A stay-green phenotype is useful for adaptation of wheat to end-of-season drought conditions. We identified quantitative trait loci (QTL) for stay-green traits, as well as for height, days to anthesis and yield, in a multireference nested association mapping (MR-NAM) population of wheat (Triticum aestivum L.) in two environments differing in degree of drought stress experienced post-anthesis. The MR-NAM population consisted of three inter-related nested association mapping populations developed by nesting 11 diverse adaptation donors within three common reference parents, adapted to the northern, southern and western cropping regions of Australia, respectively. The construction of the MR-NAM population enables the assessment of the effect on a trait of multiple alleles at any particular locus, in different genetic backgrounds, and facilitates concurrent QTL mapping and germplasm development. This approach enabled identification of parent-specific alleles and context dependent expression. Using a new statistical method specifically developed to identify QTL in MR-NAM populations, we identified 65 QTL for stay-green traits. Co-location was observed between (i) trait by loci associations for some of the different stay-green traits, (ii) for QTL between the two environments, and (iii) between QTL for stay-green traits, plant height and grain yield. Some QTL co-located with those identified in other studies however, others are likely novel. Genetic markers associated with QTL for stay-green can be applied in breeding to enrich populations for stay-green traits in early generations of selection, prior to field testing in yield plots, in particular for the development of wheat cultivars targeted to end-of-season drought-stressed environments. This information is important for breeders, because it facilitates identification of the sources of the most promising alleles at particular loci for specific genetic backgrounds and growing environments.

Agricultural stakeholders need a common set of metrics to evaluate plant pest impacts to facilitate transparency and harmonisation of pest management and prioritisation across spatial scales and jurisdictions. We propose a classification system that articulates, defines and classifies the magnitude of impacts (historical, current or potential) of pest species (alien and native) in plant production systems. Metrics were identified and criteria defined through consideration of economic parameters, risk assessment standards and guidance tools, discussions with pest risk assessment practitioners and recent advances in environmental impact classification schemes. Twenty metrics were identified and assigned to one of four key metric types: spatiotemporal, market-driven, primary response and mid-to long-term response. Host crop value, Market access, Feasibility of management and Reversibility were identified as disruptor metrics, likely to influence overall classification by at least twice that of other metrics. Application of the system found it was able to classify well-known pests by importance, capturing changes in impact status as the management programme progressed for one pest, and how it was influenced by the geographic scale of assessment for another. Our work demonstrates the value of integrating plant protection science with invasion biology to derive a comprehensive measure of pest impact in agroecosystems that can be utilised by all plant biosecurity stakeholders.

In many wheat cropping regions, water limitation is the primary production constraint. This situation is predicted to be more frequent with future climate change. The stay-green phenotype allows crops to remain green and photosynthesize for longer than standard phenotypes after anthesis which can improve yields under late season drought. Root systems with more roots at depth can contribute by increasing access to deep soil moisture late in the season. To study the genetics of root and stay-green traits in wheat, a multi reference parent nested association mapping (NAM) population was developed. Using the “speed breeding” system of rapid generation advance, over 1500 recombinant inbred lines were generated in approximately 18 months. A novel whole-genome NAM method (WG-NAM) was developed for genome-wide association mapping to identify markers associated with the target traits.

Terminal drought stress is currently a major constraint in many wheat production regions. This is predicted to worsen with future climate change. The stay-green phenotype allows crops to remain green and photosynthesize for longer after anthesis, potentially improving yields in terminal drought environments. Root systems with greater root length density at depth can contribute by increasing access to deep soil moisture late in the season. To study the genetics of root and stay-green traits in wheat, a multi reference parent nested association mapping (NAM) population was developed. Using the “speed breeding” system of rapid generation advance, over 1500 recombinant inbred lines (RIL) were generated in approximately 18 months. Genome-wide association studies (GWAS) using a novel whole-genome NAM method (WG-NAM) identified genetic regions associated with the target traits. High-throughput techniques were developed and used for the NAM lines to (i) phenotype seedling roots in controlled conditions, and (ii) objectively characterize novel stay-green traits for hundreds of genotypes in standard yield plots in the field. NAM lines were phenotyped for yield and stay-green traits at multiple water-stressed and non-stressed environments during 4 seasons. Particular traits were associated with superior adaptation to certain environments. Many lines with adaptive root and stay-green traits exhibited superior yield to the reference parent in relevant target environments and 54 such lines have been provided to commercial Australian wheat breeders for cultivar development. This combination of technologies is increasing understanding of physiological adaptation to water-limited environments in wheat and helping accelerate genetic progress.

