Dudley Huber - Academia.edu (original) (raw)

Papers by Dudley Huber

Research paper thumbnail of Performance of the loblolly pine fusiform rust disease resistance gene (Fr1) in a slashXloblolly pine hybrid family

Tree Genetics & Genomes, Jan 5, 2011

Unexpectedly high levels of field susceptibility to the fusiform rust fungus observed for slashXl... more Unexpectedly high levels of field susceptibility to the fusiform rust fungus observed for slashXloblolly hybrid families in the Cooperative Forest Genetics Research Program Pine Hybrid Trials led to several hypotheses concerning causation of the observed susceptibility. One of these hypotheses involved the failure of major resistance genes to appropriately function in this particular hybrid combination. This current work, involving the loblolly pine resistance gene Fr1 and a fusiform rust inoculum avirulent against Fr1 resistance in a greenhouse trial, delineates the investigation of major gene resistance for a particular slashXloblolly hybrid family. In this trial, the Fr1 resistance allele, derived from the heterozygous (Fr1/fr1) loblolly male parent and transferred to hybrid offspring that should have been segregating 1:1 for resistance, was fully penetrant. Likewise, in the pure-species loblolly control, the Fr1 resistance allele was again fully penetrant, and the performances of our hybrid family and the loblolly control family (both of which segregated for Fr1 resistance) were comparable. These results by inductive reasoning refute the hypothesis that major resistance genes are not appropriately functional in a slashXloblolly hybrid background.

Research paper thumbnail of Accounting for Spatial Variability in Breeding Trials: A Simulation Study

Research paper thumbnail of POSTER PRESENTATION Open Access

Effect of BLUP prediction on genomic selection: practical considerations to achieve greater accur... more Effect of BLUP prediction on genomic selection: practical considerations to achieve greater accuracy in genomic selection

Research paper thumbnail of Cuttings from a Partial

effects of rooting loblolly pine stem

Research paper thumbnail of Age–age and trait–trait correlations for Eucalyptus grandis Hill ex Maiden and their implications for optimal selection age and design of clonal trials

Theoretical and Applied Genetics, 2003

Previous results from seven locations of Eucalyptus grandis clonal trials in Colombia supported t... more Previous results from seven locations of Eucalyptus grandis clonal trials in Colombia supported the a priori contention of sub-dividing them into three different environmental zones for testing and deployment. Within these zones, the determination of age-age genetic correlations for both height and mean annual increment (MAI) showed that strong age-age correlations are present for a rotation age of 6 years starting at 3 years age and, thereafter, suggesting this age as appropriate for selection. This biological selection age coincides with an "economical" age for selection based on discounted selection efficiency in perpetuity, considering a range of interest rates between 10% and 20%. High genetic correlations between wood density at 3 years and 6 years as well as the lack of genetic correlation between this trait and growth traits, also favors selection at age 3 and facilitates breeding strategies that consider the utilization of both traits for improvement. A simulation of optimal clonal test designs indicated that by using six locations and six blocks per location in a single-tree plot design, between 80% and 90% of the maximum selection efficiency could be obtained. This type of design allows testing of a large number of genotypes across a reasonable number of locations in a cost-effective manner.

Research paper thumbnail of Heritabilities of Foliar Powdery Mildew (Podosphera aphanis) Resistance in the University of Florida Strawberry Germplasm

The Florida strawberry industry supplies the eastern United States and Canada with strawberries f... more The Florida strawberry industry supplies the eastern United States and Canada with strawberries from November through March. An annual, highly intensified growing system gives rise to cultural challenges including fungal disease control. One such ubiquitous, wind-spread disease is powdery mildew (PM) caused by the obligate parasite Podosphera aphanis. To control PM, multiple applications of fungicides are applied each season. Planting resistant cultivars would reduce the need for chemical controls; however there are no commercial cultivars with PM resistance for Florida. To date, there have been no published reports on powdery mildew resistance in the Florida strawberry breeding population. In 2010, clonally replicated individuals from seven bi-parental crosses arising from eleven parents were included in a field trial designed as a modified Latin square with four replications. Seedlings were evaluated visually for percentage of coverage of PM mycelium over the leaf surface on a sca...

Research paper thumbnail of Relative contributions of crown and phenological traits to growth of a pseudo-backcross pine family ((slash × loblolly) × slash) and its pure species progenitors

Tree Genetics & Genomes, 2012

One pseudo-backcross [(slash×loblolly)×slash] (BC1) and open-pollinated families of the pure spec... more One pseudo-backcross [(slash×loblolly)×slash] (BC1) and open-pollinated families of the pure species progenitors were established in a single test in North Central Florida. Multivariate analysis was used to estimate the intratrait correlation among the taxa, and path analyses were used to determine the relative contributions of crown architectural and phenological traits to first-year height growth. The multivariate analysis indicated that BC1, slash, and loblolly pine have different relationships among the traits studied, suggesting that a separate path analysis was required for each taxon. Path analysis coefficients of determination of the final models were 0.69, 0.73, and 0.65 for the pseudo-backcross, loblolly, and slash pine families, respectively. The ranking of traits by relative magnitude of effect on total growth was, for the pseudo-backcross crown projected area (CPA), fascicle length (FL), number of nodes (NN), number of branches (NB), number of needles per fascicle (NF), and fascicle diameter. For loblolly, this was CPA, NB, FL, NN, NF, initiation, and specific leaf area. For slash, this was CPA, NN, FL, NF, and NB. The study indicated that all crown traits considered in the path analysis had moderate effects on first-year height growth, with the exceptions of the consistently large effect of CPA and the minimal effect of the phenological traits.

