Canadian Spring Wheat Research Articles

Identification of Fusarium head blight sources of resistance and associated QTLs in historical and modern Canadian spring wheat.

Fusarium head blight (FHB) is one the most globally destructive fungal diseases in wheat and other small grains, causing a reduction in grain yield by 10-70%. The present study was conducted in a panel of historical and modern Canadian spring wheat (Triticum aestivum L.) varieties and lines to identify new sources of FHB resistance and map associated quantitative trait loci (QTLs). We evaluated 249 varieties and lines for reaction to disease incidence, severity, and visual rating index (VRI) in seven environments by artificially spraying a mixture of four Fusarium graminearum isolates. A subset of 198 them were genotyped with the Wheat 90K iSelect single nucleotide polymorphisms (SNPs) array. Genome-wide association mapping performed on the overall best linear unbiased estimators (BLUE) computed from all seven environments and the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map of 26,449 polymorphic SNPs out of the 90K identified sixteen FHB resistance QTLs that individually accounted for 5.7-10.2% of the phenotypic variance. The positions of two of the FHB resistance QTLs overlapped with plant height and flowering time QTLs. Four of the QTLs (QFhb.dms-3B.1, QFhb.dms-5A.5, QFhb.dms-5A.7, and QFhb.dms-6A.4) were simultaneously associated with disease incidence, severity, and VRI, which accounted for 27.0-33.2% of the total phenotypic variance in the combined environments. Three of the QTLs (QFhb.dms-2A.2, QFhb.dms-2D.2, and QFhb.dms-5B.8) were associated with both incidence and VRI and accounted for 20.5-22.1% of the total phenotypic variance. In comparison with the VRI of the checks, we identified four highly resistant and thirty-three moderately resistant lines and varieties. The new FHB sources of resistance and the physical map of the associated QTLs would provide wheat breeders valuable information towards their efforts in developing improved varieties in western Canada.

Multi-locus genome-wide association study of fusarium head blight in relation to days to anthesis and plant height in a spring wheat association panel.

Fusarium head blight (FHB) is a highly destructive fungal disease of wheat to which host resistance is quantitatively inherited and largely influenced by the environment. Resistance to FHB has been associated with taller height and later maturity; however, a further understanding of these relationships is needed. An association mapping panel (AMP) of 192 predominantly Canadian spring wheat was genotyped with the wheat 90K single-nucleotide polymorphism (SNP) array. The AMP was assessed for FHB incidence (INC), severity (SEV) and index (IND), days to anthesis (DTA), and plant height (PLHT) between 2015 and 2017 at three Canadian FHB-inoculated nurseries. Seven multi-environment trial (MET) datasets were deployed in a genome-wide association study (GWAS) using a single-locus mixed linear model (MLM) and a multi-locus random SNP-effect mixed linear model (mrMLM). MLM detected four quantitative trait nucleotides (QTNs) for INC on chromosomes 2D and 3D and for SEV and IND on chromosome 3B. Further, mrMLM identified 291 QTNs: 50 (INC), 72 (SEV), 90 (IND), 41 (DTA), and 38 (PLHT). At two or more environments, 17 QTNs for FHB, DTA, and PLHT were detected. Of these 17, 12 QTNs were pleiotropic for FHB traits, DTA, and PLHT on chromosomes 1A, 1D, 2D, 3B, 5A, 6B, 7A, and 7B; two QTNs for DTA were detected on chromosomes 1B and 7A; and three PLHT QTNs were located on chromosomes 4B and 6B. The 1B DTA QTN and the three pleiotropic QTNs on chromosomes 1A, 3B, and 6B are potentially identical to corresponding quantitative trait loci (QTLs) in durum wheat. Further, the 3B pleiotropic QTN for FHB INC, SEV, and IND co-locates with TraesCS3B02G024900 within the Fhb1 region on chromosome 3B and is ~3 Mb from a cloned Fhb1 candidate gene TaHRC. While the PLHT QTN on chromosome 6B is putatively novel, the 1B DTA QTN co-locates with a disease resistance protein located ~10 Mb from a Flowering Locus T1-like gene TaFT3-B1, and the 7A DTA QTN is ~5 Mb away from a maturity QTL QMat.dms-7A.3 of another study. GWAS and QTN candidate genes enabled the characterization of FHB resistance in relation to DTA and PLHT. This approach should eventually generate additional and reliable trait-specific markers for breeding selection, in addition to providing useful information for FHB trait discovery.

