A Revised Nomenclature for ToxA Haplotypes Across Multiple Fungal Species

ToxA is one of the most studied proteinaceous necrotrophic effectors produced by plant pathogens. It has been identified in four pathogens (Pyrenophora tritici-repentis, Parastagonospora nodorum, Parastagonospora pseudonodorum [formerly Parastagonospora avenaria f. sp. tritici], and Bipolaris sorokiniana) causing leaf spot diseases on cereals worldwide. To date, 24 different ToxA haplotypes have been identified. Some P. tritici-repentis and related species also express ToxB, another small protein necrotrophic effector. We present here a revised and standardized nomenclature for these effectors, which could be extended to other poly-haplotypic genes found across multiple species.

Managing spot blotch disease in wheat: Conventional to molecular aspects

Spot blotch (SB) caused by Bipolaris sorokiniana (teleomorph Cochliobolus sativus) is one of the devastating diseases of wheat in the warm and humid growing areas around the world. B. sorokiniana can infect leaves, stem, roots, rachis and seeds, and is able to produce toxins like helminthosporol and sorokinianin. No wheat variety is immune to SB; hence, an integrated disease management strategy is indispensable in disease prone areas. A range of fungicides, especially the triazole group, have shown good effects in reducing the disease, and crop-rotation, tillage and early sowing are among the favorable cultural management methods. Resistance is mostly quantitative, being governed by QTLs with minor effects, mapped on all the wheat chromosomes. Only four QTLs with major effects have been designated as Sb1 through Sb4. Despite, marker assisted breeding for SB resistance in wheat is scarce. Better understanding of wheat genome assemblies, functional genomics and cloning of resistance genes will further accelerate breeding for SB resistance in wheat.

Evaluation of Selenium Nanoparticles in Inducing Disease Resistance against Spot Blotch Disease and Promoting Growth in Wheat under Biotic Stress

In the present study, SeNPs were synthesized using Melia azedarach leaf extracts and investigated for growth promotion in wheat under the biotic stress of spot blotch disease. The phytosynthesized SeNPs were characterized using UV-visible spectroscopy, scanning electron microscopy (SEM), energy-dispersive X-ray (EDX), and Fourier-transformed infrared spectroscopy (FTIR). The in vitro efficacy of different concentrations of phytosynthesized SeNPs (i.e., 100 μg/mL, 150 μg/mL, 200 μg/mL, 250 μg/mL, and 300 μg/mL) was evaluated using the well diffusion method, which reported that 300 μg/mL showed maximum fungus growth inhibition. For in vivo study, different concentrations (10, 20, 30, and 40 mg/L) of SeNPs were applied exogenously to evaluate the morphological, physiological, and biochemical parameters under control conditions and determine when infection was induced. Among all treatments, 30 mg/L of SeNPs performed well and increased the plant height by 2.34% compared to the control and 30.7% more than fungus-inoculated wheat. Similarly, fresh plant weight and dry weight increased by 17.35% and 13.43% over the control and 20.34% and 52.48% over the fungus-treated wheat, respectively. In leaf surface area and root length, our findings were 50.11% and 10.37% higher than the control and 40% and 71% higher than diseased wheat, respectively. Plant physiological parameters i.e., chlorophyll a, chlorophyll b, and total chlorophyll content, were increased 14, 133, and 16.1 times over the control and 157, 253, and 42 times over the pathogen-inoculated wheat, respectively. Our findings regarding carotenoid content, relative water content, and the membrane stability index were 29-, 49-, and 81-fold higher than the control and 187-, 63-, and 48-fold higher than the negative control, respectively. In the case of plant biochemical parameters, proline, sugar, flavonoids, and phenolic contents were recorded at 6, 287, 11, and 34 times higher than the control and 32, 107, 33, and 4 times more than fungus-inoculated wheat, respectively. This study is considered the first biocompatible approach to evaluate the potential of green-synthesized SeNPs as growth-promoting substances in wheat under the spot blotch stress and effective management strategy to inhibit fungal growth.

