Identification of a UDP-glucosyltransferase conferring deoxynivalenol resistance in Aegilops tauschii and wheat.

Aegilops tauschii is the diploid progenitor of the wheat D subgenome and a valuable resource for wheat breeding, yet, genetic analysis of resistance against Fusarium head blight (FHB) and the major Fusarium mycotoxin deoxynivalenol (DON) is lacking. We treated a panel of 147 Ae. tauschii accessions with either Fusarium graminearum spores or DON solution and recorded the associated disease spread or toxin-induced bleaching. A k-mer-based association mapping pipeline dissected the genetic basis of resistance and identified candidate genes. After DON infiltration nine accessions revealed severe bleaching symptoms concomitant with lower conversion rates of DON into the non-toxic DON-3-O-glucoside. We identified the gene AET5Gv20385300 on chromosome 5D encoding a uridine diphosphate (UDP)-glucosyltransferase (UGT) as the causal variant and the mutant allele resulting in a truncated protein was only found in the nine susceptible accessions. This UGT is also polymorphic in hexaploid wheat and when expressed in Saccharomyces cerevisiae only the full-length gene conferred resistance against DON. Analysing the D subgenome helped to elucidate the genetic control of FHB resistance and identified a UGT involved in DON detoxification in Ae. tauschii and hexaploid wheat. This resistance mechanism is highly conserved since the UGT is orthologous to the barley UGT HvUGT13248 indicating descent from a common ancestor of wheat and barley.

Two major quantitative trait loci control wheat dwarf virus resistance in four related winter wheat populations.

KEY MESSAGE: Qwdv.ifa-6A on chromosomes 6AL and Qwdv.ifa-1B on chromosome 1B are highly effective against wheat dwarf virus and act additively when combined. Wheat dwarf virus (WDV) is among the most damaging viral pathogens. Its prevalence has increased substantially in recent years, and it is predicted to increase even further due to global warming. There are limited options to control the virus. Growing resistant cultivars would safeguard crops, but most current wheat cultivars are highly susceptible. Thus, the aim of this study was to dissect the genetic architecture of WDV resistance in resistant germplasm and to identify quantitative trait loci (QTL) to support resistance breeding. QTL mapping was conducted using four related populations comprising 168, 105, 99 and 130 recombinant inbred lines. Populations were evaluated under field conditions for three years. Natural infestation was provoked by early autumn sowing. WDV symptom severity was visually assessed at two time points in spring. QTL analysis revealed two highly significant QTL with the major QTL Qwdv.ifa-6A mapping to the long arm of chromosome 6A between markers Tdurum_contig75700_411 (601,412,152 bp) and AX-95197581 (605,868,853 bp). Qwdv.ifa-6A descends from the Dutch experimental line SVP-72017 and was of high effect in all populations, explaining up to 73.9% of the phenotypic variance. The second QTL, Qwdv.ifa-1B, mapped to chromosome 1B and is putatively associated with the 1RS.1BL translocation, which was contributed by the CIMMYT line CM-82036. Qwdv.ifa-1B explained up to 15.8% of the phenotypic variance. Qwdv.ifa-6A and Qwdv.ifa-1B are among the first identified highly effective resistance QTL and represent valuable resources for improving WDV resistance in wheat.

Wheat (Triticum aestivum) chromosome 6D harbours the broad spectrum common bunt resistance gene Bt11.

