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RADseq approaches and applications for forest tree genetics

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Abstract

As tree species vary extensively in genome size, complexity, and resource development, reduced representation methods have been increasingly employed for the generation of population genomic data. By allowing rapid marker discovery and genotyping for thousands of genomic regions in many individuals without requiring genomic resources, restriction site-associated DNA sequencing (RADseq) methods have dramatically improved our ability to bring population genomic perspectives to non-model trees. The rapid recent increase in studies of trees utilizing RADseq suggests that it is likely to become among the most common approaches for generating genome-wide data for a variety of applications. Here we provide a practical review of RADseq and its application to research areas of tree genetics. We briefly review RADseq laboratory methods and consider analytical approaches for assembly, variant calling, and bioinformatic processing. To guide considerations for study design, we use in silico analyses of eight available tree genomes to illustrate how expected marker number and density vary across laboratory approaches and genome sizes, and to consider the ability of RADseq designs to query coding regions. We review the empirical use of RADseq for different research objectives, considering its strengths and limitations. Many studies have used RADseq data to perform genome scans for selection, although limited marker density and linkage disequilibrium will often compromise its utility for such analyses. Regardless of this limitation, RADseq offers a powerful and inexpensive technique for generating genome-wide SNP data that can greatly contribute to research spanning phylogenetic and population genetic inference, linkage mapping, and quantitative genetic parameter estimation for tree genetics.

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Acknowledgements

We thank Santiago González-Martínez for inviting this review, and Chris Nice and C. Alex Buerkle for discussion and constructive comments on portions of the manuscript. During the writing of the manuscript, Thomas Parchman was supported by the National Science Foundation (DEB-1344250), Andrew Eckert was supported by the National Science Foundation (EF-1442486) and the United States Department of Agriculture (USDA 2016-67013-24469), and Kathryn Uckele was supported with a National Science Foundation Graduate Research Fellowship.

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  1. Department of Biology and Program in Ecology, Evolution, and Conservation Biology, University of Nevada Reno, Reno, NV, 89557, USA

    Thomas L. Parchman, Joshua P. Jahner, Kathryn A. Uckele & Lanie M. Galland

  2. Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA

    Andrew J. Eckert

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  1. Thomas L. Parchman
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  2. Joshua P. Jahner
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Correspondence to Thomas L. Parchman.

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Communicated by S. C. González-Martínez

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Parchman, T.L., Jahner, J.P., Uckele, K.A. et al. RADseq approaches and applications for forest tree genetics. Tree Genetics & Genomes 14, 39 (2018). https://doi.org/10.1007/s11295-018-1251-3

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