New insight into the species diversity and life cycles of rust fungi (Pucciniales) affecting bioenergy switchgrass (Panicum virgatum) in the Eastern and Central United States

Kenaley, Shawn C.; Quan, Menchus; Aime, M. Catherine; Bergstrom, Gary C.

doi:10.1007/s11557-018-1434-1

Cited by 6 publications

(10 citation statements)

References 71 publications

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“…However, we found an overwhelming predominance of one species, Puccinia novopanici, at all sites other than Mead, NE (LINC). While we were not able to sample species composition for all years of this study, the dominance of P. novopanici in the central United States is corroborated by previous reports on this system (Kenaley et al, 2018). The hypothesis that largescale climatic variation accounts for QTL variation in switchgrass was also supported in another study that used these same mapping populations (Lowry et al, 2019).…”

Section: North-south Difference In Qtl Expressionsupporting

confidence: 75%

“…Demers et al, (2017) found predominantly P. pammelii and P. graminicola in the midwestern United States, and P. novopanici predominantly in eastern states. In contrast, Kenaley et al, (2018) found that most midwestern switchgrass plantings are infected with P. novopanici, with P. pammelii and P.…”

Section: Introductionmentioning

confidence: 81%

“…We followed the same method as Kenaley et al, (2018) for DNA extraction, PCR amplification, purification, and sequencing. Briefly, we extracted genomic DNA from leaf segments cut from areas with one pustule or very few pustules using the DNeasy Plant Mini Kit (Qiagen, Valencia, CA).…”

Section: Rust Abundance and Species Compositionmentioning

confidence: 99%

“…Therefore, over geographic space, the distribution of pathogen genetic diversity can determine host resistance expression (Chappell & Rausher 2016). Rust pathogens can be geographically constrained by their low freezing tolerance and the distribution of their alternate host (Kenaley et al, 2018). Therefore, if rust population diversity is higher in southern regions, as is true for wheat rusts in Asia (Ali et al, 2014), switchgrass resistance expression may involve more loci than in northern populations, resulting in a more complicated genetic architecture.…”

Section: North-south Difference In Qtl Expressionmentioning

confidence: 99%

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Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)

VanWallendael

Bonnette

Juenger

et al. 2019

Preprint

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Section: North-south Difference In Qtl Expressionsupporting

confidence: 75%

Section: Introductionmentioning

confidence: 81%

Section: Rust Abundance and Species Compositionmentioning

confidence: 99%

Section: North-south Difference In Qtl Expressionmentioning

confidence: 99%

See 2 more Smart Citations

Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)

VanWallendael

Bonnette

Juenger

et al. 2019

Preprint

Self Cite

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show abstract

“…Demers et al (2017) found predominantly P. pammelii and P. graminicola in the midwestern USA, and P. novopanici predominantly in eastern states. By contrast, Kenaley et al (2018) found that most midwestern switchgrass plantings are infected with P. novopanici, with P. pammelii and P. graminicola showing up only rarely.…”

Section: Introductionmentioning

confidence: 79%

Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)

et al. 2020

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Summary Local adaptation is an important process in plant evolution, which can be impacted by differential pathogen pressures along environmental gradients. However, the degree to which pathogen resistance loci vary in effect across space and time is incompletely described. To understand how the genetic architecture of resistance varies across time and geographic space, we quantified rust (Puccinia spp.) severity in switchgrass (Panicum virgatum) plantings at eight locations across the central USA for 3 yr and conducted quantitative trait locus (QTL) mapping for rust progression. We mapped several variable QTLs, but two large‐effect QTLs which we have named Prr1 and Prr2 were consistently associated with rust severity in multiple sites and years, particularly in northern sites. By contrast, there were numerous small‐effect QTLs at southern sites, indicating a genotype‐by‐environment interaction in rust resistance loci. Interestingly, Prr1 and Prr2 had a strong epistatic interaction, which also varied in the strength and direction of effect across space. Our results suggest that abiotic factors covarying with latitude interact with the genetic loci underlying plant resistance to control rust infection severity. Furthermore, our results indicate that segregating genetic variation in epistatically interacting loci may play a key role in determining response to infection across geographic space.

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Towards Improved Detection and Identification of Rust Fungal Pathogens in Environmental Samples Using a Metabarcoding Approach

2022

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The dispersion of fungal inocula such as the airborne spores of rust fungi (Pucciniales) can be monitored by metabarcoding the internal transcribed spacer 2 (ITS2) of the rRNA gene in environmental DNAs. This is largely dependent upon a high-quality reference database (refDB) and primers with proper taxonomic coverage and specificity. For this study, a curated ITS2 reference database (named CR-ITS2-refDB) comprising representatives of the major cereal rust fungi and phylogenetically related species was compiled. Inter- and intra-specific variation analyses suggested that the ITS2 region had reasonable discriminating power for the majority of the Puccinia species or species complexes in the database. In silico evaluation of nine forward and seven reverse ITS2 primers, including three newly designed, revealed marked variation in DNA amplification efficiency for the rusts. The theoretical assessment of rust-enhanced (Rust2inv/ITS4var_H) and universal fungal (ITS9F/ITS4) ITS2 primer pairs was validated by profiling the airborne rust fungal communities from environmental samples using a metabarcoding approach. Species or subspecific level identification of the rusts was improved by using CR-ITS2-refDB, and the Automated Oligonucleotide Design Pipeline (AODP), which identified all mutations distinguishing highly conserved DNA markers amongst close relatives. A generic bioinformatics pipeline was developed, including all steps employed in this study from in silico evaluation of primers to accurate identification of short metabarcodes at the level of interest for defining phytopathogens. The results highlighted the importance of primer selection, refDBs that are resolved to reflect phylogenetic relationships, and the use of AODP for improving the reliability of metabarcoding in phytopathogen biosurveillance.

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New insight into the species diversity and life cycles of rust fungi (Pucciniales) affecting bioenergy switchgrass (Panicum virgatum) in the Eastern and Central United States

Cited by 6 publications

References 71 publications

Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)

Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)

Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)

Towards Improved Detection and Identification of Rust Fungal Pathogens in Environmental Samples Using a Metabarcoding Approach

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