Genetic mapping of leaf rust (Puccinia triticina Eriks) resistance genes in six Canadian spring wheat cultivars.

The Canada Western Red Spring wheat (Triticum aestivum L.) cultivars AAC Concord, AAC Prevail, CDC Hughes, Lillian, Glenlea, and elite line BW961 express a spectrum of resistance to leaf rust caused by Puccinia triticina Eriks. This study aimed to identify and map the leaf rust resistance of the cultivars using three doubled haploid populations, AAC Prevail/BW961 (PB), CDC Hughes/AAC Concord (HC), and Lillian/Glenlea (LG). The populations were evaluated for seedling resistance in the greenhouse and adult plant disease response in the field at Morden, MB for 3 years and genotyped with the 90K wheat Infinium iSelect SNP array. Genetic maps were constructed to perform QTL analysis on the seedling and field leaf rust data. A total of three field leaf rust resistance QTL segregated in the PB population, five in the HC, and six in the LG population. In the PB population, BW961 contributed two QTL on chromosomes 2DS and 7DS, and AAC Prevail contributed a QTL on 4AL consistent across trials. Of the five QTL in HC, AAC Concord contributed two QTL on 4AL and 7AL consistent across trials and a QTL on 3DL.1 that provided seedling resistance only. CDC Hughes contributed two QTL on 1DS and 3DL.2. Lillian contributed four QTL significant in at least two of the three trials on 2BS, 4AL, 5AL, and 7AL, and Glenlea two QTL on 4BL and 7BL. The 1DS QTL from CDC Hughes, the 2DS from BW961, the 4AL from the AAC Prevail, AAC Concord, and Lillian, and the 7AL from AAC Concord and Lillian conferred seedling leaf rust resistance. The QTL on 4AL corresponded with Lr30 and was the same across cultivars AAC Prevail, AAC Concord, and Lillian, whereas the 7AL corresponding with LrCen was coincident between AAC Concord and Lillian. The 7DS and 2DS QTL in BW961 corresponded with Lr34 and Lr2a, respectively, and the 1DS QTL in CDC Hughes with Lr21. The QTL identified on 5AL could represent a novel gene. The results of this study will widen our knowledge of leaf rust resistance genes in Canadian wheat and their utilization in resistance breeding.

Competitive ability of western Canadian spring wheat cultivars in a model weed system

Economic and social pressures are spurring the study of alternate weed management strategies such as the development of competitive crop cultivars, capable of being used under an integrated management plan. The primary objective of this research was to determine whether western Canadian spring wheat ( Triticum spp.) cultivars differ in their ability to compete against model weeds and whether those differences were expressed when challenged with wild weeds. A total of 71 wheat cultivars were grown in the absence or presence of simulated [cultivated oat ( Avena sativa L.) and oriental mustard ( Brassica juncea L.)] or natural [wild oat ( Avena fatua L.)] weed competition conditions. Significant ( p = 0.01) weed by cultivar interactions involving changes in yield cultivar rank were detected, indicating that the cultivars responded differently to competition. A small minority of cultivars such as Glenlea, CDC Rama, Genesis, AC Taber, AC Vista, Plenty, Napoleon, and BW652 had high-yield potential coupled with yield maintenance under weed pressure. The competitive ability advantage appeared to be associated with plant height or tillers per square meter as well as shorter vernalization requirement combined with photoperiod sensitivity. These outlier cultivar differences could be exploited in breeding new widely adapted varieties for scenarios where reduced herbicide weed control is desired, including situations where herbicide resistance limits chemical options. Cultivars with differing competitive ability under model weed conditions maintained their ranking when challenged by natural weed infestations. This suggests that selecting competitive spring wheat cultivars using a repeatable protocol based on model weeds is realistic.

