Potato cyst nematodes infesting potato fields in Ecuador: integrative diagnosis and molecular phylogeny

Abstract

Potato cyst nematodes (PCN), Globodera rostochiensis and G. pallida, are serious pests of potatoes worldwide, with some species included in the quarantine lists of many countries. Their accurate and timely identification is a prerequisite in designing effectivemanagement strategies. In Ecuador, potato is one of themain crops, and PCNrepresent an important pest. This situation led to a national surveywhere a total of 85 soil samples were collected in 2013 from the major potato-growing regions. The main objectives were to determine the prevalence of PCN and to establish a method for the integrative diagnosis of species based on the combination ofmorphological datawithmolecular analysis using rRNA regions. PCR-based techniques for species-specific amplification of the ITS region and for sequencing the D2–D3 expansion segments of the 28S rRNA gene were also developed. Results: Globodera pallida was the only PCN species found in the potato fields, but it was widespread (55% frequency of infestation).Moderate to highG. pallida population densities were found. The results from the molecular methods were congruent with the morphological data. Interspecific divergence of the D2–D3 regionof PCNis low, and it isnot possible to discriminate betweenG. pallida and G. rostrochiensis based upon thismolecular region, but it is useful for the distinction of other species. Phylogenetic analysis yielded twomajor well-defined and supported clades, where Ecuadorian sequences grouped with sequences of G. pallida and G. rostochiensis populations deposited in the GenBank database. Significance: The prevalence of G. pallidamakes it a severe threat to potato production in Ecuador.Moreover, management practices such as the short termof crop rotations and the use of the “super-chola” susceptible cultivar could be worsening the problem. A strategy based on the integration of morphological data and molecular analysis is useful for identifying PCN species. In addition, other molecular barcodes are currently being characterized (ITS-rRNA, COI-mitDNA)