Biology subjects

VanWallendael, A.

Publications and source records attributed to VanWallendael, A..

5 recordsLinked to original sources

bioRxiv2024

Local adaptation of both plant and pathogen: an arms-race compromise in switchgrass rust

O_LIIn widespread species, parasites can locally adapt to host populations, or hosts can locally adapt to resist parasites. Parasites with rapid life cycles locally adapt more quickly, but host diversity, selective pressure, and climatic factors impact coevolution. C_LIO_LITo better understand local adaptation in co-evolved host-parasite systems, we examined switchgrass (Panicum virgatum), and its leaf rust pathogen (Puccinia novopanici) across a latitudinal range in North America. We grew diverse switchgrass genotypes in ten replicated common gardens spanning 16.78{degrees} latitude for three years, measuring rust severity from natural infection. We conducted genome wide association mapping to identify genetic loci associated with rust severity. C_LIO_LIGenetically differentiated rust populations were locally adapted to northern and southern switchgrass, despite host local adaptation in the same regions. Rust resistance was highly polygenic, and distinct loci were associated with rust severity in the north and south. We narrowed a previously identified large-effect QTL for rust severity to a candidate YSL3-like gene, and linked numerous other loci to immunity-related genes. C_LIO_LIBoth hosts and parasites can be locally adapted when parasites have a lower impact on fitness than other local selection pressures. In switchgrass, our results suggest variation in fungal resistance mechanisms between locally adapted regions. C_LI

evolutionary biology↗

bioRxiv2021

Host genetic control of succession in the switchgrass leaf fungal microbiome

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across three additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association mapping and RNA-sequencing to show that three cysteine-rich receptor-like kinases were linked to a genetic locus associated with microbiome structure. These genes were more highly expressed in genotypes susceptible to fungal pathogens, which were central to microbial covariance networks, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.

ecology↗

bioRxiv2020

Alignment-free methods for polyploid genomes: quick and reliable genetic distance estimation

Polyploid genomes pose several inherent challenges to population genetic analyses. While alignment-based methods are fundamentally limited in their applicability to polyploids, alignment-free methods bypass most of these limits. We investigated the use of Mash, a k-mer analysis tool that uses the MinHash method to reduce complexity in large genomic datasets, for basic population genetic analyses of polyploid sequences. We measured the degree to which Mash correctly estimated pairwise genetic distance in simulated diploid and polyploid short-read sequences with various levels of missing data. Mash-based estimates of genetic distance were comparable to alignment-based estimates, and were less impacted by missing data. We also used Mash to analyze publicly available short-read data for three polyploid and one diploid species, then compared Mash results to published results. For both simulated and real data, Mash accurately estimated pairwise genetic differences for polyploids as well as diploids as much as 476 times faster than alignment-based methods, though we found that Mash genetic distance estimates could be biased by per-sample read depth. Mash may be a particularly useful addition to the toolkit of polyploid geneticists for rapid confirmation of alignment-based results and for basic population genetics in reference-free systems with poor quality DNA.

genetics↗

bioRxiv2020

Patterns of population genomic diversity in the invasive Japanese knotweed species complex

PremiseInvasive species are expected to experience a reduction in genetic diversity due to founder effects, which should limit their ability to adapt to new habitats. Still, many invasive species achieve widespread distributions and dense populations. This paradox of invasions could potentially be overcome through multiple introductions or hybridization, both of which increase genetic diversity. We conducted a population genomics study of Japanese knotweed (Reynoutria japonica), which is a polyploid, clonally reproducing invasive species that has been notoriously successful worldwide despite supposedly low genetic diversity. MethodsWe used Genotyping-by-Sequencing to collect 12,912 SNP markers from 88 samples collected at 38 locations across North America for the species complex. We used non-alignment based k-mer hashing analysis in addition to traditional population genetic analyses to account for the challenges of genotyping polyploids. ResultsGenotypes conformed to three genetic clusters, likely representing Japanese knotweed, Giant knotweed, and hybrid Bohemian knotweed. We found that, contrary to previous findings, the Japanese knotweed cluster had substantial genetic diversity, though it had no apparent genetic structure across the landscape. In contrast, Giant knotweed and hybrids showed distinct population groups. We did not find evidence of Isolation-by-Distance in the species complex, likely reflecting the stochastic introduction history of this species complex. Among species, we found no correlations between SNPs and several temperature- and precipitation-based climatic variables. ConclusionsThe results indicate that clonal invasive species can show substantial genetic diversity and can be successful at colonizing a variety of habitats without showing evidence of local adaptation or genetic structure.

evolutionary biology↗

bioRxiv2019

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

O_LILocal 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. C_LIO_LITo 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 United States for three years and conducted quantitative trait locus (QTL) mapping for rust progression. C_LIO_LIWe 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. In 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 strength and direction of effect across space. C_LIO_LIOur results suggest that abiotic factors covarying with latitude interact with the genetic loci underlying plant resistance to control rust infection severity. Further, our results indicate that segregating genetic variation in epistatically interacting loci may play a key role in determining response to infection across geographic space. C_LI

genomics↗