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Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories and proteins for the human diet. Compared with its wild ancestors, modern bread wheat shows lower genetic diversity, caused by polyploidisation, domestication and breeding bottlenecks1,2. Wild wheat relatives represent genetic reservoirs, and harbour diversity and beneficial alleles that have not been incorporated into bread wheat. Here we establish and analyse extensive genome resources for Tausch’s goatgrass (Aegilops tauschii), the donor of the bread wheat D genome. Our analysis of 46 Ae. tauschiigenomes enabled us to clone a disease resistance gene and perform haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, which involves contributions from genetically and geographically discrete Ae. tauschiisubpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement.

Hundreds of quantitative trait loci (QTLs) have been reported in diverse types of hexaploid wheat (Triticum aestivumL.) populations, but direct comparisons of QTLs in different studies and populations are still challenging due to the lack of physical positions for most QTLs. Here, we used the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map of all markers to map QTLs associated with leaf spot (Ls), leaf rust (Lr), stripe rust (Yr), and common bunt (Cbt) resistance in two recombinant inbred line populations. QTL mapping was conducted using the IWGSC physical map of 3158 and 5732 markers and disease severity data of Peace/Carberry and Attila/CDC Go populations evaluated in three to eight environments. We uncovered a total of 82 QTLs associated with Yr (36), Ls (18), Lr (15), and Cbt (13) resistance in the individual and overall means of all combined environments. Among them, 29 were associated with all combined environments, which accounted for 0.5%–20.9% individually and 12.4%–41.2% of the total disease severity per trait. Three (QLr.dms‐2D.2, QLs.dms‐5B, and QYr.dms‐5B.2) of the 29 QTLs were common in both populations. Fourteen out of the 29 QTLs were stable as they were identified both in the overall means and most of the individual environments. Ten chromosome arms harbored a cluster of QTLs associated with resistance to two to four diseases. This methodology would serve as one of the resources to compare QTLs identified in different populations and studies based on the improved physical information of all markers instead of population‐specific and consensus linkage maps. The methodology described in this study would serve as a basis for easily comparing QTLs in different populations and independent studies using the physical positions of all markers.This study uncovered 29 QTLs associated with the overall mean disease severity of four wheat diseases in two populations.The number of QTLs identified in Peace/Carberry population was over twofold more than Attila/CDC Go population.The total phenotypic variation explained in Peace/Carberry was two‐ to threefold more than Attila/CDC Go.Ten chromosomes harbored a cluster of QTLs associated with resistance for two to four diseases.

This study investigated the impact of protein quantity and gluten strength on mechanical properties and microstructure of cooked pasta using texture analyzer and scanning electron microscopy. Three Canadian durum varieties with wide range of gluten strength at four protein levels were selected. Four distinct microstructures were characterized for cooked pasta. Pasta with firm texture exhibited compact and dense protein networks, while that with soft texture showed open, coarse, and heterogeneous structures. Protein content was the dominant factor in determining pasta firmness, the impact of gluten strength on pasta texture depends on protein content and cooking time. Greater impact from gluten strength was observed when pasta was overcooked. The relative contribution of protein quantity and quality in cooked pasta texture depends upon the ranges of protein content, gluten strength, and degree of cooking. This study unveiled the impact of wheat protein content and gluten strength on textural and microstructural properties of pasta at three cooking times. Results generated from this study provide guidance for durum breeding programs, durum milling, and pasta processing industry in setting protein content and gluten strength targets to ensure pasta quality.

The development and improvement of crop cultivars are necessary to meet the demands of the growing global population. The ability to decrease the generation time is imperative for breeders to achieve higher rates of genetic gain annually. Understanding the way in which photoperiod affects the maturation rate of these crops, including winter wheat (Triticum aestivumL.), is required for decreasing generation time in breeding programs. The effects of prolonged photoperiod and light intensity on winter wheat generation time were studied to determine if photoperiod may contribute to a shortened cycle time. Three winter wheat cultivars (Branson, CFBA1401, and Norstar) and one spring wheat cultivar (AC Carberry) were exposed to four treatments based on the daily light integral (DLI): high light (HL) or low light and photoperiod as follows: 22 h of light and 2 h of dark (22:2) or 16 h of light and 8 h of dark (16:8). Generation time, as measured by days to maturity in the HL22:2 treatment, resulted in a decrease of 8 days or 7% of the total generation time, compared to the control, HL16:8 treatment. Photoperiod itself had a minimal effect on generation time when both DLI and temperature were controlled. An improved understanding of the effects of photoperiod, thermal time, and DLI and their interactions is required prior to implementation in a winter cereal breeding program. Accelerating plant growth using a post‐vernalization method has shown differences between spring and winter wheat.Photoperiod has a minor effect on decreasing days to anthesis when temperature is controlled.Results provide evidence for controlling all contributing factors to increase growth rate.

