Molecular Mapping of Loci Conferring Susceptibility to Spot Blotch and Resistance to Powdery Mildew in Barley Using the Sequencing-Based Genotyping Approach

Genomic regions associated with spot blotch resistance in elite barley breeding populations

Spot blotch (SB), a prevalent foliar disease of barley, is caused by the hemibiotrophic fungal pathogen Bipolaris sorokiniana. Predominately occurring in humid growing regions worldwide, SB can result in yield losses of up to 30%. Genetic resistance remains the most effective strategy for disease management; however, most Australian barley cultivars exhibit susceptibility despite the previous identification of major resistance loci. This study investigates the genetic architecture underlying spot blotch resistance within an Australian barley breeding program. Resistance was assessed at both the seedling and adult growth stages using a single conidial isolate (SB61) across two consecutive years. A total of 337 barley lines were genotyped with 16,824 polymorphic DArT-seq™ markers. Two mapping approaches were employed: a single-marker genome-wide association study (GWAS) and a haplotype-based local genomic estimated breeding values (Local GEBV) approach. Both methodologies identified two major resistance-associated regions on chromosomes 3H and 7H, effective across growth stages. Additionally, the haplotype-based Local GEBV approach revealed resistance-associated regions on 1H, 3H, and 6H that were not detected by GWAS. Haplotype stacking analysis underscored the critical role of the 7H region for adult-plant resistance when combined with other resistance haplotypes, suggesting significant gene-by-gene interactions and highlighting the complex, quantitative nature of spot blotch resistance. This research confirms the presence of key resistance loci within Australian barley breeding populations, provides novel insight into the genetic architecture of spot blotch resistance, and emphasises the potential to enhance resistance through haplotype stacking and whole-genome prediction approaches.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01537-5.

Identification of a novel mutation in the OsMRP5 gene in low phytate Basmati rice mutant and development of CAPS marker for marker-assisted breeding

Low phytate level is a desirable trait because it promotes mineral bioavailability and thus offers a solution to tackle mineral deficiencies. The objectives of the present study were to characterize low phytate (lpa) Basmati rice mutants for the identification of novel mutations in target gene(s) and to develop a PCR-based CAPS (cleaved amplified polymorphic sequence) marker for low phytate Basmati rice. For this purpose, cultivar Super Basmati (Q4) was irradiated with gamma rays (60Co source) and three mutants named Q1 (lpa-5-9), Q2 (lpa-9-13), and Q3 (lpa-59-14) were isolated. Four genes previously been reported for the low phytic acid trait in rice were sequenced in these mutants and no mutation was observed in Q1 and Q2. However, in Q3 (lpa14) mutant a novel mutation in OsMRP5 gene (LOC_Os03g04920`) was detected. Sequence analysis displayed a substitution in the first exon of OsMRP5 at position 1142 bp resulting in the amino acid change from glycine (Gly) to alanine (Ala) at position 381a.a. To facilitate low-phytate breeding program, CAPS marker was developed to confirm this mutation site using the restriction digestion by AluI restriction enzyme. After enzyme digestion, Q3 produces four bands (32, 220, 154, and 32 bp) while Q4 (parent cultivar Super Basmati) produces only 3 bands (32, 374, and 32 bp). These results showed that this CAPS marker is 100% linked with this mutation and can be used for future breeding programs. Present findings provided insights in molecular basis of low phytate trait in rice paving the way for developing low-phytate rice varieties through marker-assisted breeding.

Transcriptome analysis of Bipolaris sorokiniana - Hordeum vulgare provides insights into mechanisms of host-pathogen interaction

