title: Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing.
abstract: Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here, we developed and applied a binned genotyping-by-sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks using two large marine by freshwater F2 crosses of more than 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds to chromosomes, reorienting 40 scaffolds, and rearranging scaffolds in 4 locations. In the revised genome assembly, 94.6% of the assembly was anchored to a chromosome. To assess linkage map quality, we mapped quantitative trait loci (QTL) controlling lateral plate number, which mapped as expected to a 200-kb genomic region containing Ectodysplasin, as well as a chromosome 7 QTL overlapping a previously identified modifier QTL. Finally, we mapped eight QTL controlling convergently evolved reductions in gill raker length in the two crosses, which revealed that this classic adaptive trait has a surprisingly modular and nonparallel genetic basis.
authors.affiliation: Molecular and Cell Biology Department, University of California-Berkeley, Berkeley, California 94720.
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Glazer
authors.affiliation: Molecular and Cell Biology Department, University of California-Berkeley, Berkeley, California 94720.
authors.forename: Emily E
authors.initials: EE
authors.lastname: Killingbeck
authors.affiliation: Molecular and Cell Biology Department, University of California-Berkeley, Berkeley, California 94720.
authors.forename: Therese
authors.initials: T
authors.lastname: Mitros
authors.affiliation: Molecular and Cell Biology Department, University of California-Berkeley, Berkeley, California 94720.
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Rokhsar
authors.affiliation: Molecular and Cell Biology Department, University of California-Berkeley, Berkeley, California 94720 ctmiller@berkeley.edu.
authors.forename: Craig T
authors.initials: CT
authors.lastname: Miller
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics / Q000378:metabolism; D015723:Gene Library; D008040:Genetic Linkage; D016678:Genome; D005838:Genotype; D010641:Phenotype; D040641:Quantitative Trait Loci; D023701:Smegmamorpha / Q000235:genetics*
keywords: convergent evolution; genotyping-by-sequencing; linkage map; quantitative trait locus; stickleback