Genetics of Resistance to Common Root Rot (Spot Blotch), Fusarium Crown Rot, and Sharp Eyespot in Wheat

Genomic prediction for sugarcane diseases including hybrid Bayesian-machine learning approaches

Sugarcane smut and Pachymetra root rots are two serious diseases of sugarcane, with susceptible infected crops losing over 30% of yield. A heritable component to both diseases has been demonstrated, suggesting selection could improve disease resistance. Genomic selection could accelerate gains even further, enabling early selection of resistant seedlings for breeding and clonal propagation. In this study we evaluated four types of algorithms for genomic predictions of clonal performance for disease resistance. These algorithms were: Genomic best linear unbiased prediction (GBLUP), including extensions to model dominance and epistasis, Bayesian methods including BayesC and BayesR, Machine learning methods including random forest, multilayer perceptron (MLP), modified convolutional neural network (CNN) and attention networks designed to capture epistasis across the genome-wide markers. Simple hybrid methods, that first used BayesR/GWAS to identify a subset of 1000 markers with moderate to large marginal additive effects, then used attention networks to derive predictions from these effects and their interactions, were also developed and evaluated. The hypothesis for this approach was that using a subset of markers more likely to have an effect would enable better estimation of interaction effects than when there were an extremely large number of possible interactions, especially with our limited data set size. To evaluate the methods, we applied both random five-fold cross-validation and a structured PCA based cross-validation that separated 4702 sugarcane clones (that had disease phenotypes and genotyped for 26k genome wide SNP markers) by genomic relationship. The Bayesian methods (BayesR and BayesC) gave the highest accuracy of prediction, followed closely by hybrid methods with attention networks. The hybrid methods with attention networks gave the lowest variation in accuracy of prediction across validation folds (and lowest MSE), which may be a criteria worth considering in practical breeding programs. This suggests that hybrid methods incorporating the attention mechanism could be useful for genomic prediction of clonal performance, particularly where non-additive effects may be important.

Genome-Wide Association Studies on Chinese Wheat Cultivars Reveal a Novel Fusarium Crown Rot Resistance Quantitative Trait Locus on Chromosome 3BL

Fusarium crown rot (FCR), primarily caused by Fusarium pseudograminearum, has emerged as a new threat to wheat production and quality in North China. Genetic enhancement of wheat resistance to FCR remains the most effective approach for disease control. In this study, we phenotyped 435 Chinese wheat cultivars through FCR inoculation at the seedling stage in a greenhouse. Our findings revealed that only approximately 10.8% of the wheat germplasms displayed moderate or high resistance to FCR. A genome-wide association study (GWAS) using high-density 660K SNP led to the discovery of a novel quantitative trait locus on the long arm of chromosome 3B, designated as Qfcr.hebau-3BL. A total of 12 significantly associated SNPs were closely clustered within a 1.05 Mb physical interval. SNP-based molecular markers were developed to facilitate the practical application of Qfcr.hebau-3BL. Among the five candidate FCR resistance genes within the Qfcr.hebau-3BL, we focused on TraesCS3B02G307700, which encodes a protein kinase, due to its expression pattern. Functional validation revealed two transcripts, TaSTK1.1 and TaSTK1.2, with opposing roles in plant resistance to fungal disease. These findings provide insights into the genetic basis of FCR resistance in wheat and offer valuable resources for breeding resistant varieties.

Dissecting the genetic basis of Fusarium crown rot resistance in wheat by genome wide association study

