Molecular Techniques for Root-Knot Nematode Identification

Among plant-parasitic nematodes, root-knot nematodes (RKN), Meloidogyne spp., are the most important parasite infecting economically important crops globally and causing severe losses in crop production. The use of efficient nematode control methods against these parasites depends upon their correct detection in roots and soil samples. Currently, the use of integrated identification methods, including biochemical, molecular, and morphological-based characters, is preferred. But the techniques using morphology and phylogenetic analysis are time-consuming and not suitable for routine analysis. They have only been used for studies of cryptic species, which were identified using integrative taxonomy. Here we describe the enzymatic and molecular-based methods that have successfully been used in Brazil for more than 25 years in the Nematology Lab at Embrapa Genetic Resources and Biotechnology for routine analysis. This technique is a combination of isozyme esterase profiling and molecular markers, with the aim of having a rapid and correct diagnosis of Meloidogyne spp. populations from field and greenhouse.

Additional information on Meloidogyne polycephannulata and its proposal as a junior synonym of M. incognita

The type population ofMeloidogyne polycephannulatais synonymised withM. incognitabased on morphological and morphometric characters, as well as biochemical, molecular and phylogenetic studies. Morphological variability and a wide host range were reported forM. incognitaduring its first description and later re-description.Meloidogyne polycephannulatawas described in Brazil from specimens collected in a carrot field (type population). The esterase phenotype (Est) characterised for this species was identical to the phenotype Est I2 ofM. incognita, the most ubiquitous phenotype used for diagnostics. Morphological and morphometric characters of the descriptions of the two nominal species showed major similarities, as well as variability within the range of variation detected inM. incognita. In PCR assays, three SCAR markers species-specific forM. incognita(incK14 F/R, Mi/FR and incB06 F/R) amplified the same fragments of 399 bp, 955 bp and 1200 bp, respectively, for populations in both species. In phylogenetic studies based either on concatenated sequences of ITS1-5.8S-ITS2, D2-D3 rRNA, mitochondrialCOII regions or on RAPD and AFLP data, the populations of both species grouped in the same clade with high bootstrap support. Altogether, these results provide congruent evidence that theM. polycephannulatatype isolate deposited at the Embrapa Cryopreserved National Collection of Root-knot Nematodes is not a valid species but rather a junior synonym ofM. incognita.