Whole Genome Sequencing and Comparative Genomics of Indian Isolates of Wheat Spot Blotch Pathogen Bipolaris sorokiniana Reveals Expansion of Pathogenicity Gene Clusters

Spot blotch is a highly destructive disease in wheat caused by the fungal pathogen Bipolaris sorokiniana (teleomorph, Cochliobolus sativus). It is prevalent in warm and humid areas, including Africa, Asia, Latin America, and the USA. In the present study, twelve isolates of B. sorokiniana were collected from wheat fields in three different geographical locations in India. The pathogenicity of seven sporulating isolates was assessed on 'DDK 1025', a spot blotch-susceptible wheat variety under greenhouse conditions. The isolate 'D2' illustrated the highest virulence, followed by 'SI' and 'BS52'. These three isolates were sequenced using the Illumina HiSeq1000 platform. The estimated genome sizes of the isolates BS52, D2, and SI were 35.19 MB, 39.32 MB, and 32.76 MB, with GC contents of 48.48%, 50.43%, and 49.42%, respectively. The numbers of pathogenicity genes identified in BS52, D2, and SI isolates were 2015, 2476, and 2018, respectively. Notably, the isolate D2 exhibited a relatively larger genome with expanded arsenals of Biosynthetic Gene Clusters (BGCs), CAZymes, secretome, and pathogenicity genes, which could have contributed to its higher virulence among the tested isolates. This study provides the first comparative genome analysis of the Indian isolates of B. sorokiniana using whole genome sequencing.

Mechanisms of Resistance to Spot Blotch in Yunnan Iron Shell Wheat Based on Metabolome and Transcriptomics

Spot blotch (SB) is a fungal disease that threatens wheat yield and quality. Presently, the molecular mechanism against SB is unclear. In this study, the resistant variety Zhenkang iron shell wheat (Yunmai 0030) and susceptible variety Lincang iron shell wheat (Yunmai 0608) were selected by identifying SB of Yunnan iron shell wheat. The metabolome and transcriptome of leaves of two varieties at different positions were detected using the systemic acquired resistance theory to investigate the molecular and physiological changes in Yunnan iron shell wheat under SB stress. We found that the genes and metabolites related to benzoxazinoid biosynthesis and arginine and proline metabolism were highly enriched after infection with leaf blight. The enriched differential metabolites mainly included phenolic acids, alkaloids, and flavonoids. We further observed that DIBOA- and DIMBOA-glucoside positively affected iron shell wheat resistance to leaf blight and proline and its derivatives were important for plant self-defense. Furthermore, we confirmed that the related metabolites in benzoxazinoid biosynthesis and arginine and proline metabolism positively affected Triticum aestivum ssp. resistance to SB. This study provides new insights into the dynamic physiological changes of wheat in response to SB, helps us better understand the mechanism of resistance to SB, and contributes to the breeding and utilization of resistant varieties.

SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat (Triticum aestivum L.), an Essential Crop for Food Security

The pathogenic fungus, Bipolaris sorokiniana, that causes spot blotch (SB) disease of wheat, is a major production constraint in the Eastern Gangetic Plains of South Asia and other warm, humid regions of the world. A recombinant inbred line population was developed and phenotyped at three SB-prone locations in India. The single nucleotide polymorphism (SNP) for SB resistance was identified using a bulked segregant RNA-Seq-based approach, referred to as “BSR-Seq.” Transcriptome sequencing of the resistant parent (YS#24), the susceptible parent (YS#58), and their resistant and susceptible bulks yielded a total of 429.67 million raw reads. The bulk frequency ratio (BFR) of SNPs between the resistant and susceptible bulks was estimated, and selection of SNPs linked to resistance was done using sixfold enrichments in the corresponding bulks (BFR >6). With additional filtering criteria, the number of transcripts was further reduced to 506 with 1055 putative polymorphic SNPs distributed on 21 chromosomes of wheat. Based on SNP enrichment on chromosomal loci, five transcripts were found to be associated with SB resistance. Among the five SB resistance-associated transcripts, four were distributed on the 5B chromosome with putative 52 SNPs, whereas one transcript with eight SNPs was present on chromosome 3B. The SNPs linked to the trait were exposed to a tetra-primer ARMS-PCR assay, and an SNP-based allele-specific marker was identified for SB resistance. The in silico study of these five transcripts showed homology with pathogenesis-related genes; the metabolic pathway also exhibits similar results, suggesting their role in the plant defense mechanism.

