Identification of a major dominant gene for race-nonspecific tan spot resistance in wild emmer wheat

Potential of tetraploid wheats in plant breeding: A review

Domestication syndrome, selection pressure, and modern plant breeding programs have reduced the genetic diversity of the wheat germplasm. For the genetic gains of breeding programs to be sustainable, plant breeders require a diverse gene pool to select genes for resistance to biotic stress factors, tolerance to abiotic stress factors, and improved quality and yield components. Thus, old landraces, subspecies and wild ancestors are rich sources of genetic diversity that have not yet been fully exploited, and it is possible to utilize this diversity. Compared with durum wheat, tetraploid wheat subspecies have retained much greater genetic diversity despite genetic drift and various environmental influences, and the identification and utilization of this diversity can make a greater contribution to the genetic enrichment of wheat. In addition, using the pre-breeding method, the valuable left-behind alleles in the wheat gene pool can be re-introduced through hybridization and introgressive gene flow to create a sustainable opportunity for the genetic gain of wheat. This review provides some insights about the potential of tetraploid wheats in plant breeding and the genetic gains made by them in plant breeding across past decades, and gathers the known functional information on genes/QTLs, metabolites, traits and their direct involvement in wheat resistance/tolerance to biotic/abiotic stresses.

Association mapping of tan spot and septoria nodorum blotch resistance in cultivated emmer wheat

KEY MESSAGE

A total of 65 SNPs associated with resistance to tan spot and septoria nodorum blotch were identified in a panel of 180 cultivated emmer accessions through association mapping Tan spot and septoria nodorum blotch (SNB) are foliar diseases caused by the respective fungal pathogens Pyrenophora tritici-repentis and Parastagonospora nodorum that affect global wheat production. To find new sources of resistance, we evaluated a panel of 180 cultivated emmer wheat (Triticum turgidum ssp. dicoccum) accessions for reactions to four P. tritici-repentis isolates Pti2, 86-124, 331-9 and DW5, two P. nodorum isolate, Sn4 and Sn2000, and four necrotrophic effectors (NEs) produced by the pathogens. About 8-36% of the accessions exhibited resistance to the four P. tritici-repentis isolates, with five accessions demonstrating resistance to all isolates. For SNB, 64% accessions showed resistance to Sn4, 43% to Sn2000 and 36% to both isolates, with Spain (11% accessions) as the most common origin of resistance. To understand the genetic basis of resistance, association mapping was performed using SNP (single nucleotide polymorphism) markers generated by genotype-by-sequencing and the 9 K SNP Infinium array. A total of 46 SNPs were significantly associated with tan spot and 19 SNPs with SNB resistance or susceptibility. Six trait loci on chromosome arms 1BL, 3BL, 4AL (2), 6BL and 7AL conferred resistance to two or more isolates. Known NE sensitivity genes for disease development were undetected except Snn5 for Sn2000, suggesting novel genetic factors are controlling host-pathogen interaction in cultivated emmer. The emmer accessions with the highest levels of resistance to the six pathogen isolates (e.g., CItr 14133-1, PI 94634-1 and PI 377672) could serve as donors for tan spot and SNB resistance in wheat breeding programs.

Genome-wide association analysis of tan spot disease resistance in durum wheat accessions from Tunisia

Background: Tunisia harbors a rich collection of unexploited durum wheat landraces (Triticum durum ssp. durum) that have been gradually replaced by elite cultivars since the 1970s. These landraces represent an important potential source for broadening the genetic background of elite durum wheat cultivars and for the introgression of novel genes for key traits, including disease resistance, into these cultivars. Methods: In this study, single nucleotide polymorphism (SNP) markers were used to investigate the genetic diversity and population structure of a core collection of 235 durum wheat accessions consisting mainly of landraces. The high phenotypic and genetic diversity of the fungal pathogen Pyrenophora tritici-repentis (cause of tan spot disease of wheat) in Tunisia allowed the assessment of the accessions for tan spot resistance at the adult plant stage under field conditions over three cropping seasons. A genome-wide association study (GWAS) was performed using a 90k SNP array. Results: Bayesian population structure analysis with 9191 polymorphic SNP markers classified the accessions into two groups, where groups 1 and 2 included 49.79% and 31.49% of the accessions, respectively, while the remaining 18.72% were admixtures. Principal coordinate analysis, the unweighted pair group method with arithmetic mean and the neighbor-joining method clustered the accessions into three to five groups. Analysis of molecular variance indicated that 76% of the genetic variation was among individuals and 23% was between individuals. Genome-wide association analyses identified 26 SNPs associated with tan spot resistance and explained between 8.1% to 20.2% of the phenotypic variation. The SNPs were located on chromosomes 1B (1 SNP), 2B (4 SNPs), 3A (2 SNPs), 3B (2 SNPs), 4A (2 SNPs), 4B (1 SNP), 5A (2 SNPs), 5B (4 SNPs), 6A (5 SNPs), 6B (2 SNPs), and 7B (1 SNP). Four markers, one on each of chromosomes 1B, and 5A, and two on 5B, coincided with previously reported SNPs for tan spot resistance, while the remaining SNPs were either novel markers or closely related to previously reported SNPs. Eight durum wheat accessions were identified as possible novel sources of tan spot resistance that could be introgressed into elite cultivars. Conclusion: The results highlighted the significance of chromosomes 2B, 5B, and 6A as genomic regions associated with tan spot resistance.