KEY MESSAGE

A locus conferring Fusarium crown rot resistance was identified on chromosome arm 3DL through genome wide association study and further validated in two recombinant inbred lines populations. Fusarium crown rot (FCR) is a severe soil borne disease in many wheat growing regions of the world. In this study, we attempted to detect loci conferring FCR resistance through a new seedling inoculation assay. A total of 223 wheat accessions from different geography origins were used to assemble an association panel for GWAS analysis. Four genotypes including Heng 4332, Luwanmai, Pingan 998 and Yannong 24 showed stable resistance to FCR. A total of 54 SNPs associated with FCR resistance were identified. Among the 10 putative QTLs represented by these SNPs, seven QTLs on chromosome 2B, 3A, 3D, 4A, 7A and 7B were novel and were consistently detected in at least two of the three trials conducted. Qfcr.cau.3D-3, which was targeted by 38 SNPs clustered within a genomic region of approximately 5.57 Mb (609.12-614.69 Mb) on chromosome arm 3DL, was consistently detected in all the three trials. The effects of Qfcr.cau.3D-3 were further validated in two recombinant inbred line populations. The presence of this locus reduced FCR severity up to 21.55%. Interestingly, the collinear positions of sequences containing the four SNPs associated with two FCR loci (Qfcr.cau.3A and Qfcr.cau.3B) were within the regions of Qfcr.cau.3D-3, suggesting that genes underlying these three loci may be homologous. Our results provide useful information for improving FCR resistance in wheat.

Screening and Resistance Locus Identification of the Mutant fcrZ22 Resistant to Crown Rot Caused by Fusarium pseudograminearum

Crown rot caused by Fusarium pseudograminearum is a devastating wheat disease worldwide. In addition to yield losses, the fungi causing Fusarium crown rot (FCR) also deteriorate the quality and safety of food because of the production of mycotoxins. Planting resistant cultivars is an effective way to control FCR. However, most wheat cultivars are susceptible to FCR. Therefore, development of new sources and detection of loci for FCR resistance are necessary. In the present study, a resistant mutant, fcrZ22, was identified from an ethyl methane sulfonate (EMS)-mutagenized population of the cultivar Zhoumai 22, and then fcrZ22 was crossed with the wild type to produce an F2 population. Genetic analysis of the F2 population was carried out by the mixed inheritance model of major genes plus polygenes, and 20 resistant and 20 susceptible plants were selected to assemble mixed pools. Combining 660K SNP arrays, the resistance loci were detected by bulked segregant analysis. The resistance to FCR caused by F. pseudograminearum in the F2 population was in accordance with the "mixed model with two major genes of additive-epistasis effect + additive-dominant polygenes," and the heritability of the major gene was 0.92. Twenty-one loci were detected, which were located on 10 chromosomes, namely, 1B (1), 1D (1), 2A (3), 1B (1), 3A (3), 3B (3), 4A (2), 5A (2), 7A (3), and 7B (2). Among the 21 loci, eight were new loci for FCR resistance. This is the first report of detecting loci for FCR resistance from a mutant. The results of the present study provided excellent germplasm resources for breeding wheat cultivars with FCR resistance and laid the foundation for fine mapping of FCR resistance loci.

Does straw returning affect the root rot disease of crops in soil? A systematic review and meta-analysis

Straw returning is a sustainable way that does not destroy soil ecology in agronomic management. Some studies have found that straw returning may aggravate or reduce soilborne diseases in the past few decades. Despite the increasing number of independent studies investigated the effect of straw returning on root rot of crops, the quantitative analysis regarding the relationship between straw returning and crop root rot is still undefined. In this study, keywords co-occurrence matrix was extracted from 2489 published studies (published from 2000 to 2022, the same below) on controlling soilborne diseases of crops. The methods used for soilborne diseases prevention have shifted from chemical to biological and agricultural control since 2010. As root rot is the soilborne disease with the largest weight in keyword co-occurrence according to statistics, we further collected 531 articles focusing on crop root rot. Notably, the 531 studies are mainly distributed in the United States, Canada, China and other countries in Europe and the south and southeast of Asia, and focus on the root rot of soybean, tomato, wheat and other important grain crops or economic crops. Based on the meta-analysis of 534 measurements in 47 previous studies, we explored how 10 management factors (soil pH/texture, type/size of straw, depth/rate/cumulative amount of application, days after application, beneficial/pathogenic microorganism inoculated before application and annual N-fertilizer input) during straw returning affect root rot onset worldwide. The results showed that straw size and microorganisms inoculated before straw returning are the key factors affecting the incidence of root rot. In combination with actual agricultural production, detailed advice applicable to traditional farming system on the optimization management of straw returning was given. This study emphasized the significance of straw pretreatment and farmland management to reduce soilborne diseases during straw returning.