Genome-Wide Association Mapping Indicates Quantitative Genetic Control of Spot Blotch Resistance in Bread Wheat and the Favorable Effects of Some Spot Blotch Loci on Grain Yield

Spot blotch caused by the fungus Bipolaris sorokiniana poses a serious threat to bread wheat production in warm and humid wheat-growing regions of the world. Hence, the major objective of this study was to identify consistent genotyping-by-sequencing (GBS) markers associated with spot blotch resistance using genome-wide association mapping on a large set of 6,736 advanced bread wheat breeding lines from the International Maize and Wheat Improvement Center. These lines were phenotyped as seven panels at Agua Fria, Mexico between the 2013-2014 and 2019-2020 crop cycles. We identified 214 significant spot blotch associated GBS markers in all the panels, among which only 96 were significant in more than one panel, indicating a strong environmental effect on the trait and highlights the need for multiple phenotypic evaluations to identify lines with stable spot blotch resistance. The 96 consistent GBS markers were on chromosomes 1A, 1B, 1D, 2A, 3B, 4A, 5B, 5D, 6B, 7A, 7B, and 7D, including markers possibly linked to the Lr46, Sb1, Sb2 and Sb3 genes. We also report the association of the 2NS translocation from Aegilops ventricosa with spot blotch resistance in some environments. Moreover, the spot blotch favorable alleles at the 2NS translocation and two markers on chromosome 3BS (3B_2280114 and 3B_5601689) were associated with increased grain yield evaluated at several environments in Mexico and India, implying that selection for favorable alleles at these loci could enable simultaneous improvement for high grain yield and spot blotch resistance. Furthermore, a significant relationship between the percentage of favorable alleles in the lines and their spot blotch response was observed, which taken together with the multiple minor effect loci identified to be associated with spot blotch in this study, indicate quantitative genetic control of resistance. Overall, the results presented here have extended our knowledge on the genetic basis of spot blotch resistance in bread wheat and further efforts to improve genetic resistance to the disease are needed for reducing current and future losses under climate change.

Pathotype Identification and Virulence Variation in Cochliobolus sativus in China

Spot blotch caused by Cochliobolus sativus has become an important disease in the wheat-growing regions in China that has resulted from changes in the regional climate, agricultural cultivation patterns, and the susceptible wheat varieties that are widely grown. Little information is available about virulence variability and pathogenic specialization of the C. sativus isolates from major wheat-growing regions in China. Here, 12 representative wheat varieties and foundation breeding stocks were selected to characterize the pathotypes of C. sativus isolates from infected wheat plants. Based on the infection phenotypes in the 12 differential genotypes at the seedling stage, 70 Chinese pathotypes were identified from 110 isolates and clustered into three virulence groups. The high virulence isolates were collected from wheat leaves, crowns, and roots, with most (10 of 14) from the Henan province in the Huang-Huai plain. No relationship was evident between virulence variability of C. sativus isolates and their geographic origins or types of diseased wheat tissues. C. sativus showed a significant pathogenic specialization in hosts of wheat and barley. Most of the wheat isolates (50 of 65) were avirulent to all the differential barley genotypes, and a few were virulent only to highly susceptible barley genotypes. These results indicated that C. sativus isolates from the wheat-growing regions in China varied considerably for their virulence in wheat varieties, and showed significant pathogenic specialization to the wheat and barley hosts.

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

Due to soil changes, high density planting, and the use of straw-returning methods, wheat common root rot (spot blotch), Fusarium crown rot (FCR), and sharp eyespot (sheath blight) have become severe threats to global wheat production. Only a few wheat genotypes show moderate resistance to these root and crown rot fungal diseases, and the genetic determinants of wheat resistance to these devastating diseases are poorly understood. This review summarizes recent results of genetic studies of wheat resistance to common root rot, Fusarium crown rot, and sharp eyespot. Wheat germplasm with relatively higher resistance are highlighted and genetic loci controlling the resistance to each disease are summarized.

