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United States Department of Agriculture

Agricultural Research Service

Research Project: PECAN CULTIVATION AND DISEASE MANAGEMENT Title: A comparison of UP-PCR and RAPD markers to study genetic diversity of Fusicladium effusum (G. Winter, cause of pecan scab

Authors
item Bock, Clive
item Endalew, Tewodros -
item Biswas, B -
item Yadav, Anand -
item Hotchkiss, Michael
item Stevenson, K -
item Wood, Bruce

Submitted to: Forest Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 14, 2013
Publication Date: N/A

Interpretive Summary: Pecan scab is the major disease of pecan in the south-eastern US. There is no information on the population genetics or genetic diversity of the causal fungus, Fusicladium effusum, or the applicability of available molecular tools to study these aspects. The usefulness of two molecular marker methods (RAPDs and Universally Primed (UP)-PCR) were compared to detect polymorphisms on a group of 20 isolates of F. effusum obtained from scab-diseased leaves of pecan from 11 geographic locations in the southeastern U.S.A. (Georgia [2 locations], Louisiana, Florida, Texas, Alabama [2 locations], Oklahoma, Kansas, Illinois and Mississippi). Markers were scored manually on an agarose gel; in addition, UP-PCR markers were scored using an automated capillary system. Analysis based on source populations group showed three groupings using all three methods (RAPD, UP-PCR scored both manually and automatically), sharing up to 10 of the 11 populations in the same groupings. A Mantel test showed a strong correlation between the two methods, and between the manually scored and automatically scored UP-PCR. Based on these results RAPD and UP-PCR markers may be used to elucidate aspects of the population genetics and genetic diversity of F. effusum which will have an impact on the management of the disease.

Technical Abstract: Fusicladium effusum is a plant pathogenic fungus that infects pecan causing yield loss. There is no information on the population genetics or genetic diversity of F. effusum, or the applicability of available molecular tools to study these aspects. The usefulness of RAPDs and Universally Primed (UP)-PCR to detect polymorphisms was compared on a group of 20 isolates of F. effusum obtained from scab-diseased leaves of pecan from 11 geographic locations in the southeastern U.S.A. (Georgia [2 locations], Louisiana, Florida, Texas, Alabama [2 locations], Oklahoma, Kansas, Illinois and Mississippi). RAPD markers were scored manually on an agarose gel, but the UP-PCR markers were scored both manually and using an automated capillary system. Both RAPDs and UP-PCR markers detected a high level of polymorphism among the scored markers (87.5-96.9%, respectively). Analysis of all 20 isolates using unweighted paired groups of means averages (UPGMA) analysis resulted in dendrograms showing three groupings (which shared up to 16 of the 20 isolates in common groupings). UPGMA analysis based on source populations group showed three groupings using all three methods (RAPD, UP-PCR scored both manually and automatically) which shared up to 10 of the 11 populations in the same groupings. A Mantel test based on Nei’s measure of genetic distance between the RAPD and manually scored UP-PCR markers analyses showed a strong correlation between the two methods (r = 0.55 P<0.0001), and between the manually scored and automatically scored UP-PCR (r=0.82 P<0.0001). Based on these results RAPD and UP-PCR (scored either manually or automatically) markers may be used to elucidate aspects of the population genetics and genetic diversity of F. effusum which will have an impact on the management of the disease.

Last Modified: 11/24/2014
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