Association Genetics for Growth, Carbon Isotope Discrimination, and Stem Quality in Loblolly Pine

Association genetics offers the potential to identify molecular markers which account for variation in phenotypic traits of interest in loblolly pine. The detection of associations could be used to explain the underlying genetics architecture of complex quantitative traits, and potentially the identification of markers which could be used for selection in breeding programs to capture additional genetic variation and make greater genetic gains through selection and breeding cycles. Three experiments were conducted to explore the genetic variation in growth, water use efficiency, and stem form in loblolly pine.;The first experiment involved an association genetics approach using an unimproved population of 425 clonally replicated unrelated trees to test 3,938 single nucleotide polymorphisms (SNPs) for association with phenotypic variation in carbon isotope discrimination, total tree height, and foliar nitrogen concentration after two growing seasons. Best linear unbiased prediction was used with a spatial adjustment to remove additional environmental variation from phenotypic data. After correction for multiple testing a total of 14 SNPs were associated with carbon isotope discrimination, height, and foliar nitrogen concentration.;The second experiment was a quantitative analysis of genetic variation in growth and stem form traits related to sawtimber quality in an elite population of loblolly pine. Progeny from an elite population of loblolly pine were bred in a diallel mating design and planted at four sites across the lower coastal plain of the southeastern United States. Growth, disease incidence, stem quality and a sawtimber potential score were measured after six growing seasons. There were significant differences among families for all traits measured. Individual-tree narrow-sense heritability estimates ranged from 0.06 to 0.22. Height and volume were highly correlated with the sawtimber potential score of individual trees. From multiple regression, 79% of the variation in sawtimber potential breeding values could be attributed to variation in volume, rust incidence, stem sweep, and forking breeding values. The potential economic value of loblolly pine was increased as much as 162% over local checks when both volume and sawtimber potential were used to select the 10 best parents from the population. Implementation of a selection index on currently measured traits is a promising opportunity to make gains in the proportion of sawtimber produced from improved germplasm of loblolly pine in the southeastern United States.;The third experiment was an attempt to identify single SNPs associated with variation in growth and stem form traits in loblolly pine (Pinus taeda L.). Associations were tested between 4,200 SNPs and breeding values for a population of 200 largely unrelated selections of loblolly pine. We identified 13 SNP-phenotype associations for sawtimber index, volume, and stem straightness after multiple testing correction. Individual SNPs explained from 0% to 27% of the variance in breeding values used as phenotypes. The most significant SNPs were used to estimate genetic values for an independent population of 153 clonally replicated trees. The correlation between marker based estimated genetic values and the BLUP predictions for volume was highest when 10 to 25 SNP loci were used (r=0.27). Gain estimates from marker based selection scenarios were compared to seedling and clonal progeny testing scenarios to explore the needed reliability of marker-based estimates to assess the incorporation of marker based selection in loblolly pine breeding programs. Comparisons revealed that even low repeatability values for marker-based selection may be a potential consideration in tree breeding programs.