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Fusarium crown rot (FCR) causes significant grain yield loss in winter cereals around the world. Breeding for resistance and/or tolerance to FCR has been slow with relatively limited success. In this study, multi-species experiments were used to demonstrate an improved method to quantify FCR infection levels at plant maturity using qPCR, as well as the genotype yield retention using residual regression deviation. Using qPCR to measure FCR infection allowed a higher degree of resolution between genotypes than traditional visual stem basal browning assessments. The results were consistent across three environments with different levels of disease expression. The improved measure of FCR infection along with genotype yield retention allows for partitioning of both tolerance and partial resistance. Together these methods offer new insights to FCR partial resistance and its relative importance to tolerance in bread wheat and barley. This new approach offers a more robust, cost-effective way to select for both FCR traits within breeding programs.Key messageGenetic gain for tolerance and partial resistance against Fusarium crown rot (FCR) in winter cereals has been impeded by laborious and variable visual measures of infection severity. This paper presents results of an improved method to quantify FCR infection that are strongly correlated to yield loss and reveal previously unrecognised partial resistance in barley and wheat varieties.

Septoria tritici blotch (STB) has been ranked the third most important wheat disease in the world, threatening a large area of wheat production. Although major genes play an important role in the protection against Zymoseptoria tritici infection, the lifespan of their resistance unfortunately is very short in modern agriculture systems. Combinations of quantitative resistance with minor effects, therefore, are believed to have prolonged and more durable resistance to Z. tritici. In this study new quantitative trait loci (QTLs) were identified that are responsible for seedling-stage resistance and adult-plant stage resistance (APR). More importantly was the characterisation of a previously unidentified QTL that can provide resistance during different stages of plant growth or multi-stage resistance (MSR). At the seedling stage, we discovered a new isolate-specific QTL, QSt.wai.1A.1. At the adult-plant stage, the new QTL QStb.wai.6A.2 provided stable and consistent APR in multiple sites and years, while the QTL QStb.wai.7A.2 was highlighted to have MSR. The stacking of multiple favourable MSR alleles was found to improve resistance to Z. tritici by up to 40%.Key messageAn Australian GWAS panel discovered three new QTLs associated with seedling-stage resistance, adult-plant stage resistance, and multi-stage resistance, respectively.

Low temperatures at the young microspore stage (YMS) decreases spikelet fertility and is a major limiting factor to rice production in temperate Australia. Low temperature tolerance is a difficult trait to phenotype, hence there is a strong desire for the identification of quantitative trait loci (QTL) for their use in marker-assisted selection (MAS). Association mapping was used in several breeding populations with a known source of low temperature tolerance, Norin PL8, to identify QTL for low temperature tolerance. A novel QTL for spikelet fertility was identified on chromosome 6

Climate change may lead to an increase in both day and night time temperatures in rice (Oryza sativa L) growing regions, but the impact of such temperature increases on yields of Australian rice varieties is not known. We evaluated the biomass and grain yield response of eleven Australian rice varieties including long, medium and short grain types, and the Californian cultivar M205, to heat stress during the reproductive phase and grain filling stages. Heat stress (day/night = 35/25°C) was applied at one of three stages: from panicle exertion to anthesis (PE), from anthesis to 10 days after anthesis (EGF) and from 10–20 days after anthesis (LGF) periods after which the effect on biomass and grain yield was compared to control plants. When heat stress was applied at PE and early grain filling stages, mean grain yield losses across rice varieties were 83% and 53%, respectively, though significant genotype × heat stress treatment interactions were observed. Notably, three varieties—YRM 67, Koshihikari and Opus—appeared to possess greater tolerance to heat stress at these growth stages. A significant genotype × heat stress treatment interaction was also observed in the LGF treatment, where significant yield reductions were only observed in Opus (21% loss) and YRM 67 (25% loss). A lack of effect of heat stress on total grain yield in most varieties at late grain filling appeared to be due to late tiller grain yields which were either unaffected by the heat stress or increased significantly compared to control plants. While genetic variation for tolerance to heat stress across the three growth stages was observed, there was no rice genotype that was consistently tolerant (in terms of yield under stress) across all three heat stress treatments. In the absence of a genotype that showed broad heat stress tolerance during reproductive growth, we suggest screening of a wider pool of more diverse rice germplasm is warranted.

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.

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.

The disease scald of barley is caused by the pathogen Rhynchosporium commune and can cause up to 30-40% yield loss in susceptible varieties. In this study, the Australian barley cultivar Yerong was demonstrated to have resistance that differed from Turk (Rrs1) based on seedling tests with 11 R. commune isolates. A doubled haploid population with 177 lines derived from a cross between Yerong and Franklin was used to identify quantitative trait loci (QTL) for scald resistance. Scald resistance against four pathogen isolates was assessed at the seedling growth stage in a glasshouse experiment and at the adult growth stage in field experiments with natural infection over three consecutive years. A QTL on chromosome 3H was identified with large effect, consistent with a major gene conferring scald resistance at the seedling stage. Under field conditions, scald percentage was negatively correlated with early relative maturity. A bivariate analysis was used to model scald percentage and relative maturity together, residuals from the regression of scald percentage on relative maturity were used as our phenotype for QTL analysis. This analysis identified one major QTL on chromosome 3H, which mapped to the same position as the QTL identified for scald resistance at seedling stage. The identified QTL on 3H is proposed to be different from the Rrs1 on the basis of seedling resistance against different R. commune isolates and physical map position. The analysis also identified an additional novel QTL on chromosome 7H. This study increases the current understanding of scald resistance and identifies genetic material possessing QTLs useful for the marker-assisted selection of scald resistance in barley breeding programs.

