Alternative scoring methods of fusarium head blight resistance for genomic assisted breeding.

Fusarium head blight (FHB) is a fungal disease of wheat (Triticum aestivum.L) that causes yield losses and produces mycotoxins which could easily exceed the limits of the EU regulations. Resistance to FHB has a complex genetic architecture and accurate evaluation in breeding programs is key to selecting resistant varieties. The Area Under the Disease Progress Curve (AUDPC) is one of the commonly metric used as a standard methodology to score FHB. Although efficient, AUDPC requires significant costs in phenotyping to cover the entire disease development pattern. Here, we show that there are more efficient alternatives to AUDPC (angle, growing degree days to reach 50% FHB severity, and FHB maximum variance) that reduce the number of field assessments required and allow for fair comparisons between unbalanced evaluations across trials. Furthermore, we found that the evaluation method that captures the maximum variance in FHB severity across plots is the most optimal approach for scoring FHB. In addition, results obtained on experimental data were validated on a simulated experiment where the disease progress curve was modeled as a sigmoid curve with known parameters and assessment protocols were fully controlled. Results show that alternative metrics tested in this study captured key components of quantitative plant resistance. Moreover, the new metrics could be a starting point for more accurate methods for measuring FHB in the field. For example, the optimal interval for FHB evaluation could be predicted using prior knowledge from historical weather data and FHB scores from previous trials. Finally, the evaluation methods presented in this study can reduce the FHB phenotyping burden in plant breeding with minimal losses on signal detection, resulting in a response variable available to use in data-driven analysis such as genome-wide association studies or genomic selection.

Suppressed recombination and unique candidate genes in the divergent haplotype encoding Fhb1, a major Fusarium head blight resistance locus in wheat.

KEY MESSAGE: Fine mapping and sequencing revealed 28 genes in the non-recombining haplotype containing Fhb1 . Of these, only a GDSL lipase gene shows a pathogen-dependent expression pattern. Fhb1 is a prominent Fusarium head blight resistance locus of wheat, which has been successfully introgressed in adapted breeding material, where it confers a significant increase in overall resistance to the causal pathogen Fusarium graminearum and the fungal virulence factor and mycotoxin deoxynivalenol. The Fhb1 region has been resolved for the susceptible wheat reference genotype Chinese Spring, yet the causal gene itself has not been identified in resistant cultivars. Here, we report the establishment of a 1 Mb contig embracing Fhb1 in the donor line CM-82036. Sequencing revealed that the region of Fhb1 deviates from the Chinese Spring reference in DNA size and gene content, which explains the repressed recombination at the locus in the performed fine mapping. Differences in genes expression between near-isogenic lines segregating for Fhb1 challenged with F. graminearum or treated with mock were investigated in a time-course experiment by RNA sequencing. Several candidate genes were identified, including a pathogen-responsive GDSL lipase absent in susceptible lines. The sequence of the Fhb1 region, the resulting list of candidate genes, and near-diagnostic KASP markers for Fhb1 constitute a valuable resource for breeding and further studies aiming to identify the gene(s) responsible for F. graminearum and deoxynivalenol resistance.

Identification of QTLs for resistance to Fusarium head blight, DON accumulation and associated traits in the winter wheat variety Arina.

Fusarium head blight (FHB) of wheat has become a serious threat to wheat crops in numerous countries. In addition to loss of yield and quality, this disease is of primary importance because of the contamination of grain with mycotoxins such as deoxynivalenol (DON). The Swiss winter cultivar Arina possesses significant resistance to FHB. The objective of this study was to map quantitative trait loci (QTL) for resistance to FHB, DON accumulation and associated traits in grain in a double haploid (DH) population from a cross between Arina and the FHB susceptible UK variety Riband. FHB resistance was assessed in five trials across different years and locations. Ten QTL for resistance to FHB or associated traits were detected across the trials, with QTL derived from both parents. Very few of the QTL detected in this study were coincident with those reported by authors of two other studies of FHB resistance in Arina. It is concluded that the FHB resistance of Arina, like that of the other European winter wheat varieties studied to date, is conferred by several genes of moderate effect making it difficult to exploit in marker-assisted selection breeding programmes. The most significant and stable QTL for FHB resistance was on chromosome 4D and co-localised with the Rht-D1 locus for height. This association appears to be due to linkage of deleterious genes to the Rht-D1b (Rht2) semi-dwarfing allele rather than differences in height per se. This association may compromise efforts to enhance FHB resistance in breeding programmes using germplasm containing this allele.

