Fig. 1.

High-resolution mapping of a major QTL controlling dorsal spine length in sticklebacks. a QTL scan results for spine lengths in a family of 375 F2s from the JAMA × PAXB cross. Positions of dorsal spines 1–3, the anal spine, and pelvic spines (DS1–DS3, AS, and PS) are indicated on an alizarin-stained stickleback. The dashed line shows an α=0.05 permutation-based threshold. b Fine mapping for a subset of chromosome 4 containing the peak from (a). DS1 and DS2 were measured in additional recombinant fish from the F2 cross and genotyped more densely to refine the QTL position. Marker positions are indicated by tick marks along the bottom. The highlighted area around the peak indicates the region displayed in (c). c Genome browser view of the physical region surrounding the QTL peak. The peak marker, MEM235, is located at 13,912,800 bp (between genes MSX2A and CPEB4A). The marker MEM238 has an identical position on the linkage map, with a physical position of 13,965,800 bp (between STC2A and NKX2-5). The browser tracks show the marine/freshwater cluster separation score (CSS) and divergent regions identified in Jones et al. [27]. These represent regions showing consistent sequence differences between marine and freshwater populations, as identified by the analysis of 21 genomes using CSS and a self-organizing map/hidden Markov model method. Ensembl gene models are shown in red, with MSX2A highlighted in green. From left to right, the genes shown are RNF44, FAF2, PIN4, TSSK1, DRD1A, MSX2A, CPEB4A, STC2A, NKX2-5, BNIP1A, ATP6V0E1, RPL26, and PPP2R2BA. Names appended with A are duplicated with respect to the human genome and have a corresponding B paralog on chromosome 7. AS anal spine, CSS cluster separation score, DS dorsal spine, EDA ectodysplasin, JAMA Japanese marine population, LOD logarithm (base 10) of odds ratio for QTL model at a given locus, PAXB Paxton Lake benthic population, PS pelvic spine