Characterization of Leaf Rust Resistance in International Barley Germplasm Using Genome-Wide Association Studies

Leaf rust (LR) caused by Puccinia hordei is a serious disease of barley worldwide, causing significant yield losses and reduced grain quality. Discovery and incorporation of new sources of resistance from gene bank accessions into barley breeding programs is essential for the development of leaf rust resistant varieties. To identify Quantitative Trait Loci (QTL) conferring LR resistance in the two barley subsets, the Generation Challenge Program (GCP) reference set of 142 accessions and the leaf rust subset constructed using the Focused Identification of Germplasm Strategy (FIGS) of 76 barley accessions, were genotyped to conduct a genome-wide association study (GWAS). The results revealed a total of 59 QTL in the 218 accessions phenotyped against barley leaf rust at the seedling stage using two P. hordei isolates (ISO-SAT and ISO-MRC), and at the adult plant stage in four environments in Morocco. Out of these 59 QTL, 10 QTL were associated with the seedling resistance (SR) and 49 QTL were associated with the adult plant resistance (APR). Four QTL showed stable effects in at least two environments for APR, whereas two common QTL associated with SR and APR were detected on chromosomes 2H and 7H. Furthermore, 39 QTL identified in this study were potentially novel. Interestingly, the sequences of 27 SNP markers encoded the candidate genes (CGs) with predicted protein functions in plant disease resistance. These results will provide new perspectives on the diversity of leaf rust resistance loci for fine mapping, isolation of resistance genes, and for marker-assisted selection for the LR resistance in barley breeding programs worldwide.

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

Roy,

Dinglasan,

Fowler

et al. 2024

Preprint

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Spot blotch (SB) is a common foliar disease of barley, caused by the hemibiotrophic fungal pathogen Bipolaris sorokiniana. Predominately found in humid growing regions worldwide, the disease can cause yield losses of up to 30%. Genetic control through deployment of durable resistance in barley cultivars is the preferred, yet the majority of Australian cultivars are susceptible, despite the identification of major resistance loci in bi-parental studies. In this study, we explore the genetic architecture of spot blotch resistance in an Australian barley breeding program. Seedling (glasshouse) and adult (field) experiments using a single conidial isolate (SB61) were conducted across two consecutive years for 337 lines genotyped with 16,824 polymorphic DArT-seq™ markers. Two mapping approaches were investigated, a single-marker genome-wide association study (GWAS) and a haplotype-based local genomic estimated breeding values (GEBV) approach. Both methods detected two major regions on chromosomes 3H and 7H that contribute resistance across growth stages. Additional chromosomal regions on 1H, 3H and 6H were detected only in the local GEBV approach. Haplotype stacking revealed the importance of the 7H region for adult-plant resistance in combination with other resistance haplotypes, suggesting a significant gene by gene interaction and demonstrating the highly quantitative nature of the genetic control. Our study validates the presence of major spot blotch resistance loci in Australian breeding populations, while generating novel insight into the genetic architecture, and highlights the challenges and opportunities to improve resistance levels via haplotype stacking or whole-genome approaches.

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Characterization of Leaf Rust Resistance in International Barley Germplasm Using Genome-Wide Association Studies

Cited by 3 publications

References 42 publications

Future Prospects: High-Altitude Crop Improvement via Genomics

Future Prospects: High-Altitude Crop Improvement via Genomics

Genome wide association study of seedling and adult plant leaf rust resistance in two subsets of barley genetic resources

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

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