Genetic analysis of net form net blotch resistance in barley lines CIho 5791 and Tifang against a global collection of P. teres f. teres isolates

Variability in Chromosome 1 of Select Moroccan Pyrenophora teres f. teres Isolates Overcomes a Highly Effective Barley Chromosome 6H Source of Resistance

Barley net form net blotch (NFNB) is a destructive foliar disease caused by Pyrenophora teres f. teres. Barley line CIho5791, which harbors the broadly effective chromosome 6H resistance gene Rpt5, displays dominant resistance to P. teres f. teres. To genetically characterize P. teres f. teres avirulence/virulence on the barley line CIho5791, we generated a P. teres f. teres mapping population using a cross between the Moroccan CIho5791-virulent isolate MorSM40-3 and the avirulent reference isolate 0-1. Full genome sequences were generated for 103 progenies. Saturated chromosome-level genetic maps were generated, and quantitative trait locus (QTL) mapping identified two major QTL associated with P. teres f. teres avirulence/virulence on CIho5791. The most significant QTL mapped to chromosome (Ch) 1, where the virulent allele was contributed by MorSM40-3. A second QTL mapped to Ch8; however, this virulent allele was contributed by the avirulent parent 0-1. The Ch1 and Ch8 loci accounted for 27 and 15% of the disease variation, respectively, and the avirulent allele at the Ch1 locus was epistatic over the virulent allele at the Ch8 locus. As a validation, we used a natural P. teres f. teres population in a genome-wide association study that identified the same Ch1 and Ch8 loci. We then generated a new reference quality genome assembly of parental isolate MorSM40-3 with annotation supported by deep transcriptome sequencing of infection time points. The annotation identified candidate genes predicted to encode small, secreted proteins, one or more of which are likely responsible for overcoming the CIho5791 resistance. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2024.

High resolution mapping of a novel non-transgressive hybrid susceptibility locus in barley exploited by P. teres f. maculata

Hybrid genotypes can provide significant yield gains over conventional inbred varieties due to heterosis or hybrid vigor. However, hybrids can also display unintended negative attributes or phenotypes such as extreme pathogen susceptibility. The necrotrophic pathogen Pyrenophora teres f. maculata (Ptm) causes spot form net blotch, which has caused significant yield losses to barley worldwide. Here, we report on a non-transgressive hybrid susceptibility locus in barley identified between the three parental lines CI5791, Tifang and Golden Promise that are resistant to Ptm isolate 13IM.3. However, F2 progeny from CI5791 × Tifang and CI5791 × Golden Promise crosses exhibited extreme susceptibility. The susceptible phenotype segregated in a ratio of 1 resistant:1 susceptible representing a genetic segregation ratio of 1 parental (res):2 heterozygous (sus):1 parental (res) suggesting a single hybrid susceptibility locus. Genetic mapping using a total of 715 CI5791 × Tifang F2 individuals (1430 recombinant gametes) and 149 targeted SNPs delimited the hybrid susceptibility locus designated Susceptibility to Pyrenophora teres 2 (Spt2) to an ~ 198 kb region on chromosome 5H of the Morex V3 reference assembly. This single locus was independently mapped with 83 CI5791 × Golden Promise F2 individuals (166 recombinant gametes) and 180 genome wide SNPs that colocalized to the same Spt2 locus. The CI5791 genome was sequenced using PacBio Continuous Long Read technology and comparative analysis between CI5791 and the publicly available Golden Promise genome assembly determined that the delimited region contained a single high confidence Spt2 candidate gene predicted to encode a pentatricopeptide repeat-containing protein.

