Detection and validation of a novel major QTL for resistance to Fusarium head blight from Triticum aestivum in the terminal region of chromosome 7DL

Recent advances on genome-wide association studies (GWAS) and genomic selection (GS); prospects for Fusarium head blight research in Durum wheat

PURPOSE

Wheat is an important cereal crop that is cultivated in different parts of the world. The biotic stresses are the major concerns in wheat-growing nations and are responsible for production loss globally. The change in climate dynamics makes the pathogen more virulent in foothills and tropical regions. There is growing concern about FHB in major wheat-growing nations, and until now, there has been no known potential source of resistance identified in wheat germplasm. The plant pathogen interaction activates the cascade of pathways, genes, TFs, and resistance genes. Pathogenesis-related genes' role in disease resistance is functionally validated in different plant systems. Similarly, Genomewide association Studies (GWAS) and Genomic selection (GS) are promising tools and have led to the discovery of resistance genes, genomic regions, and novel markers. Fusarium graminearum produces deoxynivalenol (DON) mycotoxins in wheat kernels, affecting wheat productivity globally. Modern technology now allows for detecting and managing DON toxin to reduce the risk to humans and animals. This review offers a comprehensive overview of the roles played by GWAS and Genomic selection (GS) in the identification of new genes, genetic variants, molecular markers and DON toxin management strategies.

METHODS

The review offers a comprehensive and in-depth analysis of the function of Fusarium graminearum virulence factors in Durum wheat. The role of GWAS and GS for Fusarium Head Blight (FHB) resistance has been well described. This paper provides a comprehensive description of the various statistical models that are used in GWAS and GS. In this review, we look at how different detection methods have been used to analyze and manage DON toxin exposure.

RESULTS

This review highlights the role of virulent genes in Fusarium disease establishment. The role of genome-based selection offers the identification of novel QTLs in resistant wheat germplasm. The role of GWAS and GS selection has minimized the use of population development through breeding technology. Here, we also emphasized the function of recent technological developments in minimizing the impact of DON toxins and their implications for food safety.

Genetic basis of maize kernel protein content revealed by high-density bin mapping using recombinant inbred lines

Maize with a high kernel protein content (PC) is desirable for human food and livestock fodder. However, improvements in its PC have been hampered by a lack of desirable molecular markers. To identify quantitative trait loci (QTL) and candidate genes for kernel PC, we employed a genotyping-by-sequencing strategy to construct a high-resolution linkage map with 6,433 bin markers for 275 recombinant inbred lines (RILs) derived from a high-PC female Ji846 and low-PC male Ye3189. The total genetic distance covered by the linkage map was 2180.93 cM, and the average distance between adjacent markers was 0.32 cM, with a physical distance of approximately 0.37 Mb. Using this linkage map, 11 QTLs affecting kernel PC were identified, including qPC7 and qPC2-2, which were identified in at least two environments. For the qPC2-2 locus, a marker named IndelPC2-2 was developed with closely linked polymorphisms in both parents, and when tested in 30 high and 30 low PC inbred lines, it showed significant differences (P = 1.9E-03). To identify the candidate genes for this locus, transcriptome sequencing data and PC best linear unbiased estimates (BLUE) for 348 inbred lines were combined, and the expression levels of the four genes were correlated with PC. Among the four genes, Zm00001d002625, which encodes an S-adenosyl-L-methionine-dependent methyltransferase superfamily protein, showed significantly different expression levels between two RIL parents in the endosperm and is speculated to be a potential candidate gene for qPC2-2. This study will contribute to further research on the mechanisms underlying the regulation of maize PC, while also providing a genetic basis for marker-assisted selection in the future.

