Phenotypic and phylogenetic segregation of Alternaria infectoria from small-spored Alternaria species isolated from wheat in Germany and Russia

SRAP markers as an alternative tool for Alternaria classification

Alternaria is one of the main fungal contaminants of cereal grains worldwide with the potential to produce mycotoxins hazardous to human and animal health. Many studies have been carried out to characterize Alternaria sp.-grp. using traditional morphology or polyphasic approach, but a good correlation between morphological sp.-grp., molecular, and chemotaxonomic groups has not always been achieved. For this reason, this study aimed to investigate the usefulness of a cheaper alternative tool, SRAP markers, in identifying Alternaria sp.-grps. obtained from Argentinean barley grains and to compare it with preliminary characterization using morphological traits, phylogeny, and metabolite profiles. Fifty-three Alternaria isolates from barley grains of the main producing regions of Argentina were analyzed with four combinations of SRAP markers. The UPGMA dendrogram, based on the Simple Matching similarity coefficient, revealed three distinct groups. SRAP markers allowed the separation of Alternaria from Infectoriae sections in agreement with the results of a polyphasic approach previously made. Besides, isolates of A. arborescens sp.-grp. were clustered in a separate group from isolates of A. tenuissima and A. alternata sp.-grp., which were grouped in the same cluster. SRAP markers are a recommended tool for classifying Alternaria isolates because of its simplicity, reliability, and cost-effectiveness compared to other molecular markers.

Characterization of Alternaria alternata and Alternaria scrophulariae Brown Spot in Colombian quinoa (Chenopodium quinoa)

Alternaria is a saprophytic and opportunistic fungus with a worldwide distribution that can affect the quality of various agricultural products, such as fruits, cereals, and pseudocereals. This research was carried out to investigate the population of this genus associated with quinoa cultivation in plots located in the Boyacá department (Colombia), the country's third-largest quinoa-producing department. The present study found 17 Alternaria isolates, of which 13 were identified as A. alternata and 4 as A. scrophulariae (formerly A. conjuncta) employed molecular markers of internal transcribed spacer (ITS) region and translation elongation factor 1α (TEF-1α). In the pathogenicity test under greenhouse conditions, all the Alternaria isolates showed some degree of pathogenicity on Piartal quinoa cultivar plants although no significant differences were found in isolates. The severity indices ranged from 2 to 5, and the percentage of affected leaves per plant ranged between 15% and 40%. This fungus affected the foliar tissue of quinoa, resulting in chlorotic and necrotic spots, symptoms that can generate a reduction in the quality and productivity of crops. This is the first time that the pathogenicity of Alternaria spp. in the Piartal variety has been described and the first report of this genera in quinoa crops of Colombia.

Alternaria alternata, the Causal Agent of a New Needle Blight Disease on Pinus bungeana

Pinus bungeana, an endangered and native coniferous tree species in China, has considerable timber and horticulture value. However, little is known about needle diseases in P. bungeana. A needle blight of P. bungeana has been observed in Hebei Province, China. P. bungeana inoculated with mycelial plugs of fungal isolates presented symptoms similar to those observed under field conditions. Ten virulent fungal isolates were identified as a small-spored Alternaria species based on morphological observations. Maximum likelihood and Bayesian phylogenetic analyses carried out with multilocus sequence typing of eight regions (SSU, LSU, ITS, gapdh, tef1, Alt a 1, endoPG, OPA10-2) assigned the pathogen to Alternaria alternata. This is the first report of A. alternata causing needle blight on P. bungeana in China.

Alternaria species in section Alternaria associated with Iris plants in China

Plants of the Iris genus have been widely cultivated because of their medicinal, ornamental, and economic values. It commonly suffers from Alternaria leaf spot or blight disease leading to considerable losses for their commercial values. During an investigation of 14 provinces or municipalities of China from 2014 to 2022, a total of 122 Alternaria strains in section Alternaria were obtained from diseased leaves of Iris spp.. Among them, 12 representative strains were selected and identified based on morphological characterization and multi-locus phylogenetic analysis, which encompassed the internal transcribed spacer of rDNA region (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), translation elongation factor 1 alpha (TEF1), RNA polymerase second largest subunit (RPB2), Alternaria major allergen gene (Alt a 1), an anonymous gene region (OPA10-2), and endopolygalacturonase gene (EndoPG). The strains comprised two known species of A. alternata and A. iridicola, and two new species of A. setosae and A. tectorum, which were described and illustrated here. Their pathogenicity evaluated on Iris setosa indicated that all the strains could induce typical Alternaria leaf spot or blight symptoms. The results showed that the virulence was variable among those four species, from which A. tectorum sp. nov. was the most virulent one, followed by A. setosae sp. nov., A. iridicola and A. alternata.

