A Linkage Map for Brown Trout (Salmo trutta): Chromosome Homeologies and Comparative Genome Organization With Other Salmonid Fish

Abstract

We report on the construction of a linkage map for brown trout (Salmo trutta) and its comparison with those of other tetraploid-derivative fish in the family Salmonidae, including Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss), and Arctic char (Salvelinus alpinus). Overall, we identified 37 linkage groups (2n ¼ 80) from the analysis of 288 microsatellite polymorphisms, 13 allozyme markers, and phenotypic sex in four backcross families. Additionally, we used gene-centromere analysis to approximate the position of the centromere for 20 linkage groups and thus relate linkage arrangements to the physical morphology of chromosomes. Sex-specific maps derived from multiple parents were estimated to cover 346.4 and 912.5 cM of the male and female genomes, respectively. As previously observed in other salmonids, recombination rates showed large sex differences (average female-to-male ratio was 6.4), with male crossovers generally localized toward the distal end of linkage groups. Putative homeologous regions inherited from the salmonid tetraploid ancestor were identified for 10 pairs of linkage groups, including five chromosomes showing evidence of residual tetrasomy (pseudolinkage). Map alignments with orthologous regions in Atlantic salmon, rainbow trout, and Arctic char also revealed extensive conservation of syntenic blocks across species, which was generally consistent with chromosome divergence through Robertsonian translocations.

Major Quantitative Trait Loci Affect Resistance to Infectious Pancreatic Necrosis in Atlantic Salmon (Salmo salar)

“…The Atlantic salmon genome shows a great deal of homology to other salmonids, including rainbow trout, Arctic charr, and brown trout Gharbi et al 2006). The two previously identified QTL affecting IPN resistance in rainbow trout (RT) map to RT LG 3 (IPN R/S 1) and RT LG 22 (IPN R/S 2) (Ozaki et al 2001(Ozaki et al , 2005, for which there has not been any clearly identified homology to the Atlantic salmon QTL linkage groups identified here .…”

“…In addition, the two-stage analysis provides a QTL detection stage (sire based) and a confirmation and positioning stage (dam based). However, one potential drawback of the approach is that the lower male recombination is not universal across the genome, and toward the telomeres of the chromosomes the sexspecific recombination ratios may actually reverse (Sakamoto et al 2000; Gharbi et al 2006). As a result, the initial QTL screening using sire-based segregation of just two or three markers may fail to detect QTL residing toward the telomeres of the chromosomes.…”

“…These structures are also thought to constrain recombination, particularly toward centromeric regions of the chromosome (Allendorf and Danzmann 1997;Sakamoto et al 2000). Interestingly, these phenomena are unique to male meiosis, and as a result there are striking sex-specific differences in linkage maps within salmonid species, with estimations of female:male map distance ratios of 3.25 in rainbow trout (Oncorhynchus mykiss) (Sakamoto et al 2000), 3.92 (Gilbey et al 2004) or 8.26 (Moen et al 2004a) in Atlantic salmon, and 2.64 for brown trout (Salmo trutta) (Gharbi et al 2006). The implications of these recombination differences for mapping quantitative trait loci (QTL) include the increased power of QTL detection, combined with the reduced ability to position the QTL in males (Hayes et al 2006).…”

Linkage Maps for the Pacific Abalone (Genus Haliotis) Based on Microsatellite DNA Markers

“…Sex-related difference in recombination rate: Since the discovery of heterogeneous fractions of meiotic recombination between sexes in Drosophila (Morgan 1912), sex-specific differences in recombination rates have been found in a diverse range of organisms, for example, in plants (Burt et al 1991;De Vicente and Tanksley 1991;Graner et al 1991;Sewell et al 1999), mammals (Donis-Keller et al 1987;Mikawa et al 1999;Neff et al 1999;Lynn et al 2005), and aquatic animals such as teleost fishes (Sakamoto et al 2000;Kondo et al 2001;Singer et al 2002;Woram et al 2004;Kai et al 2005;Lee et al 2005;Gharbi et al 2006). Although limited information is available for molluscan species, higher recombination rates in females have been reported (eastern oyster, Yu and Guo 2003;Pacific oyster, Li and Guo 2004;Hubert and Hedgecock 2004), and in H. discus hannai as well (Liu et al 2006).…”

“…This has been done, mainly for teleost fishes, using information for quantitative trait loci (QTL) mapping to elevate aquaculture technology ( Jackson et al 1998;Danzmann et al 1999;Sakamoto et al 1999;Ozaki et al 2001;Perry et al 2001;Robinson et al 2001;Cnaani et al 2003;Somorjai et al 2003;Moen et al 2004;Reid et al 2005;Yu and Guo 2006) and for comparative mapping to understand the evolutionary processes of organisms (Barbazuk et al 2000;Postlethwait et al 2000;Woods et al 2000;Liu et al 2002;Jaillon et al 2004;Naruse et al 2004;Kai et al 2005;Gharbi et al 2006). However, such accelerated progress in genomics has not been the case with a marine gastropod, the abalone (Haliotidae).…”