Genotyping-by-Sequencing for the Study of Genetic Diversity in Puccinia triticina.

Meriem Aoun,Matthew Breiland,Robert S Brueggeman,Jonathan Richards,James A Kolmer,Les J Szabo,Maricelis Acevedo

doi:10.1094/pdis-09-19-1890-re

Abstract

Leaf rust, caused by Puccinia triticina Erikss., is globally the most widespread rust of wheat. Populations of P. triticina are highly diverse for virulence, with many different races found annually. The genetic diversity of P. triticina populations has been previously assessed using different types of DNA markers. Genotyping technologies that provide a higher density of markers distributed across the genome will be more powerful for analysis of genetic and phylogenetic relationships in P. triticina populations. In this study, we utilized restriction-associated DNA (RAD) genotyping-by-sequencing (GBS) adapted for the Ion Torrent sequencing platform for the study of population diversity in P. triticina. A collection of 102 isolates, collected mainly from tetraploid and hexaploid wheat, was used. The virulence phenotypes of the isolates were determined on 20 lines of Thatcher wheat near isogenic for leaf rust resistance genes. Seven races were found among 57 isolates collected from tetraploid wheat, and 21 races were observed among 40 hexaploid wheat type isolates. This is the first study to report durum wheat virulent races to Lr3bg in Tunisia, Lr14a in Morocco, and Lr3bg and Lr28 in Mexico. Ethiopian isolates with high virulence to durum wheat but avirulent on Thatcher (hexaploid wheat) were tested for virulence on a set of durum (tetraploid) differentials. A subset of 30 isolates representing most of the virulence phenotypes in the 102 isolates were genotyped using RAD-GBS. Phylogenetic analysis of 30 isolates using 2,125 single nucleotide polymorphism (SNP) markers showed nine distinct clusters. There was a general correlation between virulence phenotypes and SNP genotypes. The high bootstrap values between clusters of isolates in the phylogenetic tree indicated that RAD-GBS can be used as a new genotyping tool that is fast, simple, high throughput, cost effective, and provides a sufficient number of markers for the study of genetic diversity in P. triticina.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Highlights

Leaf rust is a common disease in all wheat (Triticum spp.) growing regions and is the most commonly found of the three wheat rusts (Chester 1946), reducing the quantity and quality of kernels
The objectives of this study were to (i) assess the application of restrictionassociated DNA (RAD)-GBS using the Ion Torrent sequencing platform as a new genotyping tool for the study of genetic diversity in P. triticina and (ii) develop durum differential lines to distinguish between virulence phenotypes of Ethiopian isolates that are avirulent to Thatcher wheat
Virulence phenotypes on Thatcher differential lines showed that races of P. triticina collected from tetraploid wheat differ from those collected from hexaploid common wheat

Summary

Introduction

Leaf rust is a common disease in all wheat (Triticum spp.) growing regions and is the most commonly found of the three wheat rusts (Chester 1946), reducing the quantity and quality of kernels. The severity of leaf rust is usually the highest in areas where wheat grows under warm to hot climates such as the Great Plains of North America and the steppes of Central Asia. High leaf rust severity has been reported in regions with warm and humid climate such as the Mediterranean basin, South America, and the coastal regions of North America (Liu et al 2014). Durum) mainly in the Mediterranean basin, Middle East, Ethiopia, Mexico, and South America (Ordoñez and Kolmer 2007a). The pycniospores and aeciospores are produced on the alternate hosts, mainly Thalictrum speciosissimum L.

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