Detection of Fusarium head blight resistance QTL in a wheat population using bulked segregant analysis

Identification of Two Novel QTL for Fusarium Head Blight Resistance in German Wheat Cultivar Centrum

Fusarium head blight (FHB) is a devastating disease that occurs in warm and humid environments. The German wheat 'Centrum' has displayed moderate to high levels of FHB resistance in the field for many years. In this study, an F6:8 recombinant inbred line (RIL) population derived from cross 'Centrum' × 'Xinong 979' was evaluated for FHB response following point inoculation in five environments. The population and parents were genotyped using the GenoBaits Wheat 16 K Panel. Stable quantitative trait loci (QTL) associated with FHB resistance in 'Centrum' were mapped on chromosome arms 2DS and 5BS. The most effective QTL, located in 2DS, was identified as a new chromosome region represented by a 1.4 Mb interval containing 17 candidate genes. Another novel QTL was mapped in chromosome arm 5BS of a 5BS to 7BS translocation chromosome. In addition, two environmentally sensitive QTL were mapped on chromosome arms 2BL from 'Centrum' and 5AS from 'Xinong 979'. Polymorphisms of flanking phenotypic variance explained (PVE) markers (allele-specific quantitative PCR [AQP]) AQP-6 for QFhb.nwafu-2DS and 16K-13073 for QFhb.nwafu-5BS were validated in a panel of 217 cultivars and breeding lines. These markers could be useful for marker-assisted selection (MAS) of FHB resistance and provide a starting point for fine mapping and marker-based cloning of the resistance genes.

Two QTL regions for spike length showing pleiotropic effects on Fusarium head blight resistance and thousand-grain weight in bread wheat (Triticum aestivum L.)

Spike length (SL) plays an important role in the yield improvement of wheat and is significantly associated with other traits. Here, we used a recombinant inbred line (RIL) population derived from a cross between Yangmai 12 (YM12) and Yanzhan 1 (YZ1) to construct a genetic linkage map and identify quantitative trait loci (QTL) for SL. A total of 5 QTL were identified for SL, among which QSl.yaas-3A and QSl.yaas-5B are two novel QTL for SL. The YZ1 alleles at QSl.yaas-2D and QSl.yaas-5A, and the YM12 alleles at QSl.yaas-2A, QSl.yaas-3A, and QSl.yaas-5B conferred increasing SL effects. Two major QTL QSl.yaas-5A and QSl.yaas-5B explained 9.11-15.85% and 9.01-12.85% of the phenotypic variations, respectively. Moreover, the positive alleles of QSl.yaas-5A and QSl.yaas-5B could significantly increase Fusarium head blight (FHB) resistance (soil surface inoculation and spray inoculation were used) and thousand-grain weight (TGW) in the RIL population. Kompetitive allele-specific PCR (KASP) markers for QSl.yaas-5A and QSl.yaas-5B were developed and validated in an additional panel of 180 wheat cultivars/lines. The cultivars/lines harboring both the positive alleles of QSl.yaas-5A and QSl.yaas-5B accounted for only 28.33% of the validation populations and had the longest SL, best FHB resistance (using spray inoculation), and highest TGW. A total of 358 and 200 high-confidence annotated genes in QSl.yaas-5A and QSl.yaas-5B were identified, respectively. Some of the genes in these two regions were involved in cell development, disease resistance, and so on. The results of this study will provide a basis for directional breeding of longer SL, higher TGW, and better FHB resistance varieties and a solid foundation for fine-mapping QSl.yaas-5A and QSl.yaas-5B in future.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01427-8.

Analysis of QTLs and Candidate Genes for Tassel Symptoms in Maize Infected with Sporisorium reilianum

Heat smut is a fungal soil-borne disease caused by Sporisorium reilianum, and affects the development of male and female tassels. Our previous research found that the tassel symptoms in maize infected with Sporisorium reilianum significantly differed in inbred lines with Sipingtou blood, and exhibited stable heredity over time at multiple locations. In this study, cytological analysis demonstrated that the cellular organization structures of three typical inbred lines (Huangzao4, Jing7, and Chang7-2) showed significant discrepancies at the VT stage. QTLs that control the different symptoms of maize tassels infected with Sporisorium reilianum were located in two F₂ populations, which were constructed using three typical inbred lines. The BSA (bulked segregation analysis) method was used to construct mixed gene pools based on typical tassel symptoms. The QTLs of different symptoms of maize tassels infected with Sporisorium reilianum were detected with 869 SSR markers covering the whole maize genome. The mixed gene pools were screened with polymorphic markers between the parents. Additional SSR markers were added near the above marker to detect genotypes in partially single plants in F₂ populations. The QTL controlling tassel symptoms in the Huangzao4 and Jing7 lines was located on the bin 1.06 region, between the markers of umc1590 and bnlg1598, and explained 21.12% of the phenotypic variation with an additive effect of 0.6524. The QTL controlling the tassel symptoms of the Jing7 and Chang7-2 lines was located on the bin 2.07 region, between the markers of umc1042 and bnlg1335, and explained 11.26% phenotypic variation with an additive effect of 0.4355. Two candidate genes (ZmABP2 and Zm00001D006403) were identified by a conjoint analysis of label-free quantification proteome sequencings.

High-resolution mapping reveals a Ht3-like locus against northern corn leaf blight

Northern corn leaf blight (NCLB), caused by the fungal pathogen Exserohilum turcicum, poses a grave threat to maize production worldwide. The resistance gene in A619Ht3, discovered decades ago, is an important genetic resource for NCLB control. By using a pair of near-isogenic lines (NILs) A619Ht3 and A619, together with the resistant and susceptible bulks derived from the cross of A619Ht3 and L3162 lines, we initially detected a Ht3-like (Ht3L) locus in bin 8.06 that was closely associated with NCLB resistance. We then performed five rounds of fine-mapping, which ultimately delimited the Ht3L locus to a 577-kb interval flanked by SNP markers KA002081 and KA002084. Plants homozygous for the Ht3L/Ht3L genotype exhibited an average reduction in diseased leaf area (DLA) by 16.5% compared to plants lacking Ht3L locus. The Ht3L locus showed extensive variation in genomic architecture among different maize lines and did not appear to contain any genes encoding canonical cell wall-associated kinases against NCLB. Moreover, the Ht3L locus was located ∼2.7 Mb away from the known Htn1 locus. We speculate that the Ht3L locus may contain a bona fide Ht3 gene or a novel NCLB resistance gene closely linked to Ht3. In practice, the Ht3L locus is a valuable resource for improving maize resistance to NCLB.

Identification and validation of a major QTL for kernel length in bread wheat based on two F3 biparental populations

BACKGROUND

High yield and quality are essential goals of wheat (Triticum aestivum L.) breeding. Kernel length (KL), as a main component of kernel size, can indirectly change kernel weight and then affects yield. Identification and utilization of excellent loci in wheat genetic resources is of great significance for cultivating high yield and quality wheat. Genetic identification of loci for KL has been performed mainly through genome-wide association study in natural populations or QTL mapping based on genetic linkage map in high generation populations.

RESULTS

In this study, an F₃ biparental population derived from the cross between an EMS mutant BLS1 selected from an EMS-induced wheat genotype LJ2135 (derived from the hybrid progeny of a spelt wheat (T. spelta L.) and a common wheat) mutant bank and a local breeding line 99E18 was used to rapidly identify loci controlling KL based on Bulked Segregant Analysis (BSA) and the wheat 660 K single-nucleotide polymorphism (SNP) array. The highest ratio of polymorphic SNPs was located on chromosome 4A. Linkage map analysis showed that 33 Kompetitive Allele Specific PCR markers were linked to the QTL for KL (Qkl.sicau-BLE18-4A) identified in three environments as well as the best linear unbiased prediction (BLUP) dataset. This QTL explained 10.87-19.30% of the phenotypic variation. Its effect was successfully confirmed in another F₃ population with the two flanking markers KASP-AX-111536305 and KASP-AX-110174441. Compared with previous studies and given that the of BLS1 has the genetic background of spelt wheat, the major QTL was likely a new one. A few of predicted genes related to regulation of kernel development were identified in the interval of the detected QTL.

CONCLUSION

A major, novel and stable QTL (Qkl.sicau-BLE18-4A) for KL was identified and verified in two F₃ biparental populations across three environments. Significant relationships among KL, kernel width (KW) and thousand kernel weight (TKW) were identified. Four predicted genes related to kernel growth regulation were detected in the interval of Qkl.sicau-BLE18-4A. Furthermore, this study laid foundation on subsequent fine mapping work and provided a possibility for breeding of elite wheat varieties.

