A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North America

Abstract

Pratylenchus species are among the most common plant parasitic nematodes in the Great Plains Region of North America. Our goal was to survey Pratylenchus species diversity across the Great Plains region using a mitochondrial COI DNA barcode. The objectives were to (i) determine species boundaries of the common Pratylenchus species within the region, (ii) assess the host associations of the barcoded Pratylenchus specimens, and (iii) determine Pratylenchus distribution patterns throughout the region. A total of 860 soil samples, primarily associated with eight major crops, were collected from Colorado, Kansas, Montana, Nebraska, North Dakota, and Wyoming. From this total, 246 soil samples provided the majority of 915 individual nematode specimens that were amplified by PCR and sequenced for a 727 to 739bp region of COI. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic trees all recognized 19 distinct and well-supported haplotype groups. The most common and widespread haplotype group, representing 53% of all specimens was P. neglectus, detected from 178 fields in 100 counties and associated with fields growing wheat, corn, dry beans, barley, alfalfa, sugar beets, potatoes, and a vineyard. The second most prevalent haplotype group was P. scribneri, representing 30% of all specimens and recovered from 104 fields in 45 counties, and most frequently associated with corn. Mixed field populations were encountered in approximately 20% of infested fields, with P. neglectus and P. scribneri most often occurring together in corn-soybean cropping systems. Less frequently encountered from the region were P. hexincisus, P. thornei, P. penetrans, P. alleni, and P. zeae. Eight additional haplotype groups, potentially new Pratylenchus species, were discovered in the survey.