A Moroccan Pyrenophora teres f. teres Population Defeats Rpt5, the Broadly Effective Resistance on Barley Chromosome 6H

Net form net blotch (NFNB), caused by Pyrenophora teres f. teres, is an important barley disease. The centromeric region of barley chromosome 6H has often been associated with resistance or susceptibility to NFNB, including the broadly effective dominant resistance gene Rpt5 derived from barley line CIho 5791. We characterized a population of Moroccan P. teres f. teres isolates that had overcome Rpt5 resistance and identified quantitative trait loci (QTL) that were effective against these isolates. Eight Moroccan P. teres f. teres isolates were phenotyped on barley lines CIho 5791 and Tifang. Six isolates were virulent on CIho 5791, and two were avirulent. A CIho 5791 × Tifang recombinant inbred line (RIL) population was phenotyped with all eight isolates and confirmed the defeat of the 6H resistance locus formerly mapped as Rpt5 in barley line CI9819. A major QTL on chromosome 3H with the resistance allele derived from Tifang, as well as minor QTL, was identified and provided resistance against these isolates. F2 segregation ratios supported dominant inheritance for both the 3H and 6H resistance. Furthermore, inoculation of progeny isolates derived from a cross of P. teres f. teres isolates 0-1 (virulent on Tifang/avirulent on CIho 5791) and MorSM 40-3 (avirulent on Tifang/virulent on CIho 5791) onto the RIL and F2 populations determined that recombination between isolates can generate novel genotypes that overcome both resistance genes. Markers linked to the QTL identified in this study can be used to incorporate both resistance loci into elite barley cultivars for durable resistance.

Multi-parental fungal mapping population study to detect genomic regions associated with Pyrenophora teres f. teres virulence

In recent years multi-parental mapping populations (MPPs) have been widely adopted in many crops to detect quantitative trait loci (QTLs) as this method can compensate for the limitations of QTL analyses using bi-parental mapping populations. Here we report the first multi-parental nested association mapping (MP-NAM) population study used to detect genomic regions associated with host-pathogenic interactions. MP-NAM QTL analyses were conducted on 399 Pyrenophora teres f. teres individuals using biallelic, cross-specific and parental QTL effect models. A bi-parental QTL mapping study was also conducted to compare the power of QTL detection between bi-parental and MP-NAM populations. Using MP-NAM with 399 individuals detected a maximum of eight QTLs with a single QTL effect model whilst only a maximum of five QTLs were detected with an individual bi-parental mapping population of 100 individuals. When reducing the number of isolates in the MP-NAM to 200 individuals the number of QTLs detected remained the same for the MP-NAM population. This study confirms that MPPs such as MP-NAM populations can be successfully used in detecting QTLs in haploid fungal pathogens and that the power of QTL detection with MPPs is greater than with bi-parental mapping populations.

Genome-wide association mapping of Pyrenophora teres f. maculata and Pyrenophora teres f. teres resistance loci utilizing natural Turkish wild and landrace barley populations

Unimproved landraces and wild relatives of crops are sources of genetic diversity that were lost post domestication in modern breeding programs. To tap into this rich resource, genome-wide association studies in large plant genomes have enabled the rapid genetic characterization of desired traits from natural landrace and wild populations. Wild barley (Hordeum spontaneum), the progenitor of domesticated barley (Hordeum vulgare), is dispersed across Asia and North Africa, and has co-evolved with the ascomycetous fungal pathogens Pyrenophora teres f. teres and P. teres f. maculata, the causal agents of the diseases net form of net blotch and spot form of net blotch, respectively. Thus, these wild and local adapted barley landraces from the region of origin of both the host and pathogen represent a diverse gene pool to identify new sources of resistance, due to millions of years of co-evolution. The barley—P. teres pathosystem is governed by complex genetic interactions with dominant, recessive, and incomplete resistances and susceptibilities, with many isolate-specific interactions. Here, we provide the first genome-wide association study of wild and landrace barley from the Fertile Crescent for resistance to both forms of P. teres. A total of 14 loci, four against P. teres f. maculata and 10 against P. teres f. teres, were identified in both wild and landrace populations, showing that both are genetic reservoirs for novel sources of resistance. We also highlight the importance of using multiple algorithms to both identify and validate additional loci.