Genome‐wide association mapping of agronomic traits and grain characteristics in spring wheat under conventional and organic management systems

AbstractPrevious genome‐wide association studies in Canadian spring wheat (Triticum aestivum L.) 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‐A1 and Vrn‐B1 genes, respectively. The IWGSC RefSeq v2.0 physical positions presented here would serve as the basis for easily comparing independent discovery studies in the future.

Genomic Predictions for Common Bunt, FHB, Stripe Rust, Leaf Rust, and Leaf Spotting Resistance in Spring Wheat.

Some studies have investigated the potential of genomic selection (GS) on stripe rust, leaf rust, Fusarium head blight (FHB), and leaf spot in wheat, but none of them have assessed the effect of the reaction norm model that incorporated GE interactions. In addition, the prediction accuracy on common bunt has not previously been studied. Here, we investigated within-population prediction accuracies using the baseline M1 model and two reaction norm models (M2 and M3) with three random cross-validation (CV1, CV2, and CV0) schemes. Three Canadian spring wheat populations were evaluated in up to eight field environments and genotyped with 3158, 5732, and 23,795 polymorphic markers. The M3 model that incorporated GE interactions reduced residual variance by an average of 10.2% as compared with the main effect M2 model and increased prediction accuracies on average by 2–6%. In some traits, the M3 model increased prediction accuracies up to 54% as compared with the M2 model. The average prediction accuracies of the M3 model with CV1, CV2, and CV0 schemes varied from 0.02 to 0.48, from 0.25 to 0.84, and from 0.14 to 0.87, respectively. In both CV2 and CV0 schemes, stripe rust in all three populations, common bunt and leaf rust in two populations, as well as FHB severity, FHB index, and leaf spot in one population had high to very high (0.54–0.87) prediction accuracies. This is the first comprehensive genomic selection study on five major diseases in spring wheat.

Validation of a New Sensitive Method for the Detection and Quantification of R and S-Epimers of Ergot Alkaloids in Canadian Spring Wheat Utilizing Deuterated Lysergic Acid Diethylamide as an Internal Standard.

Ergot sclerotia effect cereal crops intended for consumption. Ergot alkaloids within ergot sclerotia are assessed to ensure contamination is below safety standards established for human and animal health. Ergot alkaloids exist in two configurations, the R and S-epimers. It is important to quantify both configurations. The objective of this study was to validate a new ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method for quantification of six R and six S-epimers of ergot alkaloids in hard red spring wheat utilizing deuterated lysergic acid diethylamide (LSD-D3) as an internal standard. Validation parameters such as linearity, limit of detection (LOD), limit of quantification (LOQ), matrix effects, recovery and precision were investigated. For the 12 epimers analyzed, low LOD and LOQ values were observed, allowing for the sensitive detection of ergot epimers. Matrix effects ranged between 101–113% in a representative wheat matrix. Recovery was 68.3–119.1% with an inter-day precision of <24% relative standard deviation (RSD). The validation parameters conform with previous studies and exhibit differences between the R and S-epimers which has been rarely documented. This new sensitive method allows for the use of a new internal standard and can be incorporated and applied to research or diagnostic laboratories.

Genetic diversity and selective sweeps in historical and modern Canadian spring wheat cultivars using the 90K SNP array

Previous molecular characterization studies conducted in Canadian wheat cultivars shed some light on the impact of plant breeding on genetic diversity, but the number of varieties and markers used was small. Here, we used 28,798 markers of the wheat 90K single nucleotide polymorphisms to (a) assess the extent of genetic diversity, relationship, population structure, and divergence among 174 historical and modern Canadian spring wheat varieties registered from 1905 to 2018 and 22 unregistered lines (hereinafter referred to as cultivars), and (b) identify genomic regions that had undergone selection. About 91% of the pairs of cultivars differed by 20–40% of the scored alleles, but only 7% of the pairs had kinship coefficients of < 0.250, suggesting the presence of a high proportion of redundancy in allelic composition. Although the 196 cultivars represented eight wheat classes, our results from phylogenetic, principal component, and the model-based population structure analyses revealed three groups, with no clear structure among most wheat classes, breeding programs, and breeding periods. FST statistics computed among different categorical variables showed little genetic differentiation (< 0.05) among breeding periods and breeding programs, but a diverse level of genetic differentiation among wheat classes and predicted groups. Diversity indices were the highest and lowest among cultivars registered from 1970 to 1980 and from 2011 to 2018, respectively. Using two outlier detection methods, we identified from 524 to 2314 SNPs and 41 selective sweeps of which some are close to genes with known phenotype, including plant height, photoperiodism, vernalization, gluten strength, and disease resistance.