Research paper thumbnail of Variance component estimation techniques compared for two mating designs with forest genetic architecture through computer simulation

Theoretical and Applied Genetics, 1994

Computer simulation was used to compare minimum variance quadratic estimation (MIVQUE), minimum n... more Computer simulation was used to compare minimum variance quadratic estimation (MIVQUE), minimum norm quadratic unbiased estimation (MIN-QUE), restricted maximum likelihood (REML), maximum likelihood (ML), and Henderson's Method 3 (HM3) on the basis of variance among estimates, mean square error (MSE), bias and probability of nearness for estimation of both individual variance components and three ratios of variance components. The investigation also compared three procedures for dealing with negative estimates and included the use of both individual observations and plot means as the experimental unit of the analysis. The structure of data simulated (field design, mating designs, genetic architecture and imbalance) represented typical analysis problems in quantitative forest genetics. Results of comparing the estimation techniques demonstrated that: estimates of probability of nearness did not discriminate among techniques; bias was discriminatory among procedures for dealing with negative estimates but not among estimation techniques (except ML); sampling variance among estimates was discriminatory among procedures for dealing with negative estimates, estimation techniques and unit of observation; and MSE provided no additional information to variance of the estimates. HM3 and REML were the closest competitors under these criteria; however, REML demonstrated greater robustness to imbalance. Of the three negative estimate This is Journal Series NO. R-03768 of the Institute of Food and Agricultural Sciences Communicated by P. M. A. Tigerstedt

Research paper thumbnail of Association genetics in Pinus taeda L. II. Carbon isotope discrimination

Heredity, 2008

Dissection of complex traits that influence fitness is not only a central topic in evolutionary r... more 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 timeintegrated trait measure of stomatal conductance. A familybased 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.

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

Genetics, 2010

Genetic resistance to disease incited by necrotrophic pathogens is not well understood in plants.... more 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...

Research paper thumbnail of Genotype×environment interactions in selected loblolly and slash pine plantations in the Southeastern United States

Forest Ecology and Management, 2007

Few studies have quantified the combined effects of silvicultural treatments and genetic improvem... more Few studies have quantified the combined effects of silvicultural treatments and genetic improvement on unit area production of full-sib family blocks of loblolly (Pinus taeda L.) and slash pine (P. elliottii Engelm. var. elliotttii). Efficient operational deployment of genetic materials requires an understanding of possible site and silvicultural treatment interactions to maximize yield potential. We examined genotype (family) by environmental interactions (G  E) through age 5 years using a factorial experiment consisting of silvicultural treatment intensity (operational versus intensive), planting density (1334 versus 2990 trees ha À1) and families (seven elite full-sib loblolly and six elite full-sib slash pine families). In January of 2000, randomized complete block, split-plot experiments were installed at two locations for each species in southeast Georgia and northeast Florida. Five years after planting, both loblolly and slash pine demonstrated significant interactions among several factors: genotype  location (p < 0.028 and p < 0.016, respectively), genotype  silvicultural treatment intensity (p < 0.055 and p < 0.059), and silvicultural treatment intensity  density (p < 0.002 and p < 0.001) for basal area (BA) and standing stem volume (VOL). Genotype  silvicultural treatment interactions were positive, with the best overall performing families responding the greatest to intensive treatment. There were changes in slash pine family rankings between locations, which were partly explained by reductions in growth associated with a combination of fusiform rust infection [Cronartium quercum (Berk.) Miyabe ex Shirai f. sp. fusiforme] and wind damage from the 2004 hurricane season. No three-way interactions, which included family, were evident and all genetic sources were stable across the contrasting planting densities. At age 5, loblolly pine outperformed slash pine (p < 0.0001), especially under the intensive silvicultural intensity. While loblolly performance was similar whether deployed in mixtures or pure family blocks, slash pine tended to be more productive in intimate mixtures than when grown in pure family blocks (p = 0.0754 for aboveground biomass).

