Unlocking new alleles for leaf rust resistance in the Vavilov wheat collection

Abstract

Thirteen potentially new leaf rust resistance loci were identified in a Vavilov wheat diversity panel. We demonstrated the potential of allele stacking to strengthen resistance against this important pathogen. Leaf rust (LR) caused by Puccinia triticina is an important disease of wheat (Triticum aestivum L.), and the deployment of genetically resistant cultivars is the most viable strategy to minimise yield losses. In this study, we evaluated a diversity panel of 295 bread wheat accessions from the N. I. Vavilov Institute of Plant Genetic Resources (St Petersburg, Russia) for LR resistance and performed genome-wide association studies (GWAS) using 10,748 polymorphic DArT-seq markers. The diversity panel was evaluated at 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 adult plant resistance (APR). Of the 31 QTL, 13 were considered potentially new loci, whereas 4 co-located with previously catalogued Lr genes and 14 aligned to regions reported in other GWAS and genomic prediction studies. One seedling LR resistance QTL located on chromosome 3A showed pronounced levels of linkage disequilibrium among markers (r = 0.7), suggested a high allelic fixation. Subsequent haplotype analysis for this region found seven haplotype variants, of which two were strongly associated with LR resistance at seedling stage. Similarly, analysis of an APR QTL on chromosome 7B revealed 22 variants, of which 4 were associated with resistance at the adult plant stage. Furthermore, most of the tested lines in the diversity panel carried 10 or more combined resistance-associated marker alleles, highlighting the potential of allele stacking for long-lasting resistance.

Novel sources of resistance to Septoria nodorum blotch in the Vavilov wheat collection identified by genome-wide association studies

“…For the effector-sensitivity assay where a single inverse gene-for-gene interaction was expected, the Bonferroni corrected P = 0.05 method [− log 10 ( P ) = 5.49] was used as described by Cockram et al ( 2015 ). For whole-plant disease infection where more complex interactions contributed to the SNB severity among the Vavilov wheat accessions, an arbitrary threshold of − log 10 ( P ) = 3.5 was applied, similar to the approach adopted in recent GWAS studies by Qian et al ( 2016 ) and Riaz et al ( 2017b ).…”

“…The 5BS QTL was selected for haplotype analysis, because it co-located with the genomic location for Snn3 . Haplotypes for Snn3 sensitivity gene to SnTox3 were constructed based on markers which satisfied three criteria: (1) they were located in close proximity to the QTL detected by these traits; (2) displayed pairwise linkage disequilibrium (LD) values ≥ 0.8 (Riaz et al 2017b ); and (3) were significantly associated with the SnTox3 sensitivity response. LD between all pairs of mapped markers was calculated using PopGen package in R (R_Core_Team 2013 ).…”

Stable sources of resistance to yellow rust and powdery mildew in Indian and exotic wheat germplasm

“…Crop pathogens with worldwide prevalence and potential for long distance migration and invasions into new areas may pose a serious threat to food security regionally or globally (Dean et al, 2012;Beddowet al, 2015). Wheat (Triticum aestivum L.) is an important food crop worldwide ( Juliana et al, 2017) and it is persistently threatened by attack from diverse rapidly evolving pathogens (Riaz et al, 2018). Wheat pathogens like rusts and powdery mildew are generally managed through large-scale breeding efforts to improve disease resistance, which is economical, eco-and farmer friendly, practically feasible and sometimes the only available option to prevent disease related yield losses (Kumar et al, 2016;Singh et al, 2018).…”

Genome-wide association study of yield and related traits in common wheat under salt-stress conditions

“…With several advantages, such as the use of diverse germplasms as materials and the capability to capture superior alleles that have been missed by breeding practices, GWASs have been widely used to dissect complex genetic mechanisms regulating biotic and abiotic stress tolerance in wheat [16,19,20]. For instance, Riaz et al [21] performed a GWAS using 10,748 DArT-seq markers in a diverse panel of 295 bread wheat accessions for leaf rust resistance.…”