Mapping stem rust resistance loci effective in Kenya in Canadian spring wheat (Triticum aestivum L.) lines ‘AAC Prevail’ and ‘BW961’

This study was conducted to identify and map stem rust resistance genes in Canada Western Red Spring (CWRS) wheat variety ‘AAC Prevail’ and elite line ‘BW961ʹ. A population of 227 doubled haploid lines from ‘AAC Prevail’/‘BW961ʹ and parents were evaluated for their response to stem rust (Puccinia graminis) at Njoro, Kenya, from 2016–2019 and genotyped using a targeted genotyping by sequencing SeqSNP assay. ‘AAC Prevail’ and ‘BW961ʹ were susceptible to race TTKSK in seedling tests in Canada. We identified stable QTL (significant in most environments tested) associated with field stem rust resistance on chromosome arms 2BS and 7AL, and minor QTL on 5AL, 6AS and 7BL. The QTL on 5AL, 7AL and 7BL were contributed by ‘AAC Prevail’, while those on 2BS and 6AS were contributed by ‘BW961ʹ. The QTL on 7AL was detected across all environments and explained 9.5% to 39% of the variation in disease severity (DS) and infection response (IR). The QTL on 2BS was associated with DS in all environments and in three of four environments for IR, and explained 4.8% to 12% of the variation in DS and IR. In two environments, the combination of 2BS and 7AL significantly enhanced field stem rust resistance compared with either QTL singly. Using SNP markers closely linked to the novel QTL on 2BS and 7AL, Kompetitive Allele Specific PCR markers were developed and validated in the population. These results provide breeders with new information and markers to utilize these sources of stem rust resistance.

Examining the genetic diversity of the orange blossom wheat midge, Sitodiplosis mosellana (Géhin), across North America

AbstractThe orange blossom wheat midge, Sitodiplosis mosellana (Géhin) (Diptera: Cecidomyiidae), is a significant pest of wheat (Triticum spp.) grown in the Northern Hemisphere. It was accidently introduced to North America over 200 years ago and has subsequently spread throughout the northern Great Plains. Since 2010, several Canadian spring wheat varieties containing the resistance gene Sm1 have been released. Due to the potential of wheat midge populations to evolve virulent biotypes to Sm1, cultivars containing Sm1 are grown with a susceptible cultivar in an interspersed refuge. An understanding of the genetic diversity of wheat midge populations could provide important information on the potential development of resistance to Sm1. In the current study, we used two mitochondrial genes (CO1 and ND4) from wheat midge collected across the northern Great Plains and Québec in North America to assess population structure and genetic diversity. We found limited genetic diversity and population structure across the sampled North American populations. We also assessed North American haplotype similarity to wheat midge collected from Europe and China and found high similarity between North American and European populations, although sampling in Europe was limited. This supports the hypothesis that North American populations originated from Europe.

Mapping of Major Fusarium Head Blight Resistance from Canadian Wheat cv. AAC Tenacious.

Fusarium head blight (FHB) is one of the most devastating wheat disease due to its direct detrimental effects on grain-yield, quality and marketability. Resistant cultivars offer the most effective approach to manage FHB; however, the lack of different resistance resources is still a major bottleneck for wheat breeding programs. To identify and dissect FHB resistance, a doubled haploid wheat population produced from the Canadian spring wheat cvs AAC Innova and AAC Tenacious was phenotyped for FHB response variables incidence and severity, visual rating index (VRI), deoxynivalenol (DON) content, and agronomic traits days to anthesis (DTA) and plant height (PHT), followed by single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker genotyping. A high-density map was constructed consisting of 10,328 markers, mapped on all 21 chromosomes with a map density of 0.35 cM/marker. Together, two major quantitative trait loci for FHB resistance were identified on chromosome 2D from AAC Tenacious; one of these loci on 2DS also colocated with loci for DTA and PHT. Another major locus for PHT, which cosegregates with locus for low DON, was also identified along with many minor and epistatic loci. QTL identified from AAC Tenacious may be useful to pyramid FHB resistance.