Since it was first characterised in 1983, 2-acetyl-1-pyrroline (2AP) has been considered to be the most important aroma compound in rice. In this study, we show four other amine heterocycles: 6-methyl, 5-oxo-2,3,4,5-tetrahydropyridine (6M5OTP), 2-acetylpyrrole, pyrrole and 1-pyrroline, that correlate strongly with the production of 2AP, and are present in consistent proportions in a set of elite aromatic rice varieties from South East Asia and Australia as well as in a collection of recombinant inbred lines (RILs) derived from indica Jasmine-type varieties, Australian long grain varieties (temperate japonica) and Basmati-type rice (Grp V). These compounds were detected through untargeted metabolite profiling by two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOF-MS), and their identity were confirmed by comparison with authentic standards analysed using gas chromatography mass spectrometry (GC-MS) and High Resolution GC × GC-TOF-MS (GC × GC HRT-4D). Genome-wide association analysis indicates that all compounds co-localised with a single quantitative trait locus (QTL) that harbours the FGR gene responsible for the production of GABA. Together, these data provide new insights into the production of 2AP, and evidence for understanding the pathway leading to the accumulation of aroma in fragrant rice.

Climate change represents a threat to the productivity of staple crops which are sensitive to heat stress. While heat stress during grain filling is known to reduce rice (Oryza sativa) yields, the impact on grain quality traits such as head rice yield (HRY) has not been fully resolved. The impact of a 10 d heat stress event (31/23 °C, 33/24 °C and 35/25 °C: day/night, 12 h/12 h) from 10 days after anthesis (DAA) to 20 DAA on grain yields and HRY was investigated in two medium grain (M205, Baru) and one long grain (Lemont) japonica cultivars and one medium grain indica cultivar (Teqing). Losses during milling were partitioned into husk losses or grain breakage during de-husking, and bran losses or grain breakage during polishing. While the highest heat stress (35/25 °C) reduced grain yields by around 20% compared to control plants across the four cultivars, reductions in HRY were greater than 50%. In the control treatment, husk losses during milling ranged from 21% (Teqing) to 40% (Lemont) while breakage of white rice during milling ranged from less than 5% in M205 and Lemont to 23% in Teqing. High levels of heat stress led to increased grain breakage during dehusking and/or polishing in cultivars M205, Baru and Lemont. However, heat stress reduced cultivar Lemont HRY not by increased grain breakage during polishing but predominantly due to a 59% increase in husk loss. Given husk tissue is not a net carbon source for developing rice grains, this suggests heat stress in Lemont increased carbon partitioning from vegetative tissues to the husk at the expense of the developing caryopsis. Ultimately, our results indicate reduction in HRY due to heat stress during grain filling is complex and cannot be attributed solely to greater grain breakage during de-husking and polishing. While HRY is typically treated as a single trait, our data suggest quantifying the individual process losses that contribute to HRY as separate traits will improve the accuracy of HRY QTL analysis and selection in breeding programs.

Aromatic rices are culturally and economically important for many countries in Asia. Investigation of the volatile compounds emitted by rice during cooking is the key to understanding the flavour of elite aromatic rice varieties. The objectives of this study were to compare Jasmine-type aromatic rices from the Greater Mekong Subregion and Australia in terms of their metabolomics and sensory profiles and to draw out associations between the volatile organic compounds and human sensory perception of rice aroma. A set of aromatic rice varieties from South East Asia and Australia, along with non-aromatic controls, was grown in tropical and temperate areas of Australia. Untargeted metabolite profiling of volatile compounds, from the heated rice flour, by static headspace extraction and separation by two dimensional gas chromatography time-of-flight mass spectrometry was performed. Volatile compounds were also assayed in the standard references used in the sensory evaluation and compared to the compounds detected in the headspace of rice. While 2-acetyl-1-pyrroline (2-AP) was a discriminating compound, we identified several of its structural homologues, and a number of other metabolites that were consistently detected in fragrant Jasmine rice. 2-AP producing rice varieties have different sensory properties and these variations were defined by the discriminating compounds identified in each rice type. The results of this study are valuable in understanding the aspects of aromatic rice that are important to consumers, and in the identification of compounds that breeding programs can use to select for pleasant aromas, enabling breeding programs to target markets with greater accuracy.

Research into winter cereal breeding in Australia has focused primarily on studying the effects of rainfed environments. These studies typically show large genotype × environment (GE) interactions, and the complexity of these interactions acts as an impediment to the efficient selection of improved varieties. Wheat has been studied extensively; however, there are no published studies on the GE interactions of triticale in Australia under irrigated production systems. We conducted trials on 101 triticale genotypes at two locations over 4 years under intensive irrigated management practices and measured the yield potential, GE interactions, heritability and estimated genetic gain of yield, lodging resistance and several other traits important for breeding triticale. We found that high yield potential exceeding 10 t ha–1 exists in the Australian germplasm tested and that, in these irrigated trials, genotype accounted for a high proportion of the variability in all measured traits. All genetic parameters such as heritability and estimated genetic gain were high compared with rainfed studies. Breeding of triticale with improved yield and lodging resistance for irrigated environments is achievable and can be pursued with confidence in breeding programs.

To extend the production base of durum wheat in Australia, field trials were conducted on seven registered durum varieties across four seasons and six sites in locations where irrigation was supplied during crop growth. The purpose was to determine if the quality of the grain produced met the requirements for good milling and pasta-making quality and to understand the genotype, environment and their interaction in affecting yield and technological quality of the grain and derived pasta. High grain yields and grain protein were obtained, producing large grain weights, low screenings and low percentage of hard vitreous kernels. Yellow colour of semolina and pasta was reduced marginally but dough and other pasta technological characteristics were similar to typical dryland durum production, with some exceptions. Varieties were identified with potential for production under irrigation.