Arms Race between the Host and Pathogen Associated with Fusarium Head Blight of Wheat

Fusarium head blight (FHB), or scab, caused by Fusarium species, is an extremely destructive fungal disease in wheat worldwide. In recent decades, researchers have made unremitting efforts in genetic breeding and control technology related to FHB and have made great progress, especially in the exploration of germplasm resources resistant to FHB; identification and pathogenesis of pathogenic strains; discovery and identification of disease-resistant genes; biochemical control, and so on. However, FHB burst have not been effectively controlled and thereby pose increasingly severe threats to wheat productivity. This review focuses on recent advances in pathogenesis, resistance quantitative trait loci (QTLs)/genes, resistance mechanism, and signaling pathways. We identify two primary pathogenetic patterns of Fusarium species and three significant signaling pathways mediated by UGT, WRKY, and SnRK1, respectively; many publicly approved superstar QTLs and genes are fully summarized to illustrate the pathogenetic patterns of Fusarium species, signaling behavior of the major genes, and their sophisticated and dexterous crosstalk. Besides the research status of FHB resistance, breeding bottlenecks in resistant germplasm resources are also analyzed deeply. Finally, this review proposes that the maintenance of intracellular ROS (reactive oxygen species) homeostasis, regulated by several TaCERK-mediated theoretical patterns, may play an important role in plant response to FHB and puts forward some suggestions on resistant QTL/gene mining and molecular breeding in order to provide a valuable reference to contain FHB outbreaks in agricultural production and promote the sustainable development of green agriculture.

Chile Pepper (Capsicum) Breeding and Improvement in the "Multi-Omics" Era

Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have "defined" the state of New Mexico, USA. The official state question, "Red or Green?" refers to the preference for either red or the green stage of chile pepper, respectively, reflects the value of these important commodities. The presence of major diseases, low yields, decreased acreages, and costs associated with manual labor limit production in all growing regions of the world. The New Mexico State University (NMSU) Chile Pepper Breeding Program continues to serve as a key player in the development of improved chile pepper varieties for growers and in discoveries that assist plant breeders worldwide. Among the traits of interest for genetic improvement include yield, disease resistance, flavor, and mechanical harvestability. While progress has been made, the use of conventional breeding approaches has yet to fully address producer and consumer demand for these traits in available cultivars. Recent developments in "multi-omics," that is, the simultaneous application of multiple omics approaches to study biological systems, have allowed the genetic dissection of important phenotypes. Given the current needs and production constraints, and the availability of multi-omics tools, it would be relevant to examine the application of these approaches in chile pepper breeding and improvement. In this review, we summarize the major developments in chile pepper breeding and present novel tools that can be implemented to facilitate genetic improvement. In the future, chile pepper improvement is anticipated to be more data and multi-omics driven as more advanced genetics, breeding, and phenotyping tools are developed.

Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.)

BACKGROUND

Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between 'Criollo de Morellos-334' (CM-334), a resistant landrace from Mexico, and 'Early Jalapeno', a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified.

RESULTS

Development of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified.

CONCLUSIONS

Results support the genetic complexity of the P. capsici-Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.

Genetic control of Fusarium head blight resistance in two Yangmai 158-derived recombinant inbred line populations

Stably expressed type I and type II resistance QTL were identified using two Yangmai 158-derived RIL populations, and plant-height and flowering-time QTL intervals detected did not contribute to the FHB resistance variations. Yangmai 158 (Y158) is an elite wheat cultivar widely grown in China with stable Fusarium head blight (FHB) resistance. To enrich the genetic basis underlying FHB resistance, QTL mapping was conducted using two recombinant inbred line (RIL) populations derived from crosses of Y158 with susceptible lines Annong 8455 and Veery. Survey with makers linked to Fhb1, Fhb2, Fhb4 and Fhb5 in resistance cultivar Wangshuibai indicated that both Y158 and the susceptible lines do not contain these QTL. The RIL populations were surveyed with 65 PCR markers and 55 K chip, which generated 23,159 valid marker data, to produce genetic maps for whole genome scanning of quantitative trait loci (QTL). A total of six QTL, all with the Y158 alleles for better resistance and including one stably expressed QTL for type I resistance (Qfhi.nau-2D) and one stably expressed QTL for type II resistance (Qfhs.nau-2A), were identified. Moreover, taking advantage of the great genetic variations in plant height and flowering time, QTL conditioning these two traits were determined. Of six plant-height QTL and three flowering-time QTL intervals detected, none were associated with FHB resistance. The FHB resistance QTL in Y158 were shown to be useful alternatives in FHB resistance breeding programs. The SNP markers flanking Qfhs.nau-2A and Qfhi.nau-2D have been converted to breeder-friendly PCR-based markers to facilitate their applications.

