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.
Muhammad Nadeem, Dan Liu, Lislé Snyman et al.· Theoretical and Applied Gene...· 0 citations
Net blotch, caused by Pyrenophora teres, is a major constraint to barley production worldwide and occurs as two epidemiologically distinct forms: net form net blotch (NFNB) and spot form net blotch (SFNB). Although numerous resistance loci have been reported in recent years, their genetic relationship remains poorly understood, and the effective deployment of resistance is constrained by the complex genetic architecture of net blotch resistance. In this study, we used a haplotype-based mapping approach to dissect the genetic basis of resistance to NFNB and SFNB in a diverse panel of 950 barley accessions from the Australian Grains Genebank (AGG). Disease responses were evaluated across 13 experiments, and a total of 40 quantitative trait loci (QTL) were identified, including 26 associated with NFNB, 29 with SFNB, and 15 common for both diseases. Most loci co-localized with previously reported QTL, while six putative novel haploblocks highlighted untapped genetic diversity within the AGG collection. Correlation analyses across phenotypic, genetic and haploblock levels revealed a partial but incomplete overlap in resistance mechanisms between NFNB and SFNB. Among the 4,497 haploblocks, approximately 60% of them showed positive local genetic correlations between the two diseases, suggesting shared genomic contributions to resistance. Haplotype composition analysis further identified a resistant haplotype group, mainly comprising accessions of Asian origin, that exhibited high levels of resistance to both forms of net blotch. Through in silico haplotype stacking, we demonstrated the cumulative genetic potential achievable by combining favourable haplotypes. When the breeding objective was to improve resistance to both NFNB and SFNB, dual-disease stacking strategies outperformed single-disease approaches, highlighting the value of prioritising haplotypes with positive pleiotropic effects. Overall, this study provides a comprehensive haplotype-level framework for understanding net blotch resistance and delivers practical insights for breeding barley cultivars with durable and broad-spectrum resistance to both NFNB and SFNB.
Dan Liu, Xuechen Zhang, Lislé Snyman et al.· bioRxiv· 0 citations
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