The development and application of genetic markers for the Kuruma prawn Penaeus japonicus

Microsatellite and Amplified Fragment Length Polymorphism (AFLP) DNA marker s have been characterised for use in establishing pedigrees, linkage mappin g and identifying Quantitative Trait Loci (QTL) influencing commercially im portant traits in P. japonicus. Low efficiency of Microsatellite characteri sation from P. japonicus genomic DNA, due to the high frequency and extende d length of simple sequence repeats, make these DNA markers unsuitable for linkage mapping studies. Unique sequence flanking repeats necessary for PCR primer design were difficult to obtain due the extended lengths of the rep eats. Microsatellites that were characterised displayed between 4-24 allele s and heterozygosities between 47-91% in unrelated animals. No P. japonicus derived microsatellite successfully amplified sequences in P. monodon, P. esculentus or P. stylirostris. AFLPs were developed as an alternative to mi crosatellites. Over 570 polymorphic loci were defined using different prime r combinations. AFLPs are robust with some polymorphisms conserved across f amilies. PCR amplification and sequencing of excised bands allowed developm ent of Sequence Tagged Sites from AFLPs. A primary linkage map based on a t hree generation pedigree, genotyped at 246 AFLP loci has been constructed. It incorporates 129 markers in 44 linkage groups with an estimated genome c overage of approximately 57%. (C) 1999 Elsevier Science B.V. All rights res erved.