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.

Introgression of Thinopyrum elongatum DNA fragments carrying resistance to fusarium head blight into Triticum aestivum cultivar Chinese Spring is associated with alteration of gene expression

The tall wheatgrass species Thinopyrum elongatum carries on the long arm of chromosome 7E, a locus that contributes strongly to resistance to fusarium head blight (FHB), a devastating fungal disease affecting wheat crops in all temperate areas of the world. Introgression of Th. elongatum 7E chromatin into chromosome 7D of wheat was induced by the ph1b mutant of CS. Recombinants between chromosome 7E and wheat chromosome 7D, induced by the ph1b mutation, were monitored by a combination of molecular markers and phenotyping for FHB resistance. Progeny of up to five subsequent generations derived from two lineages, 64-8 and 32-5, were phenotyped for FHB symptoms and genotyped using published and novel 7D- and 7E-specific markers. Fragments from the distal end of 7EL, still carrying FHB resistance and estimated to be less than 114 and 66 Mbp, were identified as introgressed into wheat chromosome arm 7DL of progeny derived from 64-8 and 32-5, respectively. Gene expression analysis revealed variation in the expression levels of genes from the distal ends of 7EL and 7DL in the introgressed progeny. The 7EL introgressed material will facilitate the use of the 7EL FHB resistance locus in wheat breeding programs.

Molecular cytogenetic characterization and fusarium head blight resistance of five wheat-Thinopyrum intermedium partial amphiploids

Background

Partial amphiploids created by crossing octoploid tritelytrigia(2n = 8× = 56, AABBDDEE) and Thinopyrum intermedium (2n = 6× = 42, StStJJJ^SJ^S) are important intermediates in wheat breeding because of their resistance to major wheat diseases. We examined the chromosome compositions of five wheat-Th. intermedium partial amphiploids using GISH and multicolor-FISH.

Results

The result revealed that five lines had 10-14 J-genome chromosomes from Th. intermedium and 42 common wheat chromosomes, using the J-genomic DNA from Th. bessarabicum as GISH probe and the oligo probes pAs1-1, pAs1-3, AFA-4, (GAA) 10, and pSc119.2-1 as FISH probe. Five lines resembled their parent octoploid tritelytrigia (2n = 8× = 56, AABBDDEE) but had higher protein contents. Protein contents of two lines HS2-2 and HS2-5 were up to more than 20%. Evaluation of Fusarium head blight (FHB) resistance revealed that the percent of symptomatic spikelets (PSS) of these lines were below 30%. Lines HS2-2, HS2-4, HS2-5, and HS2-16 were less than 20% of PPS. Line HS2-5 with 14 J-genome chromosomes from Th. intermedium showed the best disease resistance, with PSS values of 10.8% and 16.6% in 2016 and 2017, respectively.

Conclusions

New wheat-Th. intermedium amphiploids with the J-genome chromosomes were identified and can be considered as a valuable source of FHB resistance in wheat breeding.

