Rattey, A. | Search bioRxiv

bioRxiv2025

QTL mapping of oat crown rust resistance in Australian fields and identification of a seedling resistance locus in oat line GS7

The development of oat cultivars with resistance to crown rust caused by Puccinia coronata f. sp. Avenae (Pca) is key for sustainable disease control. This study examined two recombinant inbred line populations, Provena x GS7 and Boyer x GS7, to identify adult plant resistance QTL in Australian fields. Seven distinct QTL associated with rust resistance were identified, with KASP markers developed for single nucleotide polymorphisms (SNPs) tightly linked to the four most significant QTL on chromosomes 4A and 7A. A major QTL named QPc_GS7_4A.2 with a resistance allele derived from line GS7 was mapped to chromosome 4A, overlapping with genomic regions previously associated with both resistance gene Pc61 and adult plant resistance. Genetic mapping for rust resistance at seedling stage using a subset of Provena x GS7 lines with contrasting alleles at QPc_GS7_4A.2 confirmed the role of this locus on seedling resistance, likely by Pc61. Furthermore, we found similar resistance profiles between GS7 and the Pc61 differential line against 20 Pca isolates at the seedling stage. Haplotype analysis of QPc_GS7_4A.2 in the oat crown rust differential set and an oat collection revealed the resistance haplotype in lines previously postulated to carry resistance gene Pc61. These results suggest that the QTL QPc_GS7_4A.2 is closely linked to the Pc61 locus on chromosome 4A. The KASP markers associated with Pc61 and QTL identified in this study will be valuable tools, allowing breeders to efficiently integrate the resistance allele for gene combinations in new cultivars, particularly in regions where Pc61 remains effective.

plant biology↗

bioRxiv2021

Novel design of imputation-enabled SNP arrays for breeding and research applications supporting multi-species hybridisation

Array-based SNP genotyping platforms have low genotype error and missing data rates compared to genotyping-by-sequencing technologies. However, design decisions used to create array-based SNP genotyping assays for both research and breeding applications are critical to their success. We describe a novel approach applicable to any animal or plant species for the design of cost-effective imputation-enabled SNP genotyping arrays with broad utility and demonstrate its application through the development of the Infinium Wheat Barley 40K SNP array. We show the approach delivers high-quality and high-resolution data for wheat and barley, including when samples are jointly hybridised. The new array aims to maximally capture haplotypic diversity in globally diverse wheat and barley germplasm while minimising ascertainment bias. Comprising mostly biallelic markers designed to be species-specific and single-copy, it permits highly accurate imputation in diverse germplasm to improve statistical power for GWAS and genomic selection. The SNP content captures tetraploid wheat (A- and B-genome) and Ae. tauschii (D-genome) diversity and delineates synthetic and tetraploid wheat from other wheats, as well as tetraploid species and subgroups. The content includes SNP tagging key trait loci in wheat and barley and that directly connect to other genotyping platforms and legacy datasets. The utility of the array is enhanced through the web-based tool Pretzel (https://plantinformatics.io/) which enables the arrays content to be visualised and interrogated interactively in the context of numerous genetic and genomic resources to more seamlessly connect research and breeding. The array is available for use by the international wheat and barley community. Short summaryDesigning SNP genotyping arrays for closely related species with broad applicability in both research and breeding is challenging. Here we describe a novel generic approach to select SNP content for such arrays and demonstrate its utility in wheat and barley to: O_LIcapture haplotypic diversity while minimising ascertainment bias; C_LIO_LIaccurately impute to high SNP density in diverse germplasm; C_LIO_LIgenerate high-quality high-resolution genotypic data; and C_LIO_LIjointly hybridise samples to the same bead chip array. C_LI

genetics↗