Distinction of Alternaria Sect. Pseudoalternaria Strains among Other Alternaria Fungi from Cereals

Species of the genus Alternaria are ubiquitous and frequently isolated from various plants, including crops. There are two phylogenetically and morphologically close Alternaria sections: the relatively well-known Infectoriae and the rarely mentioned Pseudoalternaria. Currently, the latter includes at least seven species that are less studied and sometimes misidentified. To perform precise identification, two primers (APsF and APsR) were designed and a sect. Pseudoalternaria-specific PCR method was developed. Thirty-five Russian A. infectoria-like strains were then examined. Five strains were found to be the members of the sect. Pseudoalternaria. Additionally, specificity of the previously developed primer set (Ain3F and Ain4R) was checked. It was found to be highly specific for sect. Infectoriae and did not amplify sect. Pseudoalternaria DNA. Identification of strains of the sect. Pseudoalternaria was supported and refined by phylogenetic reconstruction based on analysis of two loci, the glyceraldehyde-3-phosphate dehydrogenase gene (gpd), and the plasma membrane ATPase gene (ATP). These fungi belonged to Alternaria kordkuyana and A. rosae, which were the first detection of those taxa for the Eastern Europe. Alternaria kordkuyana was isolated from cereal seeds and eleuthero leaves. Alternaria rosae was obtained from oat seed. All strains of sect. Pseudoalternaria were not able to produce alternariol mycotoxin, as well as the majority of A. sect. Infectoriae strains.

Quantifying the Role of Ground Beetles for the Dispersal of Fusarium and Alternaria Fungi in Agricultural Landscapes

The spread by arthropods (zoochory) is an essential dispersal mechanism for many microorganisms, like plant pathogens. Carabid beetles are very abundant and mobile ground-dwelling insects. However, their role in the dispersal of economically relevant phytopathogens, like Fusarium and Alternaria fungi is basically unknown. We quantified the total fungal, Fusarium, and Alternaria load of carabid species collected in the transition zones between small water bodies and wheat fields by screening (i) their body surface for fungal propagules with a culture-dependent method and (ii) their entire bodies for fungal DNA with a qPCR approach. The analysis of entire bodies detects fungal DNA in all carabid beetles but Alternaria DNA in 98% of them. We found that 74% of the carabids carried fungal propagules on the body surface, of which only half (49%) carried Fusarium propagules. We identified eight Fusarium and four Alternaria species on the body surface; F. culmorum was dominant. The fungal, Fusarium and Alternaria, load differed significantly between the carabid species and was positively affected by the body size and weight of the carabids. Carabid beetles reveal a remarkable potential to disseminate different fungi. Dispersal by ground-dwelling arthropods could affect the spatial-temporal patterns of plant disease and microorganisms in general.

Genome-wide association study in hexaploid wheat identifies novel genomic regions associated with resistance to root lesion nematode (Pratylenchus thornei)

Root lesion nematode (RLN; Pratylenchus thornei) causes extensive yield losses in wheat worldwide and thus pose serious threat to global food security. Reliance on fumigants (such as methyl bromide) and nematicides for crop protection has been discouraged due to environmental concerns. Hence, alternative environment friendly control measures like finding and deployment of resistance genes against Pratylenchus thornei are of significant importance. In the present study, genome-wide association study (GWAS) was performed using single-locus and multi-locus methods. In total, 143 wheat genotypes collected from pan-Indian wheat cultivation states were used for nematode screening. Genotypic data consisted of  > 7K SNPs with known genetic positions on the high-density consensus map was used for association analysis. Principal component analysis indicated the existence of sub-populations with no major structuring of populations due to the origin. Altogether, 25 significant marker trait associations were detected with - log10 (p value) > 4.0. Three large linkage disequilibrium blocks and the corresponding haplotypes were found to be associated with significant SNPs. In total, 37 candidate genes with nine genes having a putative role in disease resistance (F-box-like domain superfamily, Leucine-rich repeat, cysteine-containing subtype, Cytochrome P450 superfamily, Zinc finger C2H2-type, RING/FYVE/PHD-type, etc.) were identified. Genomic selection was conducted to investigate how well one could predict the phenotype of the nematode count without performing the screening experiments. Prediction value of r = 0.40 to 0.44 was observed when 56 to 70% of the population was used as a training set. This is the first report where GWAS has been conducted to find resistance against root lesion nematode (P. thornei) in Indian wheat germplasm.