Identification of quantitative trait loci for Fusarium head blight (FHB) resistance in the cross between wheat landrace N553 and elite cultivar Yangmai 13

Fusarium head blight (FHB) of wheat poses a serious threat to food security in the Yellow-Huai River Valley Winter Wheat Region (YHW) of China. Discovery of new resistant quantitative trait loci (QTLs) or genes and application of them to highly susceptible varieties in the YHW are of great significance for ensuring the grain yield. Here, 160 recombinant inbred lines (RILs) from the cross between N553 (resistant) and Yangmai 13 (moderately susceptible) were used to evaluate FHB resistance by point inoculation, spray inoculation, and natural infection. A high-density genetic map was constructed by using a 15K SNP array and 128 polymorphism SSR markers. A total of 1452 polymorphic markers were identified, which formed 21 linkage groups and covered a total of 3555.1 cM in length. Two and four QTLs respectively related to type I and type II resistance were detected, among which QFhb-hnau.3BS.1 and QFhb-hnau.2DL were stably identified in most environments in Yangzhou and Zhengzhou, whereas QFhbn-hnau.5AL was only identified under natural infection in Jianyang. Based on the physical position (IWGSC RefSeq v1.0), QFhb-hnau.3BS.1 from the landrace N553 is likely to be Fhb1, while QFhb-hnau.2DL from Yangmai 13 may be a novel QTL. Significantly higher FHB resistance was observed in the lines with both QFhb-hnau.3BS.1 and QFhb-hnau.2DL, indicating that these two QTLs have apparent additive effects, and the RILs harboring both the two QTLs may have great application potential for the improvement of FHB resistance in wheat breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01220-5.

Updating the Breeding Philosophy of Wheat to Fusarium Head Blight (FHB): Resistance Components, QTL Identification, and Phenotyping-A Review

Fusarium head blight has posed continuous risks to wheat production worldwide due to its effects on yield, and the fungus provides additional risks with production of toxins. Plant resistance is thought to be the most powerful method. The host plant resistance is complex, Types I–V were reported. From the time of spraying inoculation (Type I), all resistance types can be identified and used to determine the total resistance. Type II resistance (at point inoculation) describes the spread of head blight from the ovary to the other parts of the head. Therefore, it cannot solve the resistance problem alone. Type II QTL (quantitative trait locus) Fhb1 on 3BS from Sumai 3 descendant CM82036 secures about the same resistance level as Type I QTL does on 5AS and 5ASc in terms of visual symptoms, FDK (Fusarium damaged kernel), and deoxynivalenol response. Recently, increasing evidence supports the association of deoxynivalenol (DON) content and low kernel infection with FHB (Fusarium head blight) resistance (Types III and IV), as QTL for individual resistance types has been identified. In plant breeding practice, the role of visual selection remains vital, but the higher correlations for FDK/DON make it possible to select low-DON genotypes via FDK value. For phenotyping, the use of more independent inocula (isolates or mixtures) makes resistance evaluation more reliable. The large heterogeneity of the mapping populations is a serious source of underestimating genetic effects. Therefore, the increasing of homogeneity is a necessity. As no wheat varieties exist with full resistance to FHB, crops must be supported by proper agronomy and fungicide use.

Genetic Characterization of Multiple Components Contributing to Fusarium Head Blight Resistance of FL62R1, a Canadian Bread Wheat Developed Using Systemic Breeding

Fusarium head blight (FHB) is a devastating fungal disease of small-grain cereals that results in severe yield and quality losses. FHB resistance is controlled by resistance components including incidence, field severity, visual rating index, Fusarium damaged kernels (FDKs), and the accumulation of the mycotoxin deoxynivalenol (DON). Resistance conferred by each of these components is partial and must be combined to achieve resistance sufficient to protect wheat from yield losses. In this study, two biparental mapping populations were analyzed in Canadian FHB nurseries and quantitative trait loci (QTL) mapped for the traits listed above. Nine genomic loci, on 2AS, 2BS, 3BS, 4AS, 4AL, 4BS, 5AS, 5AL, and 5BL, were enriched for the majority of the QTL controlling FHB resistance. The previously validated FHB resistance QTL on 3BS and 5AS affected resistance to severity, FDK, and DON in these populations. The remaining seven genomic loci colocalize with flowering time and/or plant height QTL. The QTL on 4B was a major contributor to all field resistance traits and plant height in the field. QTL on 4AL showed contrasting effects for FHB resistance between Eastern and Western Canada, indicating a local adapted resistance to FHB. In addition, we also found that the 2AS QTL contributed a major effect for DON, and the 2BS for FDK, while the 5AL conferred mainly effect for both FDK/DON. Results presented here provide insight into the genetic architecture underlying these resistant components and insight into how FHB resistance in wheat is controlled by a complex network of interactions between genes controlling flowering time, plant height, local adaption, and FHB resistance components.

