How Science Is Protecting an Iconic Fish
Atlantic salmon (Salmo salar) is a cornerstone of global aquaculture, valued at over $192 million annually in U.S. markets alone. Yet North American (NA) populations face a genomic dilemma: they are evolutionarily distinct from their European cousins, with critical differences in chromosome structure and gene content 1 4 . Historically, genetic tools designed for European salmon failed to translate accurately to NA stocks, hindering conservation and selective breeding. Now, a landmark scientific effort has produced the first chromosome-level genome and custom SNP array for NA salmon—revolutionizing how we protect and cultivate this vital species 1 .
North American salmon have 27 chromosomes compared to 29 in European salmon, requiring specialized genetic tools.
Atlantic salmon aquaculture is valued at over $192 million annually in U.S. markets alone.
Unlike European salmon's 29 chromosomes, NA salmon possess just 27. This divergence stems from dramatic evolutionary restructuring:
These rearrangements alter gene regulation and inheritance patterns, making European genomic tools inadequate for NA populations.
Like all salmonids, NA salmon retain traces of a whole-genome duplication (Ss4R) 80–100 million years ago. Over 94% of their genome still shows colinear blocks with high similarity between duplicated regions, complicating gene mapping and assembly .
A male from the St. John River (SJR) aquaculture strain became the reference individual for constructing the first NA-specific genome.
PacBio RS-II generated 104× coverage of the 2.83 Gb genome, capturing lengthy repetitive regions 2 4 .
Canu software stitched reads into 1,728 initial contigs 6 .
Bionano optical maps and Hi-C proximity ligation data linked contigs into 1,755 scaffolds 1 4 .
A genetic map with 36K SNP markers (from 141 families) ordered scaffolds into 27 chromosomes 1 5 .
Illumina short reads corrected errors, yielding a near-complete assembly with just 1,253 gaps 4 .
| Metric | Result | Significance |
|---|---|---|
| Total Length | 2.83 Gb | Matches expected genome size |
| Scaffold N50 | 17.2 Mb | Indicates high contiguity |
| BUSCO Completeness | 96.2% | Validates gene space representation |
| Gap Count | 1,253 | Fewer gaps → higher reliability |
Using whole-genome resequencing of 80 NA salmon, researchers identified 3.1 million putative SNPs. From these, 50,000 were selected for a custom array optimized for:
| Feature | Value | Utility |
|---|---|---|
| Total SNPs | 50,000 | High-density genome coverage |
| Sex Markers | 3 | Accurate sex identification |
| Origin Discriminators | 61 | Detect European/NA hybridization |
| Mapping Precision | 27 linkage groups | Chromosome-level trait mapping |
| Reagent/Technology | Function | Example in This Study |
|---|---|---|
| PacBio Long-Reads | Resolve repetitive regions | 104× coverage of SJR genome 2 |
| Bionano Optical Maps | Scaffold contigs physically | Linked contigs into 1,755 scaffolds 1 |
| Hi-C Proximity Ligation | Reveal 3D chromosome contacts | Anchored scaffolds to chromosomes 4 |
| 50K SNP Array | Genotype breeding populations | Validated in 141 full-sib families |
| BUSCO | Assess assembly completeness | Confirmed 96.2% gene coverage 1 |
This work transcends aquaculture. The chromosome-level assembly clarifies how fusions and fissions drove NA salmon evolution, offering insights into their adaptation to North American rivers 1 4 . Meanwhile, the 50K SNP array is already accelerating selective breeding:
As oceans warm and diseases spread, these tools provide hope—transforming how we safeguard an iconic species for ecosystems and farms alike.
The first chromosome-level genome and custom SNP array for North American Atlantic salmon represent a quantum leap in both aquaculture and conservation genetics, enabling precise breeding and population management for this economically and ecologically vital species.