Effect of chemical oxidizers and enzymatic treatments on the baking quality of doughs formulated with five Canadian spring wheat cultivars.

For many years, the baking industry has been using chemical improvers as a way for compensating for flour quality variation due to growing conditions or wheat cultivar. However, the replacement of chemical dough improvers with natural ingredients or processing aids (i.e. enzymes) allows for the production of 'cleaner label' products. In the present research, dough and bread properties (mixing time, oven rise, loaf volume, crumb firmness and C-cell parameters) were analysed as a function of wheat cultivar (Glenn, Harvest, Lillian, CDC Plentiful and Stettler), additive-type (ascorbic acid, azodicarbonamide, glucose oxidase and fungal xylanase) and concentration. Overall, the cultivar Glenn appeared to have improved baking performance relative to the other cultivars, regardless of the additive and additive concentration. On the other hand, Stettler showed poorer baking quality and performance even with the addition of oxidizers and enzymes in relation to the control. The concentration of additive was found to have little or no effect on improving baking properties within each cultivar. Enzymes had similar or better performance than oxidizers in most cases.

Mapping quantitative trait loci associated with leaf rust resistance in five spring wheat populations using single nucleotide polymorphism markers.

Growing resistant wheat (Triticum aestivum L) varieties is an important strategy for the control of leaf rust, caused by Puccinia triticina Eriks. This study sought to identify the chromosomal location and effects of leaf rust resistance loci in five Canadian spring wheat cultivars. The parents and doubled haploid lines of crosses Carberry/AC Cadillac, Carberry/Vesper, Vesper/Lillian, Vesper/Stettler and Stettler/Red Fife were assessed for leaf rust severity and infection response in field nurseries in Canada near Swift Current, SK from 2013 to 2015, Morden, MB from 2015 to 2017 and Brandon, MB in 2016, and in New Zealand near Lincoln in 2014. The populations were genotyped with the 90K Infinium iSelect assay and quantitative trait loci (QTL) analysis was performed. A high density consensus map generated based on 14 doubled haploid populations and integrating SNP and SSR markers was used to compare QTL identified in different populations. AC Cadillac contributed QTL on chromosomes 2A, 3B and 7B (2 loci), Carberry on 1A, 2B (2 loci), 2D, 4B (2 loci), 5A, 6A, 7A and 7D, Lillian on 4A and 7D, Stettler on 2D and 6B, Vesper on 1B, 1D, 2A, 6B and 7B (2 loci), and Red Fife on 7A and 7B. Lillian contributed to a novel locus QLr.spa-4A, and similarly Carberry at QLr.spa-5A. The discovery of novel leaf rust resistance QTL QLr.spa-4A and QLr.spa-5A, and several others in contemporary Canada Western Red Spring wheat varieties is a tremendous addition to our present knowledge of resistance gene deployment in breeding. Carberry demonstrated substantial stacking of genes which could be supplemented with the genes identified in other cultivars with the expectation of increasing efficacy of resistance to leaf rust and longevity with little risk of linkage drag.

Mapping QTL Associated with Stripe Rust, Leaf Rust, and Leaf Spotting in a Canadian Spring Wheat Population

Stripe rust, leaf rust, and the leaf spot complex are economically important diseases of wheat (Triticum aestivum L.) in western Canada, and genetic host resistance is the most successful management strategy. This study was conducted to identify quantitative trait loci (QTL) associated with these diseases and to provide wheat breeders with sources of potential disease resistance genes. A total of 208 recombinant inbred lines derived from a cross between Canadian spring wheat cultivars ‘Peace’ and ‘Carberry’ were evaluated from 2014 to 2017 in stripe rust, leaf rust, and leaf spot nurseries in Alberta and British Columbia. All lines were genotyped with sequencing‐based Diversity Arrays Technology (DArTseq) markers. Using the least square means of the combined environments, two stripe rust resistance QTL, two leaf rust resistance QTL, and three leaf spot resistance QTL were identified. The stripe rust QTL were located on chromosomes 3A and 4B, the leaf rust QTL were located on chromosomes 4A and 3D, and the leaf spot QTL were located on 2A, 4B and 7D. The stripe rust resistance QTL on 4B, contributed by ‘Carberry’, was previously identified in other studies using a population derived from ‘Carberry’. Results from this study suggest that ‘Carberry’ may be an attractive parental source for breeders to enhance resistance against stripe rust and leaf spot with minor resistance alleles.