Environmental characterization (EC) one influential approach for understanding the performance of genotypes in different environments. Sometimes interactions between environment and genotype limit the genetic gain for complex traits in breeding programs, especially drought. Stay green lines are able to retain green leaf area longer than standard lines leading to superior adaptation under water-limitation. Modelling framework has been used analytically in breeding to dissect complex traits, such as yield under water limitation, into critical trait components (e.g. stay-green, flowering time, root architecture). Characterization can help to select more heritable genotypes that can be subjected to high throughout phenotyping, and make more sensible targets for genomic selection by the following search aims: (1) Characterise stressed environments (accounting for climate and soil characteristics, management practices, and crop development) to characterise the timing and severity of the stress and non-stress, (2) Identify the potentially adaptive cultivars and traits in each specific environment, and (3) Determine the correlation between stay-green traits and yield in the different environment types.

A current challenge for plant breeders is the limited ability to phenotype and select for root characteristics to enhance crop productivity. The development of a high-throughput phenotyping method has recently offered new opportunities for the selection of root characteristics in breeding programs. Here, we investigated prospects for phenotypic and molecular selection for seminal root angle (SRA), a key trait associated with mature root system architecture in wheat ( L.). We first investigated genetic diversity for this trait in a panel of 22 wheat lines adapted to Australian environments. The angle between the first pair of seminal roots ranged from 72 to 106°. We then evaluated selection gain via direct phenotypic selection in early generations by comparing the resulting shift in population distribution in tail populations selected for "narrow" and "wide" root angle. Overall, two rounds of selection significantly shifted the mean root angle as much as 10°. Furthermore, comparison of allele frequencies in the tail populations revealed genomic regions under selection, for which marker-assisted selection appeared to be successful. By combining efficient phenotyping and rapid generation advance, lines enriched with alleles for either narrow or wide SRA were developed within only 18 mo. These results suggest that there is a valuable source of allelic variation for SRA that can be harnessed and rapidly introgressed into elite wheat lines.

Roots play a key role in plant growth regulation. It is well described that the below-ground plant architecture has a significant impact on plant performance under abiotic constraints and maintains stability under increased grain load (Lynch, 2013Lynch J.P. Steep, cheap and deep: an ideotype to optimize water and N acquisition by maize root systems.Ann. Bot. 2013; 112: 347-357Crossref PubMed Scopus (744) Google Scholar). Although loci influencing root traits have been shown to affect grain yield and agronomic performance (e.g., Canè et al., 2014Canè M.A. Maccaferri M. Nazemi G. Salvi S. Francia R. Colalongo C. Tuberosa R. Association mapping for root architectural traits in durum wheat seedlings as related to agronomic performance.Mol. Breed. 2014; 34: 1629-1645Crossref PubMed Scopus (85) Google Scholar), knowledge about the genetic control of root growth in major grain crops is limited. Here, we demonstrate that VERNALIZATION1 (VRN1), a key regulator of flowering behavior in cereals (Deng et al., 2015Deng W. Casao M.C. Wang P. Sato K. Hayes P.M. Finnegan E.J. Trevaskis B. Direct links between the vernalization response and other key traits of cereal crops.Nat. Commun. 