Association Mapping of Resistance to Tan Spot in the Global Durum Panel

Tan spot, caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr), is an important disease of durum and common wheat worldwide. Compared with common wheat, less is known about the genetics and molecular basis of tan spot resistance in durum wheat. We evaluated 510 durum lines from the Global Durum Wheat Panel (GDP) for sensitivity to the necrotrophic effectors (NEs) Ptr ToxA and Ptr ToxB and for reaction to Ptr isolates representing races 1 to 5. Overall, susceptible durum lines were most prevalent in South Asia, the Middle East, and North Africa. Genome-wide association analysis showed that the resistance locus Tsr7 was significantly associated with tan spot caused by races 2 and 3, but not races 1, 4, or 5. The NE sensitivity genes Tsc1 and Tsc2 were associated with susceptibility to Ptr ToxC- and Ptr ToxB-producing isolates, respectively, but Tsn1 was not associated with tan spot caused by Ptr ToxA-producing isolates, which further validates that the Tsn1-Ptr ToxA interaction does not play a significant role in tan spot development in durum. A unique locus on chromosome arm 2AS was associated with tan spot caused by race 4, a race once considered avirulent. A novel trait characterized by expanding chlorosis leading to increased disease severity caused by the Ptr ToxB-producing race 5 isolate DW5 was identified, and this trait was governed by a locus on chromosome 5B. We recommend that durum breeders select resistance alleles at the Tsr7, Tsc1, Tsc2, and the chromosome 2AS loci to obtain broad resistance to tan spot.

A Race Profile of Tan Spot in Australia Reveals Race 2 Isolates Harboring ToxC1

Tan spot disease is caused by Pyrenophora tritici-repentis (Ptr), one of the major necrotrophic fungal pathogens that affects wheat crops globally. Extensive research has shown that the necrotrophic fungal effectors ToxA, ToxB, and ToxC underlie the genetic interactions of Ptr race classification. ToxA and ToxB are both small proteins secreted during infection; however, the structure of ToxC remains unknown. In line with the recent discovery of the ToxC1 gene that is involved in ToxC production, a subset of 68 isolates collected from the Australian wheat cropping regions were assessed for the presence of all three effectors by pathotyping against four tan spot wheat differential lines and PCR amplification of ToxA, ToxB, and ToxC1. Based on the disease phenotypes, the 68 isolates were grouped into two races with 63 classified as race 1 and five as race 2. A representative selection of each race was tested against eight Australian commercial wheat cultivars and showed no distinction between the virulence levels. Sequencing of ToxA showed that both races had identical gene sequences of haplotype PtrA1. All the race 1 isolates possessed ToxC1 but three race 2 isolates also contained ToxC1 despite being unable to induce a spreading chlorotic symptom on the ToxC differential line. Quantitative trait loci mapping confirmed the absence of the ToxC-Tsc1 association in disease response caused by the ToxC1-containing race 2 isolate; however, ToxC1 expression was detected during plant infection. Altogether, these results suggest that there is a complex regulatory process involved in the production of ToxC within the Australian race 2 isolates.

