Root-knot nematodes are the most damaging plant-parasitic nematodes in pomegranate and are widely distributed in Iran. During the 2015/16 growth season, 195 root and soil samples were collected from major areas of pomegranate orchards in the eastern of Iran (Khorasan Razavi, Northern and Southern provinces). Species identification was carried out according to the molecular method by sequences of D2a-D3b expansion domains of 28S rDNA, sequence characterized amplified regions (SCAR). Morphological diagnostic was conducted on perineal pattern of females. Pomegranate infection to Meloidogyne spp. was observed in almost all regions, but infection severity was very variable. Several species of Meloidogyne were identified and showed band399 bp in M. incognita by Inc-14 primer, 670 bp in M. javanica by Jav primer, and 420 bp in M. arenaria by ar primer. M. cruciani showed 820 bp band by D2-D3 primer but the sequence was not distinct from other species and use perineal pattern morphology. Subcuticular punctuation around the anus on lateral posterior sides has characterized the perineal pattern in M. cruciani. M. incognita is the predominant species with 60/8% and showed the highest distribution in the city of Bardaskan orchards in Khorasan Razavi province.

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