Exploitation of a turbot (Scophthalmus maximusL.) immune‐related expressed sequence tag (EST) database for microsatellite screening and validation

Abstract

In this study, we identified and characterized 160 microsatellite loci from an expressed sequence tag (EST) database generated from immune-related organs of turbot (Scophthalmus maximus). A final set of 83 new polymorphic microsatellites were validated after the analysis of 40 individuals of Atlantic origin including both wild and farmed individuals. The allele number and the expected heterozygosity ranged from 2 to 18 and from 0.021 to 0.951, respectively. Evidences of null alleles at moderate-high frequencies were detected at six loci using population data. None of the analysed loci showed deviations from Mendelian segregation after the analysis of five full-sib families including approximately 92 individuals/family. The markers are used to consolidate the turbot genetic map, and because they are mostly EST-derived, they will be very useful for comparative genomic studies within flatfishes and with model fish species. Using an in silico approach, we detected significant homologies of microsatellite sequences with the EST databases of the flatfish species with highest genomic resources (Senegalese sole, Atlantic halibut, bastard halibut) in 31% of these turbot markers. The conservation of these microsatellites within Pleuronectiformes will pave the way for anchoring genetic maps of different species and identifying genomic regions related to productive traits.

Genetics Structure Analysis of Turbot (Scophthalmus maximus, Linnaeus, 1758) in the Black and Mediterranean Seas for Application of Innovative Management Strategies

“…This is thought to mirror their higher effective population size and less restricted migration (DeWoody and Avise, 2000). In the present microsatellite analysis, a total of 108 alleles ranging from 3 to 14 for each locus were detected within the S. maximus populations which were similar to the previous studies (Pardo et al, 2005;Florin and Höglund, 2007;Navajas-Pérez et al, 2012). Karan (2015) examined the number of alleles per locus for S. maeoticus populations and found to be the lowest in the 3/9CA15 locus as four and the highest in Sma1 locus as 11.…”

Validation and comparison of microsatellite markers derived from Senegalese sole (Solea senegalensis, Kaup) genomic and expressed sequence tags libraries

“…As expected, those containing EST-SSR (including both monomorphic and polymorphic) were annotated in a much greater proportion (58%) than the anonymous ones (9%). According to the Gene Ontology annotation, most annotated sequences are related with the following cellular components: membrane (16%), endoplasmic reticulum (12%), nucleus (8%), ribosome (8%) and cytoplasm (4%), showing a distribution similar to those found in turbot (Navajas-Pérez et al 2012).…”

A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus)

“…To ensure identification of new molecular markers, sequences similar to GenBank deposited sequences were filtered out to avoid identification of already known SSR and SNP sequences, especially the ones previously identified by turbot [18,19,48,51,94,124,125]. …”

“…These markers are the basis for genetic mapping and comparative genomic analysis, which are in turn used for detection of quantitative trait loci (QTL) and for marker assisted selection (MAS) programs [46,47]. Several types of genetic markers have been developed and investigated in turbot [48] and many of them have already been mapped [18-21]. Recently, a genome scan for sex-determination [22] and resistance/survival to A. salmonicida [49] and P. dicentrarchi [50] using the genetic map identified several consistent QTLs and associated markers in turbot, which suggests the existence of genetic factors underlying these characters and supports their application in genetic breeding strategies.…”