Dissecting the genetic interactions associated with Rph20-based leaf rust resistance in barley: ‘minor genes’ with major implications

Abstract

Recent work in Australia led to the characterisation of the first adult plant resistance (APR) gene for barley leaf rust (BLR), named Rph20. The gene confers partial resistance to the pathogen (Puccinia hordei Otth) that is best expressed in adult plants. However, when deployed alone, this gene only provides a low level of resistance, thus additional genomic regions must be identified that can be combined with Rph20 to boost levels of resistance and reduce the reliance upon a single resistance factor. Hence, this study aimed to discover 'minor' genes or genetic 'modifiers' enhancing the expression of Rph20, along with their associated DNA marker sequences.Minor gene candidates were detected and validated by applying association mapping (AM) to elite breeding populations of the northern region barley breeding program (NRBBP) situated in Queensland, Australia. Populations were genotyped using the first and second generation high-density genotyping platforms of Diversity Arrays Technology (DArT): DArT and DArT-seq. Evaluation of multiple populations across years in disease screening nurseries located in Toowoomba (Queensland) and Cobbitty (New South Wales) enabled identification of regions associated with APR to BLR. Comparison of quantitative trait loci (QTL) across populations that were genotyped with different marker platforms was achieved by positioning genomic regions on an integrated consensus map.Overall, this strategy identified 19 independent QTL associated with BLR response in the NRBBP material and confirmed the important role of Rph20 as the only active resistance region detected in all 15 environments analysed. Projection of QTL reported in previous BLR studies highlighted chromosome 6H to likely harbour a promising candidate region forpairing with Rph20. To further characterise this region, bulked segregant analysis (BSA) was employed to identify strongly linked markers and ultimately designate this locus as Rph24, a new minor APR gene.Major outcomes include the DNA marker sequences associated with resistance QTL, particularly those associated with Rph24, which provide the necessary tools to empower breeders to stabilise Rph20-based resistance. The deployment of improved barley cultivars incorporating durable and stable genetic resistance is anticipated to reduce production losses due to BLR.