Mapping seedling and adult plant leaf rust resistance genes in the durum wheat cultivar Strongfield and other Triticum turgidum (L.) lines.

Durum wheat (T. turgidum L.) is threatened by the appearance of new virulent races of leaf rust, caused by Puccinia triticina, in recent years. This study was conducted to determine the leaf rust resistance in a modern Canadian durum cultivar Strongfield. Six populations derived from crosses of Strongfield with six tetraploid wheat lines, respectively, were tested at seedling plant stage with different P. triticina races. Two of the populations were evaluated for adult plant leaf rust infection in Canada and Mexico. A stepwise regression joint linkage QTL mapping and analysis by MapQTL were performed. Strongfield contributed the majority of QTL detected, contributing seven QTL detected in field tests, and eight QTL conditioning seedling resistance. A 1B QTL, QLr-Spa-1B.1, from Strongfield had a significant effect in both Canadian and Mexican field tests, and corresponded with Lr46/Yr29. The remaining field QTL were found in only the Canadian or the Mexican environment, not both. The QTL from Strongfield on 3A, QLr-Spa-3A, conferred seedling resistance to all races tested and had a significant effect in the field in Canada. This is the first report of the QLr-Spa-3A and Lr46/Yr29 as key components of the genetic resistance in Canadian durum wheat. KASP markers were developed to detect the QLr-Spa-3A for use in marker assisted leaf rust resistance breeding. The susceptible parental lines contributed QTL on 1A, 2B and 5B that were effective in Mexican field tests that may be good targets to integrate into modern durum varieties to improve resistance to new durum virulent races.

Main effect and epistatic QTL affecting spike shattering and association with plant height revealed in two spring wheat (Triticum aestivum L.) populations.

KEY MESSAGE: A major QTL on chromosome arm 4BS was associated with reduced spike shattering and reduced plant height in coupling phase, and a second major QTL associated with reduced spike shattering was detected on chromosome arm 5AL in the same wheat variety Carberry. Spike shattering can cause severe grain yield loss in wheat. Development of cultivars with reduced shattering but having easy mechanical threshability is the target of wheat breeding programs. This study was conducted to determine quantitative trait loci (QTL) associated with shattering resistance, and epistasis among QTL in the populations Carberry/AC Cadillac and Carberry/Thatcher. Response of the populations to spike shattering was evaluated near Swift Current, SK, in four to five environments. Plant height data recorded in different locations and years were used to determine the relationship of the trait with spike shattering. Each population was genotyped and mapped with the wheat 90 K Illumina iSelect SNP array. Main effect QTL were analyzed by MapQTL 6, and epistatic interactions between main effect QTL were determined by QTLNetwork 2.0. Correlations between height and shattering ranged from 0.15 to 0.49. Carberry contributed two major QTL associated with spike shattering on chromosome arms 4BS and 5AL, detected in both populations. Carberry also contributed two minor QTL on 7AS and 7AL. AC Cadillac contributed five minor QTL on 1AL, 2DL, 3AL, 3DL and 7DS. Nine epistatic QTL interactions were identified, out of which the most consistent and synergistic interaction, that reduced the expression of shattering, occurred between 4BS and 5AL QTL. The 4BS QTL was consistently associated with reduced shattering and reduced plant height in the coupling phase. The present findings shed light on the inheritance of shattering resistance and provide genetic markers for manipulating the trait to develop wheat cultivars.

Mapping quantitative trait loci associated with common bunt resistance in a spring wheat (Triticum aestivum L.) variety Lillian.

KEY MESSAGE: Based on their consistency over environments, two QTL identified in Lillian on chromosomes 5A and 7A could be useful targets for marker assisted breeding of common bunt resistance. Common bunt of wheat (Triticum aestivum L.) caused by Tilletia tritici and T. laevis is an economically important disease because of losses in grain yield and reduced grain quality. Resistance can be quantitative, under the control of multiple small effect genes. The Canada Western Red Spring wheat variety Lillian is moderately resistant to common bunt races found on the Canadian prairies. This study was conducted to identify and map quantitative trait loci (QTL) conferring resistance against common bunt in Lillian. A doubled haploid population comprising 280 lines was developed from F1 plants of the cross of Lillian by Vesper. The lines were inoculated at seeding with the two races L16 (T. laevis) and T19 (T. tritici), grown in field near Swift Current, SK, in 2014, 2015 and 2016 and assessed for disease incidence. The lines were genotyped with the 90 K iSelect SNP genotyping assay, and a high-density genetic map was constructed. Quantitative trait locus analysis was performed with MapQTL.6® software. Two relatively stable common bunt resistance QTL, detected in two of the 3 years, were identified on chromosomes 5A and 7A from Lillian. In addition, three less stable QTL, appearing in one out of 3 years, were identified: one was contributed by Lillian on chromosome 3D and two were contributed by Vesper on chromosomes 1D and 2A. Epistatic interaction was identified for the bunt incidence between 3D and 7A resulting in greater bunt resistance. Future bunt resistance breeding will benefit from combining these QTL through gene pyramiding.

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

KEY MESSAGE: 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.

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.

A Combination of Leaf Rust Resistance Genes, Including Lr34 and Lr46, Is the Key to the Durable Resistance of the Canadian Wheat Cultivar, Carberry.

The hexaploid spring wheat cultivar, Carberry, was registered in Canada in 2009, and has since been grown over an extensive area on the Canadian Prairies. Carberry has maintained a very high level of leaf rust (Puccinia triticina Eriks.) resistance since its release. To understand the genetic basis of Carberry's leaf rust resistance, Carberry was crossed with the susceptible cultivar, Thatcher, and a doubled haploid (DH) population of 297 lines was generated. The DH population was evaluated for leaf rust in seven field environments at the adult plant stage. Seedling and adult plant resistance (APR) to multiple virulence phenotypes of P. triticina was evaluated on the parents and the progeny population in controlled greenhouse studies. The population was genotyped with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, and quantitative trait loci (QTL) analysis was performed. The analysis using field leaf rust response indicated that Carberry contributed nine QTL located on chromosomes 1B, 2B (2 loci), 2D, 4A, 4B, 5A, 5B, and 7D. The QTL located on 1B, 2B, 5B, and 7D chromosomes were observed in two or more environments, whereas the remainder were detected in single environments. The resistance on 1B, detected in five environments, was attributed to Lr46 and on 7D, detected in seven environments to Lr34. The first 2B QTL corresponded with the adult plant gene, Lr13, while the second QTL corresponded with Lr16. The seedling analysis showed that Carberry carries Lr2a, Lr16, and Lr23. Five epistatic effects were identified in the population, with synergistic interactions being observed for Lr34 with Lr46, Lr16, and Lr2a. The durable rust resistance of Carberry is attributed to Lr34 and Lr46 in combination with these other resistance genes, because the resistance has remained effective even though the P. triticina population has evolved virulent to Lr2a, Lr13, Lr16, and Lr23.

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.