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Blaise Ratcliffe - One of the best experts on this subject based on the ideXlab platform.
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A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods
Heredity, 2015Co-Authors: Blaise Ratcliffe, Omnia Gamal El-dien, Jaroslav Klápště, Ilga Porth, Charles Chen, B Jaquish, Yousry A. El-kassabyAbstract:Genomic selection (GS) potentially offers an unparalleled advantage over traditional pedigree-based selection (TS) methods by reducing the time commitment required to carry out a single cycle of tree improvement. This quality is particularly appealing to tree breeders, where lengthy improvement cycles are the norm. We explored the prospect of implementing GS for interior spruce ( Picea engelmannii × glauca ) utilizing a genotyped population of 769 trees belonging to 25 open-pollinated families. A series of repeated tree height measurements through ages 3–40 years permitted the testing of GS methods temporally. The genotyping-by-sequencing (GBS) platform was used for single nucleotide polymorphism (SNP) discovery in conjunction with three unordered imputation methods applied to a data set with 60% missing information. Further, three diverse GS models were evaluated based on predictive accuracy (PA), and their marker effects. Moderate levels of PA (0.31–0.55) were observed and were of sufficient capacity to deliver improved selection response over TS. Additionally, PA varied substantially through time accordingly with spatial competition among trees. As expected, temporal PA was well correlated with age-age genetic correlation ( r =0.99), and decreased substantially with increasing difference in age between the training and validation populations (0.04–0.47). Moreover, our imputation comparisons indicate that k-nearest neighbor and singular value decomposition yielded a greater number of SNPs and gave higher predictive accuracies than imputing with the mean. Furthermore, the ridge regression (rrBLUP) and BayesCπ (BCπ) models both yielded equal, and better PA than the generalized ridge regression heteroscedastic effect model for the traits evaluated.
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A comparison of genomic selection models across time in interior spruce ( Picea engelmannii × glauca ) using unordered SNP imputation methods
Heredity, 2015Co-Authors: Blaise Ratcliffe, Omnia Gamal El-dien, Jaroslav Klápště, Ilga Porth, Charles Chen, B Jaquish, Yousry A. El-kassabyAbstract:A comparison of genomic selection models across time in interior spruce ( Picea engelmannii × glauca ) using unordered SNP imputation methods
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a comparison of genomic selection models across time in interior spruce Picea engelmannii glauca using unordered snp imputation methods
Heredity, 2015Co-Authors: Blaise Ratcliffe, Jaroslav Klápště, Ilga Porth, Charles Chen, B Jaquish, Omnia Gamal Eldien, Yousry A ElkassabyAbstract:A comparison of genomic selection models across time in interior spruce ( Picea engelmannii × glauca ) using unordered SNP imputation methods
William K. Smith - One of the best experts on this subject based on the ideXlab platform.
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effects of cumulus clouds on microclimate and shoot level photosynthetic gas exchange in Picea engelmannii and abies lasiocarpa at treeline medicine bow mountains wyoming usa
Agricultural and Forest Meteorology, 2015Co-Authors: Nicole M Hughes, Kayly L Carpente, David K Cook, Timothy S Keidel, Charlene N Mille, Junio L Neal, Adriana Sanchez, William K. SmithAbstract:a b s t r a c t Here we describe the dynamic effects of cumulus clouds on microclimate and shoot-level photosyn- thetic gas exchange in saplings of two treeline conifer species—Picea engelmannii and Abies lasiocarpa. Measurements were made during both clear-sky and partly cloudy conditions (∼10-70% cumulus cloud cover) throughout the 2012 growing season within an alpine-treeline ecotone. Cumulus clouds generated dynamic fluctuations in photosynthetically active radiation (PAR), higher maximum PAR (>2500 mol m−2 s−1), 2-4 fold increases in diffuse PAR, reduced daily mean and cumulative PAR, lower needle temperatures, and reduced leaf-to-air vapor pressure differences relative to clear-sky conditions. Onset of cloud-shade corresponded with declines in photosynthesis, needle temperatures, and evapo- transpiration, which were proportional to cloud duration and opacity. Despite increased diffuse light and greater sunlight intensity during cloud-gaps, photosynthesis was never higher on partly cloudy days compared to clear days in either species, during cloud-gaps or cloud-shade. However, reduced transpira- tion paired with photosynthesis comparable with clear-sky levels during cloud-gaps resulted in greater instantaneous water use efficiency relative to clear-sky measurements. There was no apparent photoin- hibition of photosynthesis reflected in gas exchange measurements in response to abrupt and dramatic changes in PAR levels caused by cumulus clouds. We conclude that cumulus clouds reduce instantaneous and daily carbon gain, although lower needle temperatures and associated reductions in transpirational water loss may alleviate daily and seasonal water stress, thereby enhancing carbon gain over the growing season.