Genetic mapping of host resistance to the Pyrenophora teres f. maculata isolate 13IM8.3

Spot form net blotch (SFNB), caused by the necrotrophic fungal pathogen Pyrenophora teres f. maculata (Ptm), is a foliar disease of barley that results in significant yield losses in major growing regions worldwide. Understanding the host-parasite interactions between pathogen virulence/avirulence genes and the corresponding host susceptibility/resistance genes is important for the deployment of genetic resistance against SFNB. Two recombinant inbred mapping populations were developed to characterize genetic resistance/susceptibility to the Ptm isolate 13IM8.3, which was collected from Idaho (ID). An Illumina Infinium array was used to produce a genome wide marker set. Quantitative trait loci (QTL) analysis identified ten significant resistance/susceptibility loci, with two of the QTL being common to both populations. One of the QTL on 5H appears to be novel, while the remaining loci have been reported previously. Single nucleotide polymorphisms (SNPs) closely linked to or delimiting the significant QTL have been converted to user-friendly markers. Loci and associated molecular markers identified in this study will be useful in genetic mapping and deployment of the genetic resistance to SFNB in barley.

Potentiators of Disease During Barley Infection by Pyrenophora teres f. teres in a Susceptible Interaction

Pyrenophora teres f. teres is a necrotrophic fungal pathogen and causal agent of net form net blotch (NFNB), a significant disease of barley. RNA-seq data encompassing asymptomatic and subsequent necrotrophic phases of the pathogen was obtained for P. teres f. teres isolate W1-1 in NFNB-sensitive cultivar Baudin. Host genes notably regulated during infection included concerted induction of over half the repertoire of disease resistance genes, together with genes involved in oxidation-reduction processes, characteristic of a hypersensitive response. Several systemic acquired resistance response genes were suppressed and there was a complete absence of defense-related thionin gene expression. In P. teres f. teres, genes involved in hydrolase activities and cell-wall catabolic processes were induced during infection, while nitrate assimilation and response to oxidative stress processes were suppressed. Timecourse data allowed a number of predicted P. teres f. teres effector genes with differing expression profiles to be identified that may underlie barley sensitivity to NFNB. Candidate genes involved in the host-pathogen interaction provide a basis for functional characterization and control strategies based on fungicide or mutation targets, which will facilitate further research aimed at controlling NFNB disease.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Fire Blight Susceptibility in Lilium spp. Correlates to Sensitivity to Botrytis elliptica Secreted Cell Death Inducing Compounds

Fire blight represents a widespread disease in Lilium spp. and is caused by the necrotrophic Ascomycete Botrytis elliptica. There are >100 Lilium species that fall into distinct phylogenetic groups and these have been used to generate the contemporary commercial genotypes. It is known among lily breeders and growers that different groups of lilies differ in susceptibility to fire blight, but the genetic basis and mechanisms of susceptibility to fire blight are unresolved. The aim of this study was to quantify differences in fire blight susceptibility between plant genotypes and differences in virulence between fungal isolates. To this end we inoculated, in four biological replicates over 2 years, a set of 12 B. elliptica isolates on a panel of 18 lily genotypes representing seven Lilium hybrid groups. A wide spectrum of variation in symptom severity was observed in different isolate-genotype combinations. There was a good correlation between the lesion diameters on leaves and flowers of the Lilium genotypes, although the flowers generally showed faster expanding lesions. It was earlier postulated that B. elliptica pathogenicity on lily is conferred by secreted proteins that induce programmed cell death in lily cells. We selected two aggressive isolates and one mild isolate and collected culture filtrate (CF) samples to compare the cell death inducing activity of their secreted compounds in lily. After leaf infiltration of the CFs, variation was observed in cell death responses between the diverse lilies. The severity of cell death responses upon infiltration of the fungal CF observed among the diverse Lilium hybrid groups correlated well to their fire blight susceptibility. These results support the hypothesis that susceptibility to fire blight in lily is mediated by their sensitivity to B. elliptica effector proteins in a quantitative manner. Cell death-inducing proteins may provide an attractive tool to predict fire blight susceptibility in lily breeding programs.