Research paper thumbnail of Species differences in early growth and rust incidence of loblolly and slash pine

Forest Ecology and Management, 2000

Eleven ®eld tests with two silvicultural treatments (intensive and less intensive) with three tax... more Eleven ®eld tests with two silvicultural treatments (intensive and less intensive) with three taxa (improved and unimproved Pinus elliottii and improved P. taeda) were established by the Cooperative Forest Genetics Research Program in the lower coastal plains of the southeast USA. Results from assessment at 3-years-old indicate that P. taeda is consistently taller with less rust incidence than P. elliottii in both intensive and less intensive cultures. The early superiority of P. taeda was only partially due to its lower rust incidence. The more intensive silvicultural treatment increased third-year height growth and also height differences among taxa on all sites. A slight increase of rust incidence was produced by increasing intensive management (29.2± 33.6%). The increase in cultural management did not alter the ratios of infection percentages of any two taxa. The ratios of any two taxa, one to another, were essentially constant across all sites and in both silvicultural treatments. Signi®cant genetic gain from breeding for rust resistance was detected at this age for P. elliottii. When 50% of unimproved P. elliottii trees were infected, 36.8% of improved P. elliottii trees were infected. For height growth, improved material was 4 and 8% taller than unimproved P. elliottii in less intensive and intensive treatment, respectively.

Research paper thumbnail of Genetic parameters and gains for growth and wood properties in Florida source loblolly pine in the southeastern United States

Canadian Journal of Forest Research, 2002

One hundred and thirteen open-pollinated families from Florida source loblolly pine (Pinus taeda ... more One hundred and thirteen open-pollinated families from Florida source loblolly pine (Pinus taeda L.) were tested in four states in the southeastern United States. Heritabilities and genetic correlations were estimated for volume, specific gravity, and latewood percentage at three different growth stages: juvenile (ages 0–10 years), mature (11–17 years), and total (0–17 years). Heritabilities of growth traits (0.09–0.11) were consistently lower than for wood property traits (0.16–0.33). Growth traits for Florida loblolly exhibited high genotype × environment interaction (rB = 0.44), whereas wood properties did not (rB = 0.90). The higher heritabilities and genetic stability across environments make wood properties amenable to genetic manipulation through breeding programs. In contrast, the high genotype × environment interaction of growth traits for Florida loblolly pine requires more research to understand the possible implication of these effects on breeding programs. Trait–trait a...

Research paper thumbnail of Accounting for Spatial Variability in Breeding Trials: A Simulation Study

Research paper thumbnail of Dynamics of artificial regeneration in gaps within a longleaf pine flatwoods ecosystem

Forest Ecology and Management, 2003

The selection silvicultural system has gained popularity as a means for developing and maintainin... more The selection silvicultural system has gained popularity as a means for developing and maintaining uneven-aged stand structure in a variety of forest types. Only limited information exists, however, regarding regeneration dynamics and growth of longleaf pine (Pinus palustris Mill.) managed under the group selection silvicultural system in the southeastern USA. A replicated arti®cial gap study, established in a 65-year-old, second-growth stand in northwest Florida, was used to examine the interactions between site resource availability (light, nutrition, water) and canopy gap position on survival and growth of containerized longleaf pine seedlings over two growing seasons. A gradient in site resource availability was created using fertilizer and hand weeding treatments. Levels of light transmittance (averaged over the growing season) within the gaps varied by location and ranged from 72% near the uncut edge to 96% in the gap center. Seedlings growing in the gap center had signi®cantly lower survival rates (e.g., 1999, center 23%, edge 51%), but larger diameter increments (e.g., 2000, center 3:6 mm, edge 1:4 mm) than those found in lower light environments along the gap edge. Soil moisture content had little apparent impact on these differences in survival and growth, as surface (0±15 cm) moisture contents did not vary signi®cantly among gap positions in either growing season. Although seedling survival was signi®cantly reduced by the fertilizer and hand weeding (control 41%, treated 31%), diameter increment was 44% greater than the untreated control. Results of this study suggest that a group selection silvicultural system that provides suf®cient light and relief from competition (for nutrients) for seedlings may be a suitable silvicultural method for effectively regenerating longleaf pine forests.

Research paper thumbnail of Effects of management intensity, genetics and planting density on wood stiffness in a plantation of juvenile loblolly pine in the southeastern USA

