Pathogenicity and microsatellite characterization of Puccinia hordei in South Africa

Highlights

• New race of barley leaf rust caused by Puccinia hordei.

• Barley cultivar responses to leaf rust.

• Microsatellite marker analysis revealed low gene diversity and allelic richness.

• Propagation of Puccinia hordei appears to be clonal in South Africa.

Abstract

Cultivated barley (Hordeum vulgare) is an important winter cereal in South Africa (SA), ranked second after wheat. Leaf rust, caused by Puccinia hordei Otth. (Ph), is one of the most common diseases affecting grain yield and quality of barley. In this study, isolates of Ph were pathotyped using differential cultivars and lines with designated Rph-resistance genes, as well as a set of Bowman introgression lines (BW) containing resistance genes Rph1 to Rph15. Single pustule isolates derived from recently collected field isolates, typed as Ph race UVPh7235, showed increased virulence to Rph3 when compared with previously described races from SA. Discrepancies in phenotypic responses were recorded between standard differential lines carrying Rph2, Rph6 and Rph9 and the corresponding BW lines. Results for barley cultivars with designated sources of adult plant resistance revealed low seedling infection types (ITs) for Baronesse (Rph20 + Rph24) to all Ph isolates and for Lenka (Rph20 + Rph23 + Rph24) to isolates of Ph races UVPh3231 and UVPh7231. The barley cultivars Agulhas and Cristalia showed low seedling ITs and moderate to high levels of adult plant resistance under field and greenhouse conditions, respectively. Genotyping of 48 Ph isolates with 20 microsatellite markers revealed five closely related genetic lineages with low gene diversity and allelic richness levels. While STRUCTURE analysis revealed three clusters, no clear division of the isolates into the clusters was evident, as the isolates were admixed for all three. Linkage disequilibrium analysis, as well as higher H_O versus H_E values, supported the hypothesis that the South African Ph population is clonal, consisting of a single genetic lineage.

Introduction

Barley (Hordeum vulgare L.) is the fourth most important cereal crop in the world. Barley was mainly used for human food supply in the last century, but currently the crop is increasingly grown for animal feed and malt products (FAOSTAT, 2021). In South Africa (SA), the main barley production area is the Western Cape (WC) where malting barley is annually planted during late autumn under dryland conditions. This region, with its Mediterranean climate, is prone to foliar diseases such as barley leaf rust caused by Puccinia hordei Otth. (Ph) (Van Niekerk et al., 2001). Malting barley is also planted under irrigation in the interior including the Northern Cape, North West, Limpopo and Free State provinces (Grain, 2021). While the WC dryland barley region is much larger than the irrigation areas, the latter produces higher yields per hectare. Lately, there has been a significant increase in the productivity of barley production in SA, with a record yield of 588 000 tons produced on 94 730 ha during the 2020 season (SAGIS, 2021). This can be attributed to optimised production practises and cultivar improvement.

Four rusts occur on barley viz. stripe rust (caused by Puccinia striiformis Westend. f. sp. hordei Erikss.), stem rust (caused by Puccinia graminis Pers.), crown rust (caused by Puccinia coronata Corda. var. hordei Jin & Steff.) and the commonly occurring leaf rust caused by Ph (Park et al., 2015; Supplementary Fig. 1). There are currently 27 designated barley leaf rust resistance genes known as Reaction to Ph (Rph) genes (Hickey et al., 2011; Park et al., 2015; Singh et al., 2015; Ziems et al., 2017; Yu et al., 2018; Rothwell et al., 2020; Mehnaz et al., 2021). These include Rph20, Rph23 and Rph24, which provide adult plant resistance (APR) and Rph1 to Rph19, Rph21, Rph22, Rph25, Rph26, Rph27 and Rph28 that are known as seedling or all-stage resistance (ASR) genes. The Rph15-and Rph16-mediated resistances have been reported as the same and not allelic as previously suggested (Chen et al., 2021).

Breeding for disease resistance has become more important and is preferred over the extensive reliance on chemical control. Resistance provides a more environmentally friendly control strategy, lowers the risk of disease outbreaks, prevents yield damage due to the incorrect timing of chemical applications and presents an opportunity to save on input costs. Apart from the work reported by Van Niekerk et al. (2001), there are no recent reports on the pathogenic variation of Ph in SA and thus no contemporary data on the response of local barley cultivars. To characterize these cultivars, the racial composition of Ph using designated ASR and APR sources is firstly required. Further to this, molecular markers can be used to determine the genotypic variability among Ph isolates and the structure of the population. Knowledge of the population structure can aid to predict and minimize the harmful impact of disease outbreaks and assist in the search for more durable resistance (Gnocato et al., 2018). Thus, results of rust surveys and pathotyping, combined with genotypic data, can provide a better understanding of the evolution of the Ph pathogen in a specific production area.

Considering the importance of breeding for leaf rust resistance in barley, the objectives for this study were to: (i) determine the virulence profiles of the dominant Ph race(s) to designated ASR sources of resistance; (ii) assess the response of APR sources, as well as local barley cultivars, to the detected Ph race(s); and (iii) assess the genetic variability among Ph isolates using microsatellite markers.