Fig 3. Comparative genomics reveal QTL-associated variants in intron 4 of Bmp6.

(A) Comparing genomic sequences of the fine-mapped tooth QTL (from Fig 1C) between marine (n = 3, from crosses 2, 5, and 6) and benthic chromosomes with the tooth QTL (n = 7, from crosses 1–5) identified a set of variants with opposite homozygous genotypes, colored red for marine (top) and blue for benthic (middle). Note that only positions with opposite homozygous genotypes within this 884 kb are shown. The benthic chromosome without the QTL (chromosome B₈ from cross 6) had a cluster of variants sharing the consensus marine genotype (bottom). (B) The ten variants with perfect QTL association (red points) all lie within intron 4 of Bmp6. The y-axis shows QTL concordance score (see Methods), a metric of concordance between genotype and presence or absence of tooth QTL. Gene model of Bmp6 and surrounding genes are based on Ensembl predictions [24].