Trichothecenes are sesquiterpenoid mycotoxins produced by fungi from the order Hypocreales, including members of the Fusarium genus that infect cereal grain crops. Different trichothecene-producing Fusarium species and strains have different trichothecene chemotypes belonging to the Type A and B class. These fungi cause a disease of small grain cereals, called Fusarium head blight, and their toxins contaminate host tissues. As potent inhibitors of eukaryotic protein synthesis, trichothecenes pose a health risk to human and animal consumers of infected cereal grains. In 2009, Foroud and Eudes published a review of trichothecenes in cereal grains for human consumption. As an update to this review, the work herein provides a comprehensive and multi-disciplinary review of the Fusarium trichothecenes covering topics in chemistry and biochemistry, pathogen biology, trichothecene toxicity, molecular mechanisms of resistance or detoxification, genetics of resistance and breeding strategies to reduce their contamination of wheat and barley.

Triticale (X Triticosecale Wittm.) is a hybrid derived by crossing wheat (Triticum sp.) and rye (Secale sp.). Till date, only a limited number of simple sequence repeat (SSRs) markers have been used in triticale molecular analyses and there is a need to identify dedicated high-throughput molecular markers to better exploit this crop. The objective of this study was to develop and evaluate diversity arrays technology (DArT) markers in triticale. DArT marker technology offers a high level of multiplexing. Development of new markers from triticale accessions was combined with mining the large collection of previously developed markers in rye and wheat. Three genotyping arrays were used to analyze a collection of 144 triticale accessions. The polymorphism level ranged from 8.6 to 23.8% for wheat and rye DArT markers, respectively. Among the polymorphic markers, rye markers were the most abundant (3,109) followed by wheat (2,214) and triticale (719). The mean polymorphism information content values were 0.34 for rye DArT markers and 0.37 for those from triticale and wheat. High correlation was observed between similarity matrices derived from rye, triticale, wheat and combined marker sets, as well as for the cophenetic values matrices. Cluster analysis revealed genetic relationships among the accessions consistent with the agronomic and pedigree information available. The newly developed triticale DArT markers as well as those originated from rye and wheat provide high quality markers that can be used for diversity analyses and might be exploited in a range of molecular breeding and genomics applications in triticale.

Waterlogging is a major abiotic stress causing oxygen depletion and carbon dioxide accumulation in the rhizosphere. Barley is more susceptible to waterlogging stress than other cereals. To gain a better understanding, the genome-wide gene expression responses in roots of waterlogged barley seedlings of Yerong and Deder2 were analyzed by RNA-Sequencing. A total of 6736, 5482, and 4538 differentially expressed genes (DEGs) were identified in waterlogged roots of Yerong at 72 h and Deder2 at 72 and 120 h, respectively, compared with the non-waterlogged control. Gene Ontology (GO) enrichment analyses showed that the most significant changes in GO terms, resulted from these DEGs observed under waterlogging stress, were related to primary and secondary metabolism, regulation, and oxygen carrier activity. In addition, more than 297 transcription factors, including members of MYB, AP2/EREBP, NAC, WRKY, bHLH, bZIP, and G2-like families, were identified as waterlogging responsive. Tentative important contributors to waterlogging tolerance in Deder2 might be the highest up-regulated DEGs: Trichome birefringence, α/β-Hydrolases, Xylanase inhibitor, MATE efflux, serine carboxypeptidase, and SAUR-like auxin-responsive protein. The study provides insights into the molecular mechanisms underlying the response to waterlogging in barley, which will be of benefit for future studies of molecular responses to waterlogging and will greatly assist barley genetic research and breeding.

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Foroud, N.