2015; 6: 5882Crossref PubMed Scopus (129) Google Scholar), also modulates root architecture in wheat and barley. Our discoveries provide unexpected insight into underground functions of a major player in the flowering pathway. We initially mapped a highly significant quantitative trait locus (QTL) for nodal root angle index (NRI; Supplemental Figure 1, Supplemental Materials and Methods) on Triticum aestivum chromosome 5B using 219 hexaploid winter wheat accessions (Supplemental Figure 2, Supplemental Tables 1–3). This QTL consists of six single-nucleotide polymorphism (SNP) markers, which are in strong linkage disequilibrium (LD; r2 ≥ 0.7) and span the B-subgenome homoeolog of VERNALIZATION1 (VRN1) (223 185 538-223 597 558 bp), one of the most important and well-characterized developmental genes in the temperate cereals wheat and barley. The MADS-box transcription factor encoded by VRN1 is well known for its regulation of genes influencing reproductive plant organs and flowering (Deng et al., 2015Deng W. Casao M.C. Wang P. Sato K. Hayes P.M. Finnegan E.J. Trevaskis B. Direct links between the vernalization response and other key traits of cereal crops.Nat. Commun. 2015; 6: 5882Crossref PubMed Scopus (129) Google Scholar). The VRN1 wild-type “winter” allele, v, confers a requirement for prolonged exposure to cold (vernalization) as a prerequisite for flowering in most winter-type wheat and barley, however a deletion in the first intron enables spring-sown plants to flower without prior vernalization, thus referred to as the “spring” allele (a) (Trevaskis et al., 2006Trevaskis B. Hemming M.N. Peacock W.J. Dennis E.S. HvVRN2 responds to daylength, whereas HvVRN1 is regulated by vernalization and developmental status.Plant Physiol. 2006; 140: 1397-1405Crossref PubMed Scopus (195) Google Scholar). To investigate the connection between the major VRN1 polymorphism and variation in wheat root growth, we evaluated three hexaploid wheat near-isogenic lines (NILs) carrying different combinations of winter and spring alleles at the A, B, and D subgenome homeologs of VRN1 in a common genetic background (Supplemental Materials and Methods). The presence of the winter alleles consistently reduced root angle at all growth stages under greenhouse and field conditions (Supplemental Figures 3–5). Root length varied between the different NILs during the lifecycle (Supplemental Figures 6 and 7); winter alleles (vvv) were associated with reduced root length at seedling stage but increased length at anthesis, most likely due to delayed anthesis and an extended vegetative period (Supplemental Figure 8). Root biomass in the bottom half of the soil profile was similar for all NILs at anthesis (Supplemental Figure 9) but post-anthesis, NILs carrying the spring allele (vav and vaa) produced significantly more roots (5.3%) at depth (60–80 cm) compared with winter types (vvv). Interestingly, these lines displayed a significantly reduced root-to-shoot ratio (R/S) in comparison with winter (vvv) NILs at anthesis (Supplemental Figures 10 and 11). Our results suggest that VRN1 influences temporal and spatial root growth in wheat throughout the whole plant lifecycle, with the B-subgenome homoeolog VRN-B1 imparting the strongest phenotypic effect in our study. For cross-species comparison, we assayed similar root architectural traits in barley NILs that differ for prevalent VRN1 alleles (designated VRN-H1) in a common genetic background (Supplemental Materials and Methods). Intriguingly, each VRN-H1 spring allele was associated with a unique root phenotype under greenhouse and field conditions, suggesting divergent selection of functional allelic variants in barley (Supplemental Figures 12 and 13). As expected, VRN-H1 spring alleles significantly influenced above-ground plant development, including days to anthesis and tiller number (Supplemental Figure 14). However, in contrast to wheat, no significant differences in root length at seedling stage were evident among the barley NILs. As observed previously in wheat, spring alleles in barley were associated with reduced root elongation and maximum root length between anthesis and maturity (Supplemental Figure 15). However, each spring VRN1-HA allele was associated with unique root system architecture at the mature stage. Compared with the wild-type, all barley NILs carrying spring alleles produced a higher proportion of roots at moderate soil depths (20–60 cm), particularly during the grain-filling stage (Supplemental Figure 16), although their root biomass and R/S were lower during the seedling stage (Supplemental Figure 17). Notably, the VRN1-1 allele, which is common in Australian barley varieties grown in regions with highly variable rainfall and severe seasonal drought, was associated with narrow root growth behavior in early plant