Forest Ecology and Management, 2007

In a 6-year-old plantation of Pinus taeda in Northeast Florida, the affects on juvenile corewood ... more In a 6-year-old plantation of Pinus taeda in Northeast Florida, the affects on juvenile corewood stiffness of genotype, planting density and silviculture as well as their interactions, and some potential mechanisms for these effects were investigated. The stress wave method was used to determine the dynamic modulus of elasticity (V 2 ) of the juvenile corewood in 4091 standing trees of seven full-sib families grown at two planting densities (1334 trees ha À1 versus 2990 trees ha À1 ) with two levels of silvicultural intensity (operational versus intensive). Planting density significantly influenced V 2 ( p < 0.0001) across all families and silvicultural intensities. At 2990 trees ha À1 , V 2 averaged 7.11 and 5.44 km 2 s À2 for 1334 trees ha À1 . Family and silvicultural intensity interacted significantly for V 2 ( p = 0.0003) with values ranging from 5.03 to 7.48 km 2 s À2 . Under intensive silviculture, one family (L1) exhibited a large decrease in V 2 . In contrast, another family (L4) with a high overall V 2 rank was not very sensitive to silvicultural treatment intensity. This lack of response under intensive silviculture occurred despite the fact that family L4 demonstrated the greatest increase in growth. Across all treatments, the ratio of height to diameter at breast height (HT:DBH) was strongly related to V 2 with more slender trees being the stiffest. After adjusting for this ratio, only the main effects of initial planting density and genotype were significant. Thus, HT:DBH correlated with variation in V 2 caused by silvicultural intensity. In a subset of trees within three selected families, variation in latewood percentage (LWP) did not correlate with variation in V 2 as predicted. Analysis of the treatments on LWP, showed a significant three-way interaction between genotype, planting density, and silvicultural intensity. Surprisingly, the LWP of a single family (L4) responded differently to silvicultural treatment under contrasting planting densities. Findings from this study indicate that considerable opportunity exists to improve corewood stiffness in juvenile loblolly pine plantations through the deployment of selected genotypes in combination with appropriate initial planting density and silvicultural intensity. #

Research paper thumbnail of Comparison of Experimental Designs for Clonal Forestry Using Simulated Data

Forest Science

Various alternatives for the design of clonal field trials in forestry were studied using simulat... more Various alternatives for the design of clonal field trials in forestry were studied using simulated data to identify “optimal” or “near-optimal” scenarios for the estimation of genetic parameters. The simulated field site consisted of a rectangular grid on which 256 clones with 8 ramets each were installed. Estimates of genetic parameters were compared for (1) single-tree and four-tree row plots; (2) several experimental designs (completely randomized, randomized complete block, incomplete blocks of various sizes, and row–column); (3) no mortality versus 257% mortality; and (4) different patterns of environmental variability (only patches, only gradients, and both patches and gradients). Use of single-tree plots, on average, increased the correlations between true and predicted clonal values by 57% over four-tree row plots and increased genetic gain from selection. Starting with a parametric broad-sense heritability (H B 2) of 0.25 for a completely randomized design, the experimenta...

Research paper thumbnail of Realized genetic gains of rust resistant selections of slash pine (Pinus elliottii var. elliottii) planted in high rust hazard sites

Silvae Genetica

Realized gains from selection for resistance to the fungal disease fusiform rust caused by Cronar... more Realized gains from selection for resistance to the fungal disease fusiform rust caused by Cronartium quercuum f. sp. fusiforme were estimated using data from five field trials planted on large rectangular plots in high rust-hazard sites. These five realized gain trials, planted as a Best Management Practices study (BMP), compared resistant and susceptible mixtures of families from the first-generation breeding population of slash pine (Pinus elliottii var. elliottii Engelm.) in southeastern North America. Analyses of variance (Proc Mixed using REML in SAS), conducted to test the significance of realized gains and interactions contrasting resistant with susceptible seedlots, detected important and highly significant realized gains in both rust resistance and mid-rotation yield. Significant gains were obtained for rust resistance at age 5 and stand yield at age 16 with high stability across sites and across silvicultural treatments, indicating that gains in rust resistance and the as...

Research paper thumbnail of Provenance and family variability in slash pine (Pinus elliottii var. elliottii Engelm.) grown in southern Brazil and northeastern Argentina

ABSTRACT A total of 172 seed orchard open-pollinated families of slash pine (Pinus elliottii var.... more ABSTRACT A total of 172 seed orchard open-pollinated families of slash pine (Pinus elliottii var. elliottii Engelm.), generallysuperior for growth in the southeastern United States, wereevaluated in southern Brazil and northeastern Argentina. Mostfamilies were from selections originally made in four majorphysiographic regions within the species&#39; natural distribution:Atlantic Coastal Flatwoods, East-Central Florida Flatwoods, GulfCoastal Flatwoods, and Southern Coastal Plain (withoutflatwoods). Ninety-one families were established in 1982 inthree tests in the Brazilian states of Santa Catarina and Parana. In 1986, 119 families, including 35 common to the Braziliantests, were planted in four tests in Corrientes and Misionesstates in Argentina. Variation among provenances for individualvolume growth was significant for both countries withEast-Central Florida Flatwoods consistently having the highestmean age-eight year volume and Southern Coastal Plainconsistently the lowest. Heritabilities were 0.20 in Argentinaand 0.44 in Brazil with within country type B geneticcorrelations of 0.66 and 1.00 for age-eight individual volume,respectively. The between country type B genetic correlation was0.63. Type B genetic correlations between United States breedingvalues for age-fifteen volume and Argentinian and Brazilianbreeding values for age-eight volume were 0.10 and 0.15,respectively. Families were generally superior to local checksin both South American countries.

Research paper thumbnail of Unraveling additive from nonadditive effects using genomic relationship matrices

Genetics, 2014

The application of quantitative genetics in plant and animal breeding has largely focused on addi... more 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 ...

