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An annotated consensus genetic map for Pinus taeda L. and extent of linkage disequilibrium in three genotype-phenotype discovery populations

Jared W. Westbrook, Vikram E. Chhatre, Le-Shin Wu, Srikar Chamala, Leandro Gomide Neves, Patricio Muñoz, Pedro J. Martínez-García, David B. Neale, Matias Kirst, Keithanne Mockaitis, C. Dana Nelson, Gary F. Peter, John M. Davis, Craig S. Echt
doi: https://doi.org/10.1101/012625
Jared W. Westbrook
*School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, 32611-0410
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Vikram E. Chhatre
§Southern Research Station, USDA Forest Service, Saucier, Mississippi, 39574
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Le-Shin Wu
□National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47405-7005
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Srikar Chamala
□Department of Biology, University of Florida, Gainesville, FL 32611
**Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32603
§§Genetics Institute, University of Florida, Gainesville, FL 32608
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Leandro Gomide Neves
□□RAPiD Genomics LLC, Gainesville, FL, 32601
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Patricio Muñoz
□□Department of Agronomy, University of Florida, Gainesville, FL 32608
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Pedro J. Martínez-García
***Department of Plant Sciences, University of California, Davis, Davis, California, 95616
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David B. Neale
***Department of Plant Sciences, University of California, Davis, Davis, California, 95616
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Matias Kirst
*School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, 32611-0410
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Keithanne Mockaitis
§§§Department of Biology, Indiana University, Bloomington, IN 47405-7005
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C. Dana Nelson
§Southern Research Station, USDA Forest Service, Saucier, Mississippi, 39574
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Gary F. Peter
*School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, 32611-0410
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John M. Davis
*School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, 32611-0410
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Craig S. Echt
§Southern Research Station, USDA Forest Service, Saucier, Mississippi, 39574
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ABSTRACT

A consensus genetic map for Pinus taeda (loblolly pine) was constructed by merging three previously published maps with a map from a pseudo-backcross between P. taeda and P. elliottii (slash pine). The consensus map positioned 4981 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.48 centiMorgans and total map length was 2372 centiMorgans. Functional predictions for 4762 markers for expressed sequence tags were improved by alignment to full-length P. taeda transcripts. Alignments to the P. taeda genome mapped 4225 scaffold sequences onto linkage groups. The consensus genetic map was used to compare the extent of genome-wide linkage disequilibrium in an association population of distantly related P. taeda individuals (ADEPT2), a multiple-family pedigree used for genomic selection studies (CCLONES), and a full-sib quantitative trait locus mapping population (BC1). Weak linkage disequilibrium was observed in CCLONES and ADEPT2. Average squared correlations, R2, between genotypes at SNPs less than one centiMorgan apart was less than 0.05 in both populations and R2 did not decay substantially with genetic distance. By contrast, strong and extended linkage disequilibrium was observed among BC1 full-sibs where average R2 decayed from 0.8 to less than 0.1 over 53 centiMorgans. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association and quantitative trait locus mapping between genotype-phenotype discovery populations.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 12, 2014.
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An annotated consensus genetic map for Pinus taeda L. and extent of linkage disequilibrium in three genotype-phenotype discovery populations
Jared W. Westbrook, Vikram E. Chhatre, Le-Shin Wu, Srikar Chamala, Leandro Gomide Neves, Patricio Muñoz, Pedro J. Martínez-García, David B. Neale, Matias Kirst, Keithanne Mockaitis, C. Dana Nelson, Gary F. Peter, John M. Davis, Craig S. Echt
bioRxiv 012625; doi: https://doi.org/10.1101/012625
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An annotated consensus genetic map for Pinus taeda L. and extent of linkage disequilibrium in three genotype-phenotype discovery populations
Jared W. Westbrook, Vikram E. Chhatre, Le-Shin Wu, Srikar Chamala, Leandro Gomide Neves, Patricio Muñoz, Pedro J. Martínez-García, David B. Neale, Matias Kirst, Keithanne Mockaitis, C. Dana Nelson, Gary F. Peter, John M. Davis, Craig S. Echt
bioRxiv 012625; doi: https://doi.org/10.1101/012625

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