development and prolonged root growth at the deepest soil level (60–80 cm) during grain filling. This suggests that selection for VRN-H1 variants that simultaneously induce early flowering and maintain “steep, cheap, and deep” root systems (Lynch, 2013Lynch J.P. Steep, cheap and deep: an ideotype to optimize water and N acquisition by maize root systems.Ann. Bot. 2013; 112: 347-357Crossref PubMed Scopus (744) Google Scholar) provides a dual mechanism imparting flowering-mediated drought escape coupled with improved water or nutrient acquisition. Interestingly, the NIL carrying a deletion of VRN-H2, an important plant developmental gene and the known signaling target of VRN-H1 in the vernalization response, did not show narrow root growth angles in barley (Supplemental Figures 12 and 13) but exhibited a shorter root length at flag-leaf emergence and a unique root system distribution (Supplemental Figures 15 and 16). To confirm that the influence of VRN1 on below-ground plant development was caused by pleiotropy rather than linkage, we assessed root phenotypes in three transgenic lines of the spring barley cultivar Golden Promise that carry an additional copy of VRN1-HA (Supplemental Materials and Methods). Coordination of above-ground and below-ground architecture in barley by VRN-H1 was highlighted by the striking reflection of shoot and root architecture in transformed line GP[VRN1-HA]-14, in which a significant increase in overall VRN-H1 expression was detected as compared with the non-transformed control (Figure 1). The additional VRN1-HA allele drastically altered all root parameters measured at seedling and adult plant stages (Figure 1E–1J, Supplemental Figure 18A) and significantly reduced spike length and DTA, consistent with recent findings of additional VRN1 functions (Deng et al., 2015Deng W. Casao M.C. Wang P. Sato K. Hayes P.M. Finnegan E.J. Trevaskis B. Direct links between the vernalization response and other key traits of cereal crops.Nat. Commun. 2015; 6: 5882Crossref PubMed Scopus (129) Google Scholar; Supplemental Figure 18B and 18C), while a significant reduction in R/S was only observed in transformed lines GP[VRN1-HA]-6 and GP[VRN1-HA]-22 (Supplemental Figure 19). To gain first insights into the biological mechanism with which VRN1 influences root architecture, we investigated gene expression and used time-lapse imaging to compare root gravitropic responses between barley NILs carrying different alleles (Supplemental Figure 20). Strong differences in gravitropic response were observed depending on the VRN1 allelic state (Supplemental Movie 1) and high VRN-H1 expression levels were observed in mature root system tissues of barley NILs carrying VRN1-1 and the winter wild-type allele. No expression differences could be found between the VRN-H1 and winter wild-type barley NILs for the barley homolog of DEEPER ROOTING 1 (DRO1) (Uga et al., 2013Uga Y. Sugimoto K. Ogawa S. Rane J. Ishitani M. Hara N. Kitomi Y. Inukai Y. Ono K. Kanno N. et al.Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions.Nat. Genet. 2013; 45: 1097-1102Crossref PubMed Scopus (852) Google Scholar), the first cloned root architectural gene in rice, or the barley homolog of the auxin-induced GH3-2 gene, confirming that the observed differences in root angle are independent of DRO1 and auxin sensitivity at the whole-root system level. However, this does not exclude the possibility of significant differences in root tips, as observed for DRO1 expression in rice (Uga et al., 2013Uga Y. Sugimoto K. Ogawa S. Rane J. Ishitani M. Hara N. Kitomi Y. Inukai Y. Ono K. Kanno N. et al.Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions.Nat. Genet. 2013; 45: 1097-1102Crossref PubMed Scopus (852) Google Scholar). We then examined the VRN1 allelic composition of different wheat populations. By analyzing 132 commercial Australian wheat cultivars (Supplemental Table 4), we confirmed associations of the VRN-B1 winter-spring polymorphism to variation in root growth using data from high-throughput root phenotyping (Supplemental Materials and Methods). This revealed that seminal root angle was significantly narrower in cultivars carrying the winter allele compared with cultivars with the spring allele (p = 0.01) and that VRN-B1 accounted for 8% of the total variation in root angle, independent of spatial