Genome-wide association analysis of Fusarium crown rot resistance in Chinese wheat landraces

KEY MESSAGE

A novel locus for Fusarium crown rot (FCR) resistance was identified on chromosome 1B at 641.36-645.13 Mb using GWAS and could averagely increase 39.66% of FCR resistance in a biparental population. Fusarium crown rot can cause considerable yield losses. Developing and growing resistance cultivars is one of the most effective approaches for controlling this disease. In this study, 361 Chinese wheat landraces were evaluated for FCR resistance, and 27 with the disease index lower than 30.00 showed potential in wheat breeding programs. Using a genome-wide association study approach, putative quantitative trait loci (QTL) for FCR resistance was identified. A total of 21 putative loci on chromosomes 1A, 1B, 2B, 2D, 3B, 3D, 4B, 5A, 5B, 7A, and 7B were significantly associated with FCR resistance. Among these, a major locus Qfcr.sicau.1B-4 was consistently identified among all the trials on chromosome 1B with the physical regions from 641.36 to 645.13 Mb. A polymorphism kompetitive allele-specific polymerase (KASP) marker was developed and used to validate its effect in an F_2:3 population consisting of 136 lines. The results showed the presence of this resistance allele could explain up to 39.66% of phenotypic variance compared to its counterparts. In addition, quantitative real-time polymerase chain reaction showed that two candidate genes of Qfcr.sicau.1B-4 were differently expressed after inoculation. Our study provided useful information for improving FCR resistance in wheat.

Host Specificity of Soilborne Pathogens in Hordeum Species and Their Relatives

Soilborne pathogens destabilize the yields of Triticeae crops, including barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). Although genetic resistance derived from relatives of these species has been utilized to prevent rust diseases (i.e., in the wheat-rye 1BL-1RS translocation line), research on resistance against soilborne pathogens remains limited. Here, we performed field trials using 76 genotypes representing 28 Hordeum, six Triticum, and two Aegilops species to examine resistance against three soilborne bymoviruses: barley yellow mosaic virus (BaYMV), barley mild mosaic virus (BaMMV), and wheat yellow mosaic virus (WYMV). We also performed greenhouse tests using the soilborne fungal pathogen Fusarium pseudograminearum, which causes Fusarium crown rot (FCR). Using RT-PCR, we detected BaMMV and BaYMV in several Hordeum species, whereas WYMV induced systemic infection in the Triticum and Aegilops species. The identification of FCR susceptibility in all species examined suggests that F. pseudograminearum is a facultative fungal pathogen in Triticeae. Intraspecies variation in FCR disease severity was observed for several species, pointing to the possibility of exploring host resistance mechanisms. Therefore, by unlocking the host specificity of four soilborne pathogens in Hordeum species and their relatives, we obtained insights for the further exploration of wild sources of soilborne pathogen resistance for future wheat and barley improvement programs.

A cell wall invertase modulates resistance to fusarium crown rot and sharp eyespot in common wheat

Fusarium crown rot (FCR) and sharp eyespot (SE) are serious soil-borne diseases in wheat and its relatives that have been reported to cause wheat yield losses in many areas. In this study, the expression of a cell wall invertase gene, TaCWI-B1, was identified to be associated with FCR resistance through a combination of bulk segregant RNA sequencing and genome resequencing in a recombinant inbred line population. Two bi-parental populations were developed to further verify TaCWI-B1 association with FCR resistance. Overexpression lines and ethyl methanesulfonate (EMS) mutants revealed TaCWI-B1 positively regulating FCR resistance. Determination of cell wall thickness and components showed that the TaCWI-B1-overexpression lines exhibited considerably increased thickness and pectin and cellulose contents. Furthermore, we found that TaCWI-B1 directly interacted with an alpha-galactosidase (TaGAL). EMS mutants showed that TaGAL negatively modulated FCR resistance. The expression of TaGAL is negatively correlated with TaCWI-B1 levels, thus may reduce mannan degradation in the cell wall, consequently leading to thickening of the cell wall. Additionally, TaCWI-B1-overexpression lines and TaGAL mutants showed higher resistance to SE; however, TaCWI-B1 mutants were more susceptible to SE than controls. This study provides insights into a FCR and SE resistance gene to combat soil-borne diseases in common wheat.

