Dudley A. Huber

Association genetics in Pinus taeda L. II. Carbon isotope discrimination

Dissection of complex traits that influence fitness is not only a central topic in evolutionary research but can also assist breeding practices for economically important plant species, such as loblolly pine (Pinus taeda L). In this study, 46 single nucleotide polymorphisms (SNPs) from 41 disease and abiotic stress-inducible genes were tested for their genetic association with carbon isotope discrimination (CID), a time-integrated trait measure of stomatal conductance. A family-based approach to detect genotype/phenotype genetic association was developed for the first time in plants by applying the quantitative transmission disequilibrium test on an association population of 961 clones from 61 families (adopted from previous breeding programs) evaluated for phenotypic expression of CID at two sites. Two particularly promising candidates for their genetic effects on CID are: dhn-1, involved in stabilization of cell structures, and lp5-like, a glycine rich protein putatively related to cell wall reinforcement proteins, both of which were shown in previous studies to be water-deficit inducible. Moreover, association in lp5-like involves a nonsynonymous mutation in linkage disequilibrium with two other nonsynonymous polymorphisms that could, by acting together, enhance overall phenotypic effects. This study highlights the complexity of dissecting CID traits and provides insights for designing second-generation association studies based on candidate gene approaches in forest trees.

Association Mapping of Quantitative Disease Resistance in a Natural Population of Loblolly Pine (Pinus taeda L.)

Genetic resistance to disease incited by necrotrophic pathogens is not well understood in plants. Whereas resistance is often quantitative, there is limited information on the genes that underpin quantitative variation in disease resistance. We used a population genomic approach to identify genes in loblolly pine (Pinus taeda) that are associated with resistance to pitch canker, a disease incited by the necrotrophic pathogen Fusarium circinatum. A set of 498 largely unrelated, clonally propagated genotypes were inoculated with F. circinatum microconidia and lesion length, a measure of disease resistance, data were collected 4, 8, and 12 weeks after inoculation. Best linear unbiased prediction was used to adjust for imbalance in number of observations and to identify highly susceptible and highly resistant genotypes (“tails”). The tails were reinoculated to validate the results of the full population screen. Significant associations were detected in 10 single nucleotide polymorphisms (SNPs) (out of 3938 tested). As hypothesized for genes involved in quantitative resistance, the 10 SNPs had small effects and proposed roles in basal resistance, direct defense, and signal transduction. We also discovered associated genes with unknown function, which would have remained undetected in a candidate gene approach constrained by annotation for disease resistance or stress response.

Unraveling additive from nonadditive effects using genomic relationship matrices.

The application of quantitative genetics in plant and animal breeding has largely focused on additive models, which may also capture dominance and epistatic effects. Partitioning genetic variance into its additive and nonadditive components using pedigree-based models (P-genomic best linear unbiased predictor) (P-BLUP) is difficult with most commonly available family structures. However, the availability of dense panels of molecular markers makes possible the use of additive- and dominance-realized genomic relationships for the estimation of variance components and the prediction of genetic values (G-BLUP). We evaluated height data from a multifamily population of the tree species Pinus taeda with a systematic series of models accounting for additive, dominance, and first-order epistatic interactions (additive by additive, dominance by dominance, and additive by dominance), using either pedigree- or marker-based information. We show that, compared with the pedigree, use of realized genomic relationships in marker-based models yields a substantially more precise separation of additive and nonadditive components of genetic variance. We conclude that the marker-based relationship matrices in a model including additive and nonadditive effects performed better, improving breeding value prediction. Moreover, our results suggest that, for tree height in this population, the additive and nonadditive components of genetic variance are similar in magnitude. This novel result improves our current understanding of the genetic control and architecture of a quantitative trait and should be considered when developing breeding strategies.

Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome

The metabolome of a plant comprises all small molecule metabolites, which are produced during cellular processes. The genetic basis for metabolites in nonmodel plants is unknown, despite frequently observed correlations between metabolite concentrations and stress responses. A quantitative genetic analysis of metabolites in a nonmodel plant species is thus warranted. Here, we use standard association genetic methods to correlate 3563 single nucleotide polymorphisms (SNPs) to concentrations of 292 metabolites measured in a single loblolly pine (Pinus taeda) association population. A total of 28 single locus associations were detected, representing 24 and 20 unique SNPs and metabolites, respectively. Multilocus Bayesian mixed linear models identified 2998 additional associations for a total of 1617 unique SNPs associated to 255 metabolites. These SNPs explained sizeable fractions of metabolite heritabilities when considered jointly (56.6% on average) and had lower minor allele frequencies and magnitudes of population structure as compared with random SNPs. Modest sets of SNPs (n = 1-23) explained sizeable portions of genetic effects for many metabolites, thus highlighting the importance of multi-SNP models to association mapping, and exhibited patterns of polymorphism consistent with being linked to targets of natural selection. The implications for association mapping in forest trees are discussed.

Genetic dissection of fusiform rust and pitch canker disease traits in loblolly pine

Loblolly pine (Pinus taeda L.) exhibits genetic resistance to fusiform rust disease (incited by the biotrophic fungus, Cronartium quercuum f. sp. fusiforme) and pitch canker disease (incited by the necrotrophic fungus, Fusarium circinatum). In this study, a total of 14,015 loblolly pine cuttings from 1,065 clones were screened in controlled greenhouse conditions to identify phenotypes of clones, families, and parents that guide a genetic dissection of disease traits associated with pitch canker and fusiform rust. A total of 23,373 phenotypic data points were collected for lesion length (pitch canker) and gall score, gall length, and gall width (fusiform rust). We verified heritable fusiform rust and pitch canker traits and calculated parental, clonal, and full-sib family rankings for both diseases. Genetic correlations revealed that traits associated with fusiform rust are genetically distinct from one another, and that the genetic mechanisms underlying pitch canker and fusiform rust resistance are independent. The disease phenotyping described here is a critical step towards identifying specific loci and alleles associated with fusiform rust and pitch canker resistance.

Genetic analysis of early field growth of loblolly pine clones and seedlings from the same full-sib families

Field trials established with clones and seedlings from the same families provide an opportunity for comparing full-sib family performance across propagule types. More than 1200 different clones together with over 14 000 zygotic seedlings from the same 61 full-sib families of loblolly pine (Pinus taeda L.) were tested on multiple sites across Florida and Georgia. The genetic variance associated with several early growth traits partitioned differently depending on propagule type. Most of the genetic variance associated with growth in the clonal population was additive, while the estimate of dominance in the seedling population was greater than estimates of dominance in the clonal population, based on single-site analyses. Apparently, a lack of randomization of the seedlings prior to field establishment caused full-sib families to appear more different, inflating estimates of dominance genetic variance. Parental and full-sib family ranks were stable regardless of propagule type as indicated by type B geneti...

Genetic gain from selection for rooting ability and early growth in vegetatively propagated clones of loblolly pine

A successful clonal forestry program for loblolly pine based on rooted cutting technology needs to consider selection for both rooting ability and subsequent field growth. Rooting ability and second-year height were assessed in more than 2,000 clones from 70 full-sib families of loblolly pine. The bivariate analysis of rooting ability from five rooting trials and field growth from six field trials allowed for estimation of the genetic covariance between rooting ability and second-year height for parental effects, full-sib family effects, and the total genetic value of clones within full-sib family. There was a positive genetic relationship between rooting ability and second-year height at all three genetic levels. The genetic correlation at the parental level between rooting ability and second-year height

Association genetics of oleoresin flow in loblolly pine: discovering genes and predicting phenotype for improved resistance to bark beetles and bioenergy potential

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