variation (p = 0.01) and consistent across various imputation models (Supplemental Figure 21). Although the VRN-B1 winter allele was almost completely fixed in the EU wheat panel used for the genome-wide association study (Supplemental Table 1), investigation of haplotype variation using the six SNP markers around this locus revealed further diversity. Interestingly, individuals displaying alleles G-G at the two SNPs Kukri_c12910_908 and Excalibur_c38433_291, which are in strong LD (r2 = 0.84) and directly flank VRN-B1, had significantly increased NRI compared with lines with A-A at this position (p = 0.00002) (Supplemental Table 5, Supplemental Table 6, Supplemental Figure 22). The phenotypic difference between A-A and G-G genotypes was also detectable at flowering under temperate field conditions (Supplemental Figure 23) and was independent of vernalization or VRN1 expression in root and shoot tissues (Supplemental Figure 24). This may suggest that novel molecular variants of VRN1, distinct from the major winter-spring polymorphism, are responsible for modulation of root development in winter wheat germplasm. In summary, our results indicate that VRN1 pleiotropically shapes overall plant morphology in wheat and barley, thereby regulating the balance between above- and below-ground plant architecture. In barley, QTLs for root traits were detected previously in the vicinity of VRN1 (Arifuzzaman et al., 2014Arifuzzaman M. Sayed M.A. Muzammil S. Pillen K. Schumann H. Naz A.A. Léon J. Detection and validation of novel QTL for shoot and root traits in barley (Hordeum vulgare L.).Mol. Breed. 2014; 34: 1373-1387Crossref Scopus (37) Google Scholar, Arifuzzaman et al., 2016Arifuzzaman M. Günal S. Bungartz A. Muzammil S. P Afsharyan N. Léon J. Naz A.A. Genetic mapping reveals broader role of Vrn-H3 gene in root and shoot development beyond heading in barley.PLoS One. 2016; 11: e0158718Crossref PubMed Scopus (8) Google Scholar) and a potential involvement of VRN1 in overall plant growth was also proposed in wheat (Eagles et al., 2011Eagles H.A. Cane K. Trevaskis B. Veery wheats carry an allele of Vrn-A1 that has implications for freezing tolerance in winter wheats.Plant Breed. 2011; 130: 413-418Crossref Scopus (40) Google Scholar). Nevertheless, its direct involvement in cereal root system architecture was unknown to date. However, many related genes from the MADS-box transcription factor family are highly expressed in roots of Arabidopsis (Yu et al., 2014Yu L.-H. Miao Z.-Q. Qi G.-F. Wu J. Cai X.-T. Mao J.-L. Xiang C.-B. MADS-box transcription factor AGL21 regulates lateral root development and responds to multiple external and physiological signals.Mol. Plant. 2014; 7: 1653-1669Abstract Full Text Full Text PDF PubMed Scopus (96) Google Scholar), rice (Guo et al., 2013Guo S. Xu Y. Liu H. Mao Z. Zhang C. Ma Y. Zhang Q. Meng Z. Chong K. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14.Nat. Commun. 2013; 4: 1566Crossref PubMed Scopus (215) Google Scholar), and soybean (Liu et al., 2015Liu W. Han X. Zhan G. Zhao Z. Feng Y. Wu C. A novel sucrose-regulatory MADS-box transcription factor GmNMHC5 promotes root development and nodulation in soybean (Glycine max L. Merr.).Int. J. Mol. Sci. 2015; 16: 20657-20673Crossref PubMed Scopus (25) Google Scholar), where they affect underground plant development. Investigations in Arabidopsis have demonstrated important roles of MADS-box genes in local auxin accumulation in root primordia or root cap tissue (Yu et al., 2014Yu L.-H. Miao Z.-Q. Qi G.-F. Wu J. Cai X.-T. Mao J.-L. Xiang C.-B. MADS-box transcription factor AGL21 regulates lateral root development and responds to multiple external and physiological signals.Mol. Plant. 2014; 7: 1653-1669Abstract Full Text Full Text PDF PubMed Scopus (96) Google Scholar). Further work to identify additional downstream targets of VRN1, connecting well-characterized above-ground and unexplored below-ground expression networks, would help elucidate the molecular functions of this major developmental gene in cereals. The authors acknowledge funding from the Grains Research and Development Corporation of Australia (GRDC grants UQ00068 and GRS10940), the German Federal Ministry of Education and Research (BMBF grant 031A354E/BRIWECS), and the German Federal Ministry of Food and Agriculture (BMEL grant 22408212).

