A genetic linkage map for Arctic char (Salvelinus alpinus): evidence for higher recombination rates and segregation distortion in hybrid versus pure strain mapping parents

Abstract

We constructed a genetic linkage map for Arctic char (Salvelinus alpinus) using two backcrosses between genetically divergent strains. Forty-six linkage groups (expected = 39-41) and 19 homeologous affinities (expected = 25) were identified using 184 microsatellites, 129 amplified fragment length polymorphisms (AFLPs), 13 type I gene markers, and one phenotypic marker, SEX. Twenty-six markers remain unlinked. Female map distance (9.92 Morgans) was substantially higher than male map distance (3.90 Morgans) based on the most complete parental information (i.e., the F1 hybrids). Female recombination rates were often significantly higher than those of males across all pairwise comparisons within homologous chromosomal segments (average female to male ratios within families was 1.69:1). The female hybrid parent had significantly higher recombination rates than the pure strain female parent. Segregation distortion was detected in four linkage groups (4, 8, 13, 20) for both families. In family 3, only the largest fish were sampled for genotyping, suggesting that segregation distortion may represent regions possessing influences on growth. In family 2, almost all cases showing segregation distortion involved markers in the female hybrid parent.

Growth-related quantitative trait loci in domestic and wild rainbow trout (Oncorhynchus mykiss)

“…Additionally, although not as well characterized, it is possible to relate the BW and K QTL detected on AC-20 in Arctic charr [34] to the homologous locations of this linkage group in rainbow trout and Atlantic salmon (i.e., the RT-2/9 and AS-4/11 linkage groups)(see Additional File 8). AC-20 appears to be a metacentric chromosome composed of fused homeologs in Arctic charr [42]. This would make both arms of AC-20 homologous to RT-2q/9q and AS-4q/11q.…”

QTL for body weight and condition factor in Atlantic salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus)

“…A single marker, Ssa85DU, analyzed by Somorjai (2001) (present in the central region of RT-24 and on AC-13) (see Figure 1b for inferred homologies), demonstrated a significant BW QTL effect in an AC male mapping parent. Due to the limited density of markers on the AC linkage map (Woram et al, 2004), homologous associations between Atlantic salmon and AC must be inferred from the similarities that each species has with RT. In comparisons with the RT map, it appears that the region of RT-24 containing Ssa85DU is homologous to AS-18 and not AS-8.…”

“…Nonetheless, the data suggest that more than one BW QTL region resides within RT-24. Interestingly, homeologous affinities between AC-13 and AC-14 have been detected in AC (Woram et al, 2004), suggesting that RT-24 may also contain homeologous genome segments.…”

“…The effects of allele segregation at molecular markers throughout the genome can be used to determine the number and positions of QTL affecting a trait, and the magnitude of the QTL effect (Lynch and Walsh, 1998). Linkage maps have been developed for several salmonid fishes, including rainbow trout (RT; Oncorhynchus mykiss) (Young et al, 1998;Sakamoto et al, 2000;Nichols et al, 2003), Arctic charr (AC; Salvelinus alpinus) (Woram et al, 2004), and Atlantic salmon (Salmo salar) (Gilbey et al, 2004;Moen et al, 2004). Despite the extensive karyotypic rearrangements within the tetraploid salmonids (Hartley, 1987;Phillips and Rab, 2001) since their evolution from a diploid ancestor 25-100 MYA (Allendorf and Thorgaard, 1984), microsatellite markers have been able to identify chromosomal regions that are homologous across species (Woram et al, 2003).…”

“…Comparison of homologous regions among species and recombination rate between common markers has identified several putative inter-specific fusions, inversions, and translocations (Woram et al, 2004). These homologous regions do not always span entire linkage groups in that many linkage groups show homologies to multiple linkage groups in the other salmonid species.…”