Identification of Genetic Loci of Black Point in Chinese Common Wheat by Genome-Wide Association Study and Linkage Mapping

Black point is a common disease in wheat all over the world. The disease could downgrade wheat quality and cause human health problems. In this study, 406 wheat cultivars were used to investigate black point resistance. In the field tests, 20, 65.5, and 14.5% of the tested cultivars were resistant, moderately resistant, and susceptible, respectively, suggesting that improving black point resistance is necessary in Chinese wheat breeding. A genome-wide association study (GWAS) identified 386 single-nucleotide polymorphisms (SNPs) significantly related to black point resistance in the tested wheat cultivars, and they were located on all chromosomes. Linkage mapping in a biparental population identified three quantitative trait loci (QTL) for black point resistance-QBP.hau-3A, QBP.hau-6D, and QBP.hau-7D-with 6.76, 7.79, and 8.84% phenotypic variation explained, respectively. Based on both the GWAS and linkage analyses, QBP.hau-6D covered six significant SNPs from the GWAS, and the position of these SNPs indicated that this QTL is a new locus for black point resistance. This study provides valuable germplasm for breeding wheat cultivars with resistance to black point and information for further understanding of molecular and genetic basis of black point resistance.

Molecular Identification and Mycotoxin Production by Alternaria Species Occurring on Durum Wheat, Showing Black Point Symptoms

Black point is a fungal disease of wheat, mainly associated with mycotoxigenic Alternaria species. Affected wheat kernels are characterized by dark brown discolouration of the embryo region and reduction of grain quality. Potential risk is the possible accumulation of Alternaria mycotoxins, alternariol (AOH), alternariol-monomethyl ether (AME), tenuazonic acid (TA), and altenuene (ALT), provided by haemato-toxic, genotoxic, and mutagenic activities. One hundred and twenty durum wheat samples belonging to 30 different genotypes grown in Bologna and Modena areas, in Italy, showing black point symptoms, were analyzed for Alternaria species and their mycotoxin contamination. Alternariol was selected as an indicator of the capability of the Alternaria species to produce mycotoxin in vivo in field conditions. The data showed that Alternaria species occurred in 118 out of 120 wheat kernels samples, with the incidence of infected kernels ranging between 1% and 26%. Moreover, AOH was detected by using a HPLC with a diode array detector (LC-DAD) in 98 out of 120 samples with values ranging between 24 and 262 µg Kg⁻¹. Ninety-two Alternaria representative strains, previously identified morphologically, were identified at species/section level using gene sequencing, and therefore were analyzed for their mycotoxin profiles. Eighty-four strains, phylogenetically grouped in the Alternaria section, produced AOH, AME, and TA with values up to 8064, 14,341, and 3683 µg g⁻¹, respectively, analyzed by using a LC-DAD. On the other hand, eight Alternaria strains, included in Infectoriae Section, showed a very low or no capability to produce mycotoxins.

Pseudomonas simiae effects on the mycotoxin formation by fusaria and alternaria in vitro and in a wheat field

Fluorescent pseudomonads colonizing wheat ears have a high antagonistic potential against phytopathogenic fungi. To check this hypothesis, the bacterial antagonist Pseudomonas simiae 9 ^rif+/kan+ was spray-inoculated onto the ears of winter wheat in a locally demarcated experimental field plot. Fusarium and Alternaria fungi naturally occurring on the ears and the formation of their mycotoxins in the ripe grains were investigated. Inoculated bacteria were recovered from the plants in the inoculation cell, but not in the untreated neighboring plots or in the air above the plants. Growth of fusaria and alternaria on the ears was not influenced by the bacterial antagonist. Wheat kernels were co-inoculated in vitro with the antagonist and one mycotoxin-producing strain of Fusarium and Alternaria, respectively. Mycotoxin production was almost completely suppressed in these approaches. Concentrations of zearalenone, deoxynivalenol, alternariol, and tenuazonic acid were also significantly reduced in ripe grains in the field, but to a lesser extent than in vitro. The results of this and previous studies suggest that widespread biological control of the growth of fusaria and alternaria and their mycotoxin formation by naturally occurring pseudomonads with antagonistic activity is rather unlikely.

