Root-knot nematodes (RKN) are serious pests of tomato production in Kenya. Accurate identification of the plant parasitic nematodes is important for their effective management. A study conducted to assess their prevalence and identify RKN occurring on tomatoes in Central Kenya showed infestation of the crop in all the three districts. Of the total sampled plants (N = 900), the RKN infestation level ranged from 28 to 62%. RKN disease severity ranged from 2.5 to 5.3 in all the locations. Meloidogyne incognita,M. javanica and M. arenaria were the only species found infesting tomatoes in these areas. Female nematodes sampled from the symptomatic root system that had root galls characteristic of RKN were analysed by isozyme phenotypes of esterase (EST) and malate dehydrogenase (MDH). EST phenotype was polymorphic and enabled identification of the three different species, while MDH was monomorphic. Polymerase chain reaction-restriction fragment length polymorphism with region between mitochondrial cytochrome oxidase subunit II and large subunit ribosomal RNA (mtDNA COII-LSUrRNA) using HinfI showed that all isolates of M. incognita could be digested into three restriction fragments of about 1300, 400 and 100 bp, except for one species that showed an additional restriction site, giving four fragments of 900, 420, 380 and 100 bp. The 1800 bp PCR product of M. javanica was not digested by HinfI. Meloidogyne arenaria (EST phenotype A1) PCR product was digested into two restriction fragments of about 1700 and 100 bp, while M. arenaria (EST phenotype A2) had two restriction fragments at 1100 and 100 bp.

This work presents a cooperative effort to integrate new molecular (isozyme and SSU analyses) characters into the morphological taxonomy of the genus Gigaspora (Glomales). Previous analyses of published Gigaspora SSU sequences indicated the presence of a few polymorphic nucleotides in the region delimited by primers NS71-SSU 1492′. In our study, the SSU of 24 isolates of arbuscular mycorrhizal (AM) fungi from the Gigasporaceae were amplified and the NS71-SSU 1492′ region was directly sequenced. The corresponding sequences of four more isolates of AM fungi from Gigasporaceae, already published, were also included in our analyses. Three Gigaspora groups were identified on the basis of a 6 nucleotide-long ‘molecular signature’: Gigaspora rosea group (G. rosea+G. albida), Gigaspora margarita group (G. margarita+G. decipiens) and Gigaspora gigantea, which constituted a group by itself. The isozyme profiles (malate dehydrogenase, MDH) of 12 of these 28 isolates, and seven other isolates not sequenced, were compared. The results obtained further supported the grouping of isolates provided by the SSU analysis. Both SSU and MDH analysis indicated that two out of the 35 isolates had been misidentified, which was confirmed when their morphology was reassessed. The use of the Gigaspora intrageneric molecular signature as a quick, unambiguous and objective method to recognize Gigaspora isolates under any (field or laboratory) experimental conditions is suggested.