Genetic loci associated with winter survivorship in diverse lowland switchgrass populations

High winter mortality limits biomass yield of lowland switchgrass (Panicum virgatum L.) planted in the northern latitudes of North America. Breeding of cold tolerant switchgrass cultivars requires many years due to its perennial growth habit and the unpredictable winter selection pressure that is required to identify winter-hardy individuals. Identification of causal genetic variants for winter survivorship would accelerate the improvement of switchgrass biomass production. The objective of this study was to identify allelic variation associated with winter survivorship in lowland switchgrass populations using bulk segregant analysis (BSA). Twenty-nine lowland switchgrass populations were evaluated for winter survival at two locations in southern Wisconsin and 21 populations with differential winter survivorship were used for BSA. A maximum of 10% of the individuals (8-20) were bulked to create survivor and nonsurvivor DNA pools from each population and location. The DNA pools were evaluated using exome capture sequencing, and allele frequencies were used to conduct statistical tests. The BSA tests revealed nine quatitative trait loci (QTL) from tetraploid populations and seven QTL from octoploid populations. Many QTL were population-specific, but some were identified in multiple populations that originated across a broad geographic landscape. Four QTL (at positions 88 Mb on chromosome 2N, 115 Mb on chromosome 5K, and 1 and 100 Mb on chromosome 9N) were potentially the most useful QTL. Markers associated with winter survivorship in this study can be used to accelerate breeding cycles of lowland switchgrass populations and should lead to improvements in adaptation within USDA hardiness zones 4 and 5.

Mitochondrial phosphate transporter and methyltransferase genes contribute to Fusarium head blight Type II disease resistance and grain development in wheat

Fusarium head blight (FHB) is an economically important disease of wheat that results in yield loss and grain contaminated with fungal mycotoxins that are harmful to human and animal health. Herein we characterised two wheat genes involved in the FHB response in wheat: a wheat mitochondrial phosphate transporter (TaMPT) and a methyltransferase (TaSAM). Wheat has three sub-genomes (A, B, and D) and gene expression studies demonstrated that TaMPT and TaSAM homoeologs were differentially expressed in response to FHB infection and the mycotoxigenic Fusarium virulence factor deoxynivalenol (DON) in FHB resistant wheat cv. CM82036 and susceptible cv. Remus. Virus-induced gene silencing (VIGS) of either TaMPT or TaSAM enhanced the susceptibility of cv. CM82036 to FHB disease, reducing disease spread (Type II disease resistance). VIGS of TaMPT and TaSAM significantly reduced grain number and grain weight. This indicates TaSAM and TaMPT genes also contribute to grain development in wheat and adds to the increasing body of evidence linking FHB resistance genes to grain development. Hence, Fusarium responsive genes TaSAM and TaMPT warrant further study to determine their potential to enhance both disease resistance and grain development in wheat.

Molecular Mapping of Quantitative Trait Loci for Fusarium Head Blight Resistance in a Doubled Haploid Population of Chinese Bread Wheat

Fusarium head blight (FHB) is a destructive disease of wheat worldwide, particularly in China. To map genetic loci underlying FHB resistance, a doubled haploid (DH) population consisting of 174 lines was developed from a cross between widely grown Chinese cultivars Yangmai 16 and Zhongmai 895. The DH population and parents were evaluated in field nurseries at Wuhan in 2016 to 2017 and 2017 to 2018 crop seasons with both spray inoculation and natural infection, and at Jingzhou in 2017 to 2018 crop season with grain-spawn inoculation. The DH lines were genotyped with a wheat 660K SNP array. The FHB index, plant height, anther extrusion, and days to anthesis were recorded and used for quantitative trait loci (QTL) analysis. Seven QTL for FHB resistance were mapped to chromosome arms 3BL, 4AS, 4BS, 4DS, 5AL, 6AL, and 6BS in at least two environments. QFhb.caas-4BS and QFhb.caas-4DS co-located with semi-dwarfing alleles Rht-B1b and Rht-D1b, respectively, and were associated with anther extrusion. The other five QTL were genetically independent of the agronomic traits, indicating their potential value when breeding for FHB resistance. Based on correlations between FHB indices and agronomic traits in this population, we concluded that increasing plant height to some extent would enhance FHB resistance, that anther extrusion had a more important role in environments with less severe FHB, and that days to anthesis were independent of the FHB response when viewed across years. PCR-based markers were developed for the 3BL and 5AL QTL, which were detected in more than three environments. The InDel marker InDel_AX-89588684 for QFhb.caas-5AL was also validated on a wheat panel, confirming its effectiveness for marker-assisted breeding for improvements in FHB resistance.

Molecular Mapping of QTLs Conferring Fusarium Head Blight Resistance in Chinese Wheat Cultivar Jingzhou 66

Fusarium head blight (FHB) is a destructive disease of wheat (Triticum aestivum L.), which not only significantly reduces grain yield, but also affects end-use quality. Breeding wheat cultivars with high FHB resistance is the most effective way to control the disease. The Chinese wheat cultivar Jingzhou 66 (JZ66) shows moderately high FHB resistance; however, the genetic basis of its resistance is unknown. A doubled haploid (DH) population consisting 209 lines was developed from a cross of JZ66 and Aikang 58 (AK58), a FHB susceptible wheat cultivar, to identify quantitative trait loci (QTL) that contribute to the FHB resistance. Five field experiments were established across two consecutive crop seasons (2018 and 2019) to evaluate the DH lines and parents for FHB response. The parents and DH population were genotyped with the wheat 55K single-nucleotide polymorphism (SNP) assay. Six QTLs associated with FHB resistance in JZ66 were mapped on chromosome 2DS, 3AS, 3AL, 3DL, 4DS, and 5DL, respectively. Four of the QTL (QFhb.hbaas-2DS, QFhb.hbaas-3AL, QFhb.hbaas-4DS, and QFhb.hbaas-5DL) were detected in at least two environments, and the QTL on 3AL and 5DL might be new. The QTL with major effects, QFhb.hbaas-2DS and QFhb.hbaas-4DS, explained up to 36.2% and 17.6% of the phenotypic variance, and were co-localized with the plant semi-dwarfing loci Rht8 and Rht-D1. The dwarfing Rht8 allele significantly increased spike compactness (SC) and FHB susceptibility causing a larger effect on FHB response than Rht-D1 observed in this study. PCR–based SNP markers for QFhb.hbaas-2DS, QFhb.hbaas-3AL, QFhb.hbaas-4DS, and QFhb.hbaas-5DL, were developed to facilitate their use in breeding for FHB resistance by marker-assisted selection.

Mapping of Major Fusarium Head Blight Resistance from Canadian Wheat cv. AAC Tenacious

Fusarium head blight (FHB) is one of the most devastating wheat disease due to its direct detrimental effects on grain-yield, quality and marketability. Resistant cultivars offer the most effective approach to manage FHB; however, the lack of different resistance resources is still a major bottleneck for wheat breeding programs. To identify and dissect FHB resistance, a doubled haploid wheat population produced from the Canadian spring wheat cvs AAC Innova and AAC Tenacious was phenotyped for FHB response variables incidence and severity, visual rating index (VRI), deoxynivalenol (DON) content, and agronomic traits days to anthesis (DTA) and plant height (PHT), followed by single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker genotyping. A high-density map was constructed consisting of 10,328 markers, mapped on all 21 chromosomes with a map density of 0.35 cM/marker. Together, two major quantitative trait loci for FHB resistance were identified on chromosome 2D from AAC Tenacious; one of these loci on 2DS also colocated with loci for DTA and PHT. Another major locus for PHT, which cosegregates with locus for low DON, was also identified along with many minor and epistatic loci. QTL identified from AAC Tenacious may be useful to pyramid FHB resistance.

Sex determination in the GIFT strain of tilapia is controlled by a locus in linkage group 23

Background

Tilapias (Family Cichlidae) are the second most important group of aquaculture species in the world. They have been the subject of much research on sex determination due to problems caused by early maturation in culture and their complex sex-determining systems. Different sex-determining loci (linkage group 1, 20 and 23) have been detected in various tilapia stocks. The ‘genetically improved farmed tilapia’ (GIFT) stock, founded from multiple Nile tilapia (Oreochromis niloticus) populations, with some likely to have been introgressed with O. mossambicus, is a key resource for tilapia aquaculture. The sex-determining mechanism in the GIFT stock was unknown, but potentially complicated due to its multiple origins.