Research paper thumbnail of Performance of the loblolly pine fusiform rust disease resistance gene (Fr1) in a slashXloblolly pine hybrid family

Tree Genetics & Genomes, Jan 5, 2011

Unexpectedly high levels of field susceptibility to the fusiform rust fungus observed for slashXl... more Unexpectedly high levels of field susceptibility to the fusiform rust fungus observed for slashXloblolly hybrid families in the Cooperative Forest Genetics Research Program Pine Hybrid Trials led to several hypotheses concerning causation of the observed susceptibility. One of these hypotheses involved the failure of major resistance genes to appropriately function in this particular hybrid combination. This current work, involving the loblolly pine resistance gene Fr1 and a fusiform rust inoculum avirulent against Fr1 resistance in a greenhouse trial, delineates the investigation of major gene resistance for a particular slashXloblolly hybrid family. In this trial, the Fr1 resistance allele, derived from the heterozygous (Fr1/fr1) loblolly male parent and transferred to hybrid offspring that should have been segregating 1:1 for resistance, was fully penetrant. Likewise, in the pure-species loblolly control, the Fr1 resistance allele was again fully penetrant, and the performances of our hybrid family and the loblolly control family (both of which segregated for Fr1 resistance) were comparable. These results by inductive reasoning refute the hypothesis that major resistance genes are not appropriately functional in a slashXloblolly hybrid background.

Research paper thumbnail of Accounting for Spatial Variability in Breeding Trials: A Simulation Study

Research paper thumbnail of POSTER PRESENTATION Open Access

Effect of BLUP prediction on genomic selection: practical considerations to achieve greater accur... more Effect of BLUP prediction on genomic selection: practical considerations to achieve greater accuracy in genomic selection

Research paper thumbnail of Cuttings from a Partial

effects of rooting loblolly pine stem

Research paper thumbnail of Age–age and trait–trait correlations for Eucalyptus grandis Hill ex Maiden and their implications for optimal selection age and design of clonal trials

Theoretical and Applied Genetics, 2003

Previous results from seven locations of Eucalyptus grandis clonal trials in Colombia supported t... more Previous results from seven locations of Eucalyptus grandis clonal trials in Colombia supported the a priori contention of sub-dividing them into three different environmental zones for testing and deployment. Within these zones, the determination of age-age genetic correlations for both height and mean annual increment (MAI) showed that strong age-age correlations are present for a rotation age of 6 years starting at 3 years age and, thereafter, suggesting this age as appropriate for selection. This biological selection age coincides with an &quot;economical&quot; age for selection based on discounted selection efficiency in perpetuity, considering a range of interest rates between 10% and 20%. High genetic correlations between wood density at 3 years and 6 years as well as the lack of genetic correlation between this trait and growth traits, also favors selection at age 3 and facilitates breeding strategies that consider the utilization of both traits for improvement. A simulation of optimal clonal test designs indicated that by using six locations and six blocks per location in a single-tree plot design, between 80% and 90% of the maximum selection efficiency could be obtained. This type of design allows testing of a large number of genotypes across a reasonable number of locations in a cost-effective manner.

Research paper thumbnail of Heritabilities of Foliar Powdery Mildew (Podosphera aphanis) Resistance in the University of Florida Strawberry Germplasm

The Florida strawberry industry supplies the eastern United States and Canada with strawberries f... more The Florida strawberry industry supplies the eastern United States and Canada with strawberries from November through March. An annual, highly intensified growing system gives rise to cultural challenges including fungal disease control. One such ubiquitous, wind-spread disease is powdery mildew (PM) caused by the obligate parasite Podosphera aphanis. To control PM, multiple applications of fungicides are applied each season. Planting resistant cultivars would reduce the need for chemical controls; however there are no commercial cultivars with PM resistance for Florida. To date, there have been no published reports on powdery mildew resistance in the Florida strawberry breeding population. In 2010, clonally replicated individuals from seven bi-parental crosses arising from eleven parents were included in a field trial designed as a modified Latin square with four replications. Seedlings were evaluated visually for percentage of coverage of PM mycelium over the leaf surface on a sca...

Research paper thumbnail of Relative contributions of crown and phenological traits to growth of a pseudo-backcross pine family ((slash × loblolly) × slash) and its pure species progenitors

Tree Genetics & Genomes, 2012

One pseudo-backcross [(slash×loblolly)×slash] (BC1) and open-pollinated families of the pure spec... more One pseudo-backcross [(slash×loblolly)×slash] (BC1) and open-pollinated families of the pure species progenitors were established in a single test in North Central Florida. Multivariate analysis was used to estimate the intratrait correlation among the taxa, and path analyses were used to determine the relative contributions of crown architectural and phenological traits to first-year height growth. The multivariate analysis indicated that BC1, slash, and loblolly pine have different relationships among the traits studied, suggesting that a separate path analysis was required for each taxon. Path analysis coefficients of determination of the final models were 0.69, 0.73, and 0.65 for the pseudo-backcross, loblolly, and slash pine families, respectively. The ranking of traits by relative magnitude of effect on total growth was, for the pseudo-backcross crown projected area (CPA), fascicle length (FL), number of nodes (NN), number of branches (NB), number of needles per fascicle (NF), and fascicle diameter. For loblolly, this was CPA, NB, FL, NN, NF, initiation, and specific leaf area. For slash, this was CPA, NN, FL, NF, and NB. The study indicated that all crown traits considered in the path analysis had moderate effects on first-year height growth, with the exceptions of the consistently large effect of CPA and the minimal effect of the phenological traits.