KEY MESSAGE: A major QTL on chromosome 6DL corresponding to bunt resistance gene Bt11 was identified in four mapping populations generated through crosses with Bt11-carriers PI 166910 and M822123. Common bunt in wheat has witnessed a renaissance with the rise of organic agriculture that began in the 1980s. The abandonment of systemic fungicides in organic farming, together with a lack of resistant cultivars, has led to wide-spread problems due to common bunt infections. Knowledge about genetic sources for resistance is still scarce and only few of the known bunt resistance factors are currently used in breeding. We therefore aimed to map the resistance factor harboured by the Turkish landrace PI 166910, which is the resistance donor for the Bt11 bunt differential line. Four mapping populations (MPs) with 96-132 recombinant inbred lines (RILs) were phenotyped for common bunt resistance over 2, 3 or 4 years with one or two local bunt populations and genotyped with the 25K SNP array. A major bunt resistance locus on the distal end of chromosome 6D designated QBt.ifa-6DL was identified in all MPs and experiments. Additional QTL contributing to resistance were detected on chromosomes 4B, 1A, 1B, 2A and 7B. QBt.ifa-6DL mapped to a region overlapping with the Bt9-locus identified in previous studies, but results indicate that QBt.ifa-6DL is different from Bt9 and convincing evidence from haplotype comparisons suggests that it represents the Bt11 resistance allele. Markers for the distal region of chromosome 6D between 492.6 and 495.2 Mbp can be used to select for QBt.ifa-6DL. This resistance factor confers high and stable resistance against common bunt and should be integrated into organic and low-input wheat breeding programs.

Comparison of linear and semi-parametric models incorporating genomic, pedigree, and associated loci information for the prediction of resistance to stripe rust in an Austrian winter wheat breeding program.

KEY MESSAGE: We used a historical dataset on stripe rust resistance across 11 years in an Austrian winter wheat breeding program to evaluate genomic and pedigree-based linear and semi-parametric prediction methods. Stripe rust (yellow rust) is an economically important foliar disease of wheat (Triticum aestivum L.) caused by the fungus Puccinia striiformis f. sp. tritici. Resistance to stripe rust is controlled by both qualitative (R-genes) and quantitative (small- to medium-effect quantitative trait loci, QTL) mechanisms. Genomic and pedigree-based prediction methods can accelerate selection for quantitative traits such as stripe rust resistance. Here we tested linear and semi-parametric models incorporating genomic, pedigree, and QTL information for cross-validated, forward, and pairwise prediction of adult plant resistance to stripe rust across 11 years (2008-2018) in an Austrian winter wheat breeding program. Semi-parametric genomic modeling had the greatest predictive ability and genetic variance overall, but differences between models were small. Including QTL as covariates improved predictive ability in some years where highly significant QTL had been detected via genome-wide association analysis. Predictive ability was moderate within years (cross-validated) but poor in cross-year frameworks.

Predictor bias in genomic and phenomic selection.

KEY MESSAGE: NIRS of wheat grains as phenomic predictors for grain yield show inflated prediction ability and are biased toward grain protein content. Estimating the breeding value of individuals using genome-wide marker data (genomic prediction) is currently one of the most important drivers of breeding progress in major crops. Recently, phenomic technologies, including remote sensing and aerial hyperspectral imaging of plant canopies, have made it feasible to predict the breeding value of individuals in the absence of genetic marker data. This is commonly referred to as phenomic prediction. Hyperspectral measurements in the form of near-infrared spectroscopy have been used since the 1980 s to predict compositional parameters of harvest products. Moreover, in recent studies NIRS from grains was used to predict grain yield. The same studies showed that phenomic prediction can outperform genomic prediction for grain yield. The genome is static and not environment dependent, thereby limiting genomic prediction ability. Gene expression is tissue specific and differs under environmental influences, leading to a tissue- and environment-specific phenome, potentially explaining the higher predictive ability of phenomic prediction. Here, we compare genomic prediction and phenomic prediction from hyperspectral measurements of wheat grains for the prediction of a variety of traits including grain yield. We show that phenomic predictions outperform genomic prediction for some traits. However, phenomic predictions are biased toward the information present in the predictor. Future studies on this topic should investigate whether population parameters are retained in phenomic prediction as they are in genomic prediction. Furthermore, we find that unbiased phenomic prediction abilities are considerably lower than previously reported and recommend a method to circumvent this issue.

A major yellow rust resistance QTL on chromosome 6A shows increased frequency in recent Norwegian spring wheat cultivars and breeding lines.