The Barley HvWRKY6 Transcription Factor Is Required for Resistance Against Pyrenophora teres f. teres

Barley is an important cereal crop worldwide because of its use in the brewing and distilling industry. However, adequate supplies of quality malting barley are threatened by global climate change due to drought in some regions and excess precipitation in others, which facilitates epidemics caused by fungal pathogens. The disease net form net blotch caused by the necrotrophic fungal pathogen Pyrenophora teres f. teres (Ptt) has emerged as a global threat to barley production and diverse populations of Ptt have shown a capacity to overcome deployed genetic resistances. The barley line CI5791 exhibits remarkably effective resistance to diverse Ptt isolates from around the world that maps to two major QTL on chromosomes 3H and 6H. To identify genes involved in this effective resistance, CI5791 seed were γ-irradiated and two mutants, designated CI5791-γ3 and CI5791-γ8, with compromised Ptt resistance were identified from an M₂ population. Phenotyping of CI5791-γ3 and -γ8 × Heartland F₂ populations showed three resistant to one susceptible segregation ratios and CI5791-γ3 × -γ8 F₁ individuals were susceptible, thus these independent mutants are in a single allelic gene. Thirty-four homozygous mutant (susceptible) CI5791-γ3 × Heartland F₂ individuals, representing 68 recombinant gametes, were genotyped via PCR genotype by sequencing. The data were used for single marker regression mapping placing the mutation on chromosome 3H within an approximate 75 cM interval encompassing the 3H CI5791 resistance QTL. Sequencing of the mutants and wild-type (WT) CI5791 genomic DNA following exome capture identified independent mutations of the HvWRKY6 transcription factor located on chromosome 3H at ∼50.7 cM, within the genetically delimited region. Post transcriptional gene silencing of HvWRKY6 in barley line CI5791 resulted in Ptt susceptibility, confirming that it functions in NFNB resistance, validating it as the gene underlying the mutant phenotypes. Allele analysis and transcript regulation of HvWRKY6 from resistant and susceptible lines revealed sequence identity and upregulation upon pathogen challenge in all genotypes analyzed, suggesting a conserved transcription factor is involved in the defense against the necrotrophic pathogen. We hypothesize that HvWRKY6 functions as a conserved signaling component of defense mechanisms that restricts Ptt growth in barley.

Identification of a major dominant gene for race-nonspecific tan spot resistance in wild emmer wheat

A single dominant gene found in tetraploid and hexaploid wheat controls broad-spectrum race-nonspecific resistance to the foliar disease tan spot caused by Pyrenophora tritici-repentis. Tan spot is an important foliar disease of durum and common wheat caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis. Genetic studies in common wheat have shown that pathogen-produced necrotrophic effectors interact with host genes in an inverse gene-for-gene manner to cause disease, but quantitative trait loci (QTLs) with broad race-nonspecific resistance also exist. Less work has been done to understand the genetics of tan spot interactions in durum wheat. Here, we evaluated a set of Langdon durum-wild emmer (Triticum turgidum ssp. dicoccoides) disomic chromosome substitution lines for reaction to four P. tritici-repentis isolates representing races 1, 2, 3, and 5 to identify wild emmer chromosomes potentially containing tan spot resistance genes. Chromosome 3B from the wild emmer accession IsraelA rendered the tan spot-susceptible durum cultivar Langdon resistant to all four fungal isolates. Genetic analysis indicated that a single dominant gene, designated Tsr7, governed resistance. Detailed mapping experiments showed that the Tsr7 locus is likely the same as the race-nonspecific QTL previously identified in the hexaploid wheat cultivars BR34 and Penawawa. Four user-friendly SNP-based semi-thermal asymmetric reverse PCR (STARP) markers cosegregated with Tsr7 and should be useful for marker-assisted selection of resistance. In addition to 3B, other wild emmer chromosomes contributed moderate levels of tan spot resistance, and, as has been shown previously for tetraploid wheat, the Tsn1-Ptr ToxA interaction was not associated with susceptibility. This is the first report of a major dominant gene governing resistance to tan spot in tetraploid wheat.