Anecdotal reports have suggested wild bradyrhizobia (Bradyrhizobium spp.) were as effective as commercial inoculum for mungbean (Vigna radiata (L.)) grown in the Burdekin region of far north Queensland, Australia. To test this hypothesis, we sampled the diversity of bradyrhizobium strains at two field sites in the Burdekin region of north Queensland, and from plants grown in inoculated or uninoculated soil collected from one field site in Millmerran, southern Queensland. We then compared two wild bradyrhizobium with the commercial strain for their ability to fix nitrogen and promote biomass production on plants in a glasshouse experiment. Ten mungbean nodules were collected from each of four plants, from each of two sites in the Burdekin region. One site had been treated with commercial bradyrhizobium inoculum strain CB1015, the other had never been treated with commercial inoculum. Protein analysis of the nodules using matrix assisted desorption ionization time of flight mass spectrometry (MALDI-TOF MS) showed a total of eight different strains of bradyrhizobia, distinctly different to CB1015, were present in the nodules of these plants. Of these eight strains, two strains dominated, one at each of the two collection sites. On the other hand, mungbean plants grown in soils from Millmerran, on the Darling Downs, hosted only CB1015 where inoculated, and did not nodulate when not inoculated. The two dominant wild bradyrhizobia were cultured from nodules from these field collected plants, and used in a controlled glasshouse experiment. In the glasshouse experiment, two mungbean cultivars and one black gram (Vigna mungo (L.)) cultivar were: (i) not inoculated and not supplied with nitrogen, (ii) not inoculated and supplied with nitrogen, (iii) inoculated with the commercial bradyrhizobia strain CB1015, (iv) inoculated with the dominant wild bradyrhizobia strain from Site 1, or (v) inoculated with the dominant wild bradyrhizobia strain from Site 2. Cultivars inoculated with either of the two dominant wild bradyrhizobia strains were similar in biomass and fixed a similar amount of nitrogen, to those inoculated with CB1015. There was no significant difference between the three inoculated treatments for shoot biomass nor nodule biomass per plant. Nodule number did not differ significantly from CB1015 for either of the wild bradyrizobia treatments. For root biomass per plant, the two mungbean cultivars did not differ between the three inoculated treatments, but the black gram had significantly less root biomass compared to the CB1015 treatment for one of the two wild bradyrhizobia treatments. For nitrogen fixed per plant, none of the cultivars showed significant difference between inoculated treatments. Our findings are consistent with the hypothesis that in some parts of Queensland some wild bradyrhozobia may be as effective as commercial inoculum for mungbean and black gram, potentially abrogating the need for artificial inoculation, and perhaps offering new options for the future development of better adapted commercial inoculum.

Frost, during reproductive developmental stages, especially post head emergence frost (PHEF), can result in catastrophic yield loss for wheat producers. Breeding for improved PHEF tolerance may allow greater yield to be achieved, by (i) reducing direct frost damage and (ii) facilitating earlier crop sowing to reduce the risk of late season drought and/or heat stress. This paper provides an economic feasibility analysis of breeding options for PHEF tolerant wheat varieties. It compares the economic benefit to growers with the cost of a wheat breeding program aimed at developing PHEF tolerant varieties. The APSIM wheat model, with a frost-impact and a phenology gene-based module, was employed to simulate direct and indirect yield benefits for various levels of improved frost tolerance. The economic model considers optimal profit, based on sowing date and nitrogen use, rather than achieving maximum yield. The total estimated fixed cost of breeding program was AUD 1293 million, including large scale seed production to meet seed demand, with AUD 1.2 million year(-1) to run breeding program after advanced development and large scale field experiments. The results reveal that PHEF tolerant varieties would lead to a significant increase in economic benefits through reduction in direct damage and an increase in yield through early sowing. The economic benefits to growers of up to AUD 4841 million could be realised from growing PHEF tolerant lines if useful genetic variation can be found. Sensitivity analyses indicated that the benefits are particularly sensitive to increases in fixed costs, seed replacement, discount rate, and to delays in variety release. However, the investment still remains viable for most tested scenarios. Based on comparative economic benefits, if breeders were able to develop PHEF tolerant varieties that could withstand cold temperatures -4 degrees C below the current damage threshold, there is very little further economic value of breeding total frost tolerant varieties.

