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
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.
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...
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...
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 010 years), mature (1117 years), and total (017 years). Heritabilities of growth traits (0.090.11) were consistently lower than for wood property traits (0.160.33). 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. Traittrait a...
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...
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...
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' 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.
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 ...
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
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.
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...
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...
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 010 years), mature (1117 years), and total (017 years). Heritabilities of growth traits (0.090.11) were consistently lower than for wood property traits (0.160.33). 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. Traittrait a...
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...
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...
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' 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.
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 ...
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Papers by Dudley Huber