Results

A bulk segregant analysis (BSA) version of double-digest restriction-site associated DNA sequencing (BSA-ddRADseq) was developed and used to detect and position sex-linked single nucleotide polymorphism (SNP) markers in 19 families from the GIFT strain breeding nucleus and two Stirling families as controls (a single XY locus had been previously mapped to LG1 in the latter). About 1500 SNPs per family were detected across the genome. Phenotypic sex in Stirling families showed strong association with LG1, whereas only SNPs located in LG23 showed clear association with sex in the majority of the GIFT families. No other genomic regions linked to sex determination were apparent. This region was validated using a series of LG23-specific DNA markers (five SNPs with highest association to sex from this study, the LG23 sex-associated microsatellite UNH898 and ARO172, and the recently isolated amhy marker for individual fish (n = 284).

Conclusions

Perhaps surprisingly given its multiple origins, sex determination in the GIFT strain breeding nucleus was associated only with a locus in LG23. BSA-ddRADseq allowed cost-effective analysis of multiple families, strengthening this conclusion. This technique has potential to be applied to other complex traits. The sex-linked SNP markers identified will be useful for potential marker-assisted selection (MAS) to control sex-ratio in GIFT tilapia to suppress unwanted reproduction during growout.

Fusarium head blight in wheat: contemporary status and molecular approaches

Fusarium head blight (FHB) disease that occurs in wheat is caused by Fusarium graminearum and is a major risk to wheat yield. Although several research efforts focusing on FHB have been conducted in the past several decades, conditions have become more critical due to the increase in its virulent forms. In such a scenario, conferring complete resistance in plants seems to be difficult for handling this issue. The phenotyping for FHB and finding a solution for it at the genetic level comprises a long-term process as FHB infection is largely affected by environmental conditions. Modern molecular strategies have played a crucial role in revealing the host-pathogen interaction in FHB. The integration of molecular biology-based methods such as genome-wide association studies and marker-based genomic selection has provided potential cultivars for breeding programs. In this review, we aim at outlining the contemporary status of the studies conducted on FHB in wheat. The influence of FHB in wheat on animals and human health is also discussed. In addition, a summary of the advancement in the molecular technologies for identifying and developing the FHB-resistant wheat genetic resources is provided. It also suggests the future measures that are required to reduce the world's vulnerability to FHB which was one of the main goals of the US Wheat and Barley Scab Initiative.

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.

Trait mapping in diverse arthropods by bulked segregant analysis

Bulked segregant analysis (BSA) is a cross-based method for genetic mapping in sexually reproducing organisms. The method's use of bulked (pooled) samples markedly reduces the genotyping effort associated with traditional linkage mapping studies. Further, it can be applied to species with life histories or physical attributes (as for micro-insects) that render genetic mapping with other methods impractical. Recent studies in both insects and mites have revealed that advanced BSA experimental designs can resolve causal loci to narrow genomic intervals, facilitating follow-up investigations. As high-quality genomes become more widely available, BSA methods are poised to become an increasingly important tool for the rapid mapping of both monogenic and polygenic traits in diverse arthropod species.

Identification and mapping of expressed genes associated with the 2DL QTL for fusarium head blight resistance in the wheat line Wuhan 1

Background

Fusarium head blight (FHB) is a problem of great concern in small grain cereals, especially wheat. A quantitative trait locus (QTL) for FHB resistance (FHB_SFI) located on the long arm of chromosome 2D in the spring wheat genotype Wuhan 1 is a resistance locus which has potential to improve the FHB resistance of bread wheat since it confers effective resistance to wheat breeding lines. Recently, differentially expressed genes (DEG) have been identified by comparing near isogenic lines (NIL) carrying the susceptible and resistant alleles for the 2DL QTL, using RNA-Seq. In the present study, we aimed to identify candidate genes located within the genetic interval for the 2DL QTL for FHB resistance, as assessed by single floret inoculation (FHB_SFI), and possibly contributing to it.

Results

Combining previous and additional bioinformatics analyses, 26 DEG that were located on chromosome arm 2DL were selected for further characterization of their expression profile by RT-qPCR. Seven of those DEG showed a consistent differential expression profile between either three pairs of near isogenic lines or other genotypes carrying the R and S alleles for the 2DL QTL for FHB resistance. UN25696, which was identified in previous expression work using microarray was also confirmed to have a differential expression pattern. Those eight candidate genes were further characterized in 85 lines of a double haploid mapping population derived from the cross Wuhan 1/Nyubai, the population where the 2DL QTL was originally identified. The expression QTL for gene Traes_2DL_179570792 overlapped completely with the mapping interval for the 2DL QTL for FHB_SFI while the expression QTL for UN25696 mapped near the QTL, but did not overlap with it. None of the other genes had a significant eQTL on chromosome 2DL. Higher expression of Traes_2DL_179570792 and UN25696 was associated with the resistant allele at that locus.

Conclusions

Of the 26 DEG from the 2DL chromosome further characterized in this study, only two had an expression QTL located in or near the interval for the 2DL QTL. Traes_2DL_179570792 is the first expression marker identified as associated with the 2DL QTL.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0748-6) contains supplementary material, which is available to authorized users.

Map-based cloning of QFhb.mgb-2A identifies a WAK2 gene responsible for Fusarium Head Blight resistance in wheat

Fusarium graminearum is one of the most threating pathogen of wheat, responsible for Fusarium head blight (FHB) which annually leads to yield losses, grain quality decay and accumulation of harmful mycotoxins in kernels. Host resistance represents the most effective approach to limit disease damages; however, only a limited number of resistant loci have currently been detected in durum genotypes. In this work we report the map-based cloning of a FHB-QTL on 2A chromosome of durum wheat, introgressed from a resistant line derived from the Chinese wheat cv. Sumai-3. A marker enrichment of the QTL region was carried out leading to the inclusion of 27 new SNPs respect to the previous map. A wall-associated receptor-like kinase (WAK2) gene was identified in the region and sequenced, in the resistant parent (^RP) one gene was predicted accounting for a genomic sequence of 5,613 structured into 6 exons, whereas two adjacent genes were predicted on the same DNA plus strand of the susceptible parent (^SP).t The involvement of WAK2 gene in FHB resistance mechanism was assessed by gene expression comparison between resistant and susceptible wheat lines, and disease symptoms evaluation in 3 TILLING mutants for WAK protein function.

Meta-Analysis of the QTLome of Fusarium Head Blight Resistance in Bread Wheat: Refining the Current Puzzle

Background: Fusarium Head Blight (FHB) is a worldwide devastating disease of bread wheat (Triticum aestivum L.). Genetic resistance is the most effective way to control FHB and many QTL related to this trait have been mapped on the wheat genetic map. This information, however, must be refined to be more efficiently used in breeding programs and for the advance of the basic research. The objective of the present study was to in-depth analyze the QTLome of FHB resistance in bread wheat, further integrating genetic, genomic, and transcriptomic data, aiming to find candidate genes. Methods: An exhaustive bibliographic review on 76 scientific papers was carried out collecting information about QTL related to FHB resistance mapped on bread wheat. A dense genetic consensus map with 572,862 loci was generated for QTL projection. Meta-analysis could be performed on 323 QTL. Candidate gene mining was carried out within the most refined loci, containing genes that were cross-validated with publicly available transcriptional expression data of wheat under Fusarium infection. Most highlighted genes were investigated for protein evidence. Results: A total of 556 QTL were found in the literature, distributed on all sub-genomes and chromosomes of wheat. Meta-analysis generated 65 meta-QTL, and this refinement allows one to find markers more tightly linked to these regions. Candidate gene mining within the most refined meta-QTL, meta-QTL 1/chr. 3B, harvested 324 genes and transcriptional data cross-validated 10 of these genes, as responsive to FHB. One is of these genes encodes a Glycosiltransferase and the other encodes for a Cytochrome P450, and these such proteins have already been verified as being responsible for FHB resistance, but the remaining eight genes still have to be further studied, as promising loci for breeding. Conclusions: The QTLome of FHB resistance in wheat was successfully assembled and a refinement in terms of number and length of loci was obtained. The integration of the QTLome with genomic and transcriptomic data has allowed for the discovery of promising candidate genes for use in breeding programs.