New QTLs for Spot Blotch Disease Resistance in Wheat (Triticum aestivum L.) Using Genome-Wide Association Mapping

Spot blotch disease caused by Bipolaris sorokiniana is a major constraint for wheat production in tropics and subtropics. The introgression of spot blotch resistance alleles to the disease susceptible lines is critical to securing the wheat production in these regions. Although genome-wide association studies (GWASs) for spot blotch were attempted earlier, the present study focused on identifying new quantitative trait loci (QTLs) for spot blotch under natural disease pressure in diverse field conditions. A total of 139 advanced spring wheat lines were evaluated in three environments (three years and two locations) in India and Bangladesh. The GWAS using 14,063 polymorphic genotyping-by-sequencing (GBS) markers identified eight QTLs associated with spot blotch disease resistance belonging to eight chromosomes across the wheat genome. Here, we report the identified marker–trait associations (MTAs), along with the allele effects associated with the disease. The functional annotation of the significant markers identified NBS-LRR, MADS-box transcription factor, and 34 other plant-related protein families across multiple chromosomal regions. The results indicate four promising new QTLs on chromosomes 1A (497.2 Mb), 1D (89.84 Mb), 2B (421.92 Mb), and 6D (6.84 Mb) associated with several disease resistance protein families. These results provide insights into new genomic regions associated with spot blotch disease, and with additional validation, could be utilized in disease resistance breeding efforts in wheat development.

Characterization and Mapping of Spot Blotch in Triticum durum-Aegilops speltoides Introgression Lines Using SNP Markers

Spot blotch (SB) of wheat is emerging as a major threat to successful wheat production in warm and humid areas of the world. SB, also called leaf blight, is caused by Bipolaris sorokiniana, and is responsible for high yield losses in Eastern Gangetic Plains Zone in India. More recently, SB is extending gradually toward cooler, traditional wheat-growing North-Western part of the country which is a major contributor to the national cereal basket. Deployment of resistant cultivars is considered as the most economical and ecologically sound measure to avoid losses due to this disease. In the present study, 89 backcross introgression lines (DSBILs) derived from Triticum durum (cv. PDW274-susceptible) × Aegilops speltoides (resistant) were evaluated against SB for four consecutive years, 2016-2020. Phenotypic evaluation of these lines showed a continuous variation in disease severity indicating that the resistance to SB is certainly quantitative in nature. Phenotypic data of DSBILs were further used for mapping QTLs using SNPs obtained by genotyping by sequencing. To identify QTLs stable across the environments, Best Linear Unbiased Estimates (BLUEs) and Predictions (BLUPs) were used for mapping QTLs based on stepwise regression-based Likelihood Ratio Test (RSTEP-LRT) for additive effect of markers and single marker analysis (SMA). Five QTLs, Q.Sb.pau-2A, Q.Sb.pau-2B, Q.Sb.pau-3B, Q.Sb.pau-5B, and Q.Sb.pau-6A, linked to SB resistance were mapped across chromosomes 2A, 2B, 3B, 5B, and 6A. Genes found adjacent to the SNP markers linked to these QTLs were literature mined to identify possible candidate genes by studying their role in plant pathogenesis. Further, highly resistant DSBIL (DSBIL-13) was selected to cross with a susceptible hexaploidy cultivar (HD3086) generating BC₂F₁ population. The QTL Q.Sb.pau-5B, linked to SNP S5B_703858864, was validated on this BC₂F₁ population and thus, may prove to be a potential diagnostic marker for SB resistance.

Genome Sequence Resource for Pathogen Bipolaris sorokiniana Shoemaker GN1 Causing Spot Blotch of Barley (Hordeum vulgare L.)

Spot blotch, caused by fungal pathogen Bipolaris sorokiniana Shoemaker, is one of the most frequent diseases affecting barley-growing regions worldwide. In this study, we reported the genome sequence of the highly virulent B. sorokiniana strain GN1 using the Illumina HiSeq 4000 platform. In total, 57 million 150-nucleotide paired-end clean reads were obtained and assembled into 96 scaffolds with an estimated genome size of 34.33 Mb. Furthermore, we identified genes that may be associated with strain-specific virulence and performed phylogenetic analysis of GN1 with five other Bipolaris spp. These results for GN1 will provide important information in understanding its molecular underpinning of pathogenicity and help identify novel sources of genetic resistance for improving disease resistance in barley.