"Stay-green" plants retain green leaf area longer after flowering than senescent types. This can prolong carbon assimilation during grain filling, increasing yield, particularly under terminal drought stress. A population of doubled haploid wheats (Triticum aestivum L.) derived from a cross between stay-green SeriM82 and senescent Hartog was grown in eight environments with varying degrees of water limitation. The dynamics of normalised difference vegetative index (NDVI) was followed post-flowering to evaluate change in leaf greenness. Quantitative trait loci (QTL) were identified for components of stay-green including i) maximum NDVI (Nmax), ii) an indicator of the maximum rate of senescence (SR), iii) thermal time from flowering to commencement of senescence (OnS), iv) thermal time from flowering to mid-senescence (MidS), and v) the integral of NDVI from flowering to 1500 degrees Cd after flowering (SGint). Genetic regions associated with QTL for stay-green traits were identified (i) in both wet and dry environments on chromosomes 4A, 4B, 4D (constitutive stay-green); (ii) primarily in wetter environments on 2A and (iii) primarily in dryer environments on 5B. Other regions associated with QTL for stay-green were identified on 3B and 7B in a mixture of environment types. In some environments, stay-green QTL co-located with QTL for seminal root angle, seedling root number and/or for yield. Other stay green QTL were co-located with yield but not seminal root angle and seedling root number. This suggests genetic regions associated with seminal root angle and seedling root number are not solely responsible for the high yielding, stay-green phenotype. Selection for stay-green traits will increase the rate of genetic progress for adaptation of wheat to both well-watered and water-limited environments.

Investing in pre-breeding for exotic pests and diseases in cereals is characterised as investing in an option of preparedness regardless of whether an incursion occurs. The return to pre-breeding depends on the likelihood of pest arrival, its spread across cereal producing regions and how damaging it will be through time. Any delay in the release of resistant varieties after an incursion translates into yield losses, chemical costs and, for some pests and diseases, price discounts. However, returns to pre-breeding investment are limited by delay time without pre-breeding, management alternatives and the adoption rates for resistant varieties by producers. Our analysis has estimated returns to investment for pre-breeding for six high priority exotic wheat and barley pests and diseases. The methods developed here allows for regional disaggregation and regional pest suitability across Australia’s cereal production landscape. Results indicate that pre-breeding investment is viable for only half of the pest and diseases studied. The relatively high return to these can be explained by significant yield effects, rapid spread and widespread pest suitability across regions. Furthermore, a higher average yield loss can offset lower incursion probability. In contrast, those not viable are due to slow spread, small or erratic yield effect and biosecurity trade issues not addressed by resistance. Investing in pre-breeding is highly risky as the modal investment return for all pests and diseases is zero and returns to breeders are short lived.

