A 474 bp fragment of the mitochondrial cytochrome oxidase c subunit 1 (cox1) of Cooperia oncophora was cloned and sequenced. The overall nucleotide diversity of the cox1 fragment varied from 0.5 to 2.0% between individuals. Two nucleotide substitutions were found within two RsaI endonuclease restriction sites and were used in a PCR-based restriction fragment length polymorphism (PCR-RFLP) assay to asses the intra-population variation of C. oncophora. Testing 816 individuals revealed the existence of three different haplotypes, having either both (type I) or only one (types II and III) RsaI site. Laboratory maintained individuals obtained at different time points after infection showed no significant difference in the distribution of the three haplotypes. Neither was there a difference in the distribution between male and female worms, confirming that the mitochondrial genome of C. oncophora is also maternally inherited. Nevertheless, there was a significant difference in the prevalence of the RsaI point mutation in the cox1 gene between the laboratory maintained population of C. oncophora and a Dutch field isolate, indicating that these RFLPs can be used to study genetic variation within or among C. oncophora populations.
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