Evaluation of the Potential for Genomic Selection to Improve Spring Wheat Resistance to Fusarium Head Blight in the Pacific Northwest

Fusarium Head Blight (FHB) has emerged in spring wheat production in Pacific Northwest during the last decade due to factors including climate changes, crop rotations, and tillage practices. A breeding population with 170 spring wheat lines was established and screened over a 2-year period in multiple locations for FHB incidence (INC), severity (SEV), and deposition of the mycotoxin, deoxynivalenol (DON). A genome-wide association study suggested that the detectable number of genetic loci and effects are limited for marker-assisted selection. In conjunction with the success of breeding on FHB resistance in other programs, genomic selection (GS) was suggested as a better option. To evaluate the prediction accuracy of GS in the current breeding population, we conducted a variety of validations by varying proportions of testing populations and cohorts based on both FHB resistance and market class, including soft white spring (SWS), hard white spring (HWS), and hard red spring (HRS). We found that INC had higher heritability, higher correlation across years and locations, and higher prediction accuracy than SEV and DON. Prediction accuracy varied among the scenarios that restricted the testing population to a certain cohort. For a small set of newly developed or introduced lines (<17), prediction accuracy will be about 60% if the lines have similar genetic relationships as those among the current 170-line training population. However, we expect a lower prediction accuracy if new lines are selected for a specific characteristic, such as FHB resistance or market class. With the exception of DON in the SWS lines, the current training population is capable of making reasonably accurate predictions for FHB-resistant lines in most of the major market classes. For SWS, adding more lines or further phenotyping is required to improve prediction accuracy. These results demonstrate the potential and challenges of GS, especially for developing FHB-resistant varieties in the SWS market class.

Effective marker alleles associated with type 2 resistance to Fusarium head blight infection in fields

Molecular markers associated with known quantitative trait loci (QTLs) for type 2 resistance to Fusarium head blight (FHB) in bi-parental mapping population usually have more than two alleles in breeding populations. Therefore, understanding the association of each allele with FHB response is particularly important to marker-assisted enhancement of FHB resistance. In this paper, we evaluated FHB severities of 192 wheat accessions including landraces and commercial varieties in three field growing seasons, and genotyped this panel with 364 genome-wide informative molecular markers. Among them, 11 markers showed reproducible marker-trait association (p < 0.05) in at least two experiments using a mixed model. More than two alleles were identified per significant marker locus. These alleles were classified into favorable, unfavorable and neutral alleles according to the normalized genotypic values. The distributions of effective alleles at these loci in each wheat accession were characterized. Mean FHB severities increased with decreased number of favorable alleles at the reproducible loci. Chinese wheat landraces and Japanese accessions have more favorable alleles at the majority of the reproducible marker loci. FHB resistance levels of varieties can be greatly improved by introduction of these favorable alleles and removal of unfavorable alleles simultaneously at these QTL-linked marker loci.

Rapid Identification of Resistance Loci Effective Against Puccinia graminis f. sp. tritici Race TTKSK in 33 Spring Wheat Landraces

Wheat breeders worldwide are seeking new sources of resistance to Puccinia graminis f. sp. tritici race TTKSK. To prioritize field-resistant landraces for follow-up genetic studies to test for the presence of new resistance genes, seedling response to P. graminis f. sp. tritici race TTKSK, molecular markers linked to specific Sr genes, segregation ratios among progeny from crosses, and bulked segregant analyses (BSA) were used. In total, 33 spring wheat landraces with seedling resistance to P. graminis f. sp. tritici race TTKSK were crossed to a susceptible genotype, LMPG-6. The segregation ratios of stem rust reactions in F₂ seedlings fit a single dominant gene model in 31 populations and progeny from two crosses gave ambiguous results. Using the 90K wheat single-nucleotide polymorphism genotyping platform, BSA showed that the seedling resistance in 29 accessions is probably controlled by loci on chromosome 2BL. For the three remaining accessions, BSA revealed that the seedling resistance is most likely controlled by previously unreported genes. For confirmation, two populations were advanced to the F_2:3 and screened against P. graminis f. sp. tritici race TTKSK. Segregation of the F_2:3 families fit a 1:2:1 ratio for a single dominant gene. Using the F_2:3 families, BSA located the TTKSK locus on chromosome 6DS to the same location as Sr42.

Identification of an attenuated barley stripe mosaic virus for the virus-induced gene silencing of pathogenesis-related wheat genes

BACKGROUND

Virus-induced gene silencing (VIGS) has become an emerging technology for the rapid, efficient functional genomic screening of monocot and dicot species. The barley stripe mosaic virus (BSMV) has been described as an effective VIGS vehicle for the evaluation of genes involved in wheat and barley phytopathogenesis; however, these studies have been obscured by BSMV-induced phenotypes and defense responses. The utility of BSMV VIGS may be improved using a BSMV genetic background which is more tolerable to the host plant especially upon secondary infection of highly aggressive, necrotrophic pathogens such as Fusarium graminearum.

RESULTS

BSMV-induced VIGS in Triticum aestivum (bread wheat) cv. 'Fielder' was assessed for the study of wheat genes putatively related to Fusarium Head Blight (FHB), the necrotrophism of wheat and other cereals by F. graminearum. Due to the lack of 'Fielder' spike viability and increased accumulation of Fusarium-derived deoxynivalenol contamination upon co-infection of BSMV and FHB, an attenuated BSMV construct was generated by the addition of a glycine-rich, C-terminal peptide to the BSMV γ b protein. This attenuated BSMV effectively silenced target wheat genes while limiting disease severity, deoxynivalenol contamination, and yield loss upon Fusarium co-infection compared to the original BSMV construct. The attenuated BSMV-infected tissue exhibited reduced abscisic, jasmonic, and salicylic acid defense phytohormone accumulation upon secondary Fusarium infection. Finally, the attenuated BSMV was used to investigate the role of the salicylic acid-responsive pathogenesis-related 1 in response to FHB.

CONCLUSIONS

The use of an attenuated BSMV may be advantageous in characterizing wheat genes involved in phytopathogenesis, including Fusarium necrotrophism, where minimal viral background effects on defense are required. Additionally, the attenuated BSMV elicits reduced defense hormone accumulation, suggesting that this genotype may have applications for the investigation of phytohormone-related signaling, developmental responses, and pathogen defense.

Resistance Potential of Bread Wheat Genotypes Against Yellow Rust Disease Under Egyptian Climate

Yellow rust (stripe rust), caused by Puccinia striiformis f. sp. tritici, is one of the most destructive foliar diseases of wheat in Egypt and worldwide. In order to identify wheat genotypes resistant to yellow rust and develop molecular markers associated with the resistance, fifty F8 recombinant inbred lines (RILs) derived from a cross between resistant and susceptible bread wheat landraces were obtained. Artificial infection of Puccinia striiformis was performed under greenhouse conditions during two growing seasons and relative resistance index (RRI) was calculated. Two Egyptian bread wheat cultivars i.e. Giza-168 (resistant) and Sakha-69 (susceptible) were also evaluated. RRI values of two-year trial showed that 10 RILs responded with RRI value >6 <9 with an average of 7.29, which exceeded the Egyptian bread wheat cultivar Giza-168 (5.58). Thirty three RILs were included among the acceptable range having RRI value >2 <6. However, only 7 RILs showed RRI value <2. Five RILs expressed hypersensitive type of resistance (R) against the pathogen and showed the lowest Average Coefficient of Infection (ACI). Bulked segregant analysis (BSA) with eight simple sequence repeat (SSR), eight sequence-related amplified polymorphism (SRAP) and sixteen random amplified polymorphic DNA (RAPD) markers revealed that three SSR, three SRAP and six RAPD markers were found to be associated with the resistance to yellow rust. However, further molecular analyses would be performed to confirm markers associated with the resistance and suitable for marker-assisted selection. Resistant RILs identified in the study could be efficiently used to improve the resistance to yellow rust in wheat.

Mapping of QTL for Fusarium head blight resistance and morphological and developmental traits in three backcross populations derived from Triticum dicoccum × Triticum durum

Breeding for resistance to Fusarium head blight (FHB) in durum wheat continues to be hindered by the lack of effective resistance sources. Only limited information is available on resistance QTL for FHB in tetraploid wheat. In this study, resistance to FHB of a Triticum dicoccum line in the background of three Austrian T. durum cultivars was genetically characterized. Three populations of BC(1)F(4)-derived RILs were developed from crosses between the resistant donor line T. dicoccum-161 and the Austrian T. durum recipient varieties DS-131621, Floradur and Helidur. About 130 BC(1)F(4)-derived lines per population were evaluated for FHB response using artificial spray inoculation in four field experiments during two seasons. Lines were genetically fingerprinted using SSR and AFLP markers. Genomic regions on chromosomes 3B, 4B, 6A, 6B and 7B were significantly associated with FHB severity. FHB resistance QTL on 6B and 7B were identified in two populations and a resistance QTL on 4B appeared in three populations. The alleles that enhanced FHB resistance were derived from the T. dicoccum parent, except for the QTL on chromosome 3B. All QTL except the QTL on 6A mapped to genomic regions where QTL for FHB have previously been reported in hexaploid wheat. QTL on 3B and 6B coincided with Fhb1 and Fhb2, respectively. This implies that tetraploid and hexaploid wheat share common genomic regions associated with FHB resistance. QTL for FHB resistance on 4B co-located with a major QTL for plant height and mapped at the position of the Rht-B1 gene, while QTL on 7B overlapped with QTL for flowering time.

