A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing

Area of Science:

• Genomics
• Animal Genetics
• Aquaculture

Background:

• Single-nucleotide polymorphisms (SNPs) are crucial genetic markers for various applications in animal breeding and population genetics.
• Previous SNP discovery in rainbow trout relied on methods like RAD sequencing, limiting marker density and scope.
• A comprehensive SNP resource is needed for advanced genetic and genomic studies in rainbow trout (Oncorhynchus mykiss).

Purpose of the Study:

• To discover and characterize a large number of high-quality single-nucleotide polymorphisms (SNPs) in the rainbow trout genome.
• To establish a comprehensive SNP database for rainbow trout, enabling high-density SNP array design and other genotyping platforms.
• To assess the utility of identified SNPs for population genetics and phylogenetic analyses.

Main Methods:

• Whole genome resequencing of 61 diverse rainbow trout and steelhead samples.
• Mapping sequences to the updated rainbow trout reference genome (GCA_002163495.1).
• Variant calling using FreeBayes and SAMtools mpileup, followed by rigorous filtering and validation using double-haploid lines to remove paralogous and multi-sequence variants.

Main Results:

• Identification of over 30 million SNPs across rainbow trout chromosomes and scaffolds, with over 4 million SNPs exhibiting high minor allele frequency (>0.25).
• Achieved an average SNP density of 15.6 SNPs per kb on the chromosomes, representing a significant increase in marker availability.
• Phylogenetic analysis confirmed the utility of these SNPs for resolving population relationships, and intra-population assessments revealed high levels of polymorphism and heterozygosity.

Conclusions:

• The newly identified and filtered SNP set represents a valuable genomic resource for rainbow trout.
• These SNPs are suitable for high-density SNP array development and various genotyping applications in rainbow trout.
• The findings support the use of these markers for detailed population structure, genetic diversity, and breeding programs in this species.