Identification of quantitative trait loci for net form net blotch resistance in contemporary barley breeding germplasm from the USA using genome-wide association mapping

Association mapping study conducted in a population of 3490 elite barley breeding lines from ten barley breeding programs of the USA identified 12 QTLs for resistance/susceptibility to net form of net blotch. Breeding resistant varieties is the best management strategy for net form of net blotch (NFNB) in barley (Hordeum vulgare L.) caused by Pyrenophora teres f. teres (Ptt). Several resistance QTL have been previously identified in barley via linkage mapping and genome-wide association studies (GWAS). A GWAS conducted in a collection of advanced breeding lines (n = 3490) representing elite germplasm from ten barley breeding programs of the USA identified 42 unique marker-trait associations (MTA) for NFNB resistance. The lines were genotyped with 3072 SNP markers and phenotyped with four Ptt isolates in controlled environment. The lines were used to construct 13 different GWAS panels. Efficient mixed model association method with principal components and kinship was used for GWAS. Significance threshold for MTA was set at a false discovery rate of 0.05. Two, eight, six, one and 25 MTA were identified in chromosomes 1H, 3H, 4H, 5H and 6H, respectively. Based on genetic positions and linkage disequilibrium, these MTA's correspond to two, three, two, one and four QTLs in chromosome 1H, 3H, 4H, 5H and 6H, respectively. A comparison with previous linkage and GWAS studies revealed several previously identified and novel QTLs. Moreover, different genomic regions were found to be responsible for NFNB resistance in two-row versus six-row germplasm. The germplasm-specific SNP markers with additive effects and allelic distribution is reported to facilitate breeders in selection of markers for MAS to introgress novel net blotch resistance.

Research advances in the Pyrenophora teres-barley interaction

Pyrenophora teres f. teres and P. teres f. maculata are significant pathogens that cause net blotch of barley. An increased number of loci involved in P. teres resistance or susceptibility responses of barley as well as interacting P. teres virulence effector loci have recently been identified through biparental and association mapping studies of both the pathogen and host. Characterization of the resistance/susceptibility loci in the host and the interacting effector loci in the pathogen will provide a path for targeted gene validation for better-informed release of resistant barley cultivars. This review assembles concise consensus maps for all loci published for both the host and pathogen, providing a useful resource for the community to be used in pathogen characterization and barley breeding for resistance to both forms of P. teres.

Genetic analysis of a worldwide barley collection for resistance to net form of net blotch disease (Pyrenophora teres f. teres)

A total of 449 barley accessions were phenotyped for Pyrenophora teres f. teres resistance at three locations and in greenhouse trials. Genome-wide association studies identified 254 marker-trait associations corresponding to 15 QTLs. Net form of net blotch is one of the most important diseases of barley and is present in all barley growing regions. Under optimal conditions, it causes high yield losses of 10-40% and reduces grain quality. The most cost-effective and environmentally friendly way to prevent losses is growing resistant cultivars, and markers linked to effective resistance factors can accelerate the breeding process. Here, 449 barley accessions expressing different levels of resistance comprising landraces and commercial cultivars from the centres of diversity were selected. The set was phenotyped for seedling resistance to three isolates in controlled-environment tests and for adult plant resistance at three field locations (Belarus, Germany and Australia) and genotyped with the 50 k iSelect chip. Genome-wide association studies using 33,818 markers and a compressed mixed linear model to account for population structure and kinship revealed 254 significant marker-trait associations corresponding to 15 distinct QTL regions. Four of these regions were new QTL that were not described in previous studies, while a total of seven regions influenced resistance in both seedlings and adult plants.

