Tree Genetics & Genomes

, Volume 9, Issue 5, pp 1161–1178 | Cite as

Genetic structure and association mapping of adaptive and selective traits in the east Texas loblolly pine (Pinus taeda L.) breeding populations

  • Vikram E. Chhatre
  • Thomas D. Byram
  • David B. Neale
  • Jill L. Wegrzyn
  • Konstantin V. KrutovskyEmail author
Original Paper


First-generation selection (FGS) and second-generation selection (SGS) breeding populations of loblolly pine from east Texas were studied to estimate the genetic diversity, population structure, linkage disequilibrium (LD), signatures of selection and association of breeding traits with a genome-wide panel of 4,264 single nucleotide polymorphisms (SNPs). Relatively high levels of observed (H o = 0.178–0.198) and expected (H e = 0.180–0.198) heterozygosities were observed in all populations. The amount of inbreeding was very low with many populations exhibiting a slight excess of heterozygotes. The population structure was weak, but F ST indicated more pronounced differentiation in the SGS populations. As expected for outcrossing natural populations, the genome-wide LD was low, but marker density was insufficient to deduce the decay rate. Numerous associations were found between various phenotypic traits and SNPs, but only a few remained significant after false positive correction. Signatures of diversifying and balancing selection were found in markers representing important biological functions. These results present the first step in the application of marker-assisted selection (MAS) to the Western Gulf Forest Tree Improvement Program (WGFTIP) for loblolly pine and will contribute to the knowledgebase necessary for genomic selection technology.


Association mapping Adaptive traits Breeding Genomic variation Genome-wide linkage disequilibrium Loblolly pine Pinus taeda Population structure SNPs 



We thank the members and staff of the Western Gulf Forest Tree Improvement Program, Texas Forest Service for their contribution of germplasm to this project, and the Genetics Graduate Program of Texas A&M University for the financial support of Vikram Chhatre. This work was supported by the National Science Foundation Plant Genome Research Program award #DBI-0501763 and the US Department of Agriculture National Institute of Food and Agriculture AFRI Applied Plant Genomics CAP award #2009-85606-05680. We also thank Dr. Ronald R. Sederoff (NC State University) for his comments, which greatly helped us improve the quality of the manuscript.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Vikram E. Chhatre
    • 1
    • 2
  • Thomas D. Byram
    • 2
    • 3
  • David B. Neale
    • 4
  • Jill L. Wegrzyn
    • 4
  • Konstantin V. Krutovsky
    • 2
    • 5
    • 6
    • 7
    Email author
  1. 1.Genetics Graduate ProgramTexas A&M UniversityCollege StationUSA
  2. 2.Department of Ecosystem Science and ManagementTexas A&M UniversityCollege StationUSA
  3. 3.Western Gulf Forest Tree Improvement Program, Texas Forest ServiceCollege StationUSA
  4. 4.Department of Plant SciencesUniversity of CaliforniaDavisUSA
  5. 5.Department of Forest Genetics and Forest Tree Breeding, Büsgen-InstituteGeorg-August-University of GöttingenGöttingenGermany
  6. 6.Genome Research and Education CenterSiberian Federal UniversityKrasnoyarskRussia
  7. 7.Vavilov Institute of General GeneticsRussian Academy of SciencesMoscowRussia

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