer world.

Several stable QTL were detected using metaGWAS analysis for different agronomic and quality traits under 26 normal and heat stressed environments. Heat stress, exacerbated by global warming, has a negative influence on wheat production worldwide and climate resilient cultivars can help mitigate these impacts. Selection decisions should therefore depend on multi-environment experiments representing a range of temperatures at critical stages of development. Here, we applied a meta-genome wide association analysis (metaGWAS) approach to detect stable QTL with significant effects across multiple environments. The metaGWAS was applied to 11 traits scored in 26 trials that were sown at optimal or late times of sowing (TOS1 and TOS2, respectively) at five locations. A total of 2571 unique wheat genotypes (13,959 genotypes across all environments) were included and the analysis conducted on TOS1, TOS2 and both times of sowing combined (TOS1&2). The germplasm was genotyped using a 90 k Infinium chip and imputed to exome sequence level, resulting in 341,195 single nucleotide polymorphisms (SNPs). The average accuracy across all imputed SNPs was high (92.4%). The three metaGWAS analyses revealed 107 QTL for the 11 traits, of which 16 were detected in all three analyses and 23 were detected in TOS1&2 only. The remaining QTL were detected in either TOS1 or TOS2 with or without TOS1&2, reflecting the complex interactions between the environments and the detected QTL. Eight QTL were associated with grain yield and seven with multiple traits. The identified QTL provide an important resource for gene enrichment and fine mapping to further understand the mechanisms of gene × environment interaction under both heat stressed and unstressed conditions.

Cereal rye and its wild forms are important sources of genetic diversity for wheat breeding due to their resistances to biotic and abiotic stresses.

Suboptimal distribution of photosynthetic capacity in relation to light among leaves reduces potential whole-canopy photosynthesis. We quantified the degree of suboptimality in 160 genotypes of wheat by directly measuring photosynthetic capacity and daily irradiance in flag and penultimate leaves. Capacity per unit daily irradiance was systematically lower in flag than penultimate leaves in most genotypes, but the ratio (γ) of capacity per unit irradiance between flag and penultimate leaves varied widely across genotypes, from less than 0.5 to over 1.2. Variation in γ was most strongly associated with differences in photosynthetic capacity in penultimate leaves, rather than with flag leaf photosynthesis or canopy light penetration. Preliminary genome-wide association analysis identified nine strong marker-trait associations with this trait, which should be validated in future work in other environments and/or materials. Our modelling suggests canopy photosynthesis could be increased by up to 5 % under sunny conditions by harnessing this variation through selective breeding for increased γ., Plants invest nitrogen in photosynthetic enzymes in leaves. Although the optimal investment should be roughly proportional to how much light each leaf receives, plants tend to underinvest N in upper-canopy (sunlit) leaves. We examined, for the first time, whether this suboptimal pattern differs within species, by measuring light capture and photosynthetic capacity in flag and penultimate leaves across 160 wheat genotypes. We found wide variation in suboptimal N distribution, mostly driven by variation in plants’ ability to move N from penultimate to flag leaves as flag leaves develop. Selecting for less-suboptimal N distribution could increase canopy photosynthesis by several percent.

A new leaf rust resistance gene Lr80 was identified and closely linked markers were developed for its successful pyramiding with other marker-tagged genes to achieve durable control of leaf rust. Common wheat landrace Hango-2, collected in 2006 from the Himalayan area of Hango, District Kinnaur, in Himachal Pradesh, exhibited a very low infection type (IT;) at the seedling stage to all Indian Puccinia triticina (Pt) pathotypes, except the pathotype 5R9-7 which produced IT 3+. Genetic analysis based on Agra Local/Hango-2-derived F3 families indicated monogenic control of leaf rust resistance, and the underlying locus was temporarily named LrH2. Bulked segregant analysis using 303 simple sequence repeat (SSR) markers located LrH2 in the short arm of chromosome 2D. An additional set of 10 chromosome 2DS-specific markers showed polymorphism between the parents and these were mapped on the entire Agra Local/Hango-2 F3 population. LrH2 was flanked by markers cau96 (distally) and barc124 (proximally). The 90 K Infinium SNP array was used to identify SNP markers linked with LrH2. Markers KASP_17425 and KASP_17148 showed association with LrH2. Comparison of seedling leaf rust response data and marker locations across different maps demonstrated the uniqueness of LrH2 and it was formally named Lr80. The Lr80-linked markers KASP_17425, KASP_17148 and barc124 amplified alleles/products different to Hango-2 in 82 Australian cultivars indicating their robustness for marker-assisted selection of this gene in wheat breeding programs.

The pathogen

Periods of high temperature and an expected increase in atmospheric CO2 concentration as a result of global climate change are major threats to wheat (Triticum aestivum L.) production. Developing heat-tolerant wheat cultivars demands improved understanding of the impacts of high temperature and elevated CO2 on plant growth and development. This research investigated the interactive effects of heat stress and CO2 concentration on pollen viability and its relationship to grain formation and yield of wheat in greenhouse conditions. Nineteen wheat genotypes and a current cultivar, Suntop, were heat stressed at either meiosis or anthesis at ambient (400 µL L-1) or elevated (800 µL L-1) CO2. Elevated CO2 and heat stress at meiosis reduced pollen viability, spikelet number and grain yield per spike; however, increased tillering at the elevated CO2 level helped to minimise yield loss. Both heat-tolerant genotypes (e.g. genotype 1, 2, 10 or 12) and heat-sensitive genotypes (e.g. genotype 6 or 9) were identified and response related to pollen sensitivity and subsequent impacts on grain yield and yield components were characterised. A high-throughput protocol for screening wheat for heat stress response at elevated CO2 was established and meiosis was the most sensitive stage, affecting pollen viability, grain formation and yield.

Crown rot of wheat and barley is a serious disease caused by the fungus Fusarium pseudograminearum, a stubble-borne pathogen common in no-till farming systems in water-limited grain growing regions. Marker assisted recurrent selection (MARS) was used to more effectively pyramid minor genes controlling plant response to crown rot disease. Two populations comprising 475 genotypes were phenotyped for adult plant resistance and genotyped using a 9K SNP array. A genome-wide association study (GWAS) was used to estimate quantitative trait locus (QTL) effects as more than two parents were recombined in each population. A total of 23 significant and unique marker-trait associations (MTAs) were identified in both populations. A Kompetitive allele-specific PCR (KASP) assay was developed and used to genotype the progeny and parents of each recombination cycle. Following two cycles of recombination among progeny, up to 22 markers of a possible 23 were recombined. Two hundred ninety-seven double haploid-derived lines representing both cycles of recombination, the original parents, parents selected from the base population and local cultivars were evaluated for crown rot resistance in 2016 and 2017 in the field under crown rot inoculation pressure. A significant and positive response to each cycle of recurrent selection was observed. MARS was an effective breeding strategy for combining many QTLs of small effect for crown rot resistance in wheat.