KEY MESSAGE: A major yellow rust resistance QTL, QYr.nmbu.6A, contributed consistent adult plant resistance in field trials across Europe, China, Kenya and Mexico. Puccinia striiformis f. sp. tritici, causing wheat yellow rust (YR), is one of the most devastating biotrophic pathogens affecting global wheat yields. Owing to the recent epidemic of the PstS10 race group in Europe, yellow rust has become a reoccurring disease in Norway since 2014. As all stage resistances (ASR) (or seedling resistances) are usually easily overcome by pathogen evolution, deployment of durable adult plant resistance (APR) is crucial for yellow rust resistance breeding. In this study, we assessed a Nordic spring wheat association mapping panel (n = 301) for yellow rust field resistance in seventeen field trials from 2015 to 2021, including nine locations in six countries across four different continents. Nine consistent QTL were identified across continents by genome-wide association studies (GWAS). One robust QTL on the long arm of chromosome 6A, QYr.nmbu.6A, was consistently detected in nine out of the seventeen trials. Haplotype analysis of QYr.nmbu.6A confirmed significant QTL effects in all tested environments and the effect was also validated using an independent panel of new Norwegian breeding lines. Increased frequency of the resistant haplotype was found in new varieties and breeding lines in comparison to older varieties and landraces, implying that the resistance might have been selected for due to the recent changes in the yellow rust pathogen population in Europe.

Pyramiding Fusarium head blight resistance QTL from T. aestivum, T. dicoccum and T. dicoccoides in durum wheat.

KEY MESSAGE: FHB resistance of durum wheat was improved by introgression of Fhb1 and resistance genes from emmer wheat and by selection against adverse alleles of elite durum wheat. Durum wheat is particularly susceptible to Fusarium head blight (FHB) and breeding for resistance is impeded by the low genetic variation within the elite gene pool. To extend the genetic basis for FHB resistance in durum wheat, we analyzed 603 durum wheat lines from crosses of elite durum wheat with resistance donors carrying resistance alleles derived from Triticum aestivum, T. dicoccum and T. dicoccoides. The lines were phenotyped for FHB resistance, anthesis date, and plant height in artificially inoculated disease nurseries over 5 years. A broad variation was found for all traits, while anthesis date and plant height strongly influenced FHB severities. To correct for spurious associations, we adjusted FHB scorings for temperature fluctuations during the anthesis period and included plant height as a covariate in the analysis. This resulted in the detection of seven quantitative trait loci (QTL) affecting FHB severities. The hexaploid wheat-derived Fhb1 QTL was most significant on reducing FHB severities, highlighting its successful introgression into several durum wheat backgrounds. For two QTL on chromosomes 1B and 2B, the resistance alleles originated from the T. dicoccum line Td161 and T. dicoccoides accessions Mt. Hermon#22 and Mt. Gerizim#36, respectively. The other four QTL featured unfavorable alleles derived from elite durum wheat that increased FHB severities, with a particularly negative effect on chromosome 6A that simultaneously affected plant height and anthesis date. Therefore, in addition to pyramiding resistance genes, selecting against adverse alleles present in elite durum wheat could be a promising avenue in breeding FHB-resistant durum wheat.

The effect of the Rht1 haplotype on Fusarium head blight resistance in relation to type and level of background resistance and in combination with Fhb1 and Qfhs.ifa-5A.