Genome-wide association mapping of resistance to the foliar diseases septoria nodorum blotch and tan spot in a global winter wheat collection

Septoria nodorum blotch (SNB) and tan spot, caused by the necrotrophic fungal pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis, respectively, often occur together as a leaf spotting disease complex on wheat (Triticum aestivum L.). Both pathogens produce necrotrophic effectors (NEs) that contribute to the development of disease. Here, genome-wide association analysis of a diverse panel of 264 winter wheat lines revealed novel loci on chromosomes 5A and 5B associated with sensitivity to the NEs SnTox3 and SnTox5 in addition to the known sensitivity genes for NEs Ptr/SnToxA, SnTox1, SnTox3, and SnTox5. Sensitivity loci for SnTox267 and Ptr ToxB were not detected. Evaluation of the panel with five P. nodorum isolates for SNB development indicated the Snn3-SnTox3 and Tsn1-SnToxA interactions played significant roles in disease development along with additional QTL on chromosomes 2A and 2D, which may correspond to the Snn7-SnTox267 interaction. For tan spot, the Tsc1-Ptr ToxC interaction was associated with disease caused by two isolates, and a novel QTL on chromosome 7D was associated with a third isolate. The Tsn1-ToxA interaction was associated with SNB but not tan spot. Therefore some, but not all, of the previously characterized host gene-NE interactions in these pathosystems play significant roles in disease development in winter wheat. Based on these results, breeders should prioritize the selection of resistance alleles at the Tsc1, Tsn1, Snn3, and Snn7 loci as well as the 2A and 7D QTL to obtain good levels of resistance to SNB and tan spot in winter wheat.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01400-5.

Genetics and breeding for resistance against four leaf spot diseases in wheat (Triticum aestivum L.)

In wheat, major yield losses are caused by a variety of diseases including rusts, spike diseases, leaf spot and root diseases. The genetics of resistance against all these diseases have been studied in great detail and utilized for breeding resistant cultivars. The resistance against leaf spot diseases caused by each individual necrotroph/hemi-biotroph involves a complex system involving resistance (R) genes, sensitivity (S) genes, small secreted protein (SSP) genes and quantitative resistance loci (QRLs). This review deals with resistance for the following four-leaf spot diseases: (i) Septoria nodorum blotch (SNB) caused by Parastagonospora nodorum; (ii) Tan spot (TS) caused by Pyrenophora tritici-repentis; (iii) Spot blotch (SB) caused by Bipolaris sorokiniana and (iv) Septoria tritici blotch (STB) caused by Zymoseptoria tritici.

Evolution and origin of bread wheat

Bread wheat (Triticum aestivum, genome BBAADD) is a young hexaploid species formed only 8,500-9,000 years ago through hybridization between a domesticated free-threshing tetraploid progenitor, genome BBAA, and Aegilops tauschii, the diploid donor of the D subgenome. Very soon after its formation, it spread globally from its cradle in the fertile crescent into new habitats and climates, to become a staple food of humanity. This extraordinary global expansion was probably enabled by allopolyploidy that accelerated genetic novelty through the acquisition of new traits, new intergenomic interactions, and buffering of mutations, and by the attractiveness of bread wheat's large, tasty, and nutritious grain with high baking quality. New genome sequences suggest that the elusive donor of the B subgenome is a distinct (unknown or extinct) species rather than a mosaic genome. We discuss the origin of the diploid and tetraploid progenitors of bread wheat and the conflicting genetic and archaeological evidence on where it was formed and which species was its free-threshing tetraploid progenitor. Wheat experienced many environmental changes throughout its evolution, therefore, while it might adapt to current climatic changes, efforts are needed to better use and conserve the vast gene pool of wheat biodiversity on which our food security depends.

Varietal Screening of Durum Wheat Varieties for Resistance to Pyrenophora tritici-repentis (Tan Spot) under Field Conditions

Tan spot disease caused by Pyrenophora tritici-repentis was becoming more bred in Tunisia during the last decade. The search for resistant varieties against the increased virulence diversity of P. tritici-repentis is presently considered as a priority. Seven of the most commercialized durum wheat varieties in Tunisia (cvs. Maâli, Salim, Razzak, Monastir, Khiar, Inrat100, and Sculptur) were inoculated with five characterized fungal strains under field conditions, during two seasons. The variance analysis revealed that strains Ech8F₆ and B4.8 used in inoculation are the most virulent ones. These strains hosting ToxB gene caused chlorosis symptom on the tested varieties. The other strains induced necrosis with yellow halo and host ToxA gene were less virulent. The area under disease progress curve values revealed that Maâli is the most vulnerable genotype compared to the new selected varieties Monastir and Inrat100. A variable tolerance rate of the varieties to tan spot disease was also highly visible on yield components. The losses were about 22.2% of the thousand kernel weight in Maâli variety, 35% of spikes/m² in Inrat100 variety, 32.5% of kernel number/spike, and 25.2% of yield grain in Monastir variety. This effect evaluation of the strains harbouring ToxA and ToxB genes could be responsible for the identification of potentially susceptible genes Tsn1 and Tsc2 representing resistance sources for breeding programs.