Frost, during reproductive developmental stages, especially post head emergence frost (PHEF), can result in catastrophic yield loss for wheat producers. Breeding for improved PHEF frost tolerance may allow greater yield to be achieved, by (i) reducing direct frost damage and (ii) sowing crops earlier to reduce risks of late-season drought and or heat stress. This paper provides an economic feasibility analysis of conventional and genetically modified (GM) PHEF tolerant wheat variety breeding options. The APSIM wheat model, with a phenology gene-based module, was employed to simulate direct and indirect yield benefits for various level of improved frost tolerance. The economic model considered optimal profit, based on sowing window and nitrogen use, rather than achieving maximum yield, when calculating the economics of PHEF breeding options. The results reveal that PHEF tolerant varieties, both conventional and GM, would lead to a significant increase in economic benefits through reduction in direct damage and an increase in yield through early sowing. The economic benefits of up to $4,841million and $4,826 could be realised from breeding conventional PHEF tolerant lines and GM PHEF tolerant if useful genetic variation can be found. Sensitivity analyses indicated that the benefits are particularly sensitive to the increase in fixed costs, discount rate, and delay in variety release. However, the investment still remains viable for most tested scenarios. Based on comparative economic benefits, for both conventional and GM PHEF tolerant varieties, if breeders were able to develop PHEF tolerant varieties that could withstand cold …

Temperatures have increased and in-crop rainfall decreased over recent decades in many parts of the Australian wheat cropping region. With these trends set to continue or intensify, improving crop adaptation in the face of climate change is particularly urgent in this, already drought-prone, cropping region. Importantly, improved performance under water-limitation must be achieved while retaining yield potential during more favourable seasons.A multi-trait-based approach to improve wheat yield and yield stability in the face of water-limitation and heat has been instigated in northern Australia using novel phenotyping techniques and a nested association mapping (NAM) approach. An innovative laboratory technique allows rapid root trait screening of hundreds of lines. Using soil grown seedlings, the method offers significant advantages over many other lab-based techniques. Another recently developed method allows novel stay-green traits to he quantified objectively for hundreds of genotypes in standard field trial plots. Field trials in multiple locations and seasons allow evaluation of targeted trait values and identification of superior germplasm. Traits, including yield and yield components are measured for hundreds of NAM lines in rain fed environments under various levels of water-limitation. To rapidly generate lines of interest, the University of Queensland "speed breeding" method is being employed, allowing up to 7 plant generations per annum. A NAM population of over 1000 wheat recombinant inbred lines has been progressed to the F5 generation within 18 months. Genotyping the NAM lines with the genome-wide DArTseq molecular marker system provides up to 40,000 markers. They are now being used for association mapping to validate QTL previously identified in biparental populations and to identify novel QTL for stay-green and root traits.We believe that combining the latest techniques in physiology, phenotyping, genetics and breeding will increase genetic progress toward improved adaptation to water-limited environments. (C) 2015 The Authors. Published by Elsevier B.V.

Root architecture traits in wheat are important in deep soil moisture acquisition and may be used to improve adaptation to water-limited environments. The genetic architecture of two root traits, seminal root angle and seminal root number, were investigated using a doubled haploid population derived from SeriM82 and Hartog. Multiple novel quantitative trait loci (QTL) were identified, each one having a modest effect. For seminal root angle, four QTL (-log10(P) >3) were identified on 2A, 3D, 6A and 6B, and two suggestive QTL (-log10(P) >2) on 5D and 6B. For root number, two QTL were identified on 4A and 6A with four suggestive QTL on 1B, 3A, 3B and 4A. QTL for root angle and root number did not co-locate. Transgressive segregation was found for both traits. Known major height and phenology loci appear to have little effect on root angle and number. Presence or absence of the T1BL.1RS translocation did not significantly influence root angle. Broad sense heritability (h (2)) was estimated as 50 % for root angle and 31 % for root number. Root angle QTL were found to be segregating between wheat cultivars adapted to the target production region indicating potential to select for root angle in breeding programs.

Pre-harvest sprouting (PHS) in wheat (Triticum aestivum L.) can be a significant problem, causing deleterious effects on grain quality. PHS occurs most frequently in northern New South Wales and southern Queensland, where the harvest period coincides with the beginning of the summer storm season. The introgression of genes controlling grain dormancy into white-grained bread wheat is believed to be one means of improving resistance to PHS. Our previous study on grain dormancy in wheat grown under controlled environments (CEC) has demonstrated clear differentiation between dormant and non-dormant fixed lines. Selection based on single-grain germination within F2 and F3 generations increases the frequency of desirable alleles (i.e. markers linked to the 4A dormancy QTL), and effectively recovers the dormant phenotype by the F4 generation. This study reports on a number of follow-up experiments aiming to improve the efficiency of the screening and selection process. Results suggest that methods proposed in this study could be applied within the context of an applied breeding program, where segregating populations could be grown under CEC out of season, grain screened for dormancy and selected grains desiccated and stored, allowing direct sowing of selected grains into the field for evaluation the following growing season. Application of this technology will potentially enable breeders to be better equipped to select for grain dormancy and release new varieties offering effective resistance to PHS in the near future.