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Development, characterization and application of genomic SSR markers for the oat stem rust pathogen Puccinia graminis f. sp. avenae
Author(s) -
Gnocato F. S.,
Dracatos P. M.,
Karaoglu H.,
Zhang P.,
Berlin A.,
Park R. F.
Publication year - 2018
Publication title -
plant pathology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.928
H-Index - 85
eISSN - 1365-3059
pISSN - 0032-0862
DOI - 10.1111/ppa.12742
Subject(s) - biology , stem rust , puccinia , genetic diversity , pathogen , primer (cosmetics) , population , rust (programming language) , genetics , genotype , genome , genetic marker , molecular marker , botany , gene , mildew , demography , organic chemistry , sociology , programming language , chemistry , computer science
Oat stem rust, caused by Puccinia graminis f. sp. avenae (Pga), is one of the most severe diseases of oats worldwide. Population studies are scarce for this pathogen, mainly due to the lack of polymorphic molecular markers suitable for genetic analysis. In this study, an Australian Pga isolate was sequenced, the abundance of simple sequence repeats ( SSR s) was determined and PCR ‐based polymorphic markers suitable for genetic diversity analysis were developed. The amplification of 194 primer pairs was initially assessed using a set of 12 isolates of different cereal rust species and their formae speciales. A high frequency of cross‐species amplification was observed for most markers; however, 36 SSR s were diagnostic for P. graminis only. A subset of 19 genome‐derived SSR s were deemed useful for genetic diversity analysis of Pga and were assessed on 66 Pga isolates from Australia, Brazil and Sweden. Brazilian and Australian isolates were characterized by one and two predominant clonal lineages, respectively. In contrast, the Swedish isolates, previously shown to undergo sexual recombination, were highly diverse (nine distinct genotypes out of 10 isolates) and divided into two subpopulations. The genome‐derived SSR markers developed in this study were well suited to the population studies undertaken, and have diagnostic capabilities that should aid in the identification of unknown rust pathogen species.