KEY MESSAGE: The effect of the Rht1-genes on FHB resistance depends on anther extrusion and level of background resistance. Qfhs.ifa-5A increases resistance and anther extrusion as efficiently as semi-dwarfing alleles decrease it. The semi-dwarfing reduced height alleles Rht-D1b and Rht-B1b have been deployed in modern wheat cultivars throughout the world, but they increase susceptibility to Fusarium head blight (FHB). Here, we investigated the impact of the Rht1 genes on anther retention (AR) in relation to FHB resistance using four different sets of near-isogenic lines (NILs) with contrasting levels and types of background FHB resistance. NILs were evaluated for FHB severity, plant height and AR in three greenhouse and three field trials using artificial spray inoculation. Rht-B1b and Rht-D1b alleles increased AR and FHB susceptibility in all genetic backgrounds. The magnitude of the effects differed between NIL groups. Increased FHB susceptibility largely followed increased AR. Differences in FHB susceptibility between tall and dwarf haplotypes were largest in the NIL group with the highest changes in AR. In the most resistant NIL group, dwarfed lines had only slightly higher AR than tall lines and maintained good resistance, while both tall and dwarf lines had high levels of retained anthers in the most susceptible NIL group. We further investigated the effect of the major Fusarium resistance QTL Fhb1 and Qfhs.ifa-5A in combination with the Rht1 genes. Qfhs.ifa-5A enhanced anther extrusion in tall as well as semi-dwarf haplotypes, whereas Fhb1 did not affect AR. Qfhs.ifa-5A supported FHB resistance more efficiently than Fhb1 in lines that were more responsive to AR, while both Fhb1 and Qfhs.ifa-5A were equally efficient in NILs that had high background resistance and low response to AR.

Genome-wide association mapping identifies common bunt (Tilletia caries) resistance loci in bread wheat (Triticum aestivum) accessions of the USDA National Small Grains Collection.

KEY MESSAGE: Association mapping and phenotypic analysis of a diversity panel of 238 bread wheat accessions highlights differences in resistance against common vs. dwarf bunt and identifies genotypes valuable for bi-parental crosses. Common bunt caused by Tilletia caries and T. laevis was successfully controlled by seed dressings with systemic fungicides for decades, but has become a renewed threat to wheat yield and quality in organic agriculture where such treatments are forbidden. As the most efficient way to address this problem is the use of resistant cultivars, this study aims to broaden the spectrum of resistance sources available for breeders by identifying resistance loci against common bunt in bread wheat accessions of the USDA National Small Grains Collection. We conducted three years of artificially inoculated field trials to assess common bunt infection levels in a diversity panel comprising 238 wheat accessions for which data on resistance against the closely related pathogen Tilletia controversa causing dwarf bunt was already available. Resistance levels against common bunt were higher compared to dwarf bunt with 99 accessions showing [Formula: see text] 1% incidence. Genome-wide association mapping identified six markers significantly associated with common bunt incidence in regions already known to confer resistance on chromosomes 1A and 1B and novel loci on 2B and 7A. Our results show that resistance against common and dwarf bunt is not necessarily controlled by the same loci but we identified twenty accessions with high resistance against both diseases. These represent valuable new resources for research and breeding programs since several bunt races have already been reported to overcome known resistance genes.

Genetic architecture of fusarium head blight disease resistance and associated traits in Nordic spring wheat.

KEY MESSAGE: This study identified a significant number of QTL that are associated with FHB disease resistance in NMBU spring wheat panel by conducting genome-wide association study. Fusarium head blight (FHB) is a widely known devastating disease of wheat caused by Fusarium graminearum and other Fusarium species. FHB resistance is quantitative, highly complex and divided into several resistance types. Quantitative trait loci (QTL) that are effective against several of the resistance types give valuable contributions to resistance breeding. A spring wheat panel of 300 cultivars and breeding lines of Nordic and exotic origins was tested in artificially inoculated field trials and subjected to visual FHB assessment in the years 2013-2015, 2019 and 2020. Deoxynivalenol (DON) content was measured on harvested grain samples, and anther extrusion (AE) was assessed in separate trials. Principal component analysis based on 35 and 25 K SNP arrays revealed the existence of two subgroups, dividing the panel into European and exotic lines. We employed a genome-wide association study to detect QTL associated with FHB traits and identify marker-trait associations that consistently influenced FHB resistance. A total of thirteen QTL were identified showing consistent effects across FHB resistance traits and environments. Haplotype analysis revealed a highly significant QTL on 7A, Qfhb.nmbu.7A.2, which was further validated on an independent set of breeding lines. Breeder-friendly KASP markers were developed for this QTL that can be used in marker-assisted selection. The lines in the wheat panel harbored from zero to five resistance alleles, and allele stacking showed that resistance can be significantly increased by combining several of these resistance alleles. This information enhances breeders´ possibilities for genomic prediction and to breed cultivars with improved FHB resistance.

