Genome-Wide Verification of Isogenic Nature of Clonal Fish Lines in the Atlantic salmon (Salmo salar) through Next Generation Sequencing Technologies


ORAL M. , Penman D. J. , Taggart J. B. , McAndrew B., Fjelldal P. G. , Hansen T.

Ecology 2018, Kastamonu, Turkey, 19 - 23 June 2018, pp.304

  • Publication Type: Conference Paper / Summary Text
  • City: Kastamonu
  • Country: Turkey
  • Page Numbers: pp.304

Abstract

Introduction: Farmed Atlantic salmon (Salmo salar) is the dominant cultured species in Europe by production and value. Thus genomic resources are well established compared to other teleosts. However, isogenic clonal fish lines which are of great interest for aquaculture related research have not been successfully produced, yet. The main constrains include the low survival of doubled haploid clone founders (propagated through androgenesis or mitotic gynogenesis) and the ability to discriminate between such DH fish with biparental inheritance (arising through failure of gamete irradiation) and meiotic gynogenetics (arising through untargeted spontaneous retention of the second polar body in gynogenesis). Until recently only small numbers of genetic markers were available for genotyping and thus verification of such lines. Reliable and efficient markers technologies are needed for genome-wide screening and next generation sequencing offers this potential.

Material and Methods: A total of 46 DNA samples, starting from outbred parents to putative homozygous clone founders (G1) and to the putative isogenic clonal progeny (G2) in the second generation alongside with haploids were used as template to generate a double-digest restriction associated DNA sequencing (ddRAD-seq) library so as to verify genome-wide isogenity of putative clonal Atlantic salmon lines.

Results: A single round of sequencing by synthesis resulted in 35 million raw reads producing an average of over 1,230 polymorphic single nucleotide polymorphism (SNP) loci. All polymorphic loci were Blast searched against three available versions of salmon genome assemblies to remove multi-copy loci due to a recent whole genome duplication origin in Salmonidae family. Single copy loci (22% of total polymorphic ddRAD loci in each family) showed exclusive transmission of maternal alleles among G1 families while varying levels of sire contribution (10-25%) was detected among G2 families. Although these fish were initially genotyped using 27 microsatellite loci which suggested isogenicity of all samples, residual sire contribution was only detected in the high resolution power of next generation sequencing technologies.

Discussion: The existence of non-maternal (sire alleles) among all members of the five G2 families suggested sub-optimal UV irradiation dose during the propagation of these putative clonal families. This study represents a successful example of verification carried out in species of duplicated genomes and provides evidence for the utility of NGS technologies to discriminate between the different offspring types generated by different ploidy manipulations. Reliable establishment of isogenic clonal lines in the Atlantic salmon, prime commercial interest in Europe, is critical for their utility as a research tool.

Acknowledgement: This project has received funding from the European Union’s Horizon 2020research and innovation programme under grant agreement No. 652831 (AQUAEXCEL2020). MO gratefully acknowledges the funding of National Education Department of Turkish Government (1416/YLSY) for her PhD.

Keywords: Atlantic salmon, isogenic lines, fish