An Improved Inoculation Method to Detect Wheat and Barley Genotypes for Resistance to Fusarium Crown Rot

Fusarium crown rot (FCR), caused by Fusarium species, is a serious soilborne fungal disease in many wheat growing regions in the world. A reliable FCR assessment method is essential for germplasm screening and host resistance studies. Here, we report a new assay in which we inoculated wheat seedlings grown in a glasshouse for FCR by injecting spore suspensions into the seedling stems. The effects of inoculum concentration and injection time points on disease severity were investigated. Of different treatments, the injection of 10⁷ macroconidia/ml suspension at one leaf and one heart stage gave best results. A collection of 92 emmer-derived hexaploid bread wheats, 43 barley germplasms, and four wheat genotypes with known resistance levels to FCR was used to validate this new method. Repeatability of the two trials in the validation experiments was high (r = 0.97, P < 0.01). Two emmer-derived hexaploid bread wheat and three Chinese barley germplasms showed consistent resistance to FCR in multiple rounds of selection. The short timeframe of this assay for phenotypic screening makes it a valuable tool to eliminate germplasms with undesirable susceptibility to FCR at seedling stage before costly field assays.

Genomic Analysis and Delineation of the Tan Spot Susceptibility Locus Tsc1 in Wheat

The necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) causes the foliar disease tan spot in both bread wheat and durum wheat. Wheat lines carrying the tan spot susceptibility gene Tsc1 are sensitive to the Ptr-produced necrotrophic effector (NE) Ptr ToxC. A compatible interaction results in leaf chlorosis, reducing yield by decreasing the photosynthetic area of leaves. Developing genetically resistant cultivars will effectively reduce disease incidence. Toward that goal, the production of chlorosis in response to inoculation with Ptr ToxC-producing isolates was mapped in two low-resolution biparental populations derived from LMPG-6 × PI 626573 (LP) and Louise × Penawawa (LouPen). In total, 58 genetic markers were developed and mapped, delineating the Tsc1 candidate gene region to a 1.4 centiMorgan (cM) genetic interval spanning 184 kb on the short arm of chromosome 1A. A total of nine candidate genes were identified in the Chinese Spring reference genome, seven with protein domains characteristic of resistance genes. Mapping of the chlorotic phenotype, development of genetic markers, both for genetic mapping and marker-assisted selection (MAS), and the identification of Tsc1 candidate genes provide a foundation for map-based cloning of Tsc1.

Characterization of Mediterranean Durum Wheat for Resistance to Pyrenophora tritici-repentis

Tan spot (TS), caused by the fugus Pyrenophora tritici-repentis (Ptr), has gained significant importance in the last few years, thereby representing a threat to wheat production in all major wheat-growing regions, including Tunisia. In this context, we evaluated a Mediterranean collection of 549 durum wheat accessions under field conditions for resistance to Ptr over two cropping seasons in Jendouba (Tunisia), a hot spot for Ptr. The relative disease severities showed significant phenotypic variation from resistance to susceptibility. The correlation between disease scores over the two trials was significant, as 50% of the accessions maintained good levels of resistance (resistant–moderately resistant). Seedling and adult-stage reactions were significantly correlated. The ANOVA analysis revealed that the genotype term is highly significant at the adult stage, thus emphasizing the high genetic variability of the tested accessions. Reaction-type comparison among and between countries revealed a high diversity of TS resistance. Plant height (PH) was negatively correlated to disease scores, indicating that PH might either have a significant effect on TS severity or that it can be a potential disease escape trait. The evaluation of this collection allowed for the identification of potential diverse resistance sources to Ptr that can be incorporated in breeding programs.

Characterization of Pyrenophora tritici-repentis in Tunisia and Comparison with a Global Pathogen Population