Genome Wide Association Mapping of Spot Blotch Resistance at Seedling and Adult Plant Stages in Barley

Barley spot blotch (SB) caused by Cochliobolus sativus is one of the major constrains to barley production in warmer regions worldwide. The study was undertaken to identify and estimate effects of loci underlying quantitative resistance to SB at the seedling and adult plant stages. A panel of 261 high input (HI-AM) barley genotypes consisting of released cultivars, advanced breeding lines, and landraces, was screened for resistance to SB. The seedling resistance screening was conducted using two virulent isolates from Morocco (ICSB3 and SB54) while the adult plant stage resistance was evaluated at two hot spot locations, Faizabad and Varanasi, in India under artificial inoculation using a mixture of prevalent virulent isolates. The HI-AM panel was genotyped using DArT-Seq high-throughput genotyping platform. Genome wide association mapping (GWAM) was conducted using 13,182 PAV and 6,311 SNP markers, for seedling and adult plant resistance. Both GLM and MLM model were employed in TASSEL (v 5.0) using principal component analysis and Kinship Matrix as covariates. Final disease rating and Area Under Disease Progress Curve (AUDPC) were used for the evaluation of adult stage plant resistance. The GWAM analysis indicated 23 QTL at the seedling stage (14 for isolate ICSB3 and 9 for isolate SB54), while 15 QTL were detected at the adult plant stage resistance (6 at Faizabad and 9 at Varanasi) and 5 for AUDPC based resistance at Varanasi. Common QTL at seedling and adult plant stages were found across all barley chromosomes. Seedling stage QTL explained together 73.24% of the variance for seedling resistance to isolate ICSB3 and 49.26% for isolate SB54, whereas, QTL for adult plant stage resistance explained together 38.32%, 44.09% and 26.42% of the variance at Faizabad and Varanasi and AUDPC at Varanasi, respectively. Several QTL identified in this study were also reported in previous studies using bi-parental and association mapping populations, corroborating our results. The promising QTL detected at both stages, once validated, can be used for marker assisted selection (MAS) in SB resistance barley breeding program.

Hydrogen Peroxide Prompted Lignification Affects Pathogenicity of Hemi-biotrophic Pathogen Bipolaris sorokiniana to Wheat

Spot blotch caused by Bipolaris sorokiniana has spread to more than 9 million ha of wheat in the warm, humid areas of the Eastern Gangetic Plains (EGP) of South Asia and is a disease of major concern in other similar wheat growing regions worldwide. Differential lignin content in resistant and susceptible genotypes and its association with free radicals such as hydrogen peroxide (H₂O₂), superoxide (O₂ ^-) and hydroxyl radical (OH^-) were studied after inoculation under field conditions for two consecutive years. H₂O₂ significantly influenced lignin content in flag leaves, whereas there was a negative correlation among lignin and H₂O₂ to the Area Under Disease Progress Curve (AUDPC). The production of H₂O₂ was higher in the resistant genotypes than susceptible ones. The O₂ ^- and OH^- positively correlated with AUDPC but negatively with lignin content. This study illustrates that H₂O₂ has a vital role in prompting lignification and thereby resistance to spot blotch in wheat. We used cluster analysis to separate the resistant and susceptible genotypes by phenotypic and biochemical traits. H₂O₂ associated lignin production significantly reduced the number of appressoria and penetration pegs. We visualized the effect of lignin in disease resistance using differential histochemical staining of tissue from resistant and susceptible genotypes, which shows the variable accumulation of hydrogen peroxide and lignin around penetration sites.