Stacking quantitative trait loci (QTL) for Fusarium head blight resistance from non-adapted sources in an European elite spring wheat background and assessing their effects on deoxynivalenol (DON) content and disease severity.

Fusarium head blight (FHB) is a devastating disease in wheat that reduces grain yield, grain quality and contaminates the harvest with deoxynivalenol (DON). As potent resistance sources Sumai 3 and its descendants from China and Frontana from Brazil had been analysed by quantitative trait loci (QTL) mapping. We introgressed and stacked two donor QTL from CM82036 (Sumai 3/Thornbird) located on chromosomes 3B and 5A and one donor QTL from Frontana on chromosome 3A in elite European spring wheat and estimated the effects of the three individual donor QTL and their four combinations on DON, Fusarium exoantigen content, and FHB rating adjusted to heading date. One class with the susceptible QTL alleles served as control. Each of the eight QTL classes was represented by 12-15 F(3)-derived lines tested in F(5) generation as bulked progeny possessing the respective marker alleles homozygously. Traits were evaluated in a field experiment across four locations with spray inoculation of Fusarium culmorum. All three individual donor-QTL alleles significantly reduced DON content and FHB severity compared to the marker class with no donor QTL. The only exception was the donor-QTL allele 3A that had a low, but non-significant effect on FHB severity. The highest effect had the stacked donor-QTL alleles 3B and 5A for both traits. They jointly reduced DON content by 78% and FHB rating by 55% compared to the susceptible QTL class. Analysis of Fusarium exoantigen content illustrates that lower disease severity is associated with less mycelium content in the grain. In conclusion, QTL from non-adapted sources could be verified in a genetic background of German elite spring wheat. Within the QTL classes significant (P<0.05) genotypic differences were found among the individual genotypes. An additional phenotypic selection would, therefore, be advantageous after performing a marker-based selection.

Molecular mapping of Fusarium head blight resistance in the winter wheat population Dream/Lynx.

Fusarium head blight (FHB), mainly caused by Fusarium graminearum and F. culmorum, can significantly reduce the grain quality of wheat (Triticum aestivum L.) due to mycotoxin contamination. The objective of this study was to identify quantitative trait loci (QTLs) for FHB resistance in a winter wheat population developed by crossing the resistant German cultivar Dream with the susceptible British cultivar Lynx. A total of 145 recombinant inbred lines (RILs) were evaluated following spray inoculation with a F. culmorum suspension in field trials in 2002 in four environments across Germany. Based on amplified fragment length polymorphism and simple sequence repeat marker data, a 1,734 cM linkage map was established assuming that the majority of the polymorphic parts of the genome were covered. The area under disease progress curve (AUDPC) was calculated based on the visually scored FHB symptoms. The population segregated quantitatively for FHB severity. Composite interval mapping analysis for means across the environments identified four FHB resistance QTLs on chromosomes 6AL, 1B, 2BL and 7BS. Individually the QTLs explained 19%, 12%, 11% and 21% of the phenotypic variance, respectively, and together accounted for 41%. The QTL alleles conferring resistance on 6AL, 2BL and 7BS originated from cv. Dream. The resistance QTL on chromosome 6AL partly overlapped with a QTL for plant height. The FHB resistance QTL on 7BS coincided with a QTL for heading date, but the additive effect on heading date was of minor importance. The resistance QTL on chromosome 1B was associated with the T1BL.1RS wheat-rye translocation of Lynx.

Molecular mapping of resistance to Fusarium head blight in the spring wheat cultivar Frontana.

