Identification of quantitative trait loci associated with upper temperature tolerance in turbot, Scophthalmus maximus

Abstract

Temperature tolerance is an important trait from both an economic and evolutionary perspective in fish. Because of difficulties with measurements, genome-wide selection using quantitative trait loci (QTLs) affecting Upper temperature tolerance may be an alternative for genetic improvement. Turbot Scophthalmus maximus (L.) is a cold-water marine fish with high economic value in Europe and Asia. The genetic bases of upper temperature tolerance (UTTs) traits have been rarely studied. In this study, we constructed a genetic linkage map of turbot using simple sequence repeats (SSRs) and single nucleotide polymorphism (SNP) markers. A total of 190 SSR and 8,123 SNP were assigned to 22 linkage groups (LGs) of a consensus map, which spanned 3,648.29 cM of the turbot genome, with an average interval of 0.44 cM. Moreover, we re-anchored genome sequences, allowing 93.8% physical sequences to be clustered into 22 turbot pseudo-chromosomes. A high synteny was observed between two assemblies from the literature. QTL mapping and validation analysis identified thirteen QLTs which are major effect QTLs, of these, 206 linked SNP loci, and two linked SSR loci were considered to have significant QTL effects. Association analysis for UTTs with 129 QTL markers was performed for different families, results showed that eight SNP loci were significantly correlated with UTT, which markers could be helpful in selecting thermal tolerant breeds of turbot. 1,363 gene sequences were genomically annotated, and 26 QTL markers were annotated. We believe these genes could be valuable candidates affecting high temperatures, providing valuable genomic resources for the study of genetic mechanisms regulating thermal stress. Similarly, they may be used in marker-assisted selection (MAS) programs to improve turbot performance.

Quantitative trait loci mapping reveals important genomic regions controlling root architecture and shoot biomass under nitrogen, phosphorus, and potassium stress in rapeseed (Brassica napus L.)

“…It is important to note that crop performance is the consequence of thousands of gene interactions, as well as environmental and cultural practices ( Collins, 2008 ); it is obvious that assessing quantitative trait loci (QTLs) is a powerful tool for dissecting complex quantitative traits that have been widely studied in various crops such as in wheat ( Ren et al, 2017 ), rice ( Jewel et al, 2019 ), maize ( Sun et al, 2021 ), and rapeseed ( Wang et al, 2017 ; Dun et al, 2019 ; Ibrahim et al, 2021 ; Li et al, 2021 ). As QTLs were identified to be linked with phenotypic variance, the corresponding loci may be amplified and thus could be used for phenotypic improvement ( Liu et al, 2021 ; Ma et al, 2021 ; Peltier et al, 2021 ). Understanding the genetic basis for nutrient acquisition related to root development is crucial in plant breeding ( Wissuwa et al, 2016 ).…”

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

“…Strains were developed to have enhanced upper temperature tolerance for rainbow trout ( Chen et al, 2015 ; Tan et al, 2016 ). Similarly, QTL for UTT were identified in turbot ( Ma A. et al, 2021 ).…”

Genetic architecture of acute hyperthermia resistance in juvenile rainbow trout (Oncorhynchus mykiss) and genetic correlations with production traits

“…Another member of dnaj family was also reported in a GWAS on chronic hyperthermia stress resistance in turbot with a time to loss of equilibrium higher than one week [83]. This result was surprising as there is growing evidence that acute and chronic hyperthermia resistances are distinct traits as previously mentioned in rainbow trout [49] and Atlantic salmon [50].…”

“…This phenotypic difference between homozygotes is considerable. In comparison, differences of 12% and 28% of phenotypic standard deviation between homozygotes at peak SNP for acute hyperthermia resistance were reported in the channel catfish and turbot Scophthalmus maximus , respectively [28, 83]. Thus, despite the low percentage of genetic variance explained at the population level, SNP peaks of the detected QTL seem to be good candidates for marker-assisted selection for acute hyperthermia resistance in the studied population.…”

“…In comparison, differences of 12% and 28% of phenotypic standard deviation between homozygotes at peak SNP for acute hyperthermia resistance were reported in the channel catfish and turbot Scophthalmus maximus, respectively [28,83]. Thus, despite the low percentage of genetic variance explained at the population level, SNP peaks of the detected…”