Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout () Breeding Strains by Using Next-Generation Sequencing.
Lidia de Los Ríos-Pérez, Ronald Marco Brunner, Frieder Hadlich, Alexander Rebl, Carsten Kühn, Dörte Wittenburg, Tom Goldammer, Marieke Verleih
Author Information
Lidia de Los Ríos-Pérez: Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany. ORCID
Ronald Marco Brunner: Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
Frieder Hadlich: Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
Alexander Rebl: Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany. ORCID
Carsten Kühn: Institute of Fisheries, Mecklenburg-Vorpommern Research Centre for Agriculture and Fisheries (LFA MV), 18069 Rostock, Germany.
Dörte Wittenburg: Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
Tom Goldammer: Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany. ORCID
Marieke Verleih: Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany. ORCID
Selective breeding can significantly improve the establishment of sustainable and profitable aquaculture fish farming. For rainbow trout (), one of the main aquaculture coldwater species in Europe, a variety of selected hatchery strains are commercially available. In this study, we investigated the genetic variation between the local Born strain, selected for survival, and the commercially available Silver Steelhead strain, selected for growth. We sequenced the transcriptome of six tissues (gills, head kidney, heart, liver, spleen, and white muscle) from eight healthy individuals per strain, using RNA-seq technology to identify strain-specific gene-expression patterns and single nucleotide polymorphisms (SNPs). In total, 1760 annotated genes were differentially expressed across all tissues. Pathway analysis assigned them to different gene networks. We also identified a set of SNPs, which are heterozygous for one of the two breeding strains: 1229 of which represent polymorphisms over all tissues and individuals. Our data indicate a strong genetic differentiation between Born and Silver Steelhead trout, despite the relatively short time of evolutionary separation of the two breeding strains. The results most likely reflect their specifically adapted genotypes and might contribute to the understanding of differences regarding their robustness toward high stress and pathogenic challenge described in former studies.
