Molecular characterisation of Meloidogyne enterolobii and other Meloidogyne spp. from South Africa

Identification of Meloidogyne spp. is challenging when using only the classical techniques since some species share similar characteristics. In this study, 37 Meloidogyne populations were obtained from four provinces in South Africa during 2015 and 2016 and molecularly characterised. We used SCAR-PCR markers and sequencing of four DNA fragments, viz. the D2-D3 segment (28S rDNA), COI, viable region between COII and 16S rDNA and NADH5 (mtDNA) genes. Using SCAR-PCR, M. enterolobii, M. javanica, M. incognita and M. hapla (in descending order of prevalence) were identified. According to D2-D3, COI, COII/16S and NADH5 sequence analyses, the 23 M. enterolobii populations identified clustered together in a well-supported clade, while M. javanica (9 populations) and M. incognita (5 populations) grouped in another. Results showed that D2-D3 and COI genes were appropriate for accurate identification of M. enterolobii, but not to differentiate among M. arenaria, M. incognita and M. javanica. Conversely, SCAR-PCR and NADH5 were more accurate in distinguishing among different Meloidogyne spp. In conclusion, SCAR-PCR was best for the situation of mixed populations.