Genome-Wide Association Study for Spot Blotch Resistance in Hard Winter Wheat

Spot blotch (SB) caused by Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to B. sorokiniana (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs (p = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, QSb.sdsu-2D.1 (SNP: Kukri_c31121_1460, R2 = 4%), QSb.sdsu-3A.1 (SNP: Excalibur_c46082_440, R2 = 4%), QSb.sdsu-4A.1 (SNP: IWA8475, R2 = 5.5%), QSb.sdsu-4B.1 (SNP: Excalibur_rep_c79414_306, R2 = 4%), QSb.sdsu-5A.1 (SNP: Kukri_rep_c104877_2166, R2 = 6%), and QSb.sdsu-7B.1 (SNP: TA005844-0160, R2 = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (QSb.sdsu-3A.1, QSb.sdsu-4A.1, and QSb.sdsu-4B.1) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.

The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana

Bipolaris sorokiniana is the causal agent of multiple diseases on wheat and barley and is the primary constraint to cereal production throughout South Asia. Despite its significance, the molecular basis of disease is poorly understood. To address this, the genomes of three Australian isolates of B. sorokiniana were sequenced and screened for known pathogenicity genes. Sequence analysis revealed that the isolate BRIP10943 harboured the ToxA gene, which has been associated previously with disease in the wheat pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis. Analysis of the regions flanking ToxA within B. sorokiniana revealed that it was embedded within a 12-kb genomic element nearly identical to the corresponding regions in P. nodorum and P. tritici-repentis. A screen of 35 Australian B. sorokiniana isolates confirmed that ToxA was present in 12 isolates. Sequencing of the ToxA genes within these isolates revealed two haplotypes, which differed by a single non-synonymous nucleotide substitution. Pathogenicity assays showed that a B. sorokiniana isolate harbouring ToxA was more virulent on wheat lines that contained the sensitivity gene when compared with a non-ToxA isolate. This work demonstrates that proteins that confer host-specific virulence can be horizontally acquired across multiple species. This acquisition can dramatically increase the virulence of pathogenic strains on susceptible cultivars, which, in an agricultural setting, can have devastating economic and social impacts.

Natural Variation in Elicitation of Defense-Signaling Associates to Field Resistance Against the Spot Blotch Disease in Bread Wheat (Triticum aestivum L.)

Spot blotch, caused by the hemibiotropic fungus Bipolaris sorokiniana, is amongst the most damaging diseases of wheat. Still, natural variation in expression of biochemical traits that determine field resistance to spot blotch in wheat remain unaddressed. To understand how genotypic variations relate to metabolite profiles of the components of defense-signaling and the plant performance, as well as to discover novel sources of resistance against spot blotch, we have conducted field studies using 968 wheat genotypes at 5 geographical locations in South-Asia in 2 years. 46 genotypes were identified as resistant. Further, in independent confirmatory trials in subsequent 3 years, over 5 geographical locations, we re-characterized 55 genotypes for their resistance (above 46 along with Yangmai#6, a well characterized resistant genotype, and eight susceptible genotypes). We next determined time-dependent spot blotch-induced metabolite profiles of components of defense-signaling as well as levels of enzymatic components of defense pathway (such as salicylic acid (SA), phenolic acids, and redox components), and derived co-variation patterns with respect to resistance in these 55 genotypes. Spot blotch-induced SA accumulation was negatively correlated to disease progression. Amongst phenolic acids, syringic acid was most strongly inversely correlated to disease progression, indicating a defensive function, which was independently confirmed. Thus, exploring natural variation proved extremely useful in determining traits influencing phenotypic plasticity and adaptation to complex environments. Further, by overcoming environmental heterogeneity, our study identifies germplasm and biochemical traits that are deployable for spot blotch resistance in wheat along South-Asia.

Genome-Wide Association Study for Spot Blotch Resistance in Hard Winter Wheat

Spot blotch (SB) caused by Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to B. sorokiniana (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs (p = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, QSb.sdsu-2D.1 (SNP: Kukri_c31121_1460, R² = 4%), QSb.sdsu-3A.1 (SNP: Excalibur_c46082_440, R² = 4%), QSb.sdsu-4A.1 (SNP: IWA8475, R² = 5.5%), QSb.sdsu-4B.1 (SNP: Excalibur_rep_c79414_306, R² = 4%), QSb.sdsu-5A.1 (SNP: Kukri_rep_c104877_2166, R² = 6%), and QSb.sdsu-7B.1 (SNP: TA005844-0160, R² = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (QSb.sdsu-3A.1, QSb.sdsu-4A.1, and QSb.sdsu-4B.1) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.