Boosting Immunity and Management against Wheat Fusarium Diseases by a Sustainable, Circular Nanostructured Delivery Platform

Fusarium head blight (FHB) and Fusarium crown rot (FCR) are managed by the application of imidazole fungicides, which will be strictly limited by 2030, as stated by the European Green Deal. Here, a novel and eco-sustainable nanostructured particle formulation (NPF) is presented by following the principles of the circular economy. Cellulose nanocrystals (CNC) and resistant starch were obtained from the bran of a high amylose (HA) bread wheat and employed as carrier and excipient, while chitosan and gallic acid were functionalized as antifungal and elicitor active principles. The NPF inhibited conidia germination and mycelium growth, and mechanically interacted with conidia. The NPF optimally reduced FHB and FCR symptoms in susceptible bread wheat genotypes while being biocompatible on plants. The expression level of 21 genes involved in the induction of innate immunity was investigated in Sumai3 (FHB resistant) Cadenza (susceptible) and Cadenza SBEIIa (a mutant characterized by high-amylose starch content) and most of them were up-regulated in Cadenza SBEIIa spikes treated with the NPF, indicating that this genotype may possess an interesting genomic background particularly responsive to elicitor-like molecules. Quantification of fungal biomass revealed that the NPF controlled FHB spread, while Cadenza SBEIIa was resistant to FCR fungal spread. The present research work highlights that the NPF is a powerful weapon for FHB sustainable management, while the genome of Cadenza SBEIIa should be investigated deeply as particularly responsive to elicitor-like molecules and resistant to FCR fungal spread.

Antagonistic Strain Bacillus halotolerans Jk-25 Mediates the Biocontrol of Wheat Common Root Rot Caused by Bipolaris sorokiniana

Common root rot caused by Bipolaris sorokiniana infestation in wheat is one of the main reasons for yield reduction in wheat crops worldwide. The bacterium strain JK-25 used in the current investigation was isolated from wheat rhizosphere soil and was later identified as Bacillus halotolerans based on its morphological, physiological, biochemical, and molecular properties. The strain showed significant antagonism to B. sorokiniana, Fusarium oxysporum, Fusarium graminearum, and Rhizoctonia zeae. Inhibition of B. sorokiniana mycelial dry weight and spore germination rate by JK-25 fermentation supernatant reached 60% and 88%, respectively. The crude extract of JK-25 was found, by Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), to contain the surfactin that exerted an inhibitory effect on B. sorokiniana. The disruption of mycelial cell membranes was observed under laser scanning confocal microscope (LSCM) after treatment of B. sorokiniana mycelium with the crude extract. The antioxidant enzyme activity of B. sorokiniana was significantly reduced and the oxidation product malondialdehyde (MDA) content increased after treatment with the crude extract. The incidence of root rot was significantly reduced in pot experiments with the addition of JK-25 culture fermentation supernatant, which had a significant biological control effect of 72.06%. Its ability to produce siderophores may help to promote wheat growth and the production of proteases and pectinases may also be part of the strain's role in suppressing pathogens. These results demonstrate the excellent antagonistic effect of JK-25 against B. sorokiniana and suggest that this strain has great potential as a resource for biological control of wheat root rot strains.

Biocontrol potential and action mechanism of Bacillus amyloliquefaciens DB2 on Bipolaris sorokiniana

Introduction

Bipolaris sorokiniana is the popular pathogenic fungi fungus which lead to common root rot and leaf spot on wheat. Generally, chemical fungicides are used to control diseases. However, the environmental pollution resulting from fungicides should not be ignored. It is important to study the mode of antagonistic action between biocontrol microbes and plant pathogens to design efficient biocontrol strategies.