Previous genome‐wide association studies in Canadian spring wheat (Triticum aestivumL.) cultivars were based on consensus linkage maps of small population sizes. Here, we used a panel of 192 spring wheat cultivars widely used in western Canada to (a) explore the allelic variation and effects of six known genes and (b) identify genomic regions associated with eight agronomic traits and grain characteristics using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 map. The panel was evaluated for heading, maturity, plant height, lodging, grain yield, grain protein content, test weight, and kernel weight under four conventionally (high N) and three organically (low N) managed environments and genotyped with the wheat 90K single‐nucleotide polymorphism (SNP) array of which 23,342 SNPs were polymorphic. Using gene‐specific functional markers, the proportion of homozygous genotypes with favorable alleles was low for Fhb1(7–8%), Rht‐D1(14%), and Rht‐B1(18%); moderate for Lr34/Yr18(28–39%); and high for Glu‐A1(78%) and Glu‐D1(85%). We identified a total of 172 SNPs located at 94 genomic regions across 19 chromosomes of which 82 regions were associated with a single trait and 12 regions coincided with two to three traits. Twenty‐seven of the 94 regions (28%) were common between the conventional and organic managements systems; the remaining were management specific. Two of the identified regions on chromosome 5A (586.5–588.6 Mb) and 5B (575.8 Mb) coincided with the vernalization response Vrn‐A1and Vrn‐B1genes, respectively. The IWGSC RefSeq v2.0 physical positions presented here would serve as the basis for easily comparing independent discovery studies in the future. The allelic variation and effects of six known genes in a panel of historical and modern Canadian spring wheat were investigated.The effect of low and high nitrogen management systems on QTL detection were compared using eight phenotypic traits.Some coincident genomic regions associated with negatively correlated traits were uncovered.The IWGSC RefSeq v2.0 physical map of 23,342 of the wheat 90K SNP array presented here would serve as a basis for comparing QTL results.

Rye (Secale cerealeL.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye’s incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye–wheat introgressions.

Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticumspp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the ‘pan-genome’1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgareL.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley—comprising landraces, cultivars and a wild barley—that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.

Effective and efficient selection of key quality traits is crucial to develop new durum varieties with improved end‐use quality. This study was undertaken to develop a rapid micromilling protocol using a single Brabender Quadrumat Jr. (QJ) semolina mill without purification to predict milling performance and generate semolina for quality analysis. After grinding 200 g of durum wheat with a QJ mill with the reel sifter removed, the resulting wholemeal was sifted through a laboratory sifter equipped with a bottom screen of 180 µm to remove flour and a top screen of 630 µm to retain bran‐rich fraction. Semolina materials between the two screens were collected. A model for predicting semolina yield (R2= 0.81) was developed based on the amounts of semolina and bran‐rich fraction, thus eliminating the need for additional milling to recover semolina in the bran‐rich fraction. There were highly significant correlations (r> 0.86) for semolina ash, yellowness, yellow pigment content, protein content, wet gluten, and gluten index between semolina prepared with this proposed protocol and those generated with a Allis‐Chalmers mill. The micromilling protocol developed in this study is rapid and reliable for assessing durum milling performance and for preparing semolina for quality characterization. The proposed protocol modified QJ mill and optimized milling conditions. A robust and simplified model was developed for predicting semolina yield with one‐step milling. It is a useful tool for breeding programs or genetic mapping studies that are usually large in sample number but very limited in sample size.

