Tree Genetics & Genomes

, Volume 9, Issue 5, pp 1161–1178

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


  • Vikram E. Chhatre
    • Genetics Graduate ProgramTexas A&M University
    • Department of Ecosystem Science and ManagementTexas A&M University
  • Thomas D. Byram
    • Department of Ecosystem Science and ManagementTexas A&M University
    • Western Gulf Forest Tree Improvement Program, Texas Forest Service
  • David B. Neale
    • Department of Plant SciencesUniversity of California
  • Jill L. Wegrzyn
    • Department of Plant SciencesUniversity of California
    • Department of Ecosystem Science and ManagementTexas A&M University
    • Department of Forest Genetics and Forest Tree Breeding, Büsgen-InstituteGeorg-August-University of Göttingen
    • Genome Research and Education CenterSiberian Federal University
    • Vavilov Institute of General GeneticsRussian Academy of Sciences
Original Paper

DOI: 10.1007/s11295-013-0624-x

Cite this article as:
Chhatre, V.E., Byram, T.D., Neale, D.B. et al. Tree Genetics & Genomes (2013) 9: 1161. doi:10.1007/s11295-013-0624-x


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

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© Springer-Verlag Berlin Heidelberg 2013