Pyrenophora tritici-repentis causes tan spot, an important foliar disease of wheat. A collection of P. tritici-repentis isolates from Tunisia, located in one of the main secondary centers of diversification of durum wheat, was tested for phenotypic race classification based on virulence on a host differential set and for the presence of the necrotrophic effector (NE) genes ToxA, ToxB, and toxb by PCR analysis. While races 2, 4, 5, 6, 7, and 8 were identified according to their virulence phenotypes, PCR testing indicated the presence of "atypical" isolates that induced necrosis on the wheat differential 'Glenlea,' but lacked the expected ToxA gene, suggesting the involvement of other NEs in the P. tritici-repentis/wheat interaction. Genetic diversity and the P. tritici-repentis population structure were explored further by examining 59 Tunisian isolates and 35 isolates from Algeria, Azerbaijan, Canada, Iran, and Syria using 24 simple sequence repeat markers. Average genetic diversity, overall gene flow, and percentage polymorphic loci were estimated as 0.58, 2.09, and 87%, respectively. Analysis of molecular variance showed that 81% of the genetic variance occurred within populations and 19% occurred between populations. Cluster analysis by the unweighted pair group method indicated that ToxB^- isolates grouped together and were distantly related to ToxB⁺ isolates. Based on Nei's analysis, the global collection clustered into two distinct groups according to their region of origin. The results suggest that geographic origin and the host specificity imposed by different NEs can lead to differentiation among P. tritici-repentis populations.

Genetic characterization of adult-plant resistance to tan spot (syn, yellow spot) in wheat

QTL mapping identified key genomic regions associated with adult-plant resistance to tan spot, which are effective even in the presence of the sensitivity gene Tsn1, thus serving as a new genetic solution to develop disease-resistant wheat cultivars. Improving resistance to tan spot (Pyrenophora tritici-repentis; Ptr) in wheat by eliminating race-specific susceptibility genes is a common breeding approach worldwide. The potential to exploit variation in quantitative forms of resistance, such as adult-plant resistance (APR), offers an alternative approach that could lead to broad-spectrum protection. We previously identified wheat landraces in the Vavilov diversity panel that exhibited high levels of APR despite carrying the sensitivity gene Tsn1. In this study, we characterised the genetic control of APR by developing a recombinant inbred line population fixed for Tsn1, but segregating for the APR trait. Linkage mapping using DArTseq markers and disease response phenotypes identified a QTL associated with APR to Ptr race 1 (producing Ptr ToxA- and Ptr ToxC) on chromosome 2B (Qts.313-2B), which was consistently detected in multiple adult-plant experiments. Additional loci were also detected on chromosomes 2A, 3D, 5A, 5D, 6A, 6B and 7A at the seedling stage, and on chromosomes 1A and 5B at the adult stage. We demonstrate that Qts.313-2B can be combined with other adult-plant QTL (i.e. Qts.313-1A and Qts.313-5B) to strengthen resistance levels. The APR QTL reported in this study provide a new genetic solution to tan spot in Australia and could be deployed in wheat cultivars, even in the presence of Tsn1, to decrease production losses and reduce the application of fungicides.

Fire Blight Susceptibility in Lilium spp. Correlates to Sensitivity to Botrytis elliptica Secreted Cell Death Inducing Compounds

Fire blight represents a widespread disease in Lilium spp. and is caused by the necrotrophic Ascomycete Botrytis elliptica. There are >100 Lilium species that fall into distinct phylogenetic groups and these have been used to generate the contemporary commercial genotypes. It is known among lily breeders and growers that different groups of lilies differ in susceptibility to fire blight, but the genetic basis and mechanisms of susceptibility to fire blight are unresolved. The aim of this study was to quantify differences in fire blight susceptibility between plant genotypes and differences in virulence between fungal isolates. To this end we inoculated, in four biological replicates over 2 years, a set of 12 B. elliptica isolates on a panel of 18 lily genotypes representing seven Lilium hybrid groups. A wide spectrum of variation in symptom severity was observed in different isolate-genotype combinations. There was a good correlation between the lesion diameters on leaves and flowers of the Lilium genotypes, although the flowers generally showed faster expanding lesions. It was earlier postulated that B. elliptica pathogenicity on lily is conferred by secreted proteins that induce programmed cell death in lily cells. We selected two aggressive isolates and one mild isolate and collected culture filtrate (CF) samples to compare the cell death inducing activity of their secreted compounds in lily. After leaf infiltration of the CFs, variation was observed in cell death responses between the diverse lilies. The severity of cell death responses upon infiltration of the fungal CF observed among the diverse Lilium hybrid groups correlated well to their fire blight susceptibility. These results support the hypothesis that susceptibility to fire blight in lily is mediated by their sensitivity to B. elliptica effector proteins in a quantitative manner. Cell death-inducing proteins may provide an attractive tool to predict fire blight susceptibility in lily breeding programs.