Spot blotch disease incited by Bipolaris sorokiniana severely affects the cultivation of barley. The resistance to B. sorokiniana is quantitative in nature and its interaction with the host is highly complex which necessitates in-depth molecular analysis. Thus, the study aimed to conduct the transcriptome analysis to decipher the mechanisms and pathways involved in interactions between barley and B. sorokiniana in both the resistant (EC0328964) and susceptible (EC0578292) genotypes using the RNA Seq approach. In the resistant genotype, 6,283 genes of Hordeum vulgare were differentially expressed out of which 5,567 genes were upregulated and 716 genes were downregulated. 1,158 genes of Hordeum vulgare were differentially expressed in the susceptible genotype, out of which 654 genes were upregulated and 504 genes were downregulated. Several defense-related genes like resistant gene analogs (RGAs), disease resistance protein RPM1, pathogenesis-related protein PRB1-2-like, pathogenesis-related protein 1, thaumatin-like protein PWIR2 and defensin Tm-AMP-D1.2 were highly expressed exclusively in resistant genotype only. The pathways involved in the metabolism and biosynthesis of secondary metabolites were the most prominently represented pathways in both the resistant and susceptible genotypes. However, pathways involved in MAPK signaling, plant-pathogen interaction, and plant hormone signal transduction were highly enriched in resistant genotype. Further, a higher number of pathogenicity genes of B. sorokiniana was found in response to the susceptible genotype. The pathways encoding for metabolism, biosynthesis of secondary metabolites, ABC transporters, and ubiquitin-mediated proteolysis were highly expressed in susceptible genotype in response to the pathogen. 14 and 11 genes of B. sorokiniana were identified as candidate effectors from susceptible and resistant host backgrounds, respectively. This investigation will offer valuable insights in unraveling the complex mechanisms involved in barley- B. sorokiniana interaction.

Barley MLA3 recognizes the host-specificity effector Pwl2 from Magnaporthe oryzae

Plant nucleotide-binding leucine-rich repeat (NLRs) immune receptors directly or indirectly recognize pathogen-secreted effector molecules to initiate plant defense. Recognition of multiple pathogens by a single NLR is rare and usually occurs via monitoring for changes to host proteins; few characterized NLRs have been shown to recognize multiple effectors. The barley (Hordeum vulgare) NLR gene Mildew locus a (Mla) has undergone functional diversification, and the proteins encoded by different Mla alleles recognize host-adapted isolates of barley powdery mildew (Blumeria graminis f. sp. hordei [Bgh]). Here, we show that Mla3 also confers resistance to the rice blast fungus Magnaporthe oryzae in a dosage-dependent manner. Using a forward genetic screen, we discovered that the recognized effector from M. oryzae is Pathogenicity toward Weeping Lovegrass 2 (Pwl2), a host range determinant factor that prevents M. oryzae from infecting weeping lovegrass (Eragrostis curvula). Mla3 has therefore convergently evolved the capacity to recognize effectors from diverse pathogens.

Finding stable and closely linked QTLs against spot blotch in different planting dates during the adult stage in barley

The common resistance to Spot Blotch (SB) and drought stress in barley was studied using a RILs population caused Kavir × Badia cross. These lines were inoculated with Cochliobolus sativus Gonbad isolate during the adult stage and were evaluated for three crop seasons in different planting dates. The different osmotic potentials during the flowering were regulated by changing the planting dates. In total, 43 lines had resistant to SB and drought. The high-density linkage map covered 1045 cM of barley genome. A total of five stable and closely linked QTLs to SB resistance were mapped on chromosomes 2H, 3H, 4H and 7H using genome-wide composite interval mapping. Moreover, four stable and closely linked QTLs to SB susceptibility were located on chromosomes 3H, 4H, 5H and 7H. Additionally, the ISJ19-A, SCoT7-C, ISJ17-B, Bmac0144k, iPBS2415-1, Bmac0282b and EBmatc0016 markers can be used for positive screening of resistant cultivars. However, ISJ3-C, UMB310, ISJ9-B, UMB706, D03-D and iPBS2257-A markers can be used for negative screening of susceptible cultivars in marker-assisted selection. The bioinformatics studies showed that QRCsa-2H (ISJ19-A region), QRCsa-2H (SCoT7-C-ISJ17-B region), QRCsa-3H (Bmac0144k region), QRCsa-4H (iPBS2415-1 region) and QRCsa-7H (Bmac0282b-EBmatc0016 region) are involved in the carboxypeptidase, Glycosyltransferase, transcription factors, kinase and AP2/ERF, respectively.

Genetics and breeding for resistance against four leaf spot diseases in wheat (Triticum aestivum L.)

In wheat, major yield losses are caused by a variety of diseases including rusts, spike diseases, leaf spot and root diseases. The genetics of resistance against all these diseases have been studied in great detail and utilized for breeding resistant cultivars. The resistance against leaf spot diseases caused by each individual necrotroph/hemi-biotroph involves a complex system involving resistance (R) genes, sensitivity (S) genes, small secreted protein (SSP) genes and quantitative resistance loci (QRLs). This review deals with resistance for the following four-leaf spot diseases: (i) Septoria nodorum blotch (SNB) caused by Parastagonospora nodorum; (ii) Tan spot (TS) caused by Pyrenophora tritici-repentis; (iii) Spot blotch (SB) caused by Bipolaris sorokiniana and (iv) Septoria tritici blotch (STB) caused by Zymoseptoria tritici.

