Screening for intron-length polymorphisms in penaeid shrimps using exon-primed intron-crossing (EPIC)-PCR

Intron polymorphisms have been shown to yield substantial variability and were successfully used in several population genetics surveys (Lessa 1992; Corte-Real et al. 1994; Daguin & Borsa 1999). Most studies to date have been restricted to a few genes and, frequently, polymorphic introns have been found by chance. To amplify introns, polymerase chain reaction (PCR) primers can be designed in flanking exons. This approach, called exon-primed intron-crossing (EPIC)-PCR (Palumbi 1995), has several advantages: (i) by using primers from heterologous genes, cloning and sequencing of target sequences can be avoided (Corte-Real et al. 1994); (ii) cross-species amplification should be easier than when primers are designed in noncoding sequences because exon sequences are more conserved across species; (iii) for the same reason, within species, PCR artefacts such as null alleles are expected to be less frequent. As many species within the genus Penaeus are of commercial interest (Holthuis 1980), it would be of great benefit to get easily transferable markers. This report will focus on length polymorphism, which allows an unambiguous characterization of the two alleles in a heterozygous genotype, but other sequence polymorphisms are accessible using the primers described. Two penaeid species, Penaeus monodon and P. vannamei were used for cross-species amplification and primers resulting in polymorphic introns were also probed on P. japonicus.