Genetic analysis of the barley variegation mutant, grandpa1.a

BACKGROUND

Providing the photosynthesis factory for plants, chloroplasts are critical for crop biomass and economic yield. However, chloroplast development is a complicated process, coordinated by the cross-communication between the nucleus and plastids, and the underlying biogenesis mechanism has not been fully revealed. Variegation mutants have provided ideal models to identify genes or factors involved in chloroplast development. Well-developed chloroplasts are present in the green tissue areas, while the white areas contain undifferentiated plastids that are deficient in chlorophyll. Unlike albino plants, variegation mutants survive to maturity and enable investigation into the signaling pathways underlying chloroplast biogenesis. The allelic variegated mutants in barley, grandpa 1 (gpa1), have long been identified but have not been genetically characterized.

RESULTS

We characterized and genetically analyzed the grandpa1.a (gpa1.a) mutant. The chloroplast ultrastructure was evaluated using transmission electron microscopy (TEM), and it was confirmed that chloroplast biogenesis was disrupted in the white sections of gpa1.a. To determine the precise position of Gpa1, a high-resolution genetic map was constructed. Segregating individuals were genotyped with the barley 50 k iSelect SNP Array, and the linked SNPs were converted to PCR-based markers for genetic mapping. The Gpa1 gene was mapped to chromosome 2H within a gene cluster functionally related to photosynthesis or chloroplast differentiation. In the variegated gpa1.a mutant, we identified a large deletion in this gene cluster that eliminates a putative plastid terminal oxidase (PTOX).

CONCLUSIONS

Here we characterized and genetically mapped the gpa1.a mutation causing a variegation phenotype in barley. The PTOX-encoding gene in the delimited region is a promising candidate for Gpa1. Therefore, the present study provides a foundation for the cloning of Gpa1, which will elevate our understanding of the molecular mechanisms underlying chloroplast biogenesis, particularly in monocot plants.

Pyrenophora tritici-repentis Race 4 Isolates Cause Disease on Tetraploid Wheat

The ascomycete fungus Pyrenophora tritici-repentis is the causal agent of tan spot of wheat. The disease can occur on both common wheat (Triticum aestivum) and durum wheat (T. turgidum ssp. durum) and has potential to cause significant yield and quality losses. The fungal pathogen is known to produce necrotrophic effectors (NEs) that act as important virulence factors. Based on the NE production and virulence on a set of four differentials, P. tritici-repentis isolates have been classified into eight races. Race 4 produces no known NEs and is avirulent on the differentials. From a fungal collection in North Dakota, we identified several isolates that were classified as race 4. These isolates caused no or little disease on all common wheat lines including the differentials; however, they were virulent on some durum cultivars and tetraploid wheat accessions. Using two segregating tetraploid wheat populations and quantitative trait locus mapping, we identified several genomic regions significantly associated with disease caused by two of these isolates, some of which have not been previously reported. This is the first report that race 4 is virulent on tetraploid wheat, likely utilizing unidentified NEs. Our findings further highlight the insufficiency of the current race classification system for P. tritici-repentis.

Genome-wide association mapping of tan spot resistance in a worldwide collection of durum wheat

Resistance to tan spot in durum wheat involves race-nonspecific QTL and necrotrophic insensitivity gene. Tan spot, caused by the necrotrophic fungus Pyrenophoratritici-repentis, is a major foliar disease on all cultivated wheat crops worldwide. Compared to common wheat, much less work has been done to investigate the genetic basis of tan spot resistance in durum. Here, we conducted disease evaluations, necrotrophic effector (NE) sensitivity assays and a genome-wide association study using a collection of durum accessions. The durum panel segregated for the reaction to disease inoculations and NE infiltrations with eighteen accessions being highly resistant to all races and most of them insensitive to both PtrToxA and PtrToxB. Over 65,000SNP markers were developed from genotyping-by-sequencing for the association mapping. As expected, sensitivity to PtrToxA and PtrToxB was mapped to the chromosome arms 5BL and 2BS, respectively. For the fungal inoculations, a quantitative trait locus (QTL) on chromosome 3B was associated with resistance to all races and likely corresponds to the race-nonspecific resistance QTL previously identified in common wheat. The Tsn1locus was not significantly associated with tan spot caused by the PtrToxA-producing isolates Pti2 and 86-124, but the Tsc2 locus was significantly associated with tan spot caused by the PtrToxB-producing isolate DW5. Another QTL on chromosome arm 1AS was associated with tan spot caused by the PtrToxC-producing isolate Pti2 and likely corresponds to the Tsc1 locus. Additional QTL for specific races was identified on chromosome 1B and 3B. Our work highlights the complexity of genetic resistance to tan spot and further confirms that the Ptr ToxA-Tsn1 interaction plays no significant role in disease development in tetraploid wheat.