Research paper thumbnail of Variance component estimation techniques compared for two mating designs with forest genetic architecture through computer simulation

Theoretical and Applied Genetics, 1994

Computer simulation was used to compare minimum variance quadratic estimation (MIVQUE), minimum n... more Computer simulation was used to compare minimum variance quadratic estimation (MIVQUE), minimum norm quadratic unbiased estimation (MIN-QUE), restricted maximum likelihood (REML), maximum likelihood (ML), and Henderson's Method 3 (HM3) on the basis of variance among estimates, mean square error (MSE), bias and probability of nearness for estimation of both individual variance components and three ratios of variance components. The investigation also compared three procedures for dealing with negative estimates and included the use of both individual observations and plot means as the experimental unit of the analysis. The structure of data simulated (field design, mating designs, genetic architecture and imbalance) represented typical analysis problems in quantitative forest genetics. Results of comparing the estimation techniques demonstrated that: estimates of probability of nearness did not discriminate among techniques; bias was discriminatory among procedures for dealing with negative estimates but not among estimation techniques (except ML); sampling variance among estimates was discriminatory among procedures for dealing with negative estimates, estimation techniques and unit of observation; and MSE provided no additional information to variance of the estimates. HM3 and REML were the closest competitors under these criteria; however, REML demonstrated greater robustness to imbalance. Of the three negative estimate This is Journal Series NO. R-03768 of the Institute of Food and Agricultural Sciences Communicated by P. M. A. Tigerstedt

Research paper thumbnail of Association genetics in Pinus taeda L. II. Carbon isotope discrimination

Heredity, 2008

Dissection of complex traits that influence fitness is not only a central topic in evolutionary r... more 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 timeintegrated trait measure of stomatal conductance. A familybased 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.

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

Genetics, 2010

Genetic resistance to disease incited by necrotrophic pathogens is not well understood in plants.... more 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...

Research paper thumbnail of Genotype×environment interactions in selected loblolly and slash pine plantations in the Southeastern United States

Forest Ecology and Management, 2007

Few studies have quantified the combined effects of silvicultural treatments and genetic improvem... more Few studies have quantified the combined effects of silvicultural treatments and genetic improvement on unit area production of full-sib family blocks of loblolly (Pinus taeda L.) and slash pine (P. elliottii Engelm. var. elliotttii). Efficient operational deployment of genetic materials requires an understanding of possible site and silvicultural treatment interactions to maximize yield potential. We examined genotype (family) by environmental interactions (G  E) through age 5 years using a factorial experiment consisting of silvicultural treatment intensity (operational versus intensive), planting density (1334 versus 2990 trees ha À1) and families (seven elite full-sib loblolly and six elite full-sib slash pine families). In January of 2000, randomized complete block, split-plot experiments were installed at two locations for each species in southeast Georgia and northeast Florida. Five years after planting, both loblolly and slash pine demonstrated significant interactions among several factors: genotype  location (p < 0.028 and p < 0.016, respectively), genotype  silvicultural treatment intensity (p < 0.055 and p < 0.059), and silvicultural treatment intensity  density (p < 0.002 and p < 0.001) for basal area (BA) and standing stem volume (VOL). Genotype  silvicultural treatment interactions were positive, with the best overall performing families responding the greatest to intensive treatment. There were changes in slash pine family rankings between locations, which were partly explained by reductions in growth associated with a combination of fusiform rust infection [Cronartium quercum (Berk.) Miyabe ex Shirai f. sp. fusiforme] and wind damage from the 2004 hurricane season. No three-way interactions, which included family, were evident and all genetic sources were stable across the contrasting planting densities. At age 5, loblolly pine outperformed slash pine (p < 0.0001), especially under the intensive silvicultural intensity. While loblolly performance was similar whether deployed in mixtures or pure family blocks, slash pine tended to be more productive in intimate mixtures than when grown in pure family blocks (p = 0.0754 for aboveground biomass).