Results

An antagonistic bacterium DB2 was isolated and identified as Bacillus amyloliquefaciens. The inhibition rate of cell-free culture filtrate (CF, 20%, v/v) of DB2 against B. sorokiniana reached 92.67%. Light microscopy and scanning electron microscopy (SEM) showed that the CF significantly altered the mycelial morphology of B. sorokiniana and disrupted cellular integrity. Fluorescence microscopy showed that culture filtrate destroyed mycelial cell membrane integrity, decreased the mitochondrial transmembrane potential, induced reactive oxygen species (ROS) accumulation, and nuclear damage which caused cell death in B. sorokiniana. Moreover, the strain exhibited considerable production of protease and amylase, and showed a significant siderophore and indole-3-acetic acid (IAA) production. In the detached leaves and potted plants control assay, B. amyloliquefacien DB2 had remarkable inhibition activity against B. sorokiniana and the pot control efficacy was 75.22%. Furthermore, DB2 suspension had a significant promotion for wheat seedlings growth.

Conclusion

B. amyloliquefaciens DB2 can be taken as a potential biocontrol agent to inhibit B. sorokiniana on wheat and promote wheat growth.

Identification of new resistance loci against wheat sharp eyespot through genome-wide association study

INTRODUCTION

Wheat sharp eyespot caused by Rhizoctonia cerealis is a serious pathogenic disease affecting plants. The effective strategy for controlling this disease is breeding resistant cultivar. However, to date, no wheat varieties are fully resistant to sharp eyespot, and only a few quantitative trait loci (QTLs) have been shown to be associated with sharp eyespot resistance.

METHODS

To understand the genetic basis of this disease, a genome-wide association study (GWAS) of sharp eyespot resistance in 262 varieties from all China wheat regions was conducted.

RESULTS

After cultivation for three years, only 6.5% of the varieties were resistant to sharp eyespot. Notably, the varieties from the middle and lower Yangtze River displayed higher sharp eyespot resistance than those from Huanghuai wheat zone. Only two varieties had the same resistance level to the control Shanhongmai. The results of GWAS showed that 5 single nucleotide polymorphism (SNP) loci were markedly related to sharp eyespot resistance in the three years repeatedly, and two QTLs, qSE-6A and qSE-7B, on chromosome 6A and 7B were identified. Based on the 'CG' haplotypes of significant SNPs, we found that the two QTLs exhibited additive effects on attenuating sharp eyespot resistance.

DISCUSSION

These results provide novel insights into the genetic basis of sharp eyespot resistance in China wheat varieties. The SNPs related to sharp eyespot resistance can be applied for marker-assisted selection in plant breeding.

Wheat genomic study for genetic improvement of traits in China

Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.

Genome-Wide Association Study for Spot Blotch Resistance in Synthetic Hexaploid Wheat

Spot blotch (SB) caused by Bipolaris sorokiniana (Sacc.) Shoem is a destructive fungal disease affecting wheat and many other crops. Synthetic hexaploid wheat (SHW) offers opportunities to explore new resistance genes for SB for introgression into elite bread wheat. The objectives of our study were to evaluate a collection of 441 SHWs for resistance to SB and to identify potential new genomic regions associated with the disease. The panel exhibited high SB resistance, with 250 accessions showing resistance and 161 showing moderate resistance reactions. A genome-wide association study (GWAS) revealed a total of 41 significant marker–trait associations for resistance to SB, being located on chromosomes 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4D, 5A, 5D, 6D, 7A, and 7D; yet none of them exhibited a major phenotypic effect. In addition, a partial least squares regression was conducted to validate the marker–trait associations, and 15 markers were found to be most important for SB resistance in the panel. To our knowledge, this is the first GWAS to investigate SB resistance in SHW that identified markers and resistant SHW lines to be utilized in wheat breeding.