Mapping of barley susceptibility/resistance QTL against spot form net blotch caused by Pyrenophora teres f. maculata using RIL populations

Spot form net blotch (SFNB) caused by the necrotrophic fungal pathogen Pyrenophora teres f. maculata (Ptm) is an important disease of barley worldwide including the major barley production regions of North America. To characterize SFNB resistance/susceptibility quantitative trait loci (QTL), three recombinant inbred line (RIL) populations were developed from crosses between the malting barley cultivars, Tradition (six row) and Pinnacle (two row), and the two world barley core collection lines, PI67381 and PI84314. Tradition and Pinnacle were susceptible to many North American Ptm isolates, while PI67381 and PI84314 carry resistances to diverse Ptm isolates from across the globe. The RIL populations, Tradition/PI67381, Pinnacle/PI67381, and Pinnacle/PI84314 were genotyped using polymerase chain reaction-mediated genotype-by-sequencing single nucleotide polymorphism marker panels and phenotyped at the seedling stage with six geographically distinct Ptm isolates: FGOB10Ptm-1 (North Dakota, USA), Pin-A14 (Montana, USA), Cel-A17 (Montana, USA), SG1 (Australia), NZKF2 (New Zealand) and DEN2.6 (Denmark). The goal was to determine if the susceptible elite lines contained common susceptibility genes/QTL or if the resistant lines had common resistant genes/QTL effective against diverse Ptm isolates. The QTL analyses identified a total of 12 resistance and/or susceptibility loci on chromosomes 2H, 3H, 4H, 6H, and 7H of which three had not been previously reported. Common major QTL were detected on chromosome 2H (R² = 14-40%) and 7H (R² = 24-80%) in all three RIL populations, suggesting underlying genes with broad resistance specificity. The major 7H QTL was shown to be a dominant susceptibility gene in both susceptible malting barley varieties.

SNPs associated with barley resistance to isolates of Pyrenophora teres f. teres

BACKGROUND

Net blotch caused by Pyrenophra teres f. teres is a major foliar disease of barley. Infection can result in significant yield losses of susceptible cultivars of up to 40%. Of the two forms of net blotch (P. teres f. teres and P. teres f. maculata), P. teres f. teres (net form of net blotch) is the dominant one in Russia. The goal of the current study was to identify genomic regions associated with seedling resistance to several pathotypes of the net form of net blotch in Siberian spring barley genotypes. For this, a genome-wide association study of a Siberian barley collection, genotyped with 50 K Illumina SNP-chip, was carried out.

RESULTS

Seedling resistance of 94 spring barley cultivars and lines to four Pyrenophora teres f. teres isolates (S10.2, K5.1, P3.4.0, and A2.6.0) was investigated. According to the Tekauz rating scale, 25, 21, 14, and 14% of genotypes were highly resistant, and 19, 8, 9, and 16% of genotypes were moderate-resistant to the isolates S10.2, K5.1, P3.4.0, and A2.6.0, respectively. Eleven genotypes (Alag-Erdene, Alan-Bulag, L-259/528, Kedr, Krymchak 55, Omsky golozyorny 2, Omsky 13709, Narymchanin, Pallidum 394, Severny and Viner) were resistant to all studied isolates. Nine additional cultivars (Aley, Barkhatny, Belogorsky, Bezenchuksky 2, Emelya, G-19980, Merit 57, Mestny Primorsky, Slavaynsky) were resistant to 3 of the 4 isolates. The phenotyping and genotyping data were analysed using several statistical models: GLM + Q, GLM + PCA, GLM + PCA + Q, and the MLM + kinship matrix. In total, 40 SNPs in seven genomic regions associated with net blotch resistance were revealed: the region on chromosome 1H between 57.3 and 62.8 cM associated with resistance to 2 isolates (to P3.4.0 at the significant and K5.1 at the suggestive levels), the region on chromosome 6H between 52.6 and 55.4 cM associated with resistance to 3 isolates (to P3.4.0 at the significant and K5.1 and S10.2 at the suggestive levels), three isolate-specific significant regions (P3.4.0-specific regions on chromosome 2H between 71.0 and 74.1 cM and on chromosome 3H between 12.1 and 17.4 cM, and the A2.6.0-specific region on chromosome 3H between 50.9 and 54.8 cM), as well as two additional regions on chromosomes 2H (between 23.2 and 23.8 cM, resistant to S10.2) and 3 (between 135.6 and 137.5 cM resistant to K5.1) with suggestive SNPs, coinciding, however, with known net blotch resistance quantitative trait loci (QTLs) at the same regions.