Genome-wide association study and genomic prediction of resistance to stripe rust in current Central and Northern European winter wheat germplasm.

KEY MESSAGE: We found two loci on chromosomes 2BS and 6AL that significantly contribute to stripe rust resistance in current European winter wheat germplasm. Stripe or yellow rust, caused by the fungus Puccinia striiformis Westend f. sp. tritici, is one of the most destructive wheat diseases. Sustainable management of wheat stripe rust can be achieved through the deployment of rust resistant cultivars. To detect effective resistance loci for use in breeding programs, an association mapping panel of 230 winter wheat cultivars and breeding lines from Northern and Central Europe was employed. Genotyping with the Illumina® iSelect® 25 K Infinium® single nucleotide polymorphism (SNP) genotyping array yielded 8812 polymorphic markers. Structure analysis revealed two subpopulations with 92 Austrian breeding lines and cultivars, which were separated from the other 138 genotypes from Germany, Norway, Sweden, Denmark, Poland, and Switzerland. Genome-wide association study for adult plant stripe rust resistance identified 12 SNP markers on six wheat chromosomes which showed consistent effects over several testing environments. Among these, two marker loci on chromosomes 2BS (RAC875_c1226_652) and 6AL (Tdurum_contig29607_413) were highly predictive in three independent validation populations of 1065, 1001, and 175 breeding lines. Lines with the resistant haplotype at both loci were nearly free of stipe rust symptoms. By using mixed linear models with those markers as fixed effects, we could increase predictive ability in the three populations by 0.13-0.46 compared to a standard genomic best linear unbiased prediction approach. The obtained results facilitate an efficient selection for stripe rust resistance against the current pathogen population in the Northern and Central European winter wheat gene pool.

Fusarium head blight resistance in European winter wheat: insights from genome-wide transcriptome analysis.

BACKGROUND: Fusarium head blight (FHB) is a devastating disease of wheat worldwide. Resistance to FHB is quantitatively controlled by the combined effects of many small to medium effect QTL. Flowering traits, especially the extent of extruded anthers, are strongly associated with FHB resistance. RESULTS: To characterize the genetic basis of FHB resistance, we generated and analyzed phenotypic and gene expression data on the response to Fusarium graminearum (Fg) infection in 96 European winter wheat genotypes, including several lines containing introgressions from the highly resistant Asian cultivar Sumai3. The 96 lines represented a broad range in FHB resistance and were assigned to sub-groups based on their phenotypic FHB severity score. Comparative analyses were conducted to connect sub-group-specific expression profiles in response to Fg infection with FHB resistance level. Collectively, over 12,300 wheat genes were Fusarium responsive. The core set of genes induced in response to Fg was common across different resistance groups, indicating that the activation of basal defense response mechanisms was largely independent of the resistance level of the wheat line. Fg-induced genes tended to have higher expression levels in more susceptible genotypes. Compared to the more susceptible non-Sumai3 lines, the Sumai3-derivatives demonstrated higher constitutive expression of genes associated with cell wall and plant-type secondary cell wall biogenesis and higher constitutive and Fg-induced expression of genes involved in terpene metabolism. Gene expression analysis of the FHB QTL Qfhs.ifa-5A identified a constitutively expressed gene encoding a stress response NST1-like protein (TraesCS5A01G211300LC) as a candidate gene for FHB resistance. NST1 genes are key regulators of secondary cell wall biosynthesis in anther endothecium cells. Whether the stress response NST1-like gene affects anther extrusion, thereby affecting FHB resistance, needs further investigation. CONCLUSION: Induced and preexisting cell wall components and terpene metabolites contribute to resistance and limit fungal colonization early on. In contrast, excessive gene expression directs plant defense response towards programmed cell death which favors necrotrophic growth of the Fg pathogen and could thus lead to increased fungal colonization.