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Photosynthesis during an Episodic Drought in Abies lasiocarpa and Picea engelmannii across an Alpine Treeline
Arctic Antarctic and Alpine Research, 2006Co-Authors: Craig R. Brodersen, Matthew J. Germino, William K. SmithAbstract:Abstract Effects of abiotic factors on daily and annual photosynthetic carbon gain were evaluated in Abies lasiocarpa and Picea engelmannii at three sites across an alpine treeline ecotone in the Medicine Bow Mountains of southeastern Wyoming (U.S.A.). In addition, the year 2001–2002 was characterized as an episodic drought (seventh driest year since 1895), including a winter that generated only 45% of normal snowpack. Both species had approximately 50% lower xylem water potentials and photosynthesis compared to previous studies for the same species and locale. In A. lasiocarpa, estimated total photosynthesis for the measurement period (Atot) was greatest (28.7 mol m−2) at the mid-ecotone site (∼3198 m), followed by the alpine site (24.6 mol m−2) at ∼3286 m, and then the forest site (19.4 mol m−2) below timberline (∼2965 m). Similar results occurred in P. engelmannii (17.6, 23.4, and 25.3 mol m−2, respectively). These differences appeared to be most influenced by stomatal rather than non-stomatal effects ...
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Abiotic factors limiting photosynthesis in Abies lasiocarpa and Picea engelmannii seedlings below and above the alpine timberline.
Tree physiology, 2004Co-Authors: Daniel M. Johnson, Matthew J. Germino, William K. SmithAbstract:Most research on the occurrence and stability of alpine timberlines has focused on correlations between adult tree growth and mean temperatures rather than on specific mechanisms. Timberline migration to higher altitude is dependent on new seedling establishment in the tree-line ecotone; however, reductions in photosynthetic carbon gain in establishing seedlings have previously been interpreted solely in terms of decreased seedling survival. Our objective was to evaluate the impact of abiotic factors (temperature, light and water) on photosynthetic carbon gain in young seedlings of the two dominant conifer tree species occurring naturally above (tree-line ecotone site, TS) and below (forest site, FS) a Rocky Mountain timberline in southeastern Wyoming, USA. Coincidentally, measurements were made during an unusually dry summer. Mean daily photosynthesis in seedlings of both Abies lasiocarpa (Hook.) Nutt. (subalpine fir) and Picea engelmannii Parry ex Engelm. (Engelmann spruce) was less at TS than at FS (19 and 29%, respectively). Minimum nighttime temperatures below 2 degrees C were more frequent at TS than at FS and were associated with reduced maximum photosynthesis the following day. Low midday water potentials were associated with a reduction in carbon gain at both sites early in the season, prior to snowmelt, as well as late in the season when soils began to dry. However, the lower photosynthetic rates at TS than at FS appeared to be unrelated to seedling water status because seedlings at both sites had similar xylem pressure potentials. Solar irradiance was highly variable at both sites as a result of uneven shading by neighboring trees, although this variation was substantially reduced on cloudy days (44% of all days observed). Compared with sunny days, cloudy days resulted in greater integrated daily carbon gain at both sites (41% increase at TS and 69% increase at FS), based on a simulated photosynthesis model. Photosynthetic responses to temperature, sunlight and water suggest that variable solar irradiance and nighttime temperatures were major abiotic factors limiting photosynthetic carbon acquisition in these young seedlings, especially for seedlings growing in the tree-line ecotone.
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Structural scaling of light interception efficiency in Picea engelmannii and Abies lasiocarpa.
