Unlocking new sources of adult plant resistance to wheat leaf rust

Abstract

Leaf rust (LR), caused by Puccinia triticina Eriks., is among the most important fungal diseases of wheat (Triticum aestivum L.) crops globally. LR is prevalent in all wheat cultivating regions of Australia, inflicting both yield and grain quality losses. The most sustainable method for controlling rust diseases is to incorporate genetic resistance, particularly adult plant resistance (APR), in cultivars grown by farmers. APR is considered more durable than seedling resistance because resistance is often underpinned by multiple ‘minor effect’ genes providing partial resistance thereby reducing selection pressure on the pathogen. Seedling resistance is often conferred by a single major gene that is pathogen race specific. Yet, despite the significance of APRs only a limited number of APR genes are currently deployed for wheat cultivation. Therefore, additional genes are required to prolong resistance as use of multiple genes in different combinations slows down the pathogen to gain virulence. Hence, the overall aim of the study was to identify new sources of APR from historical wheat germplasm. A diversity panel comprising of 295 bread wheat accessions was assembled, originally sourced from the N. I. Vavilov Institute of Plant Genetic Resources (VIR), a seed bank in St Petersburg, Russia. The panel comprised landraces, cultivars, and breeding lines, collected from 28 countries around the world over a period spanning from 1920 to 1990. The diversity panel was genotyped using the Diversity Arrays Technology genotyping-by-sequencing platform (DArT-seq) and the first genomic characterisation of wheat accessions from VIR was performed. This revealed a huge array of new alleles which were either fixed or absent in a sample of modern cultivars and breeding lines from Australia and the International Maize and Wheat Improvement Center (CIMMYT) in Mexico. To enable evaluation of LR resistance all-year-round, a rapid phenotyping protocol that integrates assessment at both seedling and adult plant growth stages under controlled conditions was designed and validated. The method enables up to seven consecutive disease assays per year, compared to just one assessment in the field. The integrated method is more efficient requiring less time, space, and labour than traditional approaches where seedling and adult plants are assessed in separate assays. To accelerate the discovery of new sources of APR, a novel approach was adopted, which involved screening the diverse wheat accessions using: 1) DNA markers linked to known APR genes, 2) the rapid phenotyping method and 3) field evaluation using multiple P. triticina pathotypes. Based on DNA marker screening, 83 lines were deemed to carry known APR genes (Lr34, Lr46, and Lr67) thus were eliminated. Rapid phenotypic screening identified 50 lines carrying APR and field-testing of the subset using pathotypes with additional virulence for race-specific APR genes (Lr13 and Lr37), identified 13 lines that consistently displayed high levels resistance across years and pathotypes. These lines provide useful sources for future research. Next, genome-wide association studies (GWAS) were performed for the diversity panel using 10,748 polymorphic DArT-seq markers. The diversity panel was evaluated at both seedling and adult plant growth stages using three P. triticina pathotypes prevalent in Australia. GWAS was applied to 11 phenotypic data sets which identified a total of 52 significant marker-trait associations representing 31 quantitative trait loci (QTL). Among them, 29 QTL were associated with APR. Of the 31 QTL, 13 were considered potentially new loci, whereas four co-located with previously catalogued LR resistance genes (Lr) and fourteen aligned to regions reported in other GWAS and genomic prediction studies. Notably, highly resistant accessions carried a large number of alleles for resistance, thus highlighting the potential of allele stacking or pyramiding to strengthen resistance levels against P. triticina. Major outcomes include the establishment and genetic characterisation of a Vavilov wheat diversity panel, development of a rapid phenotyping method, development of a new screening approach to mine seed bank accessions for disease resistance, and identification of new genomic regions underpinning LR resistance. This study provides open access seed and genetic resources, along with the insight and tools to exploit them in research, pre-breeding and breeding programs. This will help pathologists, geneticists and plant breeders to assemble improved wheat cultivars with long-lasting resistance to LR.