Research paper thumbnail of Species differences in early growth and rust incidence of loblolly and slash pine

Forest Ecology and Management, 2000

Eleven ®eld tests with two silvicultural treatments (intensive and less intensive) with three tax... more Eleven ®eld tests with two silvicultural treatments (intensive and less intensive) with three taxa (improved and unimproved Pinus elliottii and improved P. taeda) were established by the Cooperative Forest Genetics Research Program in the lower coastal plains of the southeast USA. Results from assessment at 3-years-old indicate that P. taeda is consistently taller with less rust incidence than P. elliottii in both intensive and less intensive cultures. The early superiority of P. taeda was only partially due to its lower rust incidence. The more intensive silvicultural treatment increased third-year height growth and also height differences among taxa on all sites. A slight increase of rust incidence was produced by increasing intensive management (29.2± 33.6%). The increase in cultural management did not alter the ratios of infection percentages of any two taxa. The ratios of any two taxa, one to another, were essentially constant across all sites and in both silvicultural treatments. Signi®cant genetic gain from breeding for rust resistance was detected at this age for P. elliottii. When 50% of unimproved P. elliottii trees were infected, 36.8% of improved P. elliottii trees were infected. For height growth, improved material was 4 and 8% taller than unimproved P. elliottii in less intensive and intensive treatment, respectively.

Research paper thumbnail of Genetic parameters and gains for growth and wood properties in Florida source loblolly pine in the southeastern United States

Canadian Journal of Forest Research, 2002

One hundred and thirteen open-pollinated families from Florida source loblolly pine (Pinus taeda ... more One hundred and thirteen open-pollinated families from Florida source loblolly pine (Pinus taeda L.) were tested in four states in the southeastern United States. Heritabilities and genetic correlations were estimated for volume, specific gravity, and latewood percentage at three different growth stages: juvenile (ages 0–10 years), mature (11–17 years), and total (0–17 years). Heritabilities of growth traits (0.09–0.11) were consistently lower than for wood property traits (0.16–0.33). Growth traits for Florida loblolly exhibited high genotype × environment interaction (rB = 0.44), whereas wood properties did not (rB = 0.90). The higher heritabilities and genetic stability across environments make wood properties amenable to genetic manipulation through breeding programs. In contrast, the high genotype × environment interaction of growth traits for Florida loblolly pine requires more research to understand the possible implication of these effects on breeding programs. Trait–trait a...

Research paper thumbnail of Accounting for Spatial Variability in Breeding Trials: A Simulation Study

Research paper thumbnail of Dynamics of artificial regeneration in gaps within a longleaf pine flatwoods ecosystem

Forest Ecology and Management, 2003

The selection silvicultural system has gained popularity as a means for developing and maintainin... more The selection silvicultural system has gained popularity as a means for developing and maintaining uneven-aged stand structure in a variety of forest types. Only limited information exists, however, regarding regeneration dynamics and growth of longleaf pine (Pinus palustris Mill.) managed under the group selection silvicultural system in the southeastern USA. A replicated arti®cial gap study, established in a 65-year-old, second-growth stand in northwest Florida, was used to examine the interactions between site resource availability (light, nutrition, water) and canopy gap position on survival and growth of containerized longleaf pine seedlings over two growing seasons. A gradient in site resource availability was created using fertilizer and hand weeding treatments. Levels of light transmittance (averaged over the growing season) within the gaps varied by location and ranged from 72% near the uncut edge to 96% in the gap center. Seedlings growing in the gap center had signi®cantly lower survival rates (e.g., 1999, center 23%, edge 51%), but larger diameter increments (e.g., 2000, center 3:6 mm, edge 1:4 mm) than those found in lower light environments along the gap edge. Soil moisture content had little apparent impact on these differences in survival and growth, as surface (0±15 cm) moisture contents did not vary signi®cantly among gap positions in either growing season. Although seedling survival was signi®cantly reduced by the fertilizer and hand weeding (control 41%, treated 31%), diameter increment was 44% greater than the untreated control. Results of this study suggest that a group selection silvicultural system that provides suf®cient light and relief from competition (for nutrients) for seedlings may be a suitable silvicultural method for effectively regenerating longleaf pine forests.

Research paper thumbnail of Effects of management intensity, genetics and planting density on wood stiffness in a plantation of juvenile loblolly pine in the southeastern USA

