Dataset: RADseq data from Atlantic silversides used for linkage and QTL mapping.

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.924886.1Version 1 (2024-04-24)Dataset Type:experimental

Principal Investigator, Contact: Nina Overgaard Therkildsen (Cornell University)

Co-Principal Investigator: Hannes Baumann (University of Connecticut)

Student: Maria Akopyan (Cornell University)

BCO-DMO Data Manager: Karen Soenen (Woods Hole Oceanographic Institution)


Project: Collaborative research: The genomic underpinnings of local adaptation despite gene flow along a coastal environmental cline (GenomAdapt)


Abstract

ddRADseq data from 568 Atlantic silversides (Menidia menidia) that are either F1 or F2 offspring to wild-caught parents from Georgia and New York used in a controlled breeding experiment. The data were used to build linkage maps for each of the separate populations and their inter-population cross, and to perform quantitative trait locus mapping.

* Raw  data  from  the  RADseq  libraries  are  available  under  NCBI  BioProject accession number PRJNA771889 (see related dataset section).
* SNP genotype call files (VCF format) are available at doi:10.6084/m9.figshare.19521955.v1 (see related dataset section) and as supplemental files to this dataset.


Related Datasets

IsSupplementedBy

Dataset: https://doi.org/10.6084/m9.figshare.19521955.v1
Akopyan, M. (2022). <i>SNPS for linkage mapping</i> [Data set]. figshare. https://doi.org/10.6084/M9.FIGSHARE.19521955.V1
References

Dataset: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA771889
Cornell University. Menidia menidia Linkage Map. 2021/10. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA771889. NCBI:BioProject: PRJNA771889.

Related Publications

Results

Akopyan, M., Tigano, A., Jacobs, A., Wilder, A. P., Baumann, H., & Therkildsen, N. O. (2022). Comparative linkage mapping uncovers recombination suppression across massive chromosomal inversions associated with local adaptation in Atlantic silversides. Molecular Ecology, 31(12), 3323–3341. Portico. https://doi.org/10.1111/mec.16472
Methods

Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: an analysis tool set for population genomics. Molecular Ecology, 22(11), 3124–3140. Portico. https://doi.org/10.1111/mec.12354
Methods

Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species. PLoS ONE, 7(5), e37135. https://doi.org/10.1371/journal.pone.0037135