Haplotype-based insights into the genetic architecture of net blotch resistance in barley

Genome-wide association mapping and functional annotation of loci conferring resistance to Pyrenophora teres f. teres in barley

Net form net blotch (NFNB), caused by Pyrenophora teres f. teres ( Ptt ), is a major constraint to barley production. However, the genetic basis of adult plant resistance (APR) and seedling resistance remains incompletely understood. This study aimed to dissect the genetic architecture of NFNB resistance in a diverse panel of 273 spring barley accessions. APR was evaluated in two contrasting field environments in Kazakhstan, whereas seedling resistance was assessed under greenhouse conditions using two Ptt races. Genotyping with the 50K SNP array yielded 31,834 high-quality SNPs. Genome-wide association analyses were performed using four models – MLM, MLMM, FarmCPU, and BLINK – that accounted for population structure and kinship. Candidate genes within QTL intervals were prioritized using transcriptomic data from 16 barley tissues and co-expression network analysis. Substantial phenotypic variation was observed, with moderate heritability for APR ( h 2 = 50.6%) and seedling resistance ( h 2 = 41.3%), together with strong genotype × environment and genotype × race interactions. In total, 275 marker–trait associations were detected for APR and 48 for seedling resistance. These associations were consolidated into 57 genome-wide significant (P < 1.57E–6) or multi-model-supported QTLs across all seven barley chromosomes, including 39 APR and 18 seedling-resistance QTLs. Forty QTLs co-localized with known resistance genes ( Rpt1 , Rpt2 , Rpt3 , Rpt4 , Rpt6 , Rpt8 , Rpt9 , and SPN1 ) or previously reported net blotch QTLs, whereas 17 were potentially novel. Transcriptomic integration identified 87 highly expressed genes within APR QTL regions and 42 within seedling-resistance QTLs. The potentially novel QTLs Q_NB_1H.6 , Q_NB_2H.3 , and Q_NB_3H.1 harbored genes encoding proteins previously associated with pathogen resistance and stress responses. Co-expression analysis revealed stage-specific transcriptional patterns, with APR-associated genes enriched in regulatory functions and seedling-resistance genes enriched in metabolic and structural functions. The results demonstrate that NFNB resistance is polygenic and developmentally stage-dependent, with partly distinct mechanisms underlying adult plant and seedling resistance. The identified QTLs and prioritized candidate genes provide targets for independent validation, functional characterization, and the development of molecular markers to support breeding for durable NFNB resistance in barley.

Haplotype-based nested association mapping for net form net blotch response in Australian barley

Haplotype-based nested association mapping conducted in Australian barley identified 30 haploblocks for resistance/susceptibility to net form of net blotch. Stacking multiple resistance haplotypes significantly reduced disease severity. Net form net blotch (NFNB), caused by Pyrenophora teres f. teres, is a major fungal disease affecting barley, leading to significant yield losses globally. Improving the sustainability of barley production requires identifying genetic sources that confer effective resistance across genetic backgrounds and diverse environments. Considerable progress has been made through mapping studies conducted internationally, but many have largely focused on unadapted germplasm such as landraces or used foreign pathotypes. To support breeding outcomes in Australia, characterization of resistance alleles that are effective against local pathotypes is critical, along with investigating resistances that may already be present in breeding germplasm as this could reduce the time to deployment of resistant cultivars. In this study, we applied the local genomic estimated breeding value approach to perform haplotype mapping using a multi-reference parent nested association mapping (MR-NAM) population developed using resistant breeding lines as donor parents. The population was evaluated across three seasons in Queensland to investigate the genetic architecture of NFNB resistance and genotype-by-environment interactions. We identified 30 haploblocks, with seven representing novel genomic regions not previously associated with NFNB resistance. Three haploblocks on chromosomes 2H, 6H, and 7H were consistently associated with resistance across all environments, suggesting that they likely harbor stable resistance loci. Haplotype stacking analysis demonstrated that combining multiple resistance haplotypes significantly reduced disease severity, with lines carrying 6–10 resistance haplotypes showing progressive improvements in NFNB resistance. The distribution and effectiveness of these key haplotypes across environments, and in diverse genetic backgrounds adapted to Australia (Commander, Compass and La Trobe), highlight the potential to harness them in ongoing pre-breeding and breeding programs.

The Genetic Basis of ZmBGLU17 in Modulating Maize Resistance to the Fall Armyworm Spodoptera Frugiperda

Maize, as a globally important food crop, is threatened by pests including the fall armyworm (FAW, Spodoptera frugiperda) throughout its production. Current management strategies are largely limited to conventional chemical insecticides and transgenic maize varieties. However, the identification and functional characterization of endogenous insect-resistance genes within maize inbred line populations, as well as the underlying molecular mechanisms governing resistance, remain poorly understood. Here, we systematically evaluate FAW resistance on 300 modern maize inbred lines and 200 recombinant inbred lines (RIL) populations in field, followed by quantitative trait locus (QTL) and genome-wide association studies (GWAS) mapping to screen candidate genes. Our data demonstrate that a β-glucosidase ZmBGLU17 was identified as a key FAW resistance gene, which contributes to the accumulation of two defense metabolites, lignin and DIMBOA. Overexpression of the ZmBGLU17 gene confers enhanced resistance to the FAW by significantly reducing larval survival. Haplotype analysis revealed two distinct haplotypes, with haplotype 1 demonstrating significantly enhanced resistance to FAW infestation compared with haplotype 2. Jointly, our research identified ZmBGLU17 as a key resistance-associated gene against FAW and confirmed its functional role through rigorous genetic validation. Furthermore, haplotype analysis revealed prevalent resistance-linked haplotypes, thereby establishing a molecular foundation for the development of FAW-resistant maize inbred lines.

Genome-wide association mapping of adult plant resistance to Septoria tritici blotch in spring bread wheat

Genetic loci and functional genes underlying black spot disease resistance across multiple environments in chrysanthemum

Black spot disease (BSD), caused by Alternaria alternata, is a devastating threat to the chrysanthemum industry, yet its genetic basis remains largely elusive. The present study aimed to decipher the genetic architecture of chrysanthemum BSD resistance and to discover genetic loci and candidate genes using genome-wide association studies (GWAS) in a biparental F1 population (n = 164). Phenotypic evaluations of BSD resistance were conducted using both multi-stage detached-leaf assays and seedling-stage in vivo inoculations. The disease severity index (DSI) exhibited wide coefficient of variation (CV: 26.21%–54.84%) and high broad-sense heritability (0.71–0.95), with significant transgressive segregation observed in the F1 progeny. 375 865 high-quality SNPs-based GWAS identified 220 quantitative trait nucleotides (QTNs) and 36 QTN-by-environment interactions (QEIs), explaining up to 7.39% and 3.46% of the phenotypic variance, respectively. Among 26 stable QTNs, 17 favorable alleles displayed significant additive effects and a clear dosage-pyramiding effect (P < 0.001). By integrating functional annotation with transcriptome profiling, 34 candidate genes involved in immune defense were identified within the candidate intervals. Notably, three key candidate genes, CmABF1, CmSINAT3, and CmLTPG1, were validated as positive regulators of BSD resistance through transient overexpression and silencing assays. The research findings provide crucial genetic resources for the molecular improvement of resistance to BSD in chrysanthemums.

Genetic architecture of Karnal bunt resistance in wheat: A review