Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Abstract

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.

Genomic investigations provide insights into the mechanisms of resilience to heterogeneous habitats of the Indian Ocean in a pelagic fish

“…Thus, to generate a complete picture of the selective forces acting on this species, a reference genome-based analysis (which can achieve higher statistical power in the outlier analyses) is needed. Higher density reference-based genome scans can reveal some additional candidate loci under strong or moderate selection in the S. longiceps populations that were not covered in the present study 56,57 . A zone of high temperature and low Chl-a is also existing between NEAS and SEAS till the end of southwest monsoon season (June-September) which also acts as an environmental barrier restricting larval dispersal and gene flow.…”

Comparing mixed models and Random Forest association tests using naturalgwas and a Striped Bass SNP data set

“…We suggest that reduced representation sequencing is most effective when combined with immediate follow‐up to confirm significant results, such as PCR confirmations used in the RADSex technique for identifying sex determining loci (Feron et al, 2021), or using individuals from full‐sib families to increase overall power to detect associations (Barría et al, 2018; Palaiokostas et al, 2018, 2021). As the cost of high‐throughput genotyping continues to fall, low coverage WGS may already have comparable costs to RAD‐Seq data sets (Lou et al, 2021; Wright et al, 2020), and low coverage, high density RAD‐Seq data sets have also proven effective at identifying phenotype associations (Pappas & Palaiokostas, 2021).…”

Whole‐genome re‐sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia

“…On the other hand, limited research based on genomic technologies has been conducted in farmed Arctic charr (Gudbrandsson et al, 2016 ). During the last couple of years, the usage of genomic information for selective breeding was assessed in Swedish Arctic charr (Palaiokostas et al, 2022 ; Pappas & Palaiokostas, 2021 ). Nevertheless, the aforementioned studies used genomic tools of relatively low genotyping density.…”