Development of microsatellite markers from 454 transcriptome derived sequences for the scallop Pecten maximus
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TECHNICAL NOTE
Development of microsatellite markers from 454 transcriptome derived sequences for the scallop Pecten maximus Natalie Hold • Louise Dawnay • Martin I. Taylor
Received: 8 February 2013 / Accepted: 15 February 2013 / Published online: 27 February 2013 Ó Springer Science+Business Media Dordrecht 2013
Abstract Twelve microsatellite markers were developed for the scallop Pecten maximus. The markers were tested in three geographically diverse populations and all markers were polymorphic in all three populations. The mean number of alleles per locus ranged from 2 to 10.67 and the observed and expected heterozygosity ranged from 0.05 to 0.67 and 0.05 to 0.81 respectively. Some loci showed evidence of null alleles and an excess of homozygotes in some populations but 9 loci conformed to Hardy–Weinberg expectations. These new loci can be combined with previously published microsatellites to create a powerful suite of markers for genetic analyses. Keywords
Scallop Pecten maximus Microsatellites
Pecten maximus supports an important commercial fishery. France and the UK land the largest annual catches with total UK scallop landings of 34,000 tonnes in 2009, equating to a value of £47 million (FAO 2012). Despite its commercial importance, the genetic structure of P. maximus stocks remain poorly defined. Watts et al. (2005) developed nine microsatellite markers but to date no N. Hold (&) School of Ocean Sciences, Bangor University, Menai Bridge LL59 5AB, UK e-mail: [email protected] N. Hold L. Dawnay Molecular Ecology and Fisheries Genetics Laboratory, Environment Centre Wales, Bangor University, Bangor LL57, UK M. I. Taylor School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
studies of population structure have been published using them and our testing found that only four produced reliable results. Consequently, new microsatellite markers were developed using 454 transcriptome sequencing. Since the development of the microsatellites in this study, nine further microsatellite markers have been published from expressed sequence tags (Charrier et al. 2012). The power of many genetic analyses is increased more rapidly by the addition of more loci (and more variable loci) than by increasing the sample size (Felsenstein 2006; Wang and Santure 2009; Landguth et al. 2012). As such, the microsatellite markers from all three studies could be combined to create a very powerful suite of genetic markers. Microsatellite markers were identified using next generation sequencing of the scallop transcriptome. Briefly, cDNA was isolated from gill, muscle, and mantle tissue from four individual scallops and sequenced on Roche’s Titanium Flex 454 sequencer. Sequences were cleaned of vectors and primers using Seqclean (http://compbio.dfci.harvard.edu/tgi/ software/) before contig assembly using iAssembler (http:// bioinfo.bti.cornell.edu/tool/iAssembler/). Microsatellite containing contigs were then identified using microsatcommander (Faircloth 2008) and primers designed using Primer3 (Rozen and Sk
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