Weed suppression by Canadian spring cereals: relative contribution of competition for resources and allelopathy

Integrated and more sustainable weed management practices are in great demand all around the globe. The adoption of more weed-suppressive cereal cultivars could be part of an integrated weed management strategy. Recently, a study was published analysing the relative contribution of above-ground competition and allelopathy to weed suppression of Scandinavian winter cereals at the field level. The present study used the same approach with Canadian spring wheat and triticale cultivars, and confirmed the results of the previous study. The competitive traits such as leaf area index, crop height and early vigour, and the allelochemicals belonging to the chemical group of benzoxazinoids measured in the root zone were of equal importance to explain the variance of weed biomass at the field level. In addition, a dendogram showed large genetic variability for competitive and allelopathic traits in the Canadian spring cereals, providing the genetic basis for the initiation of breeding programmes for more weed-suppressive cultivars.

Genetic characterization of type II Fusarium head blight resistance derived from transgressive segregation in a cross between Eastern and Western Canadian spring wheat

Fusarium head blight (FHB) caused by Fusarium graminearum is a devastating disease affecting global wheat production, causing significant losses to yield and grain quality. The Eastern Canadian line FL62R1 was developed using a systemic breeding approach and boasts high levels of FHB resistance with good yield, desirable agronomics, and end-use quality traits. The objective of this study was to identify genetic determinants of type II resistance in a cross between FL62R1 and cv. Stettler, a Canada Western Red Spring variety rated moderately susceptible to FHB. Although neither parent displayed strong resistance to FHB spread within spikes following point inoculation (type II resistance) in greenhouses, strong type II resistance was observed in a large number of progeny, including 6% with resistance comparable to the best check line, Sumai 3. Quantitative trait locus (QTL) mapping identified a locus from chromosome 2BL of Stettler which provides Sumai 3 level type II resistance when combined with favorable FHB resistance QTLs with minor effects from FL62R1. This study provides insight into transgressive segregation for FHB, which despite its importance is poorly understood, rare, and difficult to predict. It also begins to dissect the genetic architecture of FHB resistance in wheat derived from the systemic breeding approach.

Quantitative trait loci for resistance to stripe rust of wheat revealed using global field nurseries and opportunities for stacking resistance genes.

Quantitative trait loci controlling stripe rust resistance were identified in adapted Canadian spring wheat cultivars providing opportunity for breeders to stack loci using marker-assisted breeding. Stripe rust or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss., is a devastating disease of common wheat (Triticum aestivum L.) in many regions of the world. The objectives of this research were to identify and map quantitative trait loci (QTL) associated with stripe rust resistance in adapted Canadian spring wheat cultivars that are effective globally, and investigate opportunities for stacking resistance. Doubled haploid (DH) populations from the crosses Vesper/Lillian, Vesper/Stettler, Carberry/Vesper, Stettler/Red Fife and Carberry/AC Cadillac were phenotyped for stripe rust severity and infection response in field nurseries in Canada (Lethbridge and Swift Current), New Zealand (Lincoln), Mexico (Toluca) and Kenya (Njoro), and genotyped with SNP markers. Six QTL for stripe rust resistance in the population of Vesper/Lillian, five in Vesper/Stettler, seven in Stettler/Red Fife, four in Carberry/Vesper and nine in Carberry/AC Cadillac were identified. Lillian contributed stripe rust resistance QTL on chromosomes 4B, 5A, 6B and 7D, AC Cadillac on 2A, 2B, 3B and 5B, Carberry on 1A, 1B, 4A, 4B, 7A and 7D, Stettler on 1A, 2A, 3D, 4A, 5B and 6A, Red Fife on 2D, 3B and 4B, and Vesper on 1B, 2B and 7A. QTL on 1A, 1B, 2A, 2B, 3B, 4A, 4B, 5B, 7A and 7D were observed in multiple parents. The populations are compelling sources of recombination of many stripe rust resistance QTL for stacking disease resistance. Gene pyramiding should be possible with little chance of linkage drag of detrimental genes as the source parents were mostly adapted cultivars widely grown in Canada.

