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

Abstract

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.

Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

“…This latter outlier showed a gradual cline in allele frequency from the northernmost samples, through the Mediterranean, and up to the Black Sea: the most common allele in the Baltic (0.879) showed a range between 0.938 (ICE; North Atlantic) and 0.650 (BB‐FR; Biscay Bay) in ATL populations, a frequency of 0.382 in the single Mediterranean population (AD), and the lowest frequency in BLS (0.019‐ 0.029). The two aforementioned outlier loci were located within the confidence intervals of two overlapping QTLs for resistance to the hemorrhagic septicemia virus (VHSV) and growth (Rodríguez‐Ramilo et al., 2014) and closely linked to the important growth‐related gene IGFBP3 (insulin like growth factor binding protein 3; Robledo et al., 2016). Data mining around 5397_68 identified a candidate gene related to Aeromonas salmonicida resistance, DHX30 (DExH‐box helicase 30; Figueras et al., 2016), while mining around 7574_88 identified AQP1 (aquaporin 1), a gene related to fertilization (Figueras et al., 2016), and osmoregulation (Grady, Knepper, Burg, & Ferraris, 2014).…”

“…As expected, F ST between BAS and BLS increased when these outliers were excluded (using only neutral markers). As mentioned above, two of these markers (7033_88 and 5397_68) are linked to several growth‐related loci (Robledo et al., 2016; Rodríguez‐Ramilo et al., 2014; Sánchez‐Molano et al., 2011), and also to some candidate genes associated with osmotic stress response (Norman et al., 2014; Ortells et al., 2012). Two other outlier loci reside close to genes related to osmoregulation: 1587_12 on LG13 near RAC1 and PRKCA (Di Ciano et al., 2002; Zhuang, Hirai, & Ohno, 2000), and 2921_40 on LG16 near NAP1L1 (Wang et al., 2014).…”

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

“…SNP markers located in candidate genes involved in growth were detected in turbot by integrating next generation sequencing and growthrelated QTL mapping (Robledo et al, 2016). Muscle and liver transcriptome from 18 individuals was sequenced and a total of 20 447 genes and 85 344 SNPs were found.…”

Genomic changes associated with reproductive and migratory ecotypes in sockeye salmon (Oncorhynchus nerka)

“…611 R18232 contained an outlier SNP that was significant in three kokanee/sockeye salmon 612 comparisons and maps to the hepatocyte growth factor (HGF) gene, which regulates 613 embryogenesis, organogenesis, and tissue regeneration by regulating cell growth and 614 morphogenesis, and plays a central role in angiogenesis (Fajardo-Puerta et al 2016). Previous 615 QTL studies have highlighted this gene as being associated with altering growth rates in turbot 616 (Scophthalmus maximus) (Robledo et al 2016). 617…”