A Comparative Transcriptome Analysis, Conserved Regulatory Elements and Associated Transcription Factors Related to Accumulation of Fusariotoxins in Grain of Rye (Secale cereale L.) Hybrids

Detoxification of fusariotoxin is a type V Fusarium head blight (FHB) resistance and is considered a component of type II resistance, which is related to the spread of infection within spikes. Understanding this type of resistance is vital for FHB resistance, but to date, nothing is known about candidate genes that confer this resistance in rye due to scarce genomic resources. In this study, we generated a transcriptomic resource. The molecular response was mined through a comprehensive transcriptomic analysis of two rye hybrids differing in the build-up of fusariotoxin contents in grain upon pathogen infection. Gene mining identified candidate genes and pathways contributing to the detoxification of fusariotoxins in rye. Moreover, we found cis regulatory elements in the promoters of identified genes and linked them to transcription factors. In the fusariotoxin analysis, we found that grain from the Nordic seed rye hybrid "Helltop" accumulated 4 times higher concentrations of deoxynivalenol (DON), 9 times higher nivalenol (NIV), and 28 times higher of zearalenone (ZEN) than that of the hybrid "DH372" after artificial inoculation under field conditions. In the transcriptome analysis, we identified 6675 and 5151 differentially expressed genes (DEGs) in DH372 and Helltop, respectively, compared to non-inoculated control plants. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that DEGs were associated with glycolysis and the mechanistic target of rapamycin (mTOR) signaling pathway in Helltop, whereas carbon fixation in photosynthesis organisms were represented in DH372. The gene ontology (GO) enrichment and gene set enrichment analysis (GSEA) of DEGs lead to identification of the metabolic and biosynthetic processes of peptides and amides in DH372, whereas photosynthesis, negative regulation of catalytic activity, and protein-chromophore linkage were the significant pathways in Helltop. In the process of gene mining, we found four genes that were known to be involved in FHB resistance in wheat and that were differentially expressed after infection only in DH372 but not in Helltop. Based on our results, we assume that DH372 employed a specific response to pathogen infection that led to detoxification of fusariotoxin and prevented their accumulation in grain. Our results indicate that DH372 might resist the accumulation of fusariotoxin through activation of the glycolysis and drug metabolism via cytochrome P450. The identified genes in DH372 might be regulated by the WRKY family transcription factors as associated cis regulatory elements found in the in silico analysis. The results of this study will help rye breeders to develop strategies against type V FHB.

Identification of New Sources of Resistance to Crown Rot and Fusarium Head Blight in Wheat