Phylogeny and Mycotoxin Characterization of Alternaria Species Isolated from Wheat Grown in Tuscany, Italy

Wheat, the main source of carbohydrates worldwide, can be attacked by a wide number of phytopathogenic fungi, included Alternaria species. Alternaria species commonly occur on wheat worldwide and produce several mycotoxins such as tenuazonic acid (TA), alternariol (AOH), alternariol-monomethyl ether (AME), and altenuene (ALT), provided of haemato-toxic, genotoxic, and mutagenic activities. The contamination by Alternaria species of wheat kernels, collected in Tuscany, Italy, from 2013 to 2016, was evaluated. Alternaria contamination was detected in 93 out of 100 field samples, with values ranging between 1 and 73% (mean of 18%). Selected strains were genetically characterized by multi-locus gene sequencing approach through combined sequences of allergen alt1a, glyceraldeyde-3-phosphate dehydrogenase, and translation elongation factor 1α genes. Two well defined groups were generated; namely sections Alternaria and Infectoriae. Representative strains were analyzed for mycotoxin production. A different mycotoxin profile between the sections was shown. Of the 54 strains analyzed for mycotoxins, all strains included in Section Alternaria produced AOH and AME, 40 strains (99%) produced TA, and 26 strains (63%) produced ALT. On the other hand, only a very low capability to produce both AOH and AME was recorded among the Section Infectoriae strains. These data show that a potential mycotoxin risk related to the consumption of Alternaria contaminated wheat is high.

The distribution of mycotoxins in a heterogeneous wheat field in relation to microclimate, fungal and bacterial abundance

AIM

To observe the variation in accumulation of Fusarium and Alternaria mycotoxins across a topographically heterogeneous field and tested biotic (fungal and bacterial abundance) and abiotic (microclimate) parameters as explanatory variables.

METHODS AND RESULTS

We selected a wheat field characterized by a diversified topography, to be responsible for variations in productivity and in canopy-driven microclimate. Fusarium and Alternaria mycotoxins where quantified in wheat ears at three sampling dates between flowering and harvest at 40 points. Tenuazonic acid (TeA), alternariol (AOH), alternariol monomethyl ether (AME), tentoxin (TEN), deoxynivalenol (DON), zearalenone (ZEN) and deoxynivalenol-3-Glucoside (DON.3G) were quantified. In canopy temperature, air and soil humidity were recorded for each point with data-loggers. Fusarium spp. as trichothecene producers, Alternaria spp. and fungal abundances were assessed using qPCR. Pseudomonas fluorescens bacteria were quantified with a culture based method. We only found DON, DON.3G, TeA and TEN to be ubiquitous across the whole field, while AME, AOH and ZEN were only occasionally detected. Fusarium was more abundant in spots with high soil humidity, while Alternaria in warmer and drier spots. Mycotoxins correlated differently to the observed explanatory variables: positive correlations between DON accumulation, tri 5 gene and Fusarium abundance were clearly detected. The correlations among the others observed variables, such as microclimatic conditions, varied among the sampling dates. The results of statistical model identification do not exclude that species coexistence could influence mycotoxin production.

CONCLUSIONS

Fusarium and Alternaria mycotoxins accumulation varies heavily across the field and the sampling dates, providing the realism of landscape-scale studies. Mycotoxin concentrations appear to be partially explained by biotic and abiotic variables.

SIGNIFICANCE AND IMPACT OF THE STUDY

We provide a useful experimental design and useful data for understanding the dynamics of mycotoxin biosynthesis in wheat.

Antagonistic Potential of Fluorescent Pseudomonads Colonizing Wheat Heads Against Mycotoxin Producing Alternaria and Fusaria

