Integrative Transcriptome, Genome and Quantitative Trait Loci Resources Identify Single Nucleotide Polymorphisms in Candidate Genes for Growth Traits in Turbot

Int J Mol Sci. 2016 Feb 17;17(2):243. doi: 10.3390/ijms17020243.


Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure information. Turbot is a commercially important flatfish in Europe and China, with available genomic information on QTLs and genome mapping. Muscle and liver RNA-seq from 18 individuals was carried out to obtain gene sequences and markers functionally related to growth, resulting in a total of 20,447 genes and 85,344 single nucleotide polymorphisms (SNPs). Many growth-related genes and SNPs were identified and placed in the turbot genome and genetic map to explore their co-localization with growth-QTL markers. Forty-five SNPs on growth-related genes were selected based on QTL co-localization and relevant function for growth traits. Forty-three SNPs were technically feasible and validated in a wild Atlantic population, where 91% were polymorphic. The integration of functional and structural genomic resources in turbot provides a practical approach for QTL mining in this species. Validated SNPs represent a useful set of growth-related gene markers for future association, functional and population studies in this flatfish species.

Keywords: RNA-seq; SNP; Scophthalmus maximus; candidate genes; growth; integrative genomics; turbot.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Aquaculture
  • Chromosome Mapping
  • Flatfishes / genetics
  • Flatfishes / growth & development*
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing
  • Liver / metabolism
  • Muscles / metabolism
  • Polymorphism, Single Nucleotide*
  • Quantitative Trait Loci*
  • Selective Breeding
  • Transcriptome*