The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout.

Area of Science:

• Aquaculture Genetics
• Genomics
• Animal Breeding

Background:

• Rainbow trout (Oncorhynchus mykiss) are a globally important aquaculture species.
• Genetic diversity and traceability are crucial for sustainable aquaculture and conservation of wild populations.
• Previous genetic marker studies in rainbow trout were limited in scale and scope.

Purpose of the Study:

• To develop and characterize the first high-density single nucleotide polymorphism (SNP) genotyping array for rainbow trout.
• To provide a publicly available, high-quality genomic tool for rainbow trout research.
• To assess the utility of the SNP array for population genetics, traceability, and genome anchoring.

Main Methods:

• Development of a custom high-density SNP genotyping array.
• Genotyping quality assessment through validation rates, sample reproducibility, and comparison with other methods.
• Application of the array to aquaculture and wild rainbow trout populations.
• Linkage analysis and mapping of SNPs to the reference genome assembly.

Main Results:

• The SNP array achieved a high validation rate (~90%), comparable to other livestock species.
• Genotyping quality was confirmed by high sample reproducibility and nearly 100% agreement with other methods.
• The array identified over 40,900 polymorphic markers in aquaculture populations and 10,577–24,330 in wild populations.
• Linkage analysis anchored 68% of genome scaffolds/contigs, including previously unassigned regions.

Conclusions:

• The developed high-density SNP array is a robust and valuable tool for rainbow trout genetic research.
• The array facilitates population traceability, genetic diversity assessment, and genome-wide association studies.
• This resource significantly advances genomic applications in rainbow trout aquaculture and conservation.