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This study aimed to gain insights about the status of the Swedish breeding program through studying key phenotypic traits. In total, 133 and 73 full-sib families were formed during the reproductive seasons of 2016 and 2019, respectively. Growth-related recordings were available from two occasions: ∼ 9 and 24–27 months post-hatch. A preliminary descriptive analysis of the fecundity and early embryo survival identified substantial differences in favor of G0 (year class 2016) which was partly explained by the fact that first-time 3-year-old spawners were used in G1 (year class 2019). Moderate to high heritability values (0.23–0.49) were obtained for body length and weight across both time points and generations. Furthermore, the prediction accuracy of the estimated breeding values was ∼0.65, while the expected genetic gain was 36 g per year. Overall, our results demonstrate the positive performance of the Swedish rainbow trout breeding program. [ABSTRACT FROM AUTHOR]

The Arctic charr breeding programme has been a main driving force for developing the aquaculture industry in Sweden. Selection has been performed for almost 40 years using animals from a closed breeding nucleus. The aim of the current study was to evaluate the potential of further improving growth‐related traits taking into account the existence of genotype‐by‐environment interaction. Furthermore, we investigated the magnitude of the genetic component associated with survival to the eyed stage and potential associations with inbreeding coefficients. A preliminary heritability estimate of 0.23 (SE 0.20) was obtained for survival to the eyed stage using records spanning from 2000 to 2017 (n = 230). Moreover, moderate‐to‐high heritability estimates (0.27–0.49) were obtained for growth‐related traits (body weight and length), using animals from the latest generation of selection (year class 2017). Those animals (n = 2,776), originating from 55 full‐sib families, were split into two groups and reared in separate land‐based facilities of commercial fish farms in Sweden. The growth‐related traits were recorded twice in both sites when animals were of >1 and >2 years of age. Existence of sexual growth dimorphism was indicated with the males having on average 6%–8% higher total length and 22%–34% higher body weight. Furthermore, high genetic correlations regarding growth traits were obtained amongst animals reared at the two different sites (0.82–0.95). In addition, we assessed the accuracy of best linear unbiased prediction (BLUP)‐derived estimated breeding values (EBVs) when phenotypes from each rearing site were subsequently masked and used as a validation set. A mean prediction accuracy of 0.60 (length) and 0.64 (weight) were derived for both rearing sites. Overall, our results suggest that further growth improvements should be possible in the subsequent generations of selection. Finally, even though indications for the existence of an underlying genetic component(s) involved in survival to the eyed stage were obtained additional data will be required for elucidating its magnitude. [ABSTRACT FROM AUTHOR]

Arctic charr (Salvelinus alpinus) is a species of high economic value for the aquaculture industry, and of high ecological value due to its Holarctic distribution in both marine and freshwater environments. Novel genome sequencing approaches enable the study of population and quantitative genetic parameters even on species with limited or no prior genomic resources. Low coverage genotyping by sequencing (GBS) was applied in a selected strain of Arctic charr in Sweden originating from a landlocked freshwater population. For the needs of the current study, animals from year classes 2013 (171 animals, parental population) and 2017 (759 animals; 13 full sib families) were used as a template for identifying genome wide single nucleotide polymorphisms (SNPs). GBS libraries were constructed using the PstI and MspI restriction enzymes. Approximately 14.5K SNPs passed quality control and were used for estimating a genomic relationship matrix. Thereafter a wide range of analyses were conducted in order to gain insights regarding genetic diversity and investigate the efficiency of the genomic information for parentage assignment and breeding value estimation. Heterozygosity estimates for both year classes suggested a slight excess of heterozygotes. Furthermore, FST estimates among the families of year class 2017 ranged between 0.009 - 0.066. Principal components analysis (PCA) and discriminant analysis of principal components (DAPC) were applied aiming to identify the existence of genetic clusters among the studied population. Results obtained were in accordance with pedigree records allowing the identification of individual families. Additionally, DNA parentage verification was performed, with results in accordance with the pedigree records with the exception of a putative dam where full sib genotypes suggested a potential recording error. Breeding value estimation for juvenile growth through the usage of the estimated genomic relationship matrix clearly outperformed the pedigree equivalent in terms of prediction accuracy (0.51 opposed to 0.31). Overall, low coverage GBS has proven to be a cost-effective genotyping platform that is expected to boost the selection efficiency of the Arctic charr breeding program. [ABSTRACT FROM AUTHOR]

Abstract: Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high‐density single‐nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction‐site associated DNA sequencing (RAD‐Seq) and subsequent variations have been extensively applied to generate population‐level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD‐Seq techniques have included generation of genetic linkage maps, performing genome‐wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species. [ABSTRACT FROM AUTHOR]

Simple Summary: Animal breeding in recent years has benefited greatly from the availability of large-scale genetic information. The most widely applied genomic tools in selective breeding are specialized arrays that use DNA hybridization. However, the high financial investments accompanying this practice impair the profitability of emerging aquaculture species, including Arctic charr. The aim of the current study was to assess and compare the potential of two cost-efficient genotyping strategies applicable in a variety of breeding-related tasks, such as pedigree verification, genetic diversity screening and detection of genomic regions that are associated with phenotypes of economic importance. Both strategies are based on reduced representation sequencing but differ in sequencing coverage (low and high). The low coverage strategy offers a higher density of DNA markers, but also presents a greater proportion of missing data in the marker set and is characterized by more uncertainty in determining heterozygosity compared to high coverage. Our results show that while high coverage genotyping performs better in genetic diversity and kinship analyses, a low coverage strategy is more successful in identifying genomic regions associated with phenotypic traits, leading to the conclusion that both strategies could be of value into selection schemes. Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding. [ABSTRACT FROM AUTHOR]