Association mapping and haplotype analysis of a 3.1-Mb genomic region involved in Fusarium head blight resistance on wheat chromosome 3BS

A previous study provided an in-depth understanding of molecular population genetics of European and Asian wheat gene pools using a sequenced 3.1-Mb contig (ctg954) on chromosome 3BS. This region is believed to carry the Fhb1 gene for response to Fusarium head blight. In this study, 266 wheat accessions were evaluated in three environments for Type II FHB response based on the single floret inoculation method. Hierarchical clustering (UPGMA) based on a Manhattan dissimilarity matrix divided the accessions into eight groups according to five FHB-related traits which have a high correlation between them; Group VIII comprised six accessions with FHB response levels similar to variety Sumai 3. Based on the compressed mixed linear model (MLM), association analysis between five FHB-related traits and 42 molecular markers along the 3.1-Mb region revealed 12 significant association signals at a threshold of P<0.05. The highest proportion of phenotypic variation (6.2%) in number of diseased spikelets (NDS) occurred at locus cfb6059, and the physical distance was about 2.9 Kb between umn10 and this marker. Haplotype block (HapB) analysis using a sliding window LD of 5 markers, detected six HapBs in the 3.1-Mb region at r(2)>0.1 and P<0.001 between random closely linked markers. F-tests among Haps with frequencies >0.05 within each HapB at r(2)>0.1 and P<0.001 showed significant differences between the Hap carried by FHB resistant resources, such as Sumai 3 and Wangshuibai, and susceptible genotypes in HapB3 and HapB6. These results suggest that Fhb1 is located within HapB6, with the possibility that another gene is located at or near HapB3. SSR markers and Haps detected in this study will be helpful in further understanding the genetic basis of FHB resistance, and provide useful information for marker-assisted selection of Fhb1 in wheat breeding.

Mapping QTL for resistance to eyespot of wheat in Aegilops longissima

Eyespot is an economically important disease of wheat caused by the soilborne fungi Oculimacula yallundae and O. acuformis. These pathogens infect and colonize the stem base, which results in lodging of diseased plants and reduced grain yield. Disease resistant cultivars are the most desirable control method, but resistance genes are limited in the wheat gene pool. Some accessions of the wheat wild relative Aegilops longissima are resistant to eyespot, but nothing is known about the genetic control of resistance. A recombinant inbred line population was developed from the cross PI 542196 (R) × PI 330486 (S) to map the resistance genes and better understand resistance in Ae. longissima. A genetic linkage map of the S(l) genome was constructed with 169 wheat microsatellite markers covering 1261.3 cM in 7 groups. F(5) lines (189) were tested for reaction to O. yallundae and four QTL were detected in chromosomes 1S(l), 3S(l), 5S(l), and 7S(l). These QTL explained 44 % of the total phenotypic variation in reaction to eyespot based on GUS scores and 63 % for visual disease ratings. These results demonstrate that genetic control of O. yallundae resistance in Ae. longissima is polygenic. This is the first report of multiple QTL conferring resistance to eyespot in Ae. longissima. Markers cfd6, wmc597, wmc415, and cfd2 are tightly linked to Q.Pch.wsu-1S ( l ), Q.Pch.wsu-3S ( l ), Q.Pch.wsu-5S ( l ), and Q.Pch.wsu-7S ( l ), respectively. These markers may be useful in marker-assisted selection for transferring resistance genes to wheat to increase the effectiveness of resistance and broaden the genetic diversity of eyespot resistance.

Quantitative trait loci for resistance to fusarium head blight in a Chinese wheat landrace Haiyanzhong

Fusarium head blight (FHB) of wheat causes not only significant reduction in grain yield and end-use quality, but also the contamination of the grain with mycotoxins that are detrimental to human and animal health after consumption of infected grain. Growing resistant varieties is an effective approach to minimize the FHB damage. The Chinese wheat landrace Haiyanzhong (HYZ) shows a high level of resistance to FHB. To identify quantitative trait loci (QTL) that contribute to FHB resistance in HYZ, 136 recombinant inbred lines (RIL) were developed from a cross of HYZ and Wheaton, a hard spring wheat cultivar from the USA. The RIL and their parents were evaluated for percentage of scabbed spikelets (PSS) in both greenhouse and field environments. Five QTL were detected for FHB resistance in HYZ with one major QTL on 7DL. The 7DL QTL peaked at SSR marker Xwmc121, which is flanked by the SSR markers Xcfd46 and Xwmc702. This QTL explained 20.4-22.6% of the phenotypic variance in individual greenhouse experiments and 15.9% in a field experiment. Four other minor QTL on 6BS (two QTL), 5AS and 1AS each explained less than 10% of the phenotypic variance in individual experiments. HYZ carried the favorable alleles associated with FHB resistance at the QTL on 7DL, 6BS and 5AS, and the unfavorable allele at the QTL on 1AS. The major QTL on 7D can be used to improve the FHB resistance in wheat breeding programs and add diversity to the FHB resistance gene pool.

Saturation and mapping of a major Fusarium head blight resistance QTL on chromosome 3BS of Sumai 3 wheat

Fusarium head blight (FHB) is a destructive disease in wheat. The major quantitative trait locus (QTL) on 3BS from Sumai 3 and its derivatives has been used as a major source of the resistance to FHB worldwide, but the discrepancy in reported location of the major QTL could block its using in map based cloning and marker assisted selection. In this study, Chinese Spring-Sumai 3 chromosome 3B substitution line was used as resistant parent of the mapping population to reduce the confounded effect of genetic background in Sumai 3. The major QTL region was saturated with the Sequence Tagged Microsatellite (STM) and Sequence Tagged Site (STS) markers. A linkage map of chromosome 3B with 36 markers covering a genetic distance of 112.4 cM was constructed. Twelve new markers were inserted into the chromosome region where the major QTL was located. The average interval distance between markers was 1.5 cM. Multiple QTL Models (MQM) mapping indicated that the major QTL was located in the interval of Xgwm533-Xsts9-1, and explained 45.6% of phenotypic variation of the resistance to FHB. The SSR (simple sequence repeat) marker Xgwm533 and STM marker Xstm748tcac are closely linked to the major QTL.

Fusarium head blight of wheat: pathogenic species and their mycotoxins

Fusarium head blight is a wheat disease of global importance and devastating impact in some years, especially in regions with high cereal production. Wheat grain contamination with mycotoxins is the result of head infection with several Fusarium pathogens. Among all metabolites accumulated in grain of wheat and other cereals infected with Fusarium culmorum and Fusarium graminearum, deoxynivalenol (DON) and other trichothecenes as well as zearalenone (ZEA) are accumulated with the highest levels and frequencies. Furthermore, moniliformin and enniatins were identified in several countries, where Fusarium avenaceum frequency was high. Several other species occurring with lower frequency have been reported. The chemotypes of individual isolates were established with the use of specific PCR markers. This review summarises the information on toxigenic Fusarium species infecting wheat heads, the morphological and molecular identification methods, toxic metabolites accumulated in the infected grain and on recent Fusarium genomic research. The interaction between the aggressive Fusarium pathogens and wheat host plant is discussed, particularly concerning the level of accumulation of DON and ZEA in grain samples. Various types of plant resistance against Fusarium head blight are described, together with wheat quantitative trait loci and DNA markers for their identification, that are useful for resistance breeding. Taking into account the risk of increased occurrence of several Fusarium mycotoxins, regulatory limits of DON, ZEA and fumonisins were established in EU, USA, Canada and other countries.

Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis

An F(4:5) population of 490 recombinant inbred lines (RILs) from the cross Apo/(2*)Swarna was used to detect quantitative trait loci (QTL) with large effects on grain yield under drought stress using bulk-segregant analysis (BSA). Swarna is an important rainfed lowland rice variety grown on millions of hectares in Asia, but is highly susceptible to drought and aerobic soil conditions. Apo is an aerobic-adapted variety with moderate tolerance to drought. Two rice microsatellite (RM) markers, RM324, and RM416, located on chromosomes 2 and 3, respectively, were shown via BSA to be strongly associated with yield under lowland drought stress. The effects of these QTL were tested in a total of eight hydrological environments over a period of 3 years. The QTL linked to RM416 (DTY(3.1)) had a large effect on grain yield under severe lowland drought stress, explaining about 31% of genetic variance for the trait (P < 0.0001). It also explained considerable variance for yield under mild stress in lowland conditions and aerobic environments. To our knowledge this is the first reported QTL that has a large effect on yield in both lowland drought and aerobic environments. The QTL linked to RM324 (DTY(2.1)) had a highly significant effect on grain yield in lowland drought stress (R(2) = 13-16%) and in two aerobic trials. The effect of these QTL on grain yield was verified to be not mainly due to phenology differences. Effects of DTY(3.1) on yield under stress have been observed in several other rice mapping populations studied at IRRI. Results of this study indicate that BSA is an effective method of identifying QTL alleles with large effects on rice yield under severe drought stress. The Apo alleles for these large-effect QTL for grain yield under drought and aerobic conditions may be immediately exploited in marker-assisted-breeding to improve the drought tolerance of Swarna.