Genotyping by Sequencing Advancements in Barley

Barley is considered an ideal crop to study cereal genetics due to its close relationship with wheat and diploid ancestral genome. It plays a crucial role in reducing risks to global food security posed by climate change. Genetic variations in the traits of interest in crops are vital for their improvement. DNA markers have been widely used to estimate these variations in populations. With the advancements in next-generation sequencing, breeders could access different types of genetic variations within different lines, with single-nucleotide polymorphisms (SNPs) being the most common type. However, genotyping barley with whole genome sequencing (WGS) is challenged by the higher cost and computational demand caused by the large genome size (5.5GB) and a high proportion of repetitive sequences (80%). Genotyping-by-sequencing (GBS) protocols based on restriction enzymes and target enrichment allow a cost-effective SNP discovery by reducing the genome complexity. In general, GBS has opened up new horizons for plant breeding and genetics. Though considered a reliable alternative to WGS, GBS also presents various computational difficulties, but GBS-specific pipelines are designed to overcome these challenges. Moreover, a robust design for GBS can facilitate the imputation to the WGS level of crops with high linkage disequilibrium. The complete exploitation of GBS advancements will pave the way to a better understanding of crop genetics and offer opportunities for the successful improvement of barley and its close relatives.

Postulation of Specific Disease Resistance Genes in Cereals: A Widely Used Method and Its Detailed Description

Cultivation of resistant varieties is an environmentally friendly and inexpensive method of crop protection. Numerous alleles of specific disease resistance occur in cereals and other crops, and knowledge of their presence in individual varieties has wide utilization in research and practice. Postulation based on phenotyping host-pathogen interactions and the gene-for-gene model is a common way of identifying these genes. The same technique and design of tests are used for postulating virulence when pathogen populations are studied. Powdery mildews caused by different formae speciales of Blumeria graminis (Bg) are important cereal diseases. In this contribution, experimental methods are described that use a model organism Bg f. sp. hordei, which can be employed for other cereal mildews and possibly rusts. It includes illustrations and a summary of our long-term practical experience. It also critically evaluates the benefits of leaf segment tests compared with screening whole plants.

Recent insights into barley and Rhynchosporium commune interactions

Rhynchosporium commune is the causal pathogen of scald in barley (Hordeum vulgare), a foliar disease that can reduce yield by up to 40% in susceptible cultivars. R. commune is found worldwide in all temperate growing regions and is regarded as one of the most economically important barley pathogens. It is a polycyclic pathogen with the ability to rapidly evolve new virulent strains in response to resistance genes deployed in commercial cultivars. Hence, introgression and pyramiding of different loci for resistance (qualitative or quantitative) through marker-assisted selection is an effective way to improve scald resistance in barley. This review summarizes all 148 resistance quantitative trait loci reported at the date of submission of this review and projects them onto the barley physical map, where it is clear many loci co-locate on chromosomes 3H and 7H. We have summarized the major named resistance loci and reiterated the renaming of Rrs15 (CI8288) to Rrs17. This review provides a comprehensive resource for future discovery and breeding efforts of qualitative and quantitative scald resistance loci.

Bivariate analysis of barley scald resistance with relative maturity reveals a new major QTL on chromosome 3H

The disease scald of barley is caused by the pathogen Rhynchosporium commune and can cause up to 30–40% yield loss in susceptible cultivars. In this study, the Australian barley cultivar ‘Yerong’ was demonstrated to have resistance that differed from Turk (Rrs1 (Rh3 type)) based on seedling tests with 11 R. commune isolates. A doubled haploid population with 177 lines derived from a cross between ‘Yerong’ and the susceptible Australian cultivar ‘Franklin’ was used to identify quantitative trait loci (QTL) for scald resistance. A QTL on chromosome 3H was identified with large effect, consistent with a major gene conferring scald resistance at the seedling stage. Under field conditions, a bivariate analysis was used to model scald percentage of infected leaf area and relative maturity, the residuals from the regression were used as our phenotype for QTL analysis. This analysis identified one major QTL on chromosome 3H, which mapped to the same position as the QTL at seedling stage. The identified QTL on 3H is proposed to be different from the Rrs1 on the basis of seedling resistance against different R. commune isolates and physical map position. This study increases the current understanding of scald resistance and identifies genetic material possessing QTLs useful for the marker-assisted selection of scald resistance in barley breeding programs.