Isolation and characterization of 49 polymorphic microsatellite loci for Decapterus maruadsi using SLAF-seq, and cross-amplifi cation to related species

Decapterus maruadsi is a commercially important species in China, but has been heavily exploited in some areas. There is a growing need to develop microsatellites promoting its genetic research for the adequate management of this ?shery resources. The recently developed speci?c-locus ampli?ed fragment sequencing(SLAF-seq) is an effcient and high-resolution method for genome-wide microsatellite markers discovery. In this study, 28 905 microsatellites(mono-to hexa-nucleotide repeats) were identi?ed using SLAF-seq technology, of which di-nucleotide was the most frequent(13 590, 47.02%), followed by mono-nucleotide(8 138, 28.15%), tri-nucleotide(5 727, 19.81%), tetra-nucleotide(1 104, 3.82%), pentanucleotide(234, 0.81%), and hexa-nucleotide(112, 0.39%). One hundred and thirty-two microsatellite loci(di-and tri-nucleotide) were randomly selected for ampli?cation and polymorphism, of which 49 were highly polymorphic and well-resolved. The average number of alleles per locus was 13.63, ranging from 4 to 25, and allele sizes varied between 110 bp and 309 bp. The observed heterozygosity( Ho) and expected heterozygosity( He) ranged from 0.233 to 1.000 and from 0.374 to 0.959, with mean values of 0.738 and0.836, respectively. The polymorphism information content(PIC) ranged from 0.341 to 0.941(mean=0.806).However, 12 loci deviated from Hardy-Weinberg equilibrium. Furthermore, transferability tests were also successful in validating the utility of the developed markers in ?ve phylogenetically related species of family Carangidae. A total of 48 microsatellite markers were successfully cross-ampli?ed in Decapterus macarellus, Decapterus macrosoma, Decapterus kurroides, Trachurus japonicus, and Selaroides leptolepis.The present microsatellites provided the ?rst known set of microsatellite DNA markers for D. maruadsi,D. macarellus, D. kurroides, and D. macrosoma, and would be useful for further population genetic and molecular phylogeny studies as well as help with the ?sheries management formulation and implementation of the understudied species.