Identification of Secreted Protein Gene-Based SNP Markers Associated with Virulence Phenotypes of Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen

Abstract

Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a destructive disease that occurs throughout the major wheat-growing regions of the world. This pathogen is highly variable due to the capacity of virulent races to undergo rapid changes in order to circumvent resistance in wheat cultivars and genotypes and to adapt to different environments. Intensive efforts have been made to study the genetics of wheat resistance to this disease; however, no known avirulence genes have been molecularly identified in Pst so far. To identify molecular markers for avirulence genes, a Pst panel of 157 selected isolates representing 126 races with diverse virulence spectra was genotyped using 209 secreted protein gene-based single nucleotide polymorphism (SP-SNP) markers via association analysis. Nineteen SP-SNP markers were identified for significant associations with 12 avirulence genes: AvYr1, AvYr6, AvYr7, AvYr9, AvYr10, AvYr24, AvYr27, AvYr32, AvYr43, AvYr44, AvYrSP, and AvYr76. Some SP-SNPs were associated with two or more avirulence genes. These results further confirmed that association analysis in combination with SP-SNP markers is a powerful tool for identifying markers for avirulence genes. This study provides genomic resources for further studies on the cloning of avirulence genes, understanding the mechanisms of host–pathogen interactions, and developing functional markers for tagging specific virulence genes and race groups.

Genomics: Infectious Disease and Host–Pathogen Interaction

“…tritici ( Pst ) is a destructive disease to wheat worldwide. Nineteen SNPs based on secreted proteins were found to have significant associations with twelve avirulence genes using a transcriptomics-based approach, providing prospective insights into avirulence genes and host–pathogen interactions [ 10 ]. To facilitate the study of the plant–pathogen interaction, a database of the forage crops, Alfalfa, and the emerging bacterial stem blight, Pseudomonas syringae pv.…”

“…This Special Issue of the International Journal of Molecular Sciences entitled “Genomics: Infectious Disease and Host –Pathogen Interaction” contains twelve original articles and three reviews that provide new insights into infectious diseases with regard to biofilm formation [ 1 , 2 , 3 ], diagnostics [ 4 ], vaccine development [ 5 ], and host–pathogen interaction [ 6 , 7 ]; these insights are based on genomic [ 8 , 9 , 10 , 11 , 12 ], transcriptomic [ 13 , 14 ], and microbiomic [ 15 ] studies.…”

The Biological Roles of Puccinia striiformis f. sp. tritici Effectors during Infection of Wheat

“…The development of molecular markers for Avr genes is beneficial for identifying the location of Avr genes. A total of 157 Pst isolates representing 126 races with diverse virulence spectra were selected and genotyped using 209 highly expressed secreted protein gene (SP)-based single-nucleotide polymorphism (SP-SNP) markers via association analysis [ 50 ]. It was found that 19 SP-SNP markers had significant associations with 12 Avr genes: AvYrSP , AvYr1 , AvYr6 , AvYr7 , AvYr9 , AvYr10 , AvYr24 , AvYr27 , AvYr76 , AvYr32 , AvYr43 , and AvYr44 [ 50 ].…”

“…A total of 157 Pst isolates representing 126 races with diverse virulence spectra were selected and genotyped using 209 highly expressed secreted protein gene (SP)-based single-nucleotide polymorphism (SP-SNP) markers via association analysis [ 50 ]. It was found that 19 SP-SNP markers had significant associations with 12 Avr genes: AvYrSP , AvYr1 , AvYr6 , AvYr7 , AvYr9 , AvYr10 , AvYr24 , AvYr27 , AvYr76 , AvYr32 , AvYr43 , and AvYr44 [ 50 ]. Advances in whole-genome sequencing of Pst will lead to the development of highly diagnostic SP-SNP markers, which could be used to detect more Avr genes and clone them, uncovering the virulence variation.…”