CONCLUSIONS

Seven genomic regions on chromosomes 1H, 2H, 3H, and 6H associated with the resistance to four Pyrenophora teres f. teres isolates were identified in a genome-wide association study of a Siberian spring barley panel. One novel isolate-specific locus on chromosome 3 between 12.1 and 17.4 cM was revealed. Other regions identified in the current study coincided with previously known loci conferring resistance to net blotch. The significant SNPs revealed in the current study can be converted to convenient PCR markers for accelerated breeding of resistant barley cultivars.

Fine mapping of a dominant gene conferring resistance to spot blotch caused by a new pathotype of Bipolaris sorokiniana in barley

We fine-mapped and physically anchored a dominant gene (Rbs7) conferring resistance to spot blotch caused by a new pathotype of Bipolaris sorokiniana in a genomic interval of 304 kb on barley chromosome 6H. Spot blotch, caused by Bipolaris sorokiniana, is an economically important disease on barley in the Upper Midwest region of the USA and Prairie Provinces of Canada. A new pathotype (pathotype 7, represented by isolate ND4008) of B. sorokiniana has been identified, which is highly virulent on barley cultivars with resistance to other pathotypes of the fungus. In this study, we fine-mapped a dominant gene conferring resistance to pathotype 7 in the barley line PI 235186. Genetic analysis of the F₁ and F₂ plants from a cross between PI 356741 (highly susceptible to ND4008) and PI 235186 (highly resistant to ND4008) indicated that a single dominant gene (Rbs7) controls the resistance in PI 235186. This result was confirmed by genetic analysis of the F_2:3 families and a recombinant inbred line (RIL) population derived from the same cross. Bulked segregant analysis using simple sequence repeat markers localized Rbs7 on the short arm of chromosome 6H. Additional DNA markers were developed from the 6H pseudomolecule sequence of barley cv. Morex and mapped to the genomic region carrying Rbs7 using the RIL population and F₂ recombinants derived from the PI 356741 × PI 235186 cross. Rbs7 was fine-mapped between two markers (M13.06 and M13.37), which spans a physical distance of 304 kb on Morex chromosome 6H. These results provide a foundation for future cloning of the resistance gene and development of user-friendly molecular markers that can be used for development of spot-blotch-resistant cultivars in barley breeding programs.