Fusarium head blight (FHB) caused byFusarium species, is among the most devastating wheat diseases, causing losses in numerous sectors of the grain industry through yield and quality reduction, and the accumulation of poisonous mycotoxins. A germplasm collection of spring and winter wheat, including nine reference cultivars, was tested for Type II FHB resistance and deoxynivalenol (DON) content. Genetic diversity was evaluated on the basis of Simple Sequence Repeat (SSR) markers linked to FHB resistance quantitative trait loci (QTLs) and Diversity Arrays Technology (DArT) markers. The allele size of the SSR markers linked to FHB resistance QTLs from known resistance sources was compared to a germplasm collection to determine the presence of these QTLs and to identify potentially novel sources of resistance. Forty-two accessions were identified as resistant or moderately resistant to Fusarium spread, and two also had very low DON concentrations. Genetic relationships among wheat accessions were generally consistent with their geographic distribution and pedigree. SSR analysis revealed that several resistant accessions carried up to four of the tested QTLs. Resistant and moderately resistant lines without any known QTLs are considered to be novel sources of resistance that could be used for further genetic studies.

Fusarium head blight (FHB) incited by Fusarium graminearum Schwabe is a devastating disease of barley and other cereal crops worldwide. Fusarium head blight is associated with trichothecene mycotoxins such as deoxynivalenol (DON), which contaminates grains, making them unfit for malting or animal feed industries. While genetically resistant cultivars offer the best economic and environmentally responsible means to mitigate disease, parent lines with adequate resistance are limited in barley. Resistance breeding based upon quantitative genetic gains has been slow to date, due to intensive labor requirements of disease nurseries. The production of a high-throughput genome-wide molecular marker assembly for barley permits use in development of genomic prediction models for traits of economic importance to this crop. A diverse panel consisting of 400 two-row spring barley lines was assembled to focus on Canadian barley breeding programs. The panel was evaluated for FHB and DON content in three environments and over 2 years. Moreover, it was genotyped using an Illumina Infinium High-Throughput Screening (HTS) iSelect custom beadchip array of single nucleotide polymorphic molecular markers (50 K SNP), where over 23 K molecular markers were polymorphic. Genomic prediction has been demonstrated to successfully reduce FHB and DON content in cereals using various statistical models. Herein, we have studied an alternative method based on machine learning and compare it with a statistical approach. The bi-allelic SNPs represented pairs of alleles and were encoded in two ways: as categorical (–1, 0, 1) or using Hardy-Weinberg probability frequencies. This was followed by selecting essential genomic markers for phenotype prediction. Subsequently, a Transformer-based deep learning algorithm was applied to predict FHB and DON. Apart from the Transformer method, a Residual Fully Connected Neural Network (RFCNN) was also applied. Pearson correlation coefficients were calculated to compare true vs. predicted outputs. Models which included all markers generally showed marginal improvement in prediction. Hardy-Weinberg encoding generally improved correlation for FHB (6.9%) and DON (9.6%) for the Transformer network. This study suggests the potential of the Transformer based method as an alternative to the popular BLUP model for genomic prediction of complex traits such as FHB or DON, having performed equally or better than existing machine learning and statistical methods.

Barley (Hordeum vulgare L.) is a multipurpose crop that can be harvested as grain or cut prior to maturity for use as forage. Fusarium head blight (FHB) is a devastating disease of barley that reduces quality of grain. FHB can also result in the accumulation of mycotoxins such as deoxynivalenol (DON). Breeding FHB resistant varieties has been a long-term goal of many barley-producing countries, including Canada. While the genetic basis of DON detoxification via production of less-phytotoxic conjugates such as DON-3-glucoside (DON3G) is well documented in barley, little information exists in reference to varietal response. Over two years, 16 spring, two-row barley genotypes, of importance to western Canadian barley breeding programs, were grown as short-rows and inoculated following spike emergence with a Fusarium graminearum conidia suspension. Half of the plots were harvested at soft dough stage and then dissected into rachis and grain components, whereas the remainder was harvested at maturity. Multiple Fusarium-mycotoxins were assayed using liquid chromatography-mass spectrometry. Mycotoxin content was elevated at the earlier harvest point, especially in the rachis tissue. DON3G constituted a significant percentage (26%) of total trichothecene content and thus its co-occurrence with DON should be considered by barley industries. DON3G was highly correlated with DON and 3-acetyl-deoxynivalenol (3ADON). The ratio of D3G/DON exhibited consistency across genotypes, however more-resistant genotypes were characterized by a higher ratio at the soft-dough stage followed by a decrease at maturity. Plant breeding practices that use DON content as a biomarker for resistance would likely result in the development of barley cultivars with lower total DON-like compounds.