Fusarium head blight (FHB) is a destructive disease of wheat. The objective of this study was to characterise the FHB resistance of the Brazilian spring wheat cultivar Frontana through molecular mapping. A population of 210 doubled-haploid lines from a cross of Frontana (partially resistant) and Remus (susceptible) was evaluated for FHB resistance during three seasons. Spray and single-spikelet inoculations were applied. The severity, incidence and spread of the disease were assessed by visual scoring. The population was genotyped with 566 DNA markers. The major QTL effect associated with FHB resistance mapped to chromosome 3A near the centromere, explaining 16% of the phenotypic variation for disease severity over 3 years. The most likely position is in the Xgwm720-Xdupw227 interval. The genomic region on 3A was significantly associated with FHB severity and incidence in all years evaluated, but not with FHB spread, indicating the prominent contribution of this QTL to resistance against initial infection. The map interval Xgwm129-Xbarc197 on chromosome 5A also showed consistent association with FHB severity and accounted for 9% of the phenotypic variation. In addition, smaller effects for FHB severity were identified on chromosomes 1B, 2A, 2B, 4B, 5A and 6B in single years. Individual QTLs for resistance to FHB spread accounted for less than 10% of the variation in trait expression. The present study indicates that FHB resistance of Frontana primarily inhibits fungal penetration (type I resistance), but has a minor effect on fungal spread after infection (type II resistance).

Molecular mapping of QTLs for Fusarium head blight resistance in spring wheat. II. Resistance to fungal penetration and spread.

Fusarium head blight (FHB, scab) causes severe yield and quality losses, but the most serious concern is the mycotoxin contamination of cereal food and feed. The cultivation of resistant varieties may contribute to integrated control of this fungal disease. Breeding for FHB resistance by conventional selection is feasible, but tedious and expensive. The aim of this work was to detect QTLs for combined type I and type II resistance against FHB and estimate their effects in comparison to the QTLs identified previously for type II resistance. A population of 364, F1 derived doubled-haploid (DH) lines from the cross 'CM-82036' (resistant)/'Remus' (susceptible) was evaluated for components of FHB resistance during 2 years under field conditions. Plants were inoculated at anthesis with a conidial suspension of Fusarium graminearum or Fusarium culmorum. The crop was kept wet for 20 h after inoculation by mist-irrigation. Disease severity was assessed by visual scoring. Initial QTL analysis was performed on 239 randomly chosen DH lines and extended to 361 lines for putative QTL regions. Different marker types were applied, with an emphasis on PCR markers. Analysis of variance, as well as simple and composite interval mapping, revealed that two genomic regions were significantly associated with FHB resistance. The two QTLs on chromosomes 3B (Qfhs.ndsu-3BS) and 5A (Qfhs.ifa-5A) explained 29 and 20% of the phenotypic variance, respectively, for visual FHB severity. Qfhs.ndsu-3BS appeared to be associated mainly with resistance to fungal spread, and Qfhs.ifa-5A primarily with resistance to fungal penetration. Both QTL regions were tagged with flanking SSR markers. These results indicate that FHB resistance was under the control of two major QTLs operating together with unknown numbers of minor genes. Marker-assisted selection for these two major QTLs appears feasible and should accelerate the development of resistant and locally adapted wheat cultivars.

Molecular mapping of QTLs for Fusarium head blight resistance in spring wheat. I. Resistance to fungal spread (Type II resistance).

Fusarium head blight (FHB, scab) is a fungal disease of wheat and other small cereals that is found in both temperate and semi-tropical regions. FHB causes severe yield and quality losses, but the most-serious concern is the possible mycotoxin contamination of cereal food and feed. Breeding for FHB resistance by conventional selection is feasible, but tedious and expensive. This study was conducted to identify and map DNA markers associated with FHB resistance genes in wheat. A population of 364 F(1)-derived doubled-haploid (DH) lines from the cross 'CM-82036' (resistant)/'Remus' (susceptible) was evaluated for Type II resistance (spread within the spike) during 2 years under field conditions. Marker analysis was performed on 239 randomly chosen DH lines. Different marker types were applied, with an emphasis on AFLP and SSR markers. Analysis of variance, as well as simple and composite interval mapping, were applied. Three genomic regions were found significantly associated with FHB resistance. The most-prominent effect was detected on the short arm of chromosome 3B, explaining up to 60% of the phenotypic variance for Type II FHB resistance. A further QTL was located on chromosome 5A and a third one on 1B. The QTL regions on 3B and 5A were tagged with flanking SSR markers, the 1B QTL was found associated with the high-molecular-weight glutenin locus. These results indicate that FHB resistance is under control of a few major QTLs operating together with unknown numbers of minor genes. Marker-assisted selection for these major QTLs involved in FHB resistance appears feasible and should accelerate the development of resistant and agronomically improved wheat cultivars.