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Title: Population genetic structure of Venturia effusa, cause of pecan scab, in the southeastern United States

Author
item Bock, Clive
item Hotchkiss, Michael - Mike
item YOUNG, CAROLYN - Samuel Roberts Noble Foundation, Inc
item CHARLTON, NIKKI - Samuel Roberts Noble Foundation, Inc
item CHAKRADHAR, MATTUPALLI - Samuel Roberts Noble Foundation, Inc
item STEVENSON, KATHERINE - University Of Georgia
item Wood, Bruce

Submitted to: Journal of Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/12/2017
Publication Date: 2/1/2017
Citation: Bock, C.H., Hotchkiss, M.W., Young, C.A., Charlton, N.D., Chakradhar, M., Stevenson, K.L., Wood, B.W. 2017. Population genetic structure of Venturia effusa, cause of pecan scab, in the southeastern United States. Journal of Phytopathology. doi:10.1094/PHYTO-10-16-0376-R.

Interpretive Summary: Pecan scab (caused by the plant pathogenic fungus Venturia effusa) is the most damaging disease of pecan in the southeastern USA. Little information exists on the population biology and genetic diversity of the pathogen, which is required to develop effective management strategies for the disease, particularly for use of host resistance. A total of 784 isolates were collected from 63 trees in 11 pecan orchards in the southeastern USA and screened against a set of 30 genetic markers. Although genetically diverse across the range, all populations could be differentiated from each other, and some populations were more closely related compared to other pairs of populations. This is indicative of some limited population differentiation in V. effusa in the southeastern USA. None of the populations were at genetic equilibrium. These observations are consistent with the known history of pecan and pecan scab; that V. effusa became an issue on cultivated pecan in the last ~120 years (recent population expansion). Furthermore, recently reported mating type genes and the sexual stage of this fungus may help explain the observed population characteristics, which bear a strong resemblance to those of other well-characterized sexually reproducing ascomycete pathogens. The ability of the pathogen to maintain high genetic diversity and gene flow has ramifications for host resistance breeding.

Technical Abstract: Venturia effusa is the most important pathogen of pecan in the southeastern USA. Little information exists on the population biology and genetic diversity of the pathogen. A hierarchical sampling of a total of 784 isolates from 63 trees in 11 pecan orchards in the southeastern USA were screened against a set of 30 previously characterized microsatellite markers. Populations were collected from Georgia (2), Florida (1), Alabama (2), Mississippi (1), Louisiana (1), Illinois (1), Oklahoma (1), Texas (1) and Kansas (1). Clonality was low in all orchard populations (=10.1% of isolates), and there were consistently high levels of genotypic diversity (Shannon-Weiner’s index: 3.49 to 4.59) and gene diversity (Nei’s measure: 0.513 to 0.713). Analysis of molecular variance showed that although 81% of genetic diversity occurred at the scale of the individual tree, 16% occurred between orchards, and only 3% between trees within orchards. All populations could be differentiated from each other (P=0.01), and various cluster analyses indicated some populations were more closely related compared to other pairs of populations. This is indicative of some limited population differentiation in V. effusa in the southeastern USA. Bayesian and nearest neighbor methods suggested 8 clusters, with orchards from Georgia and Florida being grouped together. A minimum spanning tree of all 784 isolates also indicated some isolate identification with source population. Linkage disequilibrium was detected in all but one population (Kansas), although 8 of the 11 populations had <20% of loci at disequilibrium. A Mantel test demonstrated a relationship between physical and genetic distance between populations (Z = 11.9, r = 0.559, P=0.001). None of the populations were at mutation-drift equilibrium. All but 3 of the 11 populations had a deficiency of gene diversity compared to that expected at mutation-drift equilibrium (indicating population expansion); the remaining populations had an excess of gene diversity compared to that expected at mutation-drift equilibrium (indicating a recent bottleneck). These observations are consistent with the known history of pecan and pecan scab; that V. effusa became an issue on cultivated pecan in the last ~120 years (recent population expansion). Recently reported mating type genes and the sexual stage of this fungus may help explain the observed population characteristics, which bear a strong resemblance to those of other well-characterized sexually reproducing ascomycete pathogens.