Introgression is a potential source of beneficial genetic diversity. The contribution of introgression to adaptive evolution and improvement of wheat as it was disseminated worldwide remains unknown. We used targeted re-sequencing of 890 diverse accessions of hexaploid and tetraploid wheat to identify wild-relative introgression. Introgression, and selection for improvement and environmental adaptation, each reduced deleterious allele burden. Introgression increased diversity genome wide and in regions harboring major agronomic genes, and contributed alleles explaining a substantial proportion of phenotypic variation. These results suggest that historic gene flow from wild relatives made a substantial contribution to the adaptive diversity of modern bread wheat.

The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement.

Inbred cultivars and advanced breeding lines have been subjected to numerous recombination cycles, have strong allelic selection for desired traits, and share important attributes for adaptation and agronomic performance. Genetic variation in elite gene pools captured using molecular markers is immediately useful for cultivar development. The primary goal of this study was to implement a genome‐wide association study for 17 agronomic traits using elite inbred lines. A panel consisting of 237 elite hard red spring wheat (Triticum aestivumL.) lines from different wheat breeding institutions in North America were evaluated in 11 locations over 2 yr. A total of 19,192 polymorphic single‐nucleotide polymorphism (SNP) markers from the Illumina 90K SNP array and markers linked to major genes controlling plant height, photoperiod sensitivity, and vernalization were used to assay the population. Linkage disequilibrium was observed to decay within a map distance of ∼3 cM in the A and B genomes and 7 cM in the D genome. A total of 226 marker‐trait associations were identified. Potentially novel associations were detected for grain yield on chromosome 2B and kernels per spike on 1B and 7D, whereas others colocalized with well‐known adaptation loci for photoperiod response, vernalization, and plant height. The frequency of positive alleles for specific marker‐trait associations differed among the programs, suggesting targets for introgression by the respective breeding programs.

Optimum seeding rate on elite durum wheat depends on environment.Seeding rate had a significant positive relationship with grain yield, leaf area index, and carbon isotope discrimination.Seeding rate should be adjusted for environment and genotype for maximum yield. Seeding rate can be manipulated to optimize the ability of the crop to capture available resources and therefore increase yield. Seeding rate may vary between regions according to the climate conditions, soil type, sowing time, and other agronomic practices. Insufficient information is available for optimum seeding rate on durum wheat (Triticum turgidumL. var durum) for some production zones, and response to seeding rate is unknown for recently registered durum cultivars in Canada. The objective of this study was to determine the effect of seeding rate (SR) on performance of Canada Western Amber Durum wheat cultivars and study the underlying physiological response to a wide range of SRs. Eight durum wheat cultivars were sown at densities of 163, 217, 272, 326, and 380 seeds m−2to study the effect of SR on several agronomic and physiological traits. Each experiment was planted as a factorial randomized complete block design with three replications near Swift Current and Regina in 2010 and 2011. High genetic and environmental response to SR was observed between cultivars. The results showed an increase in grain yield as the SR increased. The optimum SR for cultivars grown at Swift Current and Regina was 272 to 326 seeds m−2and 217 to 272 seeds m−2. Grain yield showed a positive relationship with carbon isotope discrimination (CID) and leaf area index (LAI). In turn, LAI showed a linear increase with SR. Information generated from this study could enable producers to maximize crop grain profitability by optimizing plant density.

Leaf rust, yellow (stripe) rust, common bunt, and tan spot are economically significant diseases affecting wheat (Triticum aestivumL.) production in Canada. In this study, we investigated the genetic relationship and population structure of 81 Canadian western spring wheat cultivars released primarily between 1963 and 2011 and identified genomic regions associated with resistance to the above four diseases and insensitivity to three Pyrenophora tritici‐repentis(Ptr) toxins (Ptr ToxA, Ptr ToxB and Ptr ToxC). The cultivars were evaluated for field reaction to the four diseases and for reaction to the three Ptr toxins in a greenhouse and were genotyped with a subset of 19,919 of the wheat 90K single‐nucleotide polymorphic array and 11 gene‐specific markers. There were large genetic differences among pairwise comparisons of cultivars, except six pairs that showed <0.05 genetic distance. The cultivars exhibited clear population structure, generally in agreement with the major western Canada spring wheat classes. Using a threshold of p≤ 5 × 10−5and a weighted mixed linear model, we identified 94 markers from seven chromosomes associated with all traits except Ptr ToxC. Two major‐effect genomic regions on chromosomes 5B (71–74 cM) and 1A (52–53 cM) were associated with Ptr ToxA, of which the former coincided with the Tsn1gene. For Ptr ToxB, we identified two other major‐effect regions on chromosomes 2B and 5B. The genomic regions associated with common bunt mapped on 2B, 4B, and 7A, whereas those associated with leaf rust mapped at two positions on 2B. We were only able to uncover a single marker‐trait association for tan spot on 7B and for yellow rust on 2A.