A major QTL for resistance against Fusarium head blight in European winter wheat

We report on the verification of a resistance quantitative trait locus (QTL) on chromosome 1BL (now designated Qfhs.lfl-1BL) which had been previously identified in the winter wheat cultivar Cansas. For a more precise estimation of the QTL effect and its influence on plant height and heading date lines with a more homogeneous genetic background were created and evaluated in four environments after spray inoculation with Fusarium culmorum. Qfhs.lfl-1BL reduced FHB severity by 42% relative to lines without the resistance allele. This QTL did not influence plant height, but significantly delayed heading date by one day. All of the most resistant genotypes of the verification population carried this major QTL displaying its importance for disease resistance. This resistance QTL has not only been found in the cultivar Cansas, but also in the three European winter wheat cultivars Biscay, History and Pirat. A subsequent meta-analysis confirmed the presence of a single QTL on the long arm of chromosome 1B originating from the four mentioned cultivars. Altogether, the results of the present study indicate that Qfhs.lfl-1BL is an important component of FHB resistance in European winter wheat and support the view that this QTL would be effective and valuable in backcross breeding programmes.

Family-based mapping of quantitative trait loci in plant breeding populations with resistance to Fusarium head blight in wheat as an illustration

Traditional quantitative trait loci (QTL) mapping approaches are typically based on early or advanced generation analysis of bi-parental populations. A limitation associated with this methodology is the fact that mapping populations rarely give rise to new cultivars. Additionally, markers linked to the QTL of interest are often not immediately available for use in breeding and they may not be useful within diverse genetic backgrounds. Use of breeding populations for simultaneous QTL mapping, marker validation, marker assisted selection (MAS), and cultivar release has recently caught the attention of plant breeders to circumvent the weaknesses of conventional QTL mapping. The first objective of this study was to test the feasibility of using family-pedigree based QTL mapping techniques generally used with humans and animals within plant breeding populations (PBPs). The second objective was to evaluate two methods (linkage and association) to detect marker-QTL associations. The techniques described in this study were applied to map the well characterized QTL, Fhb1 for Fusarium head blight resistance in wheat (Triticum aestivum L.). The experimental populations consisted of 82 families and 793 individuals. The QTL was mapped using both linkage (variance component and pedigree-wide regression) and association (using quantitative transmission disequilibrium test, QTDT) approaches developed for extended family-pedigrees. Each approach successfully identified the known QTL location with a high probability value. Markers linked to the QTL explained 40-50% of the phenotypic variation. These results show the usefulness of a human genetics approach to detect QTL in PBPs and subsequent use in MAS.

Evaluation of genetic diversity of Fusarium head blight resistance in European winter wheat

Genetic diversity in relation to Fusarium head blight (FHB) resistance was investigated among 295 European winter wheat cultivars and advanced breeding lines using 47 wheat SSR markers. Twelve additional wheat lines with known FHB resistance were included as reference material. At least one SSR marker per chromosome arm, including SSR markers reported in the literature with putative associations with QTLs for FHB resistance, were assayed to give an even distribution of SSR markers across the wheat genome. A total of 404 SSR alleles were detected. The number of alleles per locus ranged from 2 to 21, with an average of 8.6 alleles. The polymorphism information content of the SSR markers ranged from 0.13 (Xwmc483) to 0.87 (Xwmc607), with an average of 0.54. Cluster analysis was performed by both genetic distance-based and model-based methods. In general, the dendrogram based on unweighted pair-group method with arithmetic averages showed similar groupings to the model-based analysis. Seven clusters were identified by the model-based method, which did not strictly correspond to geographical origin. The FHB resistance level of the wheat lines was evaluated in field trials conducted over multiple years or locations by assessing the following traits: % FHB severity, % FHB incidence, % diseased kernels, in spray inoculation trials, and % FHB spread and % wilted tips, in point inoculation trials. Association analysis between SSR markers and the FHB disease traits detected markers significantly associated with FHB resistance, including some that have not been previously reported. The percentage of variance explained by each individual marker was, however, rather low. Haplotype analysis revealed that the FHB-resistant European wheat lines do not contain the 3BS locus derived from Sumai 3. The information generated in this study will assist in the selection of parental lines in order to increase the efficiency of breeding efforts for FHB resistance.

Expression analysis of defense-related genes in wheat in response to infection by Fusarium graminearum

Fusarium head blight (FHB), caused by the fungi Fusarium graminearum and Fusarium culmorum, is a worldwide disease of wheat (Triticum aestivum L.). The Chinese cultivar Ning 7840 is one of a few wheat cultivars with resistance to FHB. GeneCalling, an open-architecture mRNA-profiling technology, was used to identify differentially expressed genes induced or suppressed in spikes of Ning 7840 after infection by F. graminearum. One hundred and twenty-five cDNA fragments representing transcripts differentially expressed in wheat spikes were identified. Based on BLASTN and BLASTX analyses, putative functions were assigned to some of the genes: 28 were assigned functions in primary metabolism and photosynthesis, 7 were involved in defense response, 14 were involved in gene expression and regulation, 24 encoded proteins associated with structure and protein synthesis, 42 lacked homology to sequences in the database, and 3 were similar to cloned multidrug resistance or disease resistance proteins. Of particular interest in this study were genes associated with resistance and defense against pathogen infection. Real-time quantitative reverse-transcription PCR indicated that of 51 genes tested, 19 showed 2-fold or greater induction or suppression in infected Ning 7840 in comparison with the water-treated control. The remaining 32 genes were not significantly induced or suppressed in infected Ning 7840 compared with the control. Subsequently, these 19 induced or suppressed genes were examined in the wheat line KS24-1, containing FHB resistance derived from Lophopyrum elongatum, and Len, an FHB-susceptible wheat cultivar. The temporal expression of some of these sequences encoding resistance proteins or defense-related proteins showed FHB (resistance specific) induction, suggesting that these genes play a role in protection against toxic compounds in plant-fungus interactions. On the basis of comprehensive expression profiling of various biotic or abiotic stress response genes revealed by quantitative PCR in this study and other supporting data, we hypothesized that the plant-pathogen interactions may be highly integrated into a network of diverse biosynthetic pathways.

Marker-based introduction of three quantitative-trait loci conferring resistance to Fusarium head blight into an independent elite winter wheat breeding population

Fusarium head blight (FHB) is one of the most important wheat diseases that causes yield and quality losses as well as contamination with deoxynivalenol (DON). This study aimed for marker-based introduction of three previously mapped QTLs from two German winter wheat resistance sources into an elite background unrelated to the mapping population. A double cross (DC) served as initial population that combined two resistance donor-QTL alleles from "Dream" (Qfhs.lfl-6AL, Qfhs.lfl-7BS) and one donor-QTL allele from "G16-92" on chromosome 2BL with two high yielding, susceptible elite winter wheats ("Brando", "LP235.1"). The initial population of 600 DC-derived F(1) lines was selected with SSR markers for the respective QTLs. After two marker-selection steps, each of eight marker classes was represented by 9-22 lines possessing the respective donor-QTL allele or all possible combinations thereof in the homozygous state. The effect of the QTLs was estimated by field tests at four locations inoculated with Fusarium culmorum. Resistance was measured as the mean of multiple FHB ratings (0-100%). Marker classes incorporating only one QTL were not significantly more resistant than the class without any QTL, the combination of two donor-QTL alleles reduced FHB significantly. On average, lines with Qfhs.lfl-6AL were significantly taller than lines without this QTL. A considerable variation for FHB resistance was found in all marker classes. Marker-based introduction of two QTLs enhanced mean FHB rating by about 40 percentage points, the selected plants, however, were, on average, significantly taller. Both findings strongly support a phenotypic selection following after marker-based introduction of effective QTLs.