Forest Ecology and Management, 2007

In a 6-year-old plantation of Pinus taeda in Northeast Florida, the affects on juvenile corewood ... more In a 6-year-old plantation of Pinus taeda in Northeast Florida, the affects on juvenile corewood stiffness of genotype, planting density and silviculture as well as their interactions, and some potential mechanisms for these effects were investigated. The stress wave method was used to determine the dynamic modulus of elasticity (V 2 ) of the juvenile corewood in 4091 standing trees of seven full-sib families grown at two planting densities (1334 trees ha À1 versus 2990 trees ha À1 ) with two levels of silvicultural intensity (operational versus intensive). Planting density significantly influenced V 2 ( p < 0.0001) across all families and silvicultural intensities. At 2990 trees ha À1 , V 2 averaged 7.11 and 5.44 km 2 s À2 for 1334 trees ha À1 . Family and silvicultural intensity interacted significantly for V 2 ( p = 0.0003) with values ranging from 5.03 to 7.48 km 2 s À2 . Under intensive silviculture, one family (L1) exhibited a large decrease in V 2 . In contrast, another family (L4) with a high overall V 2 rank was not very sensitive to silvicultural treatment intensity. This lack of response under intensive silviculture occurred despite the fact that family L4 demonstrated the greatest increase in growth. Across all treatments, the ratio of height to diameter at breast height (HT:DBH) was strongly related to V 2 with more slender trees being the stiffest. After adjusting for this ratio, only the main effects of initial planting density and genotype were significant. Thus, HT:DBH correlated with variation in V 2 caused by silvicultural intensity. In a subset of trees within three selected families, variation in latewood percentage (LWP) did not correlate with variation in V 2 as predicted. Analysis of the treatments on LWP, showed a significant three-way interaction between genotype, planting density, and silvicultural intensity. Surprisingly, the LWP of a single family (L4) responded differently to silvicultural treatment under contrasting planting densities. Findings from this study indicate that considerable opportunity exists to improve corewood stiffness in juvenile loblolly pine plantations through the deployment of selected genotypes in combination with appropriate initial planting density and silvicultural intensity. #

Research paper thumbnail of Comparison of Experimental Designs for Clonal Forestry Using Simulated Data

Forest Science

Various alternatives for the design of clonal field trials in forestry were studied using simulat... more Various alternatives for the design of clonal field trials in forestry were studied using simulated data to identify “optimal” or “near-optimal” scenarios for the estimation of genetic parameters. The simulated field site consisted of a rectangular grid on which 256 clones with 8 ramets each were installed. Estimates of genetic parameters were compared for (1) single-tree and four-tree row plots; (2) several experimental designs (completely randomized, randomized complete block, incomplete blocks of various sizes, and row–column); (3) no mortality versus 257% mortality; and (4) different patterns of environmental variability (only patches, only gradients, and both patches and gradients). Use of single-tree plots, on average, increased the correlations between true and predicted clonal values by 57% over four-tree row plots and increased genetic gain from selection. Starting with a parametric broad-sense heritability (H B 2) of 0.25 for a completely randomized design, the experimenta...

Research paper thumbnail of Realized genetic gains of rust resistant selections of slash pine (Pinus elliottii var. elliottii) planted in high rust hazard sites

Silvae Genetica

Realized gains from selection for resistance to the fungal disease fusiform rust caused by Cronar... more Realized gains from selection for resistance to the fungal disease fusiform rust caused by Cronartium quercuum f. sp. fusiforme were estimated using data from five field trials planted on large rectangular plots in high rust-hazard sites. These five realized gain trials, planted as a Best Management Practices study (BMP), compared resistant and susceptible mixtures of families from the first-generation breeding population of slash pine (Pinus elliottii var. elliottii Engelm.) in southeastern North America. Analyses of variance (Proc Mixed using REML in SAS), conducted to test the significance of realized gains and interactions contrasting resistant with susceptible seedlots, detected important and highly significant realized gains in both rust resistance and mid-rotation yield. Significant gains were obtained for rust resistance at age 5 and stand yield at age 16 with high stability across sites and across silvicultural treatments, indicating that gains in rust resistance and the as...

Research paper thumbnail of Provenance and family variability in slash pine (Pinus elliottii var. elliottii Engelm.) grown in southern Brazil and northeastern Argentina

ABSTRACT A total of 172 seed orchard open-pollinated families of slash pine (Pinus elliottii var.... more ABSTRACT A total of 172 seed orchard open-pollinated families of slash pine (Pinus elliottii var. elliottii Engelm.), generallysuperior for growth in the southeastern United States, wereevaluated in southern Brazil and northeastern Argentina. Mostfamilies were from selections originally made in four majorphysiographic regions within the species&#39; natural distribution:Atlantic Coastal Flatwoods, East-Central Florida Flatwoods, GulfCoastal Flatwoods, and Southern Coastal Plain (withoutflatwoods). Ninety-one families were established in 1982 inthree tests in the Brazilian states of Santa Catarina and Parana. In 1986, 119 families, including 35 common to the Braziliantests, were planted in four tests in Corrientes and Misionesstates in Argentina. Variation among provenances for individualvolume growth was significant for both countries withEast-Central Florida Flatwoods consistently having the highestmean age-eight year volume and Southern Coastal Plainconsistently the lowest. Heritabilities were 0.20 in Argentinaand 0.44 in Brazil with within country type B geneticcorrelations of 0.66 and 1.00 for age-eight individual volume,respectively. The between country type B genetic correlation was0.63. Type B genetic correlations between United States breedingvalues for age-fifteen volume and Argentinian and Brazilianbreeding values for age-eight volume were 0.10 and 0.15,respectively. Families were generally superior to local checksin both South American countries.

Research paper thumbnail of Unraveling additive from nonadditive effects using genomic relationship matrices

Genetics, 2014

The application of quantitative genetics in plant and animal breeding has largely focused on addi... more 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 ...