Genomic arrangement of salinity tolerance QTLs in salmonids: A comparative analysis of Atlantic salmon ( Salmo salar ) with Arctic charr ( Salvelinus alpinus ) and rainbow trout ( Oncorhynchus mykiss )

• Published in: BMC Genomics
• Main Authors: Norman Joseph D, Robinson Mike, Glebe Brian, Ferguson Moira M, Danzmann Roy G
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2012
• Subjects: Atlantic salmon; Arctic charr; Rainbow trout; Salinity tolerance; Genome rearrangements; Whole-genome duplications; Genome synteny; Candidate genes; Teleost fishes; Biotechnology; TP248.13-248.65; Genetics; QH426-470; Arctic; Salmo salar; Salvelinus alpinus
• Online Access: https://doi.org/10.1186/1471-2164-13-420; https://doaj.org/article/748a0b0608244bbb8185fafa3754dd2f

Abstract Background Quantitative trait locus (QTL) studies show that variation in salinity tolerance in Arctic charr and rainbow trout has a genetic basis, even though both these species have low to moderate salinity tolerance capacities. QTL were observed to localize to homologous linkage group segments within putative chromosomal regions possessing multiple candidate genes. We compared salinity tolerance QTL in rainbow trout and Arctic charr to those detected in a higher salinity tolerant species, Atlantic salmon. The highly derived karyotype of Atlantic salmon allows for the assessment of whether disparity in salinity tolerance in salmonids is associated with differences in genetic architecture. To facilitate these comparisons, we examined the genomic synteny patterns of key candidate genes in the other model teleost fishes that have experienced three whole-genome duplication (3R) events which preceded a fourth (4R) whole genome duplication event common to all salmonid species. Results Nine linkage groups contained chromosome-wide significant QTL (AS-2, -4p, -4q, -5, -9, -12p, -12q, -14q -17q, -22, and −23), while a single genome-wide significant QTL was located on AS-4q. Salmonid genomes shared the greatest marker homology with the genome of three-spined stickleback. All linkage group arms in Atlantic salmon were syntenic with at least one stickleback chromosome, while 18 arms had multiple affinities. Arm fusions in Atlantic salmon were often between multiple regions bearing salinity tolerance QTL. Nine linkage groups in Arctic charr and six linkage group arms in rainbow trout currently have no synteny alignments with stickleback chromosomes, while eight rainbow trout linkage group arms were syntenic with multiple stickleback chromosomes. Rearrangements in the stickleback lineage involving fusions of ancestral arm segments could account for the 21 chromosome pairs observed in the stickleback karyotype. Conclusions Salinity tolerance in salmonids from three genera is to some extent controlled by the same ...