QTL analysis of resistance to Fusarium head blight in the novel wheat germplasm CJ 9306. I. Resistance to fungal spread

Fusarium head blight (FHB or scab) caused by Fusarium species is a destructive disease in wheat and barley worldwide. The objectives of our study were to identify quantitative trait loci (QTLs) for resistance to FHB spread (Type II resistance) and to quantify the magnitude of their effects in a novel highly resistant wheat germplasm, CJ 9306. A set of 152 F(7) recombinant inbred lines (RILs) derived from a cross Veery/CJ 9306 and two parents were evaluated for FHB resistance by single-floret inoculation in three greenhouse experiments in 2002 and 2004. Percentage (PSS) and number (NSS) of scabby spikelets at 25 days post-inoculation were analyzed. In total 682 simple sequence repeat (SSR) markers were screened for polymorphism between the two parents, and a genetic linkage map was constructed with 208 polymorphic markers. Ten QTLs associated with FHB resistance were detected, five from CJ 9306 and five from Veery. The major QTL on 3BS (QFhs.ndsu-3BS) was validated in CJ 9306, exhibiting greatest additive effects and explained 30.7% of phenotypic variation for PSS on the overall average of three experiments. Another major QTL on 2DL (QFhs.nau-2DL) from CJ 9306 explained 9.9-28.4% of phenotypic variation, with a significant QTL x environment interaction. QFhs.nau-1AS and QFhs.nau-7BS showed lower additive effects and explained lower variance (4.5-9.5%). A QTL on 5AS, decreasing PSS by 10.3% on average, was validated by simple marker analysis and joint trait/experiment IM/CIM analysis despite insignificance for single-experiment IM and CIM analyses. Likewise, QFhs.nau-2BL and QFhs.nau-1BC from Veery could reduce PSS by 13.2 and 11.4%, respectively. The effects of other three minor QTLs from Veery were significant for one experiment and combined analysis. Comparisons of two- and three-locus combinations suggested that the effects of FHB resistance QTLs/genes could be accumulated, and the resistance could be feasibly enhanced by selection of favorable alleles for multiple loci. Four two-locus combinations and two three-locus combinations were suggested as the preferential choices in practical marker-assisted selection program.

QTL analysis of resistance to Fusarium head blight in the novel wheat germplasm CJ 9306. II. Resistance to deoxynivalenol accumulation and grain yield loss

Fusarium head blight (FHB or scab) caused by Fusarium species is a destructive disease in wheat, not only causing dramatic decrease of grain yield and quality, but also leading to serious mycotoxin contamination in the infected grains. This study was conducted to identify and quantify quantitative trait loci (QTLs) contributing to resistance to deoxynivalenol (DON) accumulation as well as to grain yield loss in a population of 152 F(7) recombinant inbred lines (RILs) derived from the cross Veery/CJ 9306. DON content in scabby grains and relative decreases of yield components were analyzed. Two new QTLs (QFhs.nau-2DL and QFhs.nau-1AS) for resistance to DON accumulation caused by FHB in wheat were detected, and QTLs QFhs.ndsu-3BS and QFhs.nau-5AS were also validated in CJ 9306, based on a constructed genetic linkage map. On the average of three experiments, major QTLs QFhs.ndsu-3BS and QFhs.nau-2DL explained up to 23 and 20% of phenotypic variation, respectively. QFhs.nau-1AS and QFhs.nau-5AS separately explained 4-6% of phenotypic variation. The differences among years/experiments were significant for all the four QTLs. However, the QTL x environment interaction was significant only for QFhs.nau-2DL, but not for the others. The results suggest that simple sequence repeat (SSR) markers Xgwm533b associated with QFhs.ndsu-3BS, and Xgwm539 associated with QFhs.nau-2DL could be used in marker-assisted selection to enhance resistance to DON accumulation. QFhs.ndsu-3BS + QFhs.nau-2DL and QFhs.nau-2DL + QFhs.nau-5AS would be the optimum choices for two-locus combinations. QFhs.ndsu-3BS was also validated in CJ 9306 for resistance to grain yield loss, explaining 8-15% of phenotypic variation. No QTLs for resistance to DON accumulation or grain yield loss independent of Type II resistance were found. By comparison, however, either of QFhs.nau-2DL or QFhs.nau-5AS alone and their combination were more contributive to resistance to DON accumulation than to Type II resistance.

QTL associated with Fusarium head blight resistance in the soft red winter wheat Ernie

Fusarium head blight (FHB), mainly caused by Fusarium graminearum Schwabe [telomorph: Gibberella zeae Schw. (Petch)], is an increasingly important disease of wheat (Triticum aestivum L.). Host-plant resistance provides the best hope for reducing economic losses associated with FHB, but new sources of resistance are limited. The moderately resistant winter wheat cultivar, Ernie, may provide a source of resistance that differs from Sumai 3 but these genes have not been mapped. Also hindering resistance breeding may be associations of resistance with agronomic traits such as late maturity that may be undesirable in some production environments. This research was conducted to identify QTL associated with type II FHB resistance (FHB severity, FHBS), and to determine if they are associated with days to anthesis (DTA), number of spikelets (NOS), and the presence/absence of awns. Two hundred and forty-three F(8) recombinant inbred lines from a cross between the resistant cultivar, Ernie and susceptible parent, MO 94-317 were phenotyped for type II FHB resistance using point inoculation in the greenhouse during 2002 and 2003. Genetic linkage maps were constructed using 94 simple sequence repeat (SSR) and 146 amplified fragment length polymorphic (AFLP) markers. Over years four QTL regions on chromosomes 2B, 3B, 4BL and 5A were consistently associated with FHB resistance. These QTL explained 43.3% of the phenotypic variation in FHBS. Major QTL conditioning DTA and NOS were identified on chromosome 2D. Neither the QTL associated with DTA and NOS nor the presence/absence of awns were associated with FHB resistance in Ernie. Our results suggest that the FHB resistance in Ernie appears to differ from that in Sumai 3, thus pyramiding the QTL in Ernie with those from Sumai 3 could result in enhanced levels of FHB resistance in wheat.

Mapping of Fhb2 on chromosome 6BS: a gene controlling Fusarium head blight field resistance in bread wheat (Triticum aestivum L.)

Fusarium head blight (FHB) is one of the most important fungal wheat diseases worldwide. Understanding the genetics of FHB resistance is key to facilitate the introgression of different FHB resistance genes into adapted wheat. The objective of this project was to study the FHB resistance QTL on chromosome 6B, quantify the phenotypic variation, and qualitatively map the resistance gene as a Mendelian factor. The FHB resistant parent BW278 (AC Domain*2/Sumai 3) was used as the source of the resistance allele. A large recombinant inbred line (RIL) mapping population was developed from the cross BW278/AC Foremost. The population segregated for three known FHB resistance QTL located on chromosomes 3BSc, 5A, and 6B. Molecular markers on chromosome 6B (WMC104, WMC397, GWM219), 5A (GWM154, GWM304, WMC415), and 3BS (WMC78, GWM566, WMC527) were amplified on approximately 1,440 F2:7 RILs. The marker information was used to select 89 RILs that were fixed homozygous susceptible for the 3BSc and 5A FHB QTLs and were recombinant in the 6B interval. Disease response was evaluated on 89 RILs and parental checks in the greenhouse and field nurseries. Dual floret injection (DFI) was used in greenhouse trials to evaluate disease severity (DS). Macroconidial spray inoculations were used in field nurseries conducted at two locations in southern Manitoba (Carman and Glenlea) over two years 2003 and 2004, to evaluate disease incidence, disease severity, visual rating index, and Fusarium-damaged kernels. The phenotypic distribution for all five-disease infection measurements was bimodal, with lines resembling either the resistant or susceptible checks and parents. All of the four field traits for FHB resistance mapped qualitatively to a coincident position on chromosome 6BS, flanked by GWM133 and GWM644, and is named Fhb2. The greenhouse-DS trait mapped 2 cM distal to Fhb2. Qualitative mapping of Fhb2 in wheat provides tightly linked markers that can reduce linkage drag associated with marker assisted selection of Fhb2 and aid the pyramiding of different resistance loci for wheat improvement.

The effect of 3BS locus of Sumai 3 on Fusarium head blight resistance in Australian wheats

The 3BS allele of Sumai 3 has been the main source of Fusarium head blight (FHB) resistance worldwide. Using molecular markers and FHB resistance screenings, we have analysed the effects of this allele in two backcross and two 4-way F2 populations derived from elite Australian cultivars. Compared to individuals without the Sumai 3 allele, individuals with the allele showed an average 32.0% reduction in FHB severity as measured by number of diseased spikelets. This value was slightly reduced to 29.2% when the total number of spikelets was taken into account by expressing severity as the proportion of diseased spikelets. When compared to the parental cultivars, progeny with the 3BS allele of Sumai 3 offered, on average, 43.3% reduction in FHB severity. Significant differences were not detected between progeny that were homozygous or heterozygous for the 3BS locus, indicating a dominant inheritance of this locus. These results confirm that the 3BS allele controls a large component of the FHB resistance in Sumai 3, which can be readily incorporated and detected in backcross populations using molecular markers. The materials derived from this study could offer significant benefits to the Australian wheat breeding programs.

