Genotyping-by-sequencing for the study of genetic variation in Puccinia triticina

Authors: AOUN, MERIEM - North Dakota State University; Kolmer, James; BREILAND, MATTHEW - North Dakota State University; RICHARDS, JONATHAN - North Dakota State University; BRUEGGEMAN, ROBERT - North Dakota State University; Szabo, Les; ACEVEDO, MARICELIS - North Dakota State University

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/4/2019
Publication Date: 1/7/2020
Citation: Aoun, M., Kolmer, J.A., Breiland, M., Richards, J., Brueggeman, R.S., Szabo, L.J., Acevedo, M. 2020. Genotyping-by-sequencing for the study of genetic variation in Puccinia triticina. Plant Disease. 104(3):752-760. https://doi.org/10.1094/PDIS-09-19-1890-RE.
DOI: https://doi.org/10.1094/PDIS-09-19-1890-RE

Interpretive Summary: Wheat is attacked by the rust fungus called Puccinia triticina, which causes the disease wheat leaf rust. There are many different forms or races of the wheat leaf rust fungus that vary in their ability to attack different resistance genes in wheat. Various DNA markers have been developed to characterize populations of Puccinia triticina. Genotype by sequence (GBS) is a DNA marker approach that can be used to quickly and efficiently genotype individual isolates of Puccinia triticina. In this study, 30 isolates of Puccinia triticina from collected from durum wheat and common wheat in the Mediterranean region, Ethiopia, Mexico, Chile, and Pakistan were characterized using the GBS technique. The isolates were grouped into nine distinct cluster based on 2125 DNA markers. The grouping based on DNA markers also corresponded to grouping of the isolates based on virulence to durum and common wheat. GBS is a highly effective method for characterizing isolates of P. triticina.

Technical 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 highe 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)-Genotype 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 markers showed nine distinct clusters. There was a general correlation between virulence phenotypes and SNP genotypes. The high boostrap 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-thoughput, cost effective and provides a sufficient number of markers for the study of genetic variation in P. triticina.