Characterization by next-generation sequencing of 24 new microsatellite loci for the barred sand-bass, Paralabrax nebulifer (Girard, 1854), from the Baja California Peninsula, Mexico

Abstract

We characterized a set of new hypervariable microsatellite loci for the barred sand-bass (Paralabrax nebulifer), a marine fish that supports important recreational and artisanal fisheries in California, USA and the west coast of the Baja California Peninsula, Mexico. We performed a shotgun genome sequencing with the 454 XL titanium chemistry and used bioinformatics to search for microsatellite loci with perfect repeats. We selected 40 primer pairs that were synthesized and genotyped in an ABI PRISM 3730XL DNA sequencer in 32 individuals from San Juanico, Baja California Sur. We estimated levels of genetic diversity, deviations from linkage and Hardy-Weinberg equilibrium, the frequency of null alleles and the probability of individual identity for the new markers. We successfully scored 24 microsatellite loci (13 tetranucleotides and 11 dinucleotides). The average number of alleles per locus was 12.5 (range 4-23). The average observed and expected heterozygosities were 0.779 (range 0.313-0.969) and 0.774 (range 0.350-0.939), respectively. We detected significant linkage disequilibrium in two pairs of loci. Genotype frequencies at seven loci showed significant deviations from the expectations of Hardy-Weinberg equilibrium and had estimated null allele frequencies 10%. The probability of individual identity for the new loci was 8.5(-36). The new markers will be useful for investigating patterns of fine-scale genetic structure and diversity to estimate larval dispersal and assess metapopulation dynamics, information necessary for the sustainable management of P. nebulifer fisheries at the west coast of the Baja California Peninsula.