Agronomy and Horticulture, Department of

 

First Advisor

Thomas O. Powers

Date of this Version

5-2019

Comments

A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science, Major: Agronomy, Under the Supervision of Professor Thomas O. Powers. Lincoln, Nebraska: May, 2019.

Copyright (c) 2019 Mehmet Ozbayrak

Abstract

Pratylenchus species are among the most common plant parasitic nematodes in the Great Plains Region. The objectives of this study were to barcode Pratylenchus specimens for species identification in the Great Plains region using mitochondrial CO1 DNA barcode. In order to (1) determine species boundaries, (2) assess the host associations of barcoded Pratylenchus, (3) to determine the distribution patterns across the Great Plains Region and, (4) to evaluate the species status of P. scribneri and P. hexincisus by a multivariate morphological analysis of haplotype groups identified by DNA barcoding. Soil samples, primarily associated with eight major crops, were collected from Colorado, Kansas, Montana, Nebraska, North Dakota, and Wyoming. A total of 439 infested field samples from 122 counties representing 11 states were selected for CO1 DNA barcoding. The CO1 region of each individual nematode was amplified by PCR resulting in a 727-739 CO1 nucleotide sequence. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic trees each displayed 19 distinct haplotype groups that were well supported by bootstrap, genetic distances, and posterior probabilities, ages of lineages. Species delimitation analysis (ABGD-GMYC-TCS) revealed variation in detecting putative species number. Most of the tentatively labeled haplotype groups were not easily associated with a named species of Pratylenchus and ambiguous results were especially evident for P. scribneri and P. hexincisus. The most common haplotype group was P. neglectus detected from 178 fields from 100 counties associated with potatoes, wheat, corn, barley, alfalfa, dry beans, vineyard, and sugar beet soils. The second most prevalent haplotype group was P. scribneri recovered from 104 fields from 45 counties. Mixed field populations were encountered of approximately 20% of infested fields, suggesting most often P. neglectus and P. scribneri together. Morphological assessment of Great Plains specimens of P. hexincisus and P. scribneri revealed difficulties in the morphological discrimination of this pair species, as evident by overlapping on plot of canonical discriminant analysis. Identification of Pratylenchus species by DNA barcoding should lead to specific, focused, and effective management strategies for lesion nematodes.

Advisor: Thomas O. Powers

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