Source Identification and Genome-Wide Association Analysis of Crown Rot Resistance in Wheat

Crown rot (CR) is a soil-borne disease of wheat in arid and semiarid areas of the world. The incidence rate and severity of CR are increasing with each passing year, which seriously threatens the safety of world wheat production. Here, 522 wheat varieties/lines representing genetic diversity were used to identify and evaluate the resistance source to CR disease. Six varieties, including Zimai 12, Xinong 509, Mazhamai, Sifangmai, and Dawson, were classified as resistant ® to CR. Seventy-nine varieties were classified as moderately resistant (MR) to CR, accounting for 15.13% of the tested varieties. The wheat 660 K SNP array was used to identify resistance loci by genome-wide association analysis (GWAS). A total of 33 SNPs, located on chromosomes 1A, 1B, 1D, 4A, and 4D, were significantly correlated with seedling resistance to CR in two years. Among them, one SNP on chromosome 1A and nine SNPs on chromosome 1B showed most significant resistance to disease, phenotypic variance explained (PVE) by these SNPs were more than 8.45%. Except that significant locus AX-110436287 and AX109621209 on chromosome 1B and AX-94692276 on 1D are close to the already reported QTL, other SNPs are newly discovered resistance loci. These results could lay a strong theoretical foundation for the genetic improvement and breeding for CR resistance in wheat.

Exogenous expression of barley HvWRKY6 in wheat improves broad-spectrum resistance to leaf rust, Fusarium crown rot, and sharp eyespot

Systemic acquired resistance (SAR) is a broad-spectrum plant defense phenomena controlled by the salicylic acid receptor NPR1. Key regulators of the SAR signaling pathway showed great potentials to improve crop resistance to various diseases. In our previous investigation, a barley transcription factor gene HvWRKY6 was identified as downstream of NPR1 during SAR. However, the broad-spectrum resistance features and molecular mechanisms of HvWRKY6 remain to be explored. In this study, a transgenic wheat line exogenously expressing HvWRKY6 showed improved resistance to leaf rust, Fusarium crown rot (FCR), and sharp eyespot. The model pathogen Pseudomonas syringae pv. tomato DC3000 was employed to induce the SAR response in wheat plants' leaf region adjacent to the infiltration area. Transcriptome sequencing revealed activation of broad-spectrum defense responses by expressing HvWRKY6 in a pathogen-independent manner. Based on the differentially expressed genes in plant hormone signal transduction, we speculated that the enhanced resistance in HvWRKY6-OE wheat transgenic line was associated with activation of the salicylic acid pathway and suppression of the abscisic acid and jasmonic acid pathways. These findings suggest that the transgenic line HvWRKY6-OE might be applied for the genetic improvement of wheat to several fungal diseases; the underlying resistance mechanism was clarified.

Fungal Pathogens Associated with Crown and Root Rot of Wheat in Central, Eastern, and Southeastern Kazakhstan

Kazakhstan is the fourteenth largest wheat producer in the world. Despite this fact, there has not been a comprehensive survey of wheat root and crown rot. A quantitative survey was conducted for the purpose of establishing the distribution of fungi associated with root and crown rot on wheat (Triticum spp.). During the 2019 growing season, samples were taken from the affected plants’ roots and stem bases. A total of 1221 fungal isolates were acquired from 65 sites across the central (Karagandy region), eastern (East Kazakhstan region), and southeastern (Almaty region) parts of the country and identified using morphological and molecular tools. The internal transcribed spacer (ITS), translation elongation factor 1-alpha (EF1-α), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) sequences were successfully used to identify the species of fungal isolates. It was found that Bipolaris sorokiniana (44.80%) and Fusarium acuminatum (20.39%) were the most predominant fungal species isolated, which were present in 86.15 and 66.15% of the fields surveyed, respectively, followed by F. equiseti (10.16%), Curvularia spicifera (7.62%), F. culmorum (4.75%), F. oxysporum (4.10%), F. redolens (2.38%), Rhizoctonia solani AG2-1 (1.06%), Nigrospora oryzae (0.98%), C. inaequalis (0.90%), F. pseudograminearum (0.74%), F. flocciferum (0.74%), Macrophomina phaseolina (0.66%), F. cf. incarnatum (0.33%), Fusarium sp. (0.25%), and F. torulosum (0.16%). A total of 74 isolates representing 16 species were tested via inoculation tests on the susceptible Triticum aestivum cv. Seri 82 and the results revealed that F. culmorum and F. pseudograminearum, B. sorokiniana, Fusarium sp., R. solani, F. redolens, C. spicifera, C. inaequalis, and N. oryzae were virulent, whereas others were non-pathogenic. The findings of this investigation demonstrate the presence of a diverse spectrum of pathogenic fungal species relevant to wheat crown and root rot in Kazakhstan. To the best of our knowledge, this is the first report of F. pseudograminearum, Fusarium sp., C. spicifera, and C. inaequalis as pathogens on wheat in Kazakhstan.

