Introns may accumulate much higher genetic variation than exons. Universal primers were designed from the conservative nucleotide sequences of exons to amplify the flanking intron. Length variations in the S7 ribosomal protein (RP) gene intron 1 and mitochondrial creatine kinase (CK) gene intron 6 of the swordfish Xiphias gladius were found. Single or two banded fragment patterns in each individual were observed by agarose gel electrophoresis. Nucleotide sequence analysis revealed that highly polymorphic fragment patterns observed in the RP gene intron 1 were due to different numbers of a TG repeat (microsatellite). The length of the CK gene intron 6 was dimorphic, in which presence or absence of a 24 bp block was responsible for longer or shorter introns. Additional minor nucleotide insertion/deletions were observed independent of the RP microsatellite and the CK 24 bp block regions. The results of this investigation indicate that introns may be good sources of intraspecific genetic variation for population genetic studies and that the same set of primers can be used to amplify homologous intron regions even among distant species. Further, the conserved exon primed PCR strategy may be useful to prevent appearance of priming site polymorphism (null allele).
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