Elucidation of defense-related signaling responses to spot blotch infection in bread wheat (Triticum aestivum L.)

Spot blotch disease, caused by Bipolaris sorokiniana, is an important threat to wheat, causing an annual loss of ~17%. Under epidemic conditions, these losses may be 100%, yet the molecular responses of wheat to spot blotch remain almost uncharacterized. Moreover, defense-related phytohormone signaling genes have been poorly characterized in wheat. Here, we have identified 18 central components of salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and enhanced disease susceptibility 1 (EDS1) signaling pathways as well as the genes of the phenylpropanoid pathway in wheat. In time-course experiments, we characterized the reprogramming of expression of these pathways in two contrasting genotypes: Yangmai #6 (resistant to spot blotch) and Sonalika (susceptible to spot blotch). We further evaluated the performance of a population of recombinant inbred lines (RILs) by crossing Yangmai#6 and Sonalika (parents) and subsequent selfing to F10 under field conditions in trials at multiple locations. We characterized the reprogramming of defense-related signaling in these RILs as a consequence of spot blotch attack. During resistance to spot blotch attack, wheat strongly elicits SA signaling (SA biogenesis as well as the NPR1-dependent signaling pathway), along with WRKY33 transcription factor, followed by an enhanced expression of phenylpropanoid pathway genes. These may lead to accumulation of phenolics-based defense metabolites that may render resistance against spot blotch. JA signaling may synergistically contribute to the resistance. Failure to elicit SA (and possibly JA) signaling may lead to susceptibility against spot blotch infection in wheat.

Accumulation of Transcripts Abundance after Barley Inoculation with Cochliobolus sativus

Spot blotch caused by the hemibiotrophic pathogen Cochliobolus sativus has been the major yield-reducing factor for barley production during the last decade. Monitoring transcriptional reorganization triggered in response to this fungus is an essential first step for the functional analysis of genes involved in the process. To characterize the defense responses initiated by barley resistant and susceptible cultivars, a survey of transcript abundance at early time points of C. sativus inoculation was conducted. A notable number of transcripts exhibiting significant differential accumulations in the resistant and susceptible cultivars were detected compared to the non-inoculated controls. At the p-value of 0.0001, transcripts were divided into three general categories; defense, regulatory and unknown function, and the resistant cultivar had the greatest number of common transcripts at different time points. Quantities of differentially accumulated gene transcripts in both cultivars were identified at 24 h post infection, the approximate time when the pathogen changes trophic lifestyles. The unique and common accumulated transcripts might be of considerable interest for enhancing effective resistance to C. sativus.

Development and characterization of simple sequence repeats for Bipolaris sorokiniana and cross transferability to related species

Simple sequence repeats (SSR) markers were developed from a small insert genomic library for Bipolaris sorokiniana, a mitosporic fungal pathogen that causes spot blotch and root rot in switchgrass. About 59% of sequenced clones (n = 384) harbored SSR motifs. After eliminating redundant sequences, 196 SSR loci were identified, of which 84.7% were dinucleotide repeats and 9.7% and 5.6% were tri- and tetra-nucleotide repeats, respectively. Primer pairs were designed for 105 loci and 85 successfully amplified loci. Sixteen polymorphic loci were characterized with 15 B. sorokiniana isolates obtained from infected switchgrass plant materials collected from five states in USA. These loci successfully cross-amplified isolates from at least one related species, including Bipolaris oryzae, Bipolaris spicifera and Bipolaris victoriae, that causes leaf spot on switchgrass. Haploid gene diversity per locus across all isolates studied varied 0.633-0.861. Principal component analysis of SSR data clustered isolates according to their respective species. These SSR markers will be a valuable tool for genetic variability and population studies of B. sorokiniana and related species that are pathogenic on switchgrass and other host plants. In addition, these markers are potential diagnostic tools for species in the genus Bipolaris.