Quinoa genome assembly employing genomic variation for guided scaffolding.

KEY MESSAGE: We propose to use the natural variation between individuals of a population for genome assembly scaffolding. In today's genome projects, multiple accessions get sequenced, leading to variant catalogs. Using such information to improve genome assemblies is attractive both cost-wise as well as scientifically, because the value of an assembly increases with its contiguity. We conclude that haplotype information is a valuable resource to group and order contigs toward the generation of pseudomolecules. Quinoa (Chenopodium quinoa) has been under cultivation in Latin America for more than 7500 years. Recently, quinoa has gained increasing attention due to its stress resistance and its nutritional value. We generated a novel quinoa genome assembly for the Bolivian accession CHEN125 using PacBio long-read sequencing data (assembly size 1.32 Gbp, initial N50 size 608 kbp). Next, we re-sequenced 50 quinoa accessions from Peru and Bolivia. This set of accessions differed at 4.4 million single-nucleotide variant (SNV) positions compared to CHEN125 (1.4 million SNV positions on average per accession). We show how to exploit variation in accessions that are distantly related to establish a genome-wide ordered set of contigs for guided scaffolding of a reference assembly. The method is based on detecting shared haplotypes and their expected continuity throughout the genome (i.e., the effect of linkage disequilibrium), as an extension of what is expected in mapping populations where only a few haplotypes are present. We test the approach using Arabidopsis thaliana data from different populations. After applying the method on our CHEN125 quinoa assembly we validated the results with mate-pairs, genetic markers, and another quinoa assembly originating from a Chilean cultivar. We show consistency between these information sources and the haplotype-based relations as determined by us and obtain an improved assembly with an N50 size of 1079 kbp and ordered contig groups of up to 39.7 Mbp. We conclude that haplotype information in distantly related individuals of the same species is a valuable resource to group and order contigs according to their adjacency in the genome toward the generation of pseudomolecules.

Genomic signatures of selection for resistance to stripe rust in Austrian winter wheat.

KEY MESSAGE: We combined quantitative and population genetic methods to identify loci under selection for adult plant resistance to stripe rust in an Austrian winter wheat breeding population from 2008 to 2018. Resistance to stripe rust, a foliar disease caused by the fungus P. striiformis f. sp. tritici, in wheat (Triticum aestivum L.) is both qualitatively and quantitatively controlled. Resistance genes confer complete, race-specific resistance but are easily overcome by evolving pathogen populations, while quantitative resistance is controlled by many small- to medium-effect loci that provide incomplete yet more durable protection. Data on resistance loci can be applied in marker-assisted selection and genomic prediction frameworks. We employed genome-wide association to detect loci associated with stripe rust and selection testing to identify regions of the genome that underwent selection for stripe rust resistance in an Austrian winter wheat breeding program from 2008 to 2018. Genome-wide association mapping identified 150 resistance loci, 62 of which showed significant evidence of selection over time. The breeding population also demonstrated selection for resistance at the genome-wide level.

Comparative mapping and validation of multiple disease resistance QTL for simultaneously controlling common and dwarf bunt in bread wheat.