Natural control of phytopathogenic microorganisms is assumed as a priority function of the commensal plant microbiota. In this study, the suitability of fluorescent pseudomonads in the phyllosphere of crop plants as natural control agents was evaluated. Under field conditions, ears of winter wheat were found to be colonized with high consistency and at a high density by pseudomonads at the late milk dough stage. Isolates of these bacteria were evaluated for their potential to protect the plants from phytopathogenic Alternaria and Fusarium fungi. More Pseudomonas isolates were antagonistically active against alternaria than against fusaria in the dual culture test. The alternaria responded species-specifically and more sensitively to bacterial antagonism than the strain-specific reacting fusaria. A total of 110 randomly selected Pseudomonas isolates were screened for genes involved in the biosynthesis of the antibiotics 2,4-diacetylphloroglucinol, phenazine-1-carboxylic acid, pyoluteorin, and pyrrolnitrin. The key gene for production of the phloroglucinol was found in none of these isolates. At least one of the genes, encoding the biosynthesis of the other antibiotics was detected in 81% of the isolates tested. However, the antagonistic effect found in the dual culture assay was not necessarily associated with the presence of these antibiotic genes. Wheat grains as natural substrate were inoculated with selected antagonistic Pseudomonas isolates and Alternaria and Fusarium strains, respectively. The fungal growth was only slightly delayed, but the mycotoxin production was significantly reduced in most of these approaches. In conclusion, the distribution of phytopathogenic fungi of the genera Alternaria and Fusarium in the field is unlikely to be inhibited by naturally occurring pseudomonads, also because the bacterial antagonists were not evenly distributed in the field. However, pseudomonads can reduce the production of Alternaria and Fusarium mycotoxins in wheat grains and thus have the potential to improve the crop quality.

Chemotaxonomy of Mycotoxigenic Small-Spored Alternaria Fungi - Do Multitoxin Mixtures Act as an Indicator for Species Differentiation?

Necrotrophic as well as saprophytic small-spored Alternaria (A.) species are annually responsible for major losses of agricultural products, such as cereal crops, associated with the contamination of food and feedstuff with potential health-endangering Alternaria toxins. Knowledge of the metabolic capabilities of different species-groups to form mycotoxins is of importance for a reliable risk assessment. 93 Alternaria strains belonging to the four species groups Alternaria tenuissima, A. arborescens, A. alternata, and A. infectoria were isolated from winter wheat kernels harvested from fields in Germany and Russia and incubated under equal conditions. Chemical analysis by means of an HPLC-MS/MS multi-Alternaria-toxin-method showed that 95% of all strains were able to form at least one of the targeted 17 non-host specific Alternaria toxins. Simultaneous production of up to 15 (modified) Alternaria toxins by members of the A. tenuissima, A. arborescens, A. alternata species-groups and up to seven toxins by A. infectoria strains was demonstrated. Overall tenuazonic acid was the most extensively formed mycotoxin followed by alternariol and alternariol mono methylether, whereas altertoxin I was the most frequently detected toxin. Sulfoconjugated modifications of alternariol, alternariol mono methylether, altenuisol and altenuene were frequently determined. Unknown perylene quinone derivatives were additionally detected. Strains of the species-group A. infectoria could be segregated from strains of the other three species-groups due to significantly lower toxin levels and the specific production of infectopyrone. Apart from infectopyrone, alterperylenol was also frequently produced by 95% of the A. infectoria strains. Neither by the concentration nor by the composition of the targeted Alternaria toxins a differentiation between the species-groups A. alternata, A. tenuissima and A. arborescens was possible.

Alternaria and Fusarium Fungi: Differences in Distribution and Spore Deposition in a Topographically Heterogeneous Wheat Field

Fusarium spp. and Alternaria spp., two genera of filamentous fungi, are common colonizers of the wheat phyllosphere. Both can be pathogenic and produce mycotoxins that are harmful to consumers. Their in-field infection dynamics have been a focus for the development of new control strategies. We analysed the abundance on plant ears and spore deposition patterns of Fusarium spp. and Alternaria spp. in a topographically heterogeneous field. Abundances were assessed genetically, using qPCR-based techniques, and passive spore traps were installed for quantifying the spore deposition at different plant heights. Data loggers were placed to measure the differences in microclimate across the field. Results indicate different distribution and spore deposition patterns for the two fungi. Fusarium spp. spore and genetic abundances were higher in spots with a more humid and colder under-canopy microclimate. Alternaria spp. showed the opposite trend for genetic abundance, while its spore deposition was not correlated to any of the microclimatic conditions and was more uniform across the field. Our study extends the knowledge on the dispersal and in-field infection dynamics of Fusarium spp. and Alternaria spp., important for a better understanding of the epidemiology of these wheat pathogens. It also illustrates that topographically heterogeneous fields are a suitable environment for studying the ecology of phyllosphere-colonizing fungi.

Genome-wide association mapping of black point reaction in common wheat (Triticum aestivum L.)

BACKGROUND

Black point is a serious threat to wheat production and can be managed by host resistance. Marker-assisted selection (MAS) has the potential to accelerate genetic improvement of black point resistance in wheat breeding. We performed a genome-wide association study (GWAS) using the high-density wheat 90 K and 660 K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of black point resistance and identify associated molecular markers.

