Quantitative Trait Loci Involved in Sex Determination and Body Growth in the Gilthead Sea Bream (Sparus aurata L.) through Targeted Genome Scan

Among vertebrates, teleost fish exhibit a considerably wide range of sex determination patterns that may be influenced by extrinsic parameters. However even for model fish species like the zebrafish Danio rerio the precise mechanisms involved in primary sex determination have not been studied extensively. The zebrafish, a gonochoristic species, is lacking discernible sex chromosomes and the sex of juvenile fish is difficult to determine. Sequential protandrous hermaphrodite species provide distinct determination of the gender and allow studying the sex determination process by looking at the mechanism of sex reversal. This is the first attempt to understand the genetic basis of phenotypic variation for sex determination and body weight in a sequential protandrous hermaphrodite species, the gilthead sea bream (Sparus aurata). This work demonstrates a fast and efficient strategy for Quantitative Trait Loci (QTL) detection in the gilthead sea bream, a non-model but target hermaphrodite fish species. Therefore a comparative mapping approach was performed to query syntenies against two other Perciformes, the European sea bass (Dicentrarchus labrax), a gonochoristic species and the Asian sea bass (Lates calcarifer) a protandrous hermaphrodite. In this manner two significant QTLs, one QTL affecting both body weight and sex and one QTL affecting sex, were detected on the same linkage group. The co-segregation of the two QTLs provides a genomic base to the observed genetic correlation between these two traits in sea bream as well as in other teleosts. The identification of QTLs linked to sex reversal and growth, will contribute significantly to a better understanding of the complex nature of sex determination in S. aurata where most individuals reverse to the female sex at the age of two years through development and maturation of the ovarian portion of the gonad and regression of the testicular area. [Genomic sequences reported in this manuscript have been submitted to GenBank under accession numbers HQ021443–HQ021749.

Advances in european sea bass genomics and future perspectives

Only recently available sequenced and annotated teleost fish genomes were restricted to a few model species, none of which were for aquaculture. Application of Marker Assisted Selection for improved production traits had been largely restricted to the salmon industry and genetic and Quantitative Trait Loci (QTL) maps were available for only a few species. With the advent of Next Generatio Sequencing the landscape is rapidly changing and today the genomes of several aquaculture species have been sequenced. The European sea bass, Dicentrarchus labrax, is a good example of a 17 commercially important aquaculture species in Europe for which in the last decade a wealth of genomic resources, including a chromosomal scale genome assembly, physical and linkage maps as well as relevant QTL have been generated. The current challenge is to stimulate the uptake of the resources by the industry so that the full potential of this scientific endeavour can be exploited and produce benefits for producers and the public alike

Mapping of quantitative trait loci for flesh colour and growth traits in Atlantic salmon (Salmo salar)

<p>Abstract</p> <p>Background</p> <p>Flesh colour and growth related traits in salmonids are both commercially important and of great interest from a physiological and evolutionary perspective. The aim of this study was to identify quantitative trait loci (QTL) affecting flesh colour and growth related traits in an F2 population derived from an isolated, landlocked wild population in Norway (Byglands Bleke) and a commercial production population.</p> <p>Methods</p> <p>One hundred and twenty-eight informative microsatellite loci distributed across all 29 linkage groups in Atlantic salmon were genotyped in individuals from four F2 families that were selected from the ends of the flesh colour distribution. Genotyping of 23 additional loci and two additional families was performed on a number of linkage groups harbouring putative QTL. QTL analysis was performed using a line-cross model assuming fixation of alternate QTL alleles and a half-sib model with no assumptions about the number and frequency of QTL alleles in the founder populations.</p> <p>Results</p> <p>A moderate to strong phenotypic correlation was found between colour, length and weight traits. In total, 13 genome-wide significant QTL were detected for all traits using the line-cross model, including three genome-wide significant QTL for flesh colour (Chr 6, Chr 26 and Chr 4). In addition, 32 suggestive QTL were detected (chromosome-wide P < 0.05). Using the half-sib model, six genome-wide significant QTL were detected for all traits, including two for flesh colour (Chr 26 and Chr 4) and 41 suggestive QTL were detected (chromosome-wide P < 0.05). Based on the half-sib analysis, these two genome-wide significant QTL for flesh colour explained 24% of the phenotypic variance for this trait.</p> <p>Conclusions</p> <p>A large number of significant and suggestive QTL for flesh colour and growth traits were found in an F2 population of Atlantic salmon. Chr 26 and Chr 4 presented the strongest evidence for significant QTL affecting flesh colour, while Chr 10, Chr 5, and Chr 4 presented the strongest evidence for significant QTL affecting growth traits (length and weight). These QTL could be strong candidates for use in marker-assisted selection and provide a starting point for further characterisation of the genetic components underlying flesh colour and growth.</p

A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer

10.1186/1471-2164-12-174BMC Genomics12-BGME

Transcriptome characterization of the South African abalone Haliotis midae using sequencing-by-synthesis

<p>Abstract</p> <p>Background</p> <p>Worldwide, the genus <it>Haliotis </it>is represented by 56 extant species and several of these are commercially cultured. Among the six abalone species found in South Africa, <it>Haliotis midae </it>is the only aquacultured species. Despite its economic importance, genomic sequence resources for <it>H. midae</it>, and for abalone in general, are still scarce. Next generation sequencing technologies provide a fast and efficient tool to generate large sequence collections that can be used to characterize the transcriptome and identify expressed genes associated with economically important traits like growth and disease resistance.</p> <p>Results</p> <p>More than 25 million short reads generated by the Illumina Genome Analyzer were <it>de novo </it>assembled in 22,761 contigs with an average size of 260 bp. With a stringent <it>E</it>-value threshold of 10^-10, 3,841 contigs (16.8%) had a BLAST homologous match against the Genbank non-redundant (NR) protein database. Most of these sequences were annotated using the gene ontology (GO) and eukaryotic orthologous groups of proteins (KOG) databases and assigned to various functional categories. According to annotation results, many gene families involved in immune response were identified. Thousands of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) were detected. Setting stringent parameters to ensure a high probability of amplification, 420 primer pairs in 181 contigs containing SSR loci were designed.</p> <p>Conclusion</p> <p>This data represents the most comprehensive genomic resource for the South African abalone <it>H. midae </it>to date. The amount of assembled sequences demonstrated the utility of the Illumina sequencing technology in the transcriptome characterization of a non-model species. It allowed the development of several markers and the identification of promising candidate genes for future studies on population and functional genomics in <it>H. midae </it>and in other abalone species.</p

Variability of 13C-14C in soil CO2: Impact on 14C groundwater ages

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Experimental study of D/H isotopic fractionation factor of water adsorbed on porous silica tubes

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