KEY MESSAGE: Resistance QTL on chromosomes 1AL and 7AL are effective against common and dwarf bunt, QTL on 1BS affects common bunt and QTL on 7DS affects dwarf bunt in bread wheat. Common bunt, caused by Tilletia caries and T. laevis, and dwarf bunt, caused by T. controversa, negatively affect grain yield and quality of wheat and are particularly destructive in low-input and organic production systems. Two recombinant inbred line (RIL) populations derived by crossing the highly and durably resistant cultivars 'Blizzard' and 'Bonneville' to the susceptible cultivar 'Rainer' were evaluated for their resistance to common and dwarf bunt in artificially inoculated field and greenhouse trials over two growing seasons and genotyped with a 15 K SNP array. Bunt resistance QTL were mapped to chromosomes 1AL, 1BS, 7AL and 7DS. Common bunt resistance was regulated by the major QTL QBt.ifa-1BS and QBt.ifa-1AL together with the moderate effect QTL QBt.ifa-7AL. Dwarf bunt resistance was on the other hand regulated by the QTL QBt.ifa-1AL, QBt.ifa-7AL and QBt.ifa-7DS. Common bunt resistance QTL exhibited pronounced epistatic effects, while epistatic effects were of smaller magnitude for dwarf bunt QTL. Kompetitive Allele-Specific PCR (KASP) markers were developed from SNPs associated with bunt resistance QTL and successfully used for QTL validation in an independent set of RILs. These KASP markers have the potential to support targeted introgression of QTL into elite wheat germplasm and accelerate breeding for enhanced bunt resistance. Durable protection against both common and dwarf bunt can be achieved by combining multiple resistance genes in the same genetic background.

QTL mapping and successful introgression of the spring wheat-derived QTL Fhb1 for Fusarium head blight resistance in three European triticale populations.

KEY MESSAGE: The spring wheat-derived QTL Fhb1 was successfully introgressed into triticale and resulted in significantly improved FHB resistance in the three triticale mapping populations. Fusarium head blight (FHB) is a major problem in cereal production particularly because of mycotoxin contaminations. Here we characterized the resistance to FHB in triticale breeding material harboring resistance factors from bread wheat. A highly FHB-resistant experimental line which derives from a triticale × wheat cross was crossed to several modern triticale cultivars. Three populations of recombinant inbred lines were generated and evaluated in field experiments for FHB resistance using spray inoculations during four seasons and were genotyped with genotyping-by-sequencing and SSR markers. FHB severity was assessed in the field by visual scorings and on the harvested grain samples using digital picture analysis for quantifying the whitened kernel surface (WKS). Four QTLs with major effects on FHB resistance were identified, mapping to chromosomes 2B, 3B, 5R, and 7A. Those QTLs were detectable with both Fusarium severity traits. Measuring of WKS allows easy and fast grain symptom quantification and appears as an effective scoring tool for FHB resistance. The QTL on 3B collocated with Fhb1, and the QTL on 5R with the dwarfing gene Ddw1. This is the first report demonstrating the successful introgression of Fhb1 into triticale. It comprises a significant step forward for enhancing FHB resistance in this crop.

Chitosan Hydrochloride Decreases Fusarium graminearum Growth and Virulence and Boosts Growth, Development and Systemic Acquired Resistance in Two Durum Wheat Genotypes.

Fusarium head blight (FHB) is a devastating disease for cereals. FHB is managed by fungicides at anthesis, but their efficacy is variable. Conventional fungicides accumulate in the soil and are dangerous for animal and human health. This study assayed the antifungal ability of chitosan hydrochloride against Fusarium graminearum. Chitosan reduced F. graminearum growth and downregulated the transcript of the major genes involved in the cell growth, respiration, virulence, and trichothecenes biosynthesis. Chitosan promoted the germination rate, the root and coleoptile development, and the nitrogen balance index in two durum wheat genotypes, Marco Aurelio (FHB-susceptible) and DBC480 (FHB-resistant). Chitosan reduced FHB severity when applied on spikes or on the flag leaves. FHB severity in DBC480 was of 6% at 21 dpi after chitosan treatments compared to F. graminearum inoculated control (20%). The elicitor-like property of chitosan was confirmed by the up-regulation of TaPAL, TaPR1 and TaPR2 (around 3-fold). Chitosan decreased the fungal spread and mycotoxins accumulation. This study demonstrated that the non-toxic chitosan is a powerful molecule with the potential to replace the conventional fungicides. The combination of a moderately resistant genotype (DBC480) with a sustainable compound (chitosan) will open new frontiers for the reduction of conventional compounds in agriculture.