Deletion of a Chromosome Arm Altered Wheat Resistance to Fusarium Head Blight and Deoxynivalenol Accumulation in Chinese Spring

Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe, is an important disease of wheat worldwide. Production of deoxynivalenol (DON) in infected wheat grain by F. graminearum is a major safety concern when considering use of the grain as feed for livestock or for human consumption. Determining chromosome locations of FHB-related genes may facilitate enhancement of wheat resistance to FHB and DON accumulation. In this study, a set of 30 ditelosomic lines derived from Chinese Spring, a moderately FHB-resistant landrace from China, were evaluated for proportion of scabbed spikelets per inoculated spike in the greenhouse and for DON contamination in harvested grain over 2 years. Significant variation in the proportion of scabbed spikelets was observed among ditelosomic lines, ranging from 13 to 95%. Seven ditelosomic lines exhibited a greater proportion of scabbed spikelets and three of these also had greater DON content than Chinese Spring (P = 0.01), suggesting that those missing chromosome arms may carry genes that contribute to resistance to FHB. Six ditelosomic lines had a reduction in proportion of scabbed spikelets, suggesting that susceptibility factors or resistance suppressors may be on these missing chromosomal arms. Selection for low proportion of scabbed spikelets in general will select for low DON content.

A resistance-like gene identified by EST mapping and its association with a QTL controllingFusariumhead blight infection on wheat chromosome 3BS

Fusarium head blight (FHB) is a major disease in the wheat growing regions of the world. A quantitative trait locus (QTL) on the short arm of chromosome 3B controls much of the variation for resistance. The cloning of candidate disease-resistance genes for FHB QTLs on chromosome 3B can provide further elucidation of the mechanisms that control resistance. However, rearrangements and divergence during plant genome evolution often hampers the identification of sequences with similarity to known disease-resistance genes. This study focuses on the use of wheat expressed sequence tags (ESTs) that map to the region on chromosome 3B containing the QTL for FHB resistance and low-stringency BLAST searching to identify sequences with similarity to known disease-resistance genes. One EST rich with leucine repeats and low similarity to a protein kinase domain of the barley Rpg1 gene was identified. Genetic mapping using a Ning894037 × Alondra recombinant inbred (RI) population showed that this EST mapped to the QTL on the short arm of chromosome 3B and may represent a portion of a newly diverged gene contributing to FHB resistance. The EST is a new marker suitable for marker-assisted selection and provides a starting point to begin map-based cloning for chromosome walking and investigate new diverged genes at this locus.Key words: Fusarium head blight resistance, expressed sequence tags, quantitative trait loci, Rpg1, wheat.

Main effects, epistasis, and environmental interactions of quantitative trait Loci for fusarium head blight resistance in a recombinant inbred population

ABSTRACT Chinese Spring Sumai 3 chromosome 7A disomic substitution line (CS-SM3-7ADS) is highly resistant to Fusarium head blight (FHB), and an F(7) population of recombinant inbred lines derived from the cross CS-SM3-7ADS x Annong 8455 was evaluated for resistance to FHB to investigate main effects, epistasis, and environmental interactions of quantitative trait loci (QTLs) for FHB resistance. A molecular linkage map consists of 501 simple sequence repeat and amplified fragment length polymorphism markers. A total of 10 QTLs were identified with significant main effects on the FHB resistance using MapQTL and QTLMapper software. Among them, CS-SM3-7ADS carries FHB-resistance alleles at five QTLs on chromosomes 2D, 3B, 4D, and 6A. One QTL on 3BS had the largest effect and explained 30.2% of the phenotypic variance. Susceptible QTLs were detected on chromosomes 1A, 1D, 4A, and 4B. A QTL for enhanced FHB resistance was not detected on chromosome 7A of CS-SM3-7ADS; therefore, the increased FHB resistance in CS-SM3-7ADS was not due to any major FHB-resistance QTL on 7A of Sumai 3, but more likely was due to removal of susceptible alleles of QTLs on 7A of Chinese Spring. QTLMapper detected nine pairs of additive-additive interactions at 17 loci that explained 26% phenotypic variance. QTL-environment interactions explained 49% of phenotypic variation, indicating that the environments significantly affected the expression of the QTLs, especially these epistasis QTLs. Adding FHB-enhancing QTLs or removal of susceptible QTLs both may significantly enhance the degree of wheat resistance to FHB in a wheat cultivar.

Mapping QTL associated with resistance to Fusarium head blight in the Nanda2419 x Wangshuibai population. II: type I resistance

Fusarium head blight (FHB) is a serious disease in wheat and barley affecting both yield and quality. To identify genes for resistance to infection, the RIL population derived from 'Nanda2419' x 'Wangshuibai' and the parents were evaluated for percentage of infected spikes (PIS) in four different environments. Using a 2,960 cM marker framework map constructed for this population, ten chromosome regions were detected for their association with type I resistance through interval mapping with Mapmaker/QTL, among which QTLs mapped in the intervals of Xwmc349--Xgwm149 on chromosome 4B, of Xwmc96--Xgwm304 on chromosome 5A and of Xgwm408--Xbarc140 on chromosome 5B were revealed in at least three environments and have Wangshuibai as the source of resistance alleles. Qfhi.nau-4B and Qfhi.nau-5A had larger effects and explained up to 17.5 and 27.0% of the phenotypic variance, respectively. To detect epistasis QTLs, two-locus interactions were examined by whole genome scan. Interactions of five locus pairs were found to have significant effects on type I resistance with the LOD score ranging 3.8-6.5 and four of them conferred resistance in parental phase. The one with the most significant effect was Xcfd42--Xgwm469 (6D)/Xwmc390-2--Xbd04 (2A) pair. No QTL x E interaction was detected for PIS. It was found that flowering time did not have significant effects on PIS in this population. Our studies indicated that Wangshuibai is useful for breeding for both type I and type II scab resistance and the markers associated with the QTLs could be used in marker-assisted selection and isolation of scab-resistance QTLs.

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.

Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust

The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n = 409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods-resampling, selective genotyping, and selective phenotyping-to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping.

Identification of type I resistance to Fusarium head blight controlled by a major gene located on chromosome 4A of Triticum macha

Using a set of 21 substitution lines of Triticum macha in a 'Hobbit Sib' background, it was previously demonstrated that chromosome 4A of T. macha carries significant resistance to Fusarium head blight. In the present study, the T. macha 4A resistance was further characterized in a 'Hobbit Sib' (T. macha 4A) single-recombinant chromosome doubled haploid (DH) population. Lines were phenotyped for disease resistance, yield components and deoxynivalenol (DON) mycotoxin content over two consecutive seasons. Both resistance to spread and resistance to initial infection were examined, and it was established that the resistance residing on T. macha 4A is predominantly of type I (resistance to initial infection). It was demonstrated that this type I resistance significantly lowered levels of DON accumulation in the grain and improved yield components under high disease pressure. Genotyping the DH lines using microsatellite genetic markers enabled the location of the gene(s) for resistance to be assigned to a region of the short arm of chromosome 4A, distal to microsatellite marker Xgwm601 and co-segregating with microsatellite marker Xgwm165 in this population.

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 characterization of Fusarium head blight resistance in Wangshuibai with simple sequence repeat and amplified fragment length polymorphism markers

Molecular mapping of Fusarium head blight (FHB) resistance quantitative trait loci (QTL) and marker-assisted selection of these QTL will aid in the development of resistant cultivars. Most reported FHB resistance QTL are from 'Sumai 3' and its derivatives. 'Wangshuibai' is a FHB-resistant landrace that originated from China and is not known to be related to 'Sumai 3'. A mapping population of 139 F(5:6) recombinant inbred lines was developed from a cross of 'Wangshuibai' and 'Wheaton'. This population was developed to map the FHB-resistant QTL in 'Wangshuibai' and was evaluated twice for Type II FHB resistance. A total of 1196 simple sequence repeat and amplified fragment length polymorphism markers were screened on this population, and four FHB resistance QTL were detected. A major QTL near the end of 3BS explained 37.3% of the phenotypic variation. Another QTL on 3BS, located close to the centromere, explained 7.4% of the phenotypic variation. Two additional QTL on 7AL and 1BL explained 9.8% and 11.9% of the phenotypic variation, respectively. The simple sequence repeat and amplified fragment length polymorphism markers closely linked to these QTL may be useful for stacking QTL from 'Wangshuibai' and other sources to develop cultivars with transgressive FHB resistance.