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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #316275

Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: A high density genetic linkage map for rainbow trout (Onchorynchus mykiss) containing 47,839 SNPS

item Palti, Yniv
item MOEN, THOMAS - Aquagen
item LIEN, SIGBJORN - Centre For Integrative Genetics (CIGENE)
item Gao, Guangtu
item Liu, Sixin
item KENT, MATTHEW - Centre For Integrative Genetics (CIGENE)
item Rexroad, Caird

Submitted to: International Symposium on Genetics in Aquaculture
Publication Type: Abstract Only
Publication Acceptance Date: 4/19/2015
Publication Date: 6/21/2015
Citation: Baranski, M., Palti, Y., Moen, T., Lien, S., Gao, G., Liu, S., Kent, M., Rexroad Iii, C.E. 2015. A high density genetic linkage map for rainbow trout (Onchorynchus mykiss) containing 47,839 SNPS [abstract]. International Symposium on Genetics in Aquaculture. P04263.

Interpretive Summary:

Technical Abstract: High-density SNP arrays have become the tool of choice for QTL mapping, genome-wide association studies and genomic selection. More recently, high-density linkage maps generated by SNP array data have proven to be crucial for the accurate assembly of scaffolds and contigs in whole-genome sequencing efforts. Rainbow trout is an important aquaculture species world-wide, and a first draft of the genome sequence of this species is now available. Earlier mapping studies have identified QTL for important commercial traits including disease resistance, and combining the resources of a high density genetic map with genome sequence data will facilitate the fine mapping of these loci and the identification of candidate genes and mutations. In this study, a 57K Affymetrix SNP array was used to genotype 2,464 samples collected across 46 full-sib families from a commercial Norwegian population and 10 from an experimental USDA breeding population. Following quality control of raw genotype data, linkage mapping was performed with Lep-MAP software. First, SNPs were assigned to linkage groups with the 'SeparateChromosomes' command using increasing LOD thresholds until the observed number of linkage groups corresponded with the haploid chromosome number in this species. Additional SNPs were subsequently added to the groups with the 'JoinSingles' command at a more relaxed LOD threshold, and finally SNPs were ordered in each linkage group with the 'OrderMarkers' command. Numerous iterations were performed to optimise error and recombination parameters. A total of 47,839 SNPs were mapped to 29 linkage groups, with an average of 1,650 SNPs per group. The number of SNPs assigned to each group ranged from 754 to 2,934. The total distances covered by the male and female maps were 2,214 cM and 4,248 cM, respectively. In all 13 chromosomes known to have homeologous pairing with at least one other chromosome arm, the female/male recombination ratios were >2.0, while in non-duplicated chromosomes the female/male recombination ratio ranged from 1.0 to 2.0, with the exception of chromosomes Omy15 and Omy21. This map is currently being used to map QTL for a number of commercially important traits, and will be used to improve the assembly of the rainbow trout genome.