Fine-mapping of the Fusarium head blight resistance QTL Qfhs.ifa-5A identifies two resistance QTL associated with anther extrusion.

KEY MESSAGE: Fine-mapping separated Qfhs.ifa-5A into a major QTL mapping across the centromere and a minor effect QTL positioned at the distal half of 5AS. Both increase Fusarium resistance and anther extrusion. The Fusarium head blight (FHB) resistance QTL Qfhs.ifa-5A resides in the low-recombinogenic pericentromeric region of chromosome 5A making fine-mapping particularly arduous. Qfhs.ifa-5A primarily contributes resistance to fungal entry with the favorable allele descending from the highly Fusarium resistant cultivar Sumai-3. Fine-mapping a near-isogenic recombinant inbred line population partitioned the Qfhs.ifa-5A interval into 12 bins. Near-isogenic lines recombining at the interval were phenotyped for FHB severity, anther retention and plant height. Composite interval mapping separated the initially single QTL into two QTL. The major effect QTL Qfhs.ifa-5Ac mapped across the centromere and the smaller effect QTL Qfhs.ifa-5AS mapped to the distal half of 5AS. Although Qfhs.ifa-5Ac and Qfhs.ifa-5AS intervals were as small as 0.1 and 0.2 cM, their corresponding physical distances were large, comprising 44.1 Mbp and 49.2 Mbp, respectively. Sumai-3 alleles at either QTL improved FHB resistance and increased anther extrusion suggesting a pleiotropic effect of anthers on resistance. This hypothesis was supported by greenhouse experiments using the susceptible cultivar Remus and its resistant near-isogenic line NIL3 carrying the entire Qfhs.ifa-5A segment. By manually removing anthers prior to spray inoculation both, Remus and NIL3 became almost equally resistant in the early phase of the disease development and were significantly less diseased than variants without anther manipulation. At late time points the positive effect of the anther removal became smaller for Remus and disappeared completely for NIL3. Results affirm that absence of anthers enhanced resistance to initial infection but did not protect plants from fungal spreading within spikes.

Exploring and exploiting the genetic variation of Fusarium head blight resistance for genomic-assisted breeding in the elite durum wheat gene pool.

KEY MESSAGE: Genomic selection had a higher selection response for FHB resistance than phenotypic selection, while association mapping identified major QTL on chromosome 3B unaffected by plant height and flowering date. Fusarium head blight (FHB) is one of the most destructive diseases of durum wheat. Hence, minimizing losses in yield, quality and avoiding contamination with mycotoxins are of pivotal importance, as durum wheat is mostly used for human consumption. While growing resistant varieties is the most promising approach for controlling this fungal disease, FHB resistance breeding in durum wheat is hampered by the limited variation in the elite gene pool and difficulties in efficiently combining the numerous small-effect resistance quantitative trait loci (QTL) in the same line. We evaluated an international collection of 228 genotyped durum wheat cultivars for FHB resistance over 3 years to investigate the genetic architecture and potential of genomic-assisted breeding for FHB resistance in durum wheat. Plant height was strongly positively correlated with FHB resistance and led to co-localization of plant height and resistance QTL. Nevertheless, a major QTL on chromosome 3B independent of plant height was identified in the same chromosomal interval as reported for the prominent hexaploid resistance QTL Fhb1, though haplotype analysis highlighted the distinctiveness of both QTL. Comparison between phenotypic and genomic selection for FHB resistance revealed a superior prediction ability of the former. However, simulated selection experiments resulted in higher selection responses when using genomic breeding values for early generation selection. An earlier identification of the most promising lines and crossing parents was feasible with a genomic selection index, which suggested a much faster short-term population improvement than previously possible in durum wheat, complementing long-term strategies with exotic resistance donors.