Crown rot (CR) and Fusarium head blight (FHB) are two serious wheat diseases caused by Fusarium pathogens in China. To identify new resistant sources for CR and FHB, 205 Chinese wheat cultivars collected from Huang-Huai wheat-growing region in China were screened for resistance. Cunmai633, LS4607, Pubing01, and Hongyun2 showed seedling resistance to CR with disease index (DI) less than 0.25. Sixteen cultivars showed adult-plant resistance to CR with DI lower than 0.10. Twenty-six cultivars showed moderate resistance to CR at seedling stage with DI from 0.26 to 0.35, and 63 cultivars showed moderate adult-plant resistance with DI from 0.11 to 0.20. Among them, Cunmai633, LS4607, Pubing01, Xinong916, Zhengda161, Xumai14017, Zhengpinmai30, Bainong8822, Jimai216, Huacheng865, Fengyumai5, and Tianmin319 showed resistance or moderate resistance to CR at both seedling and adult plant stages, with Cunmai633 showing the best resistance. Most of the cultivars (>76%) were susceptible to FHB in both the 2017 and 2018 experiments with DI > 0.40. However, some cultivars demonstrated excellent FHB resistance. For example, Zhongyu1526, Tianminxiaoyan369, and Yangao168 were resistant (DI ≤ 0.25) in 2017 and moderately resistant (0.26 ≤ DI ≤ 0.40) in 2018; Zhongwo9 was moderately resistant in 2017 (DI = 0.38) and resistant in 2018 (DI = 0.25). Eight cultivars (Cunmai608, Zhengmai162, Minfeng266, Junda159, LS4607, Deyan1603, Pumai1165, and Fengmai12) showed moderate FHB resistance with DI lower than 0.40 in both experiments. LS4607 showed moderate resistance to both diseases. The resistant cultivars identified in this study can be used for mapping the resistance genes and improving resistance to CR and/or FHB.

Germplasms, genetics and genomics for better control of disastrous wheat Fusarium head blight

Fusarium head blight (FHB), or scab, for its devastating nature to wheat production and food security, has stimulated worldwide attention. Multidisciplinary efforts have been made to fight against FHB for a long time, but the great progress has been achieved only in the genomics era of the past 20 years, particularly in the areas of resistance gene/QTL discovery, resistance mechanism elucidation and molecular breeding for better resistance. This review includes the following nine main sections, (1) FHB incidence, epidemic and impact, (2) causal Fusarium species, distribution and virulence, (3) types of host resistance to FHB, (4) germplasm exploitation for FHB resistance, (5) genetic control of FHB resistance, (6) fine mapping of Fhb1, Fhb2, Fhb4 and Fhb5, (7) cloning of Fhb1, (8) omics-based gene discovery and resistance mechanism study and (9) breeding for better FHB resistance. The advancements that have been made are outstanding and exciting; however, judged by the complicated nature of resistance to hemi-biotrophic pathogens like Fusarium species and lack of immune germplasm, it is still a long way to go to overcome FHB.

Genome-wide association mapping revealed syntenic loci QFhb-4AL and QFhb-5DL for Fusarium head blight resistance in common wheat (Triticum aestivum L.)

BACKGROUND

Fusarium head blight (FHB), primarily caused by Fusarium graminearum, is a major threat to wheat production and food security worldwide. Breeding stably and durably resistant cultivars is the most effective approach for managing and controlling the disease. The success of FHB resistance breeding relies on identification of an effective resistant germplasm. We conducted a genome-wide association study (GWAS) using the high-density wheat 90 K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of FHB resistance in natural population and identify associated molecular markers.

RESULTS

The resistance to FHB fungal spread along the rachis (Type II resistance) was evaluated on 171 wheat cultivars in the 2016-2017 (abbr. as 2017) and 2017-2018 (abbr. as 2018) growing seasons. Using Illumina Infinum iSelect 90 K SNP genotyping data, a genome-wide association study (GWAS) identified 26 loci (88 marker-trait associations), which explained 6.65-14.18% of the phenotypic variances. The associated loci distributed across all chromosomes except 2D, 6A, 6D and 7D, with those on chromosomes 1B, 4A, 5D and 7A being detected in both years. New loci for Type II resistance were found on syntenic genomic regions of chromsome 4AL (QFhb-4AL, 621.85-622.24 Mb) and chromosome 5DL (QFhb-5DL, 546.09-547.27 Mb) which showed high collinearity in gene content and order. SNP markers wsnp_JD_c4438_5568170 and wsnp_CAP11_c209_198467 of 5D, reported previously linked to a soil-borne wheat mosaic virus (SBWMV) resistance gene, were also associated with FHB resistance in this study.

CONCLUSION

The syntenic FHB resistant loci and associated SNP markers identified in this study are valuable for FHB resistance breeding via marker-assisted selection.

