Tree Genetics & Genomes

, Volume 8, Issue 6, pp 1307–1318 | Cite as

SNP markers trace familial linkages in a cloned population of Pinus taeda—prospects for genomic selection

  • Jaime Zapata-Valenzuela
  • Fikret Isik
  • Christian Maltecca
  • Jill Wegrzyn
  • David Neale
  • Steve McKeand
  • Ross Whetten
Original Paper

Abstract

Advances in DNA sequencing technology have made possible the genotyping of thousands of single-nucleotide polymorphism (SNP) markers, and new methods of statistical analysis are emerging to apply these advances in plant breeding programs. We report the utility of markers for prediction of breeding values in a forest tree species using empirical genotype data (3,406 polymorphic SNP loci). A total of 526 Pinus taeda L. clones tested widely in field trials were phenotyped at age 5 years. Only 149 clones from 13 full-sib crosses were genotyped. Markers were fit simultaneously to predict marker additive and dominance effects. Subsets of the 149 genotyped clones were used to train a model using all markers. Cross-validation strategies were followed for the remaining subset of genotyped individuals. The accuracy of genomic estimated breeding values ranged from 0.61 to 0.83 for wood lignin and cellulose content, and from 0.30 to 0.68 for height and volume traits. The accuracies of predictions based on markers were comparable with the accuracies based on pedigree. Because of the small number of SNP markers used and the relatively small population size, we suggest that observed accuracies in this study trace familial linkage rather than historical linkage disequilibrium with trait loci. Prediction accuracies of models that use only a subset of markers were generally comparable with the accuracies of the models using all markers, regardless of whether markers are associated with the phenotype. The results suggest that using SNP loci for selection instead of phenotype is efficient under different relative lengths of the breeding cycle, which would allow cost-effective applications in tree breeding programs. Prospects for applications of genomic selection to P. taeda breeding are discussed.

Keywords

Loblolly pine Marker-aided selection Quantitative genetics Genomic selection Marker–trait association 

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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Jaime Zapata-Valenzuela
    • 1
  • Fikret Isik
    • 1
  • Christian Maltecca
    • 2
  • Jill Wegrzyn
    • 3
  • David Neale
    • 3
  • Steve McKeand
    • 1
  • Ross Whetten
    • 1
  1. 1.Department of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighUSA
  2. 2.Department of Animal ScienceNorth Carolina State UniversityRaleighUSA
  3. 3.Department of Plant ScienceUniversity of California-DavisDavisUSA

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