Genome-wide association mapping of Fusarium crown rot resistance in Aegilops tauschii

Fusarium crown rot (FCR), caused by various Fusarium species, is a primary fungal disease in most wheat-growing regions worldwide. A. tauschii, the diploid wild progenitor of the D-genome of common wheat, is a reservoir of genetic diversity for improving bread wheat biotic and abiotic resistance/tolerance. A worldwide collection of 286 A. tauschii accessions was used to evaluate FCR resistance. Population structure analysis revealed that 115 belonged to the A. tauschii ssp. strangulata subspecies, and 171 belonged to the A. tauschii ssp. tauschii subspecies. Five accessions with disease index values lower than 20 showed moderate resistance to FCR. These five originated from Afghanistan, China, Iran, Uzbekistan, and Turkey, all belonging to the tauschii subspecies. Genome-wide association mapping using 6,739 single nucleotide polymorphisms (SNPs) revealed that two SNPs on chromosome 2D and four SNPs on chromosome 7D were significantly associated with FCR resistance. Almost all FCR resistance alleles were presented in accessions from the tauschii subspecies, and only 4, 11, and 19 resistance alleles were presented in accessions from the strangulata subspecies. Combining phenotypic correlation analysis and genome-wide association mapping confirmed that FCR resistance loci were independent of flowering time, heading date, and plant height in this association panel. Six genes encoding disease resistance-related proteins were selected as candidates for further validation. The identified resistant A. tauschii accessions will provide robust resistance gene sources for breeding FCR-resistant cultivars. The associated loci/genes will accelerate and improve FCR in breeding programs by deploying marker-assisted selection.

Antagonistic Strain Bacillus amyloliquefaciens XZ34-1 for Controlling Bipolaris sorokiniana and Promoting Growth in Wheat

Common root rot, caused by Bipolaris sorokiniana, is one of the most prevalent diseases of wheat and has led to major declines in wheat yield and quality worldwide. Here, strain XZ34-1 was isolated from soil and identified as Bacillus amyloliquefaciens based on the morphological, physiological, biochemical characteristics and 16S rDNA sequence. Culture filtrate (CF) of strain XZ34-1 showed a high inhibition rate against B.sorokiniana and had a broad antifungal spectrum. It also remarkably inhibited the mycelial growth and spore germination of B. sorokiniana. In pot control experiments, the incidence and disease index of common root rot in wheat seedlings were decreased after treatment with CF, and the biological control efficacy was significant, up to 78.24%. Further studies showed XZ34-1 could produce antifungal bioactive substances and had the potential of promoting plant growth. Lipopeptide genes detection with PCR indicated that strain XZ34-1 may produce lipopeptides. Furthermore, activities of defense-related enzymes were enhanced in wheat seedlings after inoculation with B.sorokiniana and treatment with CF, which showed induced resistance could be produced in wheat to resist pathogens. These results reveal that strain XZ34-1 is a promising candidate for application as a biological control agent against B.sorokiniana.