RESULTS

Black point reactions were evaluated in 166 elite wheat cultivars in five environments. Twenty-five unique loci were identified on chromosomes 2A, 2B, 3A, 3B (2), 3D, 4B (2), 5A (3), 5B (3), 6A, 6B, 6D, 7A (5), 7B and 7D (2), respectively, explaining phenotypic variation ranging from 7.9 to 18.0%. The highest number of loci was detected in the A genome (11), followed by the B (10) and D (4) genomes. Among these, 13 were identified in two or more environments. Seven loci coincided with known genes or quantitative trait locus (QTL), whereas the other 18 were potentially novel loci. Linear regression showed a clear dependence of black point scores on the number of favorable alleles, suggesting that QTL pyramiding will be an effective approach to increase resistance. In silico analysis of sequences of resistance-associated SNPs identified 6 genes possibly involved in oxidase, signal transduction and stress resistance as candidate genes involved in black point reaction.

CONCLUSION

SNP markers significantly associated with black point resistance and accessions with a larger number of resistance alleles can be used to further enhance black point resistance in breeding. This study provides new insights into the genetic architecture of black point reaction.

Spotlight on the Underdogs-An Analysis of Underrepresented Alternaria Mycotoxins Formed Depending on Varying Substrate, Time and Temperature Conditions

Alternaria (A.) is a genus of widespread fungi capable of producing numerous, possibly health-endangering Alternaria toxins (ATs), which are usually not the focus of attention. The formation of ATs depends on the species and complex interactions of various environmental factors and is not fully understood. In this study the influence of temperature (7 °C, 25 °C), substrate (rice, wheat kernels) and incubation time (4, 7, and 14 days) on the production of thirteen ATs and three sulfoconjugated ATs by three different Alternaria isolates from the species groups A. tenuissima and A. infectoria was determined. High-performance liquid chromatography coupled with tandem mass spectrometry was used for quantification. Under nearly all conditions, tenuazonic acid was the most extensively produced toxin. At 25 °C and with increasing incubation time all toxins were formed in high amounts by the two A. tenuissima strains on both substrates with comparable mycotoxin profiles. However, for some of the toxins, stagnation or a decrease in production was observed from day 7 to 14. As opposed to the A. tenuissima strains, the A. infectoria strain only produced low amounts of ATs, but high concentrations of stemphyltoxin III. The results provide an essential insight into the quantitative in vitro AT formation under different environmental conditions, potentially transferable to different field and storage conditions.

Genome-wide linkage mapping of QTL for black point reaction in bread wheat (Triticum aestivum L.)

Nine QTL for black point resistance in wheat were identified using a RIL population derived from a Linmai 2/Zhong 892 cross and 90K SNP assay. Black point, discoloration of the embryo end of the grain, downgrades wheat grain quality leading to significant economic losses to the wheat industry. The availability of molecular markers will accelerate improvement of black point resistance in wheat breeding. The aims of this study were to identify quantitative trait loci (QTL) for black point resistance and tightly linked molecular markers, and to search for candidate genes using a high-density genetic linkage map of wheat. A recombinant inbred line (RIL) population derived from the cross Linmai 2/Zhong 892 was evaluated for black point reaction during the 2011-2012, 2012-2013 and 2013-2014 cropping seasons, providing data for seven environments. A high-density linkage map was constructed by genotyping the RILs with the wheat 90K single nucleotide polymorphism (SNP) chip. Composite interval mapping detected nine QTL on chromosomes 2AL, 2BL, 3AL, 3BL, 5AS, 6A, 7AL (2) and 7BS, designated as QBp.caas-2AL, QBp.caas-2BL, QBp.caas-3AL, QBp.caas-3BL, QBp.caas-5AS, QBp.caas-6A, QBp.caas-7AL.1, QBp.caas-7AL.2 and QBp.caas-7BS, respectively. All resistance alleles, except for QBp.caas-7AL.1 from Linmai 2, were contributed by Zhong 892. QBp.caas-3BL, QBp.caas-5AS, QBp.caas-7AL.1, QBp.caas-7AL.2 and QBp.caas-7BS probably represent new loci for black point resistance. Sequences of tightly linked SNPs were used to survey wheat and related cereal genomes identifying three candidate genes for black point resistance. The tightly linked SNP markers can be used in marker-assisted breeding in combination with the kompetitive allele specific PCR technique to improve black point resistance.