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. 2025 Feb 14;14(2):194.
doi: 10.3390/pathogens14020194.

Virulence and Genetic Diversity of Puccinia spp., Causal Agents of Rust on Switchgrass (Panicum virgatum L.) in the USA

Bochra A Bahri  1   2 , Peng Tian  3 , Samikshya Rijal  2 , Katrien M Devos  2   4   5 , Jeffrey L Bennetzen  6 , Shavannor M Smith  1
Affiliations

Virulence and Genetic Diversity of Puccinia spp., Causal Agents of Rust on Switchgrass (Panicum virgatum L.) in the USA

Bochra A Bahri et al. Pathogens. .

Abstract

Switchgrass (Panicum virgatum L.) is an important cellulosic biofuel grass native to North America. Rust, caused by Puccinia spp. is the most predominant disease of switchgrass and has the potential to impact biomass conversion. In this study, virulence patterns were determined on a set of 38 switchgrass genotypes for 14 single-spore rust isolates from 14 field samples collected in seven states. Single nucleotide polymorphism (SNP) variation was also assessed in 720 sequenced cloned amplicons representing 654 base pairs of the elongation factor 1-α gene from the field samples. Five major haplotypes were identified differing by 11 out of the 39 SNP positions identified. STRUCTURE, Principal Coordinate Analysis, and phylogenetic analyses divided the rust population into two genetic clusters. Virginia and Georgia had the highest and lowest rust genetic diversity, respectively. Only nine accessions showed a differential disease response between the 14 isolates, allowing the identification of eight races, differing by 1-3 virulence factors. Overall, the results suggested clonal reproduction of the pathogen and a North-South differentiation via local adaptation. However, similar haplotypes and races were also recovered from several states, suggesting migration events, and highlighting the need to further investigate the switchgrass rust population structure and evolution in the USA.

Keywords: genetic diversity; rust; switchgrass; virulence.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Geographic location of the five major haplotypes of switchgrass rust populations in seven U.S. states. Pie charts are at scale, with the exception of Virginia and Wisconsin, which are 50% larger.
Figure 2
Figure 2
Principal Coordinates Analysis of the 720 Puccinia spp. haplotypes from switchgrass based on 39 SNPs in the elongation factor 1-α gene. The haplotypes are color-coded based on: (A) their affiliation to STRUCTURE genetic clusters at K  =  2; and (B) their state of origin. Pop1 and Pop2 are in red and green, respectively. WI, VA, TX, TN, OK, GA, AL represents the States of Wisconsin, Virginia, Texas, Tennessee, Oklahoma, Georgia, and Alabama, respectively.
Figure 3
Figure 3
Phylogenetic relationships between 97 Puccinia spp. haplotypes from switchgrass based on 39 SNPs in the elongation factor 1-α gene: (A) Maximum likelihood tree with red and green branches, indicating Pop1 and Pop2 genetic clusters, respectively; (B) Network analysis showing reticulated evolution.
Figure 4
Figure 4
Haplotype frequencies by year of 192 Puccinia spp. haplotypes from switchgrass based on 39 SNPs in the elongation factor 1-α gene, recorded in the State of Georgia.
Figure 5
Figure 5
Maximum likelihood tree showing the emergence of new switchgrass rust haplotypes by step mutations in the elongation factor 1-α gene in the State of Georgia. Mutations are indicated by ‘+’ sign in the branches followed by the SNP position. SNP222 (highlighted in yellow) and SNP146 (highlighted in pink) mutations appeared independently in Pop1 (red) and Pop2 (green) genetic clusters. The number of times a haplotype was present in the GA dataset is indicated in parenthesis.
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