Genetic diversity of Puccinia kuehnii, the causal agent of orange rust of sugarcane, from Brazil

Abstract

The use of resistant genotypes is the preferred method to control orange rust of sugarcane (Saccharum spp) caused by Puccinia kuehnii. This approach has been adopted in Brazil but outbreaks of the disease on previously resistant varieties showed that the efficacy of this method is limited and requires a better understanding of pathogen diversity. Nevertheless, adequate molecular markers for examining pathogen diversity at population level are not available, which limits the success of orange rust control by genetic resistance. Therefore, two independent investigations were conducted to examine genetic diversity of P. kuehnii from São Paulo state, the most important sugarcane growing state of Brazil. First, simple‐sequence repeat (SSR) markers were developed in the present work and genotypic diversity of orange rust isolates from different locations investigated. Second, phenotypic diversity was examined by the single‐pustule inoculation technique on P. kuehnii isolates retrieved from three susceptible commercial sugarcane cultivars. A total of 96 SSR markers were generated and tested for this species. Subsequently, 29 isolates of P. kuehnii were fingerprinted with nine SSR markers to estimate the genotypic diversity by neighbour‐joining and 3D principal coordinates. The 29 isolates of the pathogen clustered into four main groups, which were identified by three SSR markers (NPRL_PK_108a, NPRL_PK_162_spka and NPRL_PK_221_spka). Phenotypic data at 21 days after the single‐pustule inoculation showed that P. kuehnii from highly susceptible commercial cultivars harboured a small proportion of variants capable of causing disease on resistant cultivars. A differential reaction was demonstrated for the most virulent variant in a repeated experiment confirming the existence of races within P. kuehnii in Brazil.

Occurrence of two races of Puccinia kuehnii causing orange rust of sugarcane in Florida

“…The AFLP patterns of P. kuehnii differed among the 22 clonal isolates from Florida collected from two cultivars inoculated with two different races of the pathogen. Isolates of P. kuehnii from Brazil also exhibited genetic diversity based on single-repeat sequence (SSR) markers (Urashima et al, 2020). This genetic diversity may be generated by nuclear exchange between dikaryons (two distinct haploid nuclei occurring in rust fungi), as was shown for the wheat stem rust pathogen (Li et al, 2019).…”

“…Phenotypic and genotypic variation was reported in the populations of P . kuehnii that emerged recently in Brazil (Mistura et al, 2016; Moreira et al, 2018; Urashima et al, 2020). Orange rust may have been introduced into the western hemisphere as a mixture of isolates that progressively adapted to different cultivars as they were produced, or until they were grown by the industry over large areas.…”

“…Isolates of P . kuehnii from Brazil also exhibited genetic diversity based on single‐repeat sequence (SSR) markers (Urashima et al, 2020). This genetic diversity may be generated by nuclear exchange between dikaryons (two distinct haploid nuclei occurring in rust fungi), as was shown for the wheat stem rust pathogen (Li et al, 2019).…”

“…Several techniques have been used to determine differential reactions of sugarcane cultivars to brown or orange rust isolates, including detached leaf and leaf whorl inoculations, and inoculation of young plants in controlled environments (Asnaghi et al, 2001; Hoy et al, 2014; Moreira et al, 2018; Sood et al, 2009; Urashima et al, 2020). We developed herein a detached leaf bioassay to reproduce symptoms of orange rust under controlled conditions.…”

Molecular evaluation and phenotypic screening of brown and orange rust in Saccharum germplasm

“…There are different ways to classify resistant genotypes using a rating scale, and there is some evidence that more aggressive isolates or races of P . kuehnii [ 74 – 76 ] influence the predictive efficiency of the G1 marker.…”