Reference Assembly and Annotation of the Pyrenophora teres f. teres Isolate 0-1

Pyrenophora teres f. teres, the causal agent of net form net blotch (NFNB) of barley, is a destructive pathogen in barley-growing regions throughout the world. Typical yield losses due to NFNB range from 10 to 40%; however, complete loss has been observed on highly susceptible barley lines where environmental conditions favor the pathogen. Currently, genomic resources for this economically important pathogen are limited to a fragmented draft genome assembly and annotation, with limited RNA support of the P. teres f. teres isolate 0-1. This research presents an updated 0-1 reference assembly facilitated by long-read sequencing and scaffolding with the assistance of genetic linkage maps. Additionally, genome annotation was mediated by RNAseq analysis using three infection time points and a pure culture sample, resulting in 11,541 high-confidence gene models. The 0-1 genome assembly and annotation presented here now contains the majority of the repetitive content of the genome. Analysis of the 0-1 genome revealed classic characteristics of a “two-speed” genome, being compartmentalized into GC-equilibrated and AT-rich compartments. The assembly of repetitive AT-rich regions will be important for future investigation of genes known as effectors, which often reside in close proximity to repetitive regions. These effectors are responsible for manipulation of the host defense during infection. This updated P. teres f. teres isolate 0-1 reference genome assembly and annotation provides a robust resource for the examination of the barley–P. teres f. teres host–pathogen coevolution.

Identification of quantitative trait loci associated with resistance to net form net blotch in a collection of Nordic barley germplasm

Association mapping of resistance to Pyrenophora teres f. teres in a collection of Nordic barley germplasm at different developmental stages revealed 13 quantitative loci with mostly small effects. Net blotch, caused by the necrotrophic fungus Pyrenophora teres, is one of the major diseases in barley in Norway causing quantitative and qualitative yield losses. Resistance in Norwegian cultivars and germplasm is generally insufficient and resistance sources have not been extensively explored yet. In this study, we mapped quantitative trait loci (QTL) associated with resistance to net blotch in Nordic germplasm. We evaluated a collection of 209 mostly Nordic spring barley lines for reactions to net form net blotch (NFNB; Pyrenophora teres f. teres) in inoculations with three single conidia isolates at the seedling stage and in inoculated field trials at the adult stage in 4 years. Using 5669 SNP markers genotyped with the Illumina iSelect 9k Barley SNP Chip and a mixed linear model accounting for population structure and kinship, we found a total of 35 significant marker-trait associations for net blotch resistance, corresponding to 13 QTL, on all chromosomes. Out of these QTL, seven conferred resistance only in adult plants and four were only detectable in seedlings. Two QTL on chromosomes 3H and 6H were significant during both seedling inoculations and adult stage field trials. These are promising candidates for breeding programs using marker-assisted selection strategies. The results elucidate the genetic background of NFNB resistance in Nordic germplasm and suggest that NB resistance is conferred by a number of genes each with small-to-moderate effects, making it necessary to pyramid these genes to achieve sufficient levels of resistance.

Mapping of quantitative trait loci associated with resistance to net form net blotch (Pyrenophora teres f. teres) in a doubled haploid Norwegian barley population

Barley net blotch caused by the necrotrophic fungus Pyrenophora teres is a major barley disease in Norway. It can cause grain shriveling and yield losses, and resistance in currently grown cultivars is insufficient. In this study, a set of 589 polymorphic SNP markers was used to map resistance loci in a population of 109 doubled haploid lines from a cross between the closely related Norwegian cultivars Arve (moderately susceptible) and Lavrans (moderately resistant). Resistance to three net form net blotch (P. teres f. teres) single spore isolates was evaluated at the seedling stage in the greenhouse and at the adult plant stage under field conditions during three years. Days to heading and plant height were scored to assess their influence on disease severity. At the seedling stage, three to four quantitative trait loci (QTL) associated with resistance were found per isolate used. A major, putatively novel QTL was identified on chromosome 5H, accounting for 23-48% of the genetic variation. Additional QTL explaining between 12 and 16.5% were found on chromosomes 4H, 5H, 6H and 7H, with the one on 6H being race-specific. The major QTL on 5H was also found in adult plants under field conditions in three years (explaining up to 55%) and the 7H QTL was found in field trials in one year. Additional adult plant resistance QTL on 3H, 6H and 7H were significant in single years. The resistance on chromosomes 3H, 5H, 6H and 7H originates from the more resistant parent Lavrans, while the resistance on 4H is conferred by Arve. The genetic markers associated with the QTL found in this study will benefit marker-assisted selection for resistance against net blotch.