Our group previously reported five quantitative trait loci (QTL) associated with plant height, test weight, thousand-kernel weight, and grain protein content in a recombinant inbred line population derived from spring wheat (Triticum aestivumL.) cultivars ‘Attila’ and ‘CDC Go’, evaluated across three environments (2008–2010) under organic management and genotyped with 579 diversity arrays technology and Rht-B1markers. No QTL was identified for flowering time, maturity, grain yield, and number of tillers across all three environments. In the present study, we reanalyzed the same phenotypic data with a subset of 1200 informative single-nucleotide polymorphic (SNP) markers out of the 90K SNP array and three gene-specific markers (Ppd-D1, Vrn-A1, and Rht-B1) to investigate if high marker density improves QTL detection. Here, five moderate- and eleven minor-effect QTLs were detected across all three organic environments using the new genotypic data, including 13 QTLs that were not previously detected. Up to five QTLs were detected for each trait, except grain protein content, which individually accounted for 5.5 to 18.8% of phenotypic variance. For each trait, the total phenotypic and genetic variance explained by all detected QTLs varied from 9.3 to 39.4 and from 24.6 to 96.8%, respectively, which was much greater than in our previous study. One of the moderate-effect QTLs on 5A was coincidental for flowering time and maturity and mapped close to the Vrn-A1gene, while the second moderate-effect coincidental QTL on 4B was associated with both plant height and maturity but was 27 cM from the Rht-B1gene. Results from this study provide additional information for wheat researchers and organic wheat breeders.

Breeding efforts have been important in addressing the challenges of wheat production in western Canada. We studied the effect of breeding on grain yield and other important traits of 100 wheat cultivars released in Canada from 1885 to 2012. The cultivars were grown in seven environments during 2011 to 2013. Grain yield was positively correlated with days to maturity and kernel weight but negatively correlated with plant height, lodging, and grain protein content. Results indicate that grain yield increased at a rate of 0.28% year–1in 62 cultivars of Canada western red spring (CWRS) class, 1.2% year–1in 9 cultivars of Canada prairie spring (CPS) class, but not in 14 studied cultivars of Canada western amber durum (CWAD) class due to breeding efforts. Grain protein content exhibited an increasing trend in cultivars of CWRS (0.05% year–1) and CPS (0.79% year–1) classes, and a decreasing trend in those of CWAD (0.23% year–1). Days to maturity decreased in CWRS (0.02% year‐1) and CWAD (0.09% year‐1) classes but remained unchanged in CPS class. Plant height exhibited a gradual decline in cultivars of CWRS (0.16% year–1) and CWAD class (0.44% year–1), but an increase in those of CPS class (0.50% year–1). Test weights showed an increasing trend in CWRS (0.04% year–1) and CPS (0.17% year–1) classes but not in CWAD class. Grain weight also increased over time in CWRS (0.06% year–1) and in CPS (0.41% year–1), but not in CWAD class. These results suggest that breeding efforts have improved yield, quality and other attributes in wheat cultivars of different Canadian wheat classes over the last 100 years.