Stable Isotope-Assisted Plant Metabolomics: Investigation of Phenylalanine-Related Metabolic Response in Wheat Upon Treatment With the Fusarium Virulence Factor Deoxynivalenol

The major Fusarium mycotoxin deoxynivalenol (DON) is a virulence factor in wheat and has also been shown to induce defense responses in host plant tissue. In this study, global and tracer labeling with 13C were combined to annotate the overall metabolome of wheat spikes and to evaluate the response of phenylalanine-related pathways upon treatment with DON. At anthesis, spikes of resistant and susceptible cultivars as well as two related near isogenic wheat lines (NILs) differing in the presence/absence of the major resistance QTL Fhb1 were treated with 1 mg DON or water (control), and samples were collected at 0, 12, 24, 48, and 96 h after treatment (hat). A total of 172 Phe-derived wheat constituents were detected with our untargeted approach employing 13C-labeled phenylalanine and subsequently annotated as flavonoids, lignans, coumarins, benzoic acid derivatives, hydroxycinnamic acid amides (HCAAs), as well as peptides. Ninety-six hours after the DON treatment, up to 30% of the metabolites biosynthesized from Phe showed significantly increased levels compared to the control samples. Major metabolic changes included the formation of precursors of compounds implicated in cell wall reinforcement and presumed antifungal compounds. In addition, also dipeptides, which presumably are products of proteolytic degradation of truncated proteins generated in the presence of the toxin, were significantly more abundant upon DON treatment. An in-depth comparison of the two NILs with correlation clustering of time course profiles revealed some 70 DON-responsive Phe derivatives. While several flavonoids had constitutively different abundance levels between the two NILs differing in resistance, other Phe-derived metabolites such as HCAAs and hydroxycinnamoyl quinates were affected differently in the two NILs after treatment with DON. Our results suggest a strong activation of the general phenylpropanoid pathway and that coumaroyl-CoA is mainly diverted towards HCAAs in the presence of Fhb1, whereas the metabolic route to monolignol(-conjugates), lignans, and lignin seems to be favored in the absence of the Fhb1 resistance quantitative trait loci.

Identification of a major QTL on chromosome arm 2AL for reducing yellow rust severity from a Chinese wheat landrace with evidence for durable resistance

A QTL on 2AL for reducing yellow rust severity was identified from a Chinese wheat landrace, being more effective than Yr18, with evidence for durable resistance from field observations. Utilization of wheat resistance is an important strategy to control yellow rust. The Chinese wheat landrace Hong Qimai (HQM) and the advanced breeding line AQ24788-83 (AQ; a progeny of HQM) can significantly reduce disease severity at the adult-plant growth stage. HQM has maintained adult-plant resistance for a prolonged period of time. To study the inheritance of the resistance, 126 recombinant inbred lines (RILs) derived from the cross Thatcher (TC) × HQM and 138 RILs from Luke × AQ were assessed for disease severity in six field trials. A genetic map of TC × HQM was constructed by genotyping these RILs using the 90 K wheat single-nucleotide polymorphism chip. Luke × AQ map was previously constructed for another disease study and also utilized here. Based on these maps and disease data, a quantitative trait locus (QTL) was detected on the chromosome arm 2AL from both TC × HQM and Luke × AQ and designated as QYr.cau-2AL. The resistance allele at QYr.cau-2AL came from HQM and AQ. QYr.cau-2AL was significantly effective across all the test environments and different genetic backgrounds, with its effect magnitude being higher than that of Yr18. QYr.cau-2AL synergistically acted with Yr18 and a QTL for high-temperature adult-plant resistance on 2BS, resulting in an elevated resistance from the juvenile plant growth stage onward, although QYr.cau-2AL alone displayed no substantial resistance at juvenile stage. Evidence indicates that QYr.cau-2AL is novel and confers durable resistance, and thus, should have high potential value for practical breeding.