The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for the St John River aquaculture strain of North American Atlantic salmon

Authors: Gao, Guangtu; Waldbieser, Geoffrey - Geoff; RAMEY, YOUNGBLOOD - Mississippi State University; ZAHO, DONGYAN - Cornell University; Pietrak, Michael; STANNARD, JASON - The Center For Aquaculture Technologies; BUCHMAN, JOHN - The Center For Aquaculture Technologies; Scheffler, Brian; Peterson, Brian; Palti, Yniv; Rexroad, Caird; Long, Roseanna; Burr, Gary; Milligan, Melissa

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/14/2023
Publication Date: 7/19/2023
Citation: Gao, G., Waldbieser, G.C., Ramey, Y.C., Zaho, D., Pietrak, M.R., Stannard, J.A., Buchman, J.T., Scheffler, B.E., Peterson, B.C., Palti, Y., Rexroad III, C.E., Long, R., Burr, G.S., Milligan, M.T. 2023. The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for the St. John River aquaculture strain of North American Atlantic salmon. G3, Genes/Genomes/Genetics. jkad138. https://doi.org/10.1093/g3journal/jkad138.
DOI: https://doi.org/10.1093/g3journal/jkad138

Interpretive Summary: Atlantic salmon is the most economically-important cold-water aquaculture species worldwide. Atlantic salmon farming in eastern U.S. and Canada is restricted to genetic stocks of North American (N.A.) origin due to ecological and conservation concerns. The N.A. Atlantic salmon is a different sub-species with substantial genomic and genetic differences from the European sub-species. Recent biotechnological advancements have enhanced our ability to improve selective breeding in Atlantic salmon and other aquaculture species through the utilization of molecular genetics and genomics. To this end, an assay called high-density single nucleotide polymorphism (SNP) chip is used to assess relationships between the DNA make-up of the animal and desired production traits, which enables accurate prediction of the genetic merit and breeding potential of the animal. Here we report on genome sequencing and the development of the first reference genome map and the development and validation of the first public high density SNP chip for N.A. Atlantic salmon, that is now commercially available for genetic research and commercial breeding. The genome resources we developed will facilitate the identification of genes affecting important aquaculture production traits, wild fisheries management and basic biological research, and will enhance strategies targeting the genetic improvement of this fish for better production efficiency.

Technical Abstract: Given the genetic and genomic differences between Atlantic salmon of European origin and North American (N.A.) origin, it is crucial to develop genomic resources that are unique for the N.A. Atlantic salmon. Here we describe the resources that we have recently developed for genomic and genetic research in N.A. Atlantic salmon. Firstly, a new single nucleotide polymorphism (SNP) databases for N.A. Atlantic salmon consisting of 3.1 million high quality putative SNPs was generated using data from whole genome resequencing of 80 N.A. Atlantic salmon individuals; Secondly, a high density 50K SNP array enriched for the genic regions of the genome and containing three sex determination and 61 continent of origin markers was developed and validated; Thirdly, a genetic map composed of 27 linkage groups with 36K SNP markers, was generated from 2,512 individuals in 141 full-sib families; Finally, a chromosome level de-novo assembly of a male N.A. Atlantic salmon genome was generated using PacBio long-reads. Information from Hi-C proximity ligation sequences and Bionano optical mapping was used to concatenate the contigs into scaffolds. The assembly contains 1,755 scaffolds and only 1,253 gaps, with a total length of 2.83 Gb and N50 of 17.2 Mb. A BUSCO analysis detected 96.2% of conserved Actinopterygii genes in the assembly and the genetic linkage information was used to guide the formation of 27 chromosome sequences. In contrast, the karyotype of the European Atlantic salmon lineage is composed of 29 chromosomes. Comparative analysis with the reference genome assembly of the European Atlantic salmon confirmed that the karyotype differences between the two linages are caused by a fission in chromosome Ssa01 and three chromosome fusions including the p arm of chromosome Ssa01 with Ssa23, Ssa08 with Ssa29 and Ssa26 with Ssa28. The resources we have generated and describe in this report provide a crucial boost for genetic and genomic research in N.A. Atlantic salmon.