The wheat stem sawfly (WSS) (Cephus cinctus; Hymenoptera: Cephidae) is a destructive insect pest of spring, winter (Triticum aestivumL.), and durum wheat (Triticum turgidumL. var. durum) in North America. Sawfly larvae hatch from eggs deposited inside the stem, and their subsequent feeding damages vascular tissue, reducing photosynthetic capacity and grain yields. Growing solid‐stemmed wheat cultivars that develop pith in the culm lumen is the most effective method to minimize yield losses. Recent work has focused on optimizing sowing densities to achieve maximum levels of pith expression and grain yields in common wheat; however, little research has been conducted on durum wheat. We investigated the influence of four sowing densities (150, 250, 350, 450 seeds m−2) on pith expression in two newly released solid‐stemmed durum cultivars, CDC Fortitude and AAC Raymore, and compared them to the solid‐stemmed common wheat cultivar, Lillian. CDC Fortitude and AAC Raymore displayed consistently high levels of pith expression across environments and sowing densities, in contrast to Lillian, which produced only slightly more pith than the hollow‐stemmed durum check cultivar, Strongfield. A yield drag often associated with high pith expression was not evident as CDC Fortitude and AAC Raymore produced grain yield similar to Strongfield. When averaged over cultivars, increasing sowing density had a positive effect on grain yield, but was negatively associated with stem solidness. Our findings suggest that, unlike with CWRS solid‐stemmed cultivars, altering sowing density is not required to achieve effective sawfly resistance with CDC Fortitude and AAC Raymore.

Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets.

Changes in total yellow pigment (TYP) content and carotenoid composition were examined at different stages of pasta processing. Semolina samples were milled from durum genotypes with and without the Lpx-B1.1gene deletion and then processed into dry pasta. Significant pigment loss (12.8–15.3%) based on TYP content was observed from semolina to dough in genotypes without the gene deletion. Such loss remained low (2.0–2.8%) for genotypes with the Lpx-B1.1gene deletion. Extrusion and drying processes did not result in substantial pigment loss. The overall pigment loss (from semolina to dried pasta) of genotypes with the gene deletion was 9.1–12.8%, in comparison with 19.0–21.7% in genotypes without the deletion. Changes in carotenoids examined by ultra-performance liquid chromatography showed that lutein decreased gradually from representing 80% of total carotenoids to 70% of total carotenoids during pasta processing. The reduction of lutein was mostly during dough mixing, with a decrease of 16.7% in genotypes with the Lpx-B1.1deletion and 27.8% in genotypes without the deletion. Minor carotenoids increased during pasta drying, possibly at the expense of lutein. Results of this study showed that although breeding for elevated yellow pigments is the key, pasta color can be further improved by reducing pigment losses at different stages of pasta processing through selection of genotypes with Lpx-B1.1deletion and applying a vacuum during mixing and extrusion processes.

A need has been identified for alternative crop(s) with high grain yield, low grain protein concentration, and high starch for the ethanol industry. The objective of this study was to benchmark the relative performance of triticale (×Triticosecalessp.) to wheat (Triticum aestivumL.) classes currently utilized for ethanol production. Sixteen cultivars—three triticale, four Canada prairie spring (CPS) wheat, three Canada western soft white spring wheat (CWSWS), two Canada western red spring (CWRS) wheat, and four Canada western general purpose (CWGP) candidate cultivars—were grown at 36 locations across western Canada from 2006 to 2009. The performance of these cereal classes can generally be summarized as triticale = Hoffman (CWGP) = CWSWS > CPS white > CPS red > CWRS for most variables. The triticale and white wheats produced 12 and 13% more grain, respectively, than the hard red spring wheats. Among the triticales, AC Ultima’s and Pronghorn’s yield potential were most notable because they exceeded the CWRS cultivars AC Barrie and AC Superb by an average of 32% and the CPS red cultivars 5700PR and AC Crystal by 18%. The triticales and Hoffman matured later than most other cultivars. Pronghorn consistently displayed low levels of fusarium head blight (FHB), Septoria nodorumblotch, and powdery mildew, but elevated ergot levels were observed for all triticales. We conclude that triticale would be superior to CPS and CWRS wheat and similar to CWSWS in many agronomic traits desired by ethanol fermentation plants and is superior for biomass production.

