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

Microsatellite and Amplified Fragment Length Polymorphism (AFLP) DNA markers have been characterised for use in establishing pedigrees, linkage mapping and identifying Quantitative Trait Loci (QTL) influencing commercially important traits in P. japonicus. Low efficiency of Microsatellite characterisation from P. japonicus genomic DNA, due to the high frequency and extended 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 repeats. Microsatellites that were characterised displayed between 4-24 alleles 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 microsatellites. Over 570 polymorphic loci were defined using different primer combinations. AFLPs are robust with some polymorphisms conserved across families. PCR amplification and sequencing of excised bands allowed development of Sequence Tagged Sites from AFLPs. A primary linkage map based on a three generation pedigree, genotyped at 246 AFLP loci has been constructed. It incorporates 129 markers in 44 linkage groups with an estimated genome coverage of approximately 57%. (C) 1999 Elsevier Science B.V. All rights reserved.