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Combination of multipoint maximum likelihood (MML) and regression mapping algorithms to construct a high-density genetic linkage map for loblolly pine (Pinus taeda L.)

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Abstract

Genetic maps have been successfully applied to assist in the dissection of complex traits, provide insight on genome structure, and estimate recombination in conjunction with physical maps. Despite an extensive list of genetic maps developed for loblolly pine (Pinus taeda L.) over the past two decades, a high-density consensus map has not yet been constructed. In this study, we used two reference three-generation outbred pedigrees, base and qtl, obtained from the North Carolina State University Cooperative Tree Improvement Program, to obtain a high-density genetic consensus map. Both populations were genotyped with ≈ 7,000 different markers (restriction fragment length polymorphisms, expressed sequence tag polymorphisms, simple sequence repeats, SNPs). The grouping, ordering, and spacing of the markers on each linkage group were performed with JoinMap® 4.1, which implements the multipoint maximum likelihood algorithm for outbred populations. The final consensus map contains 2,466 markers, with a total length of 1,476 centimorgans (cM). The average marker density across the 12 linkage groups was 0.62 cM/marker. This high-density map provides an important resource for breeders and geneticists and will enable comparative studies across species, as well as improve the loblolly pine genome sequence assembly.

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Acknowledgments

This research was supported by the National Research Initiative of USDA’s National Institute of Food and Agriculture (grant #2011-67009-30030).

Data archiving statement

All SNP sequence and related SNP calls have been deposited at DiversiTree (https://dendrome.ucdavis.edu/DiversiTree/). All the marker/position information for the consensus map has been submitted and is already publicly available in TreeGenes (https://dendrome.ucdavis.edu/treegenes/). In addition, the Pine Reference Sequence project has just released a preliminary draft for loblolly pine (unpublished data, http://www.pinegenome.org/pinerefseq).

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Authors and Affiliations

  1. Department of Plant Sciences, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA

    Pedro J. Martínez-García, Jill L. Wegrzyn, John Liechty & David B. Neale

  2. Department of Evolution and Ecology, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA

    Kristian A. Stevens, Marc Crepeau & Charles H. Langley

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  1. Pedro J. Martínez-García
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  2. Kristian A. Stevens
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  3. Jill L. Wegrzyn
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  7. David B. Neale
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Correspondence to David B. Neale.

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Communicated by: S. Gonzalez-Martinez

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Martínez-García, P.J., Stevens, K.A., Wegrzyn, J.L. et al. Combination of multipoint maximum likelihood (MML) and regression mapping algorithms to construct a high-density genetic linkage map for loblolly pine (Pinus taeda L.). Tree Genetics & Genomes 9, 1529–1535 (2013). https://doi.org/10.1007/s11295-013-0646-4

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  • DOI: https://doi.org/10.1007/s11295-013-0646-4

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