|VAGHEFI, NILOOFAR - Cornell University|
|KIKKERT, JULIE R - Cornell University|
|SECOR, GARY - North Dakota State University|
|NELSON, SCOT - University Of Hawaii|
|PETHYBRIDGE, SARAH - Cornell University|
Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/12/2017
Publication Date: 10/24/2017
Citation: Vaghefi, N., Kikkert, J.R., Bolton, M.D., Hanson, L.E., Secor, G.A., Nelson, S.C., Pethybridge, S.J. 2017. Global genotype flow in Cercospora beticola populations confirmed through genotyping-by-sequencing. PLoS One. 12(10): e0186488. https://doi.org/10.1371/journal.pone.0186488.
Interpretive Summary: Studies on the genetics of plant pathogen populations provide insight into pathogen biology, epidemiology, and co-evolutionary interactions with plants, which in turn help define management units and dynamic management strategies in response to ever-changing pathogen populations. For example, pathogen populations showing a high degree of genetic diversity may suggest that sexual recombination is occurring, which may imply that these populations are more likely to break down plant resistance genes or be more likely to evolve resistance to fungicides. Although population genetic studies have often relied on various types of molecular markers to gain insight into population structure, these technologies have several limitations. A relatively new technique called genotype-by-sequencing relies on breaking down pathogen genomes into smaller pieces followed by partial genome sequencing. In this study, genotyping-by-sequencing was used to analyze Cercospora beticola populations from New York, Hawaii, and Europe. Comparisons were made using traditional population genetic strategies to genotyping-by-sequencing. Interestingly, one unique strain was identified in New York and England, perhaps suggesting that C. beticola can travel such distances in contaminated seed. Future work directed towards identifying strains directly from seed will need to be carried out to confirm this hypothesis.
Technical Abstract: Genotyping-by-sequencing (GBS) was conducted on 333 Cercospora isolates collected from Beta vulgaris (sugar beet, table beet and Swiss chard) in the USA and Europe. Cercospora beticola was confirmed as the species predominantly isolated from leaves with Cercospora leaf spot (CLS) symptoms. However, C. cf. flagellaris also was detected at a frequency of 3% in two table beet fields in New York. Resolution of the spatial structure and identification of clonal lineages in C. beticola populations using genome-wide single nucleotide polymorphisms (SNPs) obtained from GBS was compared to genotyping using microsatellites. Varying distance thresholds (bitwise distance = 0, 1.854599 × 10-4, and 1.298 × 10-3) were used for delineation of clonal boundaries in C. beticola populations. Results supported previous reports of long distance dispersal of C. beticola through genotype flow. The GBS-SNP data set provided higher resolution in discriminating clonal lineages, however, genotype identification was impacted by filtering parameters and the distance threshold at which the multi-locus genotypes were contracted to multi-locus lineages. The type of marker or different filtering strategies did not impact estimates of population differentiation and structure. Results emphasize the importance of robust filtering strategies and designation of distance thresholds for delineating clonal boundaries in population genomics analyses that depend on individual assignment and identification of clonal lineages. The implications of intercontinental genotype flow among C. beticola populations for CLS management are discussed.