Cereal grain ethanol production may need to supplement biomass ethanol production to meet the increasing long‐term demand for ethanol. A study was initiated to benchmark the relative performance of triticale (×Triticosecalessp.) to wheat (Triticum aestivumL.) classes utilized for ethanol production. Ten cultivars: three triticale, two Canada prairie spring (CPS) wheat, three Canada western soft white spring (CWSWS) wheat, one Canada western red spring (CWRS) wheat, and one Canada western general purpose (CWGP) wheat cultivars were grown at 45 locations across Canada from 2006 to 2009. The locations were subgrouped by agroecological zone for western Canada, by province for Ontario and Quebec, and Charlottetown, PEI, for the Maritimes. The greatest grain yield was usually observed for Hoffman (red spring wheat) followed by triticale cultivars and CWSWS cultivars. Ethanol yield varied by region as a reflection of grain yield, and differences among cultivars generally were: triticale (excluding Tyndal) = Hoffman = CWSWS > CPS > CWRS. Ethanol concentration was least for Tyndal triticale and AC Superb CWRS. Stability assessments indicated that Pronghorn and AC Ultima triticales and Bhishaj CWSWS wheat provide consistent and high ethanol yields. The other CWSWS cultivars, AC Sadash and AC Andrew, had similarly high ethanol yields but were variable, indicating that utilization outside the Parkland and Western Prairies agroecological zones could pose greater risk for ethanol plants over Pronghorn and AC Ultima. Ethanol fermentation plants could therefore increase efficiency by replacing CPS wheat feedstocks with select triticales and potentially improve the consistency of production by using select triticales in regions where CWSWS wheats are less stable.

Wheat (Triticum aestivumL.) has inherent genetic potential to synchronize its flowering and maturity to a broad growing period and is therefore one of the most widely adapted and grown food crops. Vernalization and photoperiod response genes are of primary importance to this adaptability. We screened 102 Canadian spring wheat cultivars and/or lines, developed between 1885 and 2008, from the Canada Western Red Spring (CWRS), Canada Prairie Spring Red (CPSR), and Canada Western Soft White Spring (CWSWS) classes and studied their phenotypic response both in the field and the greenhouse. Almost all the hard red cultivars possessed the Vrn‐A1agene either alone or in combination with the dominant Vrn‐B1while 74% of the higher yielding soft white lines possessed the Vrn‐B1gene alone or in combination with other Vrngenes. The Vrn‐A1aalone or in combination with the Vrn‐B1gene was the most potent gene conferring early maturity. Ppd‐D1adid not alter flowering and maturity in the hard red cultivars tested in the field but did in the greenhouse. Ppd‐D1areduced days to flowering for soft white spring wheat but did not alter maturity. The photoperiod sensitive gene (Ppd‐D1b) is being replaced with the insensitive gene, Ppd‐D1a, in most modern Canadian germplasm, suggesting its adaptive advantages in the prairies. An overall analysis of the data for the hard red class revealed a declining trend of 0.04 d yr−1in days to maturity in cultivars released from 1885 to 2008 and an increase of 8 kg ha−1yr−1in grain yield. The findings of this study may aid wheat breeders selecting parents with appropriate vernalization and photoperiod gene complexes.

While imidazolinone herbicides are an attractive alternative for weed control, spring wheat (Triticum aestivumL.) is susceptible to most of these herbicides. Three mutant alleles conferring resistance to the imidazolinone herbicides were previously identified in spring wheat following seed mutagenesis, but little is known about the physiological and molecular basis of resistance conferred by these alleles. On the basis of acetohydroxyacid synthase (AHAS; E.C. 4.1.3.18) assays, imazethapyr resistance in genotypes TealIMI 10A (AhasL‐D1), TealIMI 11A (AhasL‐B1), TealIMI 15A, and BW755 (AhasL‐D1) was due to a herbicide resistant form of AHAS. TealIMI 15A, which is homozygous for two resistance alleles, was the most resistant at the enzyme level, suggesting resistance in wheat is additive. Nucleotide sequence analysis of clones derived from susceptible cultivar CDC Teal and resistant lines indicated the presence of three genes coding for the catalytic subunit of AHAS. Using a collection of T. aestivumcv. Chinese Spring aneuploid and deletion lines, ahasL‐D1, ahasL‐B1,and ahasL‐A1mapped to the long arm of chromosomes 6D, 6B, and 6A, respectively. Comparison of partial AhasL‐D1,and AhasL‐B1deduced amino acid allele sequences with wild‐type sequences indicated resistance was due to a Ser‐Asn substitution near the carboxyl terminal of resulting AHAS catalytic subunits. This substitution was not present on the single isolated clone of AhasL‐A1from TealIMI 15A. This is the first report of the molecular characterization of the AHAS gene family from wheat.

Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.