Population Structure and Genomewide Association Analysis of Resistance to Disease and Insensitivity to Ptr Toxins in Canadian Spring Wheat Using 90K SNP Array

Leaf rust, yellow (stripe) rust, common bunt, and tan spot are economically significant diseases affecting wheat (Triticum aestivum L.) 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 &lt;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 × 10−5 and 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 Tsn1 gene. 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.

Allelic variation and effects of 16 candidate genes on disease resistance in western Canadian spring wheat cultivars

Recently, we mapped genomic regions associated with resistance to wheat diseases and insensitivity to Pyrenophora tritici-repentis (Ptr) toxins using 81 historical and modern Canadian western spring wheat cultivars genotyped with genome-wide single nucleotide polymorphic (SNP) markers. Here, we investigate the frequency and effects of allelic variants of 50 markers associated with 16 candidate genes that regulate resistance to leaf rust (Puccinia triticina), yellow or stripe rust (P. striiformis f. sp. tritici), tan spot (P. tritici-repentis), and Ptr ToxA reaction in a subset of 70 of the 81 spring wheat cultivars. We evaluated the 70 cultivars in the field for all diseases except Ptr ToxA, which was evaluated in a greenhouse. Using Spearman rank correlation, stepwise discriminant analysis, and partial least squares regression, we identified between 4 and 11 markers as best predictors of each phenotypic trait. Overall, 23 of the 50 markers were associated with one or more of the phenotypic traits of which analysis of variance showed significant differences between allelic variants of 19 markers. In most analyses, markers for Lr34/Yr18 and Tsn1 loci were identified consistently as the best predictor of disease resistance and Ptr ToxA sensitivity, respectively. The same alleles from two Lr34/Yr18 diagnostic SNP markers (wMAS000003 and wMAS000004) not only decreased stripe rust scores up to 1.6 (on a 1 to 9 scale), but also increased grain yield up to 196 kg ha−1 without affecting maturity. Results from this study could aid spring wheat breeders in selecting the best parental combinations and/or marker-assisted selection to integrate disease resistance with early maturity and short stature.

Fusarium Head Blight Resistance QTL in the Spring Wheat Cross Kenyon/86ISMN 2137

Fusarium head blight (FHB), caused by Fusarium graminearum, is a very important disease of wheat globally. Damage caused by F. graminearum includes reduced grain yield, reduced grain functional quality, and results in the presence of the trichothecene mycotoxin deoxynivalenol in Fusarium-damaged kernels. The development of FHB resistant wheat cultivars is an important component of integrated management. The objective of this study was to identify QTL for FHB resistance in a recombinant inbred line (RIL) population of the spring wheat cross Kenyon/86ISMN 2137. Kenyon is a Canadian spring wheat, while 86ISMN 2137 is an unrelated spring wheat. The RIL population was evaluated for FHB resistance in six FHB nurseries. Nine additive effect QTL for FHB resistance were identified, six from Kenyon and three from 86ISMN 2137. Rht8 and Ppd-D1a co-located with two FHB resistance QTL on chromosome arm 2DS. A major QTL for FHB resistance from Kenyon (QFhb.crc-7D) was identified on chromosome 7D. The QTL QFhb.crc-2D.4 from Kenyon mapped to the same region as a FHB resistance QTL from Wuhan-1 on chromosome arm 2DL. This result was unexpected since Kenyon does not share common ancestry with Wuhan-1. Other FHB resistance QTL on chromosomes 4A, 4D, and 5B also mapped to known locations of FHB resistance. Four digenic epistatic interactions were detected for FHB resistance, which involved eight QTL. None of these QTL were significant based upon additive effect QTL analysis. This study provides insight into the genetic basis of native FHB resistance in Canadian spring wheat.