Tree physiology, 1994Co-Authors: Mark T. Hemmerlein, William K. SmithAbstract:Sunlight interception efficiency was compared at the leaf, shoot, branch and crown levels for Picea engelmannii (Parry) and Ahies lasiocarpa ((Hook.) NW.), dominant tree species of the central Rocky Mountains, USA. The ratio of silhouette to total leaf area (STAR) was used to quantify the efficiency of direct-beam sunlight interception at each structural scale. Total mean reductions in STAR from the leaf to the crown level were 0.39 to 0.06 in P engelmannii and 0.46 to 0.02 in A. lasiocarpa. These reductions in STAR occurred for both species as structural scale increased due to a more upright leaf inclination, increased leaf twisting and curvature, or greater mutual shading among plant structures. A steeper leaf inclination between the leaf and shoot level accounted for 26 + 19% (95% C.I.) of the total leaf-to-crown STAR reduction; mutual shading among leaves on shoots caused a 14 + 7% reduction, whereas leaf curvature and twisting accounted for 22 + 3% for a total reduction of 62 + 8%. The STAR varied slightly from the shoot to the branch level (+ 7%) except for a 26% reduction in shade shoots of A. lasiocarpa as a result of increased mutual shading among leaves at lateral nodes. Another substantial reduction in STAR occurred from the branch to the crown level (35 + 3% of total) as a result of shading of one branch layer by another within the crown. Thus, light interception efficiency decreased as structural scale increased in both species, especially from the leaf to the shoot level and from the branch to the crown level.
Jaroslav Klápště - One of the best experts on this subject based on the ideXlab platform.
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A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods
Heredity, 2015Co-Authors: Blaise Ratcliffe, Omnia Gamal El-dien, Jaroslav Klápště, Ilga Porth, Charles Chen, B Jaquish, Yousry A. El-kassabyAbstract:Genomic selection (GS) potentially offers an unparalleled advantage over traditional pedigree-based selection (TS) methods by reducing the time commitment required to carry out a single cycle of tree improvement. This quality is particularly appealing to tree breeders, where lengthy improvement cycles are the norm. We explored the prospect of implementing GS for interior spruce ( Picea engelmannii × glauca ) utilizing a genotyped population of 769 trees belonging to 25 open-pollinated families. A series of repeated tree height measurements through ages 3–40 years permitted the testing of GS methods temporally. The genotyping-by-sequencing (GBS) platform was used for single nucleotide polymorphism (SNP) discovery in conjunction with three unordered imputation methods applied to a data set with 60% missing information. Further, three diverse GS models were evaluated based on predictive accuracy (PA), and their marker effects. Moderate levels of PA (0.31–0.55) were observed and were of sufficient capacity to deliver improved selection response over TS. Additionally, PA varied substantially through time accordingly with spatial competition among trees. As expected, temporal PA was well correlated with age-age genetic correlation ( r =0.99), and decreased substantially with increasing difference in age between the training and validation populations (0.04–0.47). Moreover, our imputation comparisons indicate that k-nearest neighbor and singular value decomposition yielded a greater number of SNPs and gave higher predictive accuracies than imputing with the mean. Furthermore, the ridge regression (rrBLUP) and BayesCπ (BCπ) models both yielded equal, and better PA than the generalized ridge regression heteroscedastic effect model for the traits evaluated.
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A comparison of genomic selection models across time in interior spruce ( Picea engelmannii × glauca ) using unordered SNP imputation methods
Heredity, 2015Co-Authors: Blaise Ratcliffe, Omnia Gamal El-dien, Jaroslav Klápště, Ilga Porth, Charles Chen, B Jaquish, Yousry A. El-kassabyAbstract:A comparison of genomic selection models across time in interior spruce ( Picea engelmannii × glauca ) using unordered SNP imputation methods
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a comparison of genomic selection models across time in interior spruce Picea engelmannii glauca using unordered snp imputation methods
Heredity, 2015Co-Authors: Blaise Ratcliffe, Jaroslav Klápště, Ilga Porth, Charles Chen, B Jaquish, Omnia Gamal Eldien, Yousry A ElkassabyAbstract:A comparison of genomic selection models across time in interior spruce ( Picea engelmannii × glauca ) using unordered SNP imputation methods
Yousry A. El-kassaby - One of the best experts on this subject based on the ideXlab platform.
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A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods
Heredity, 2015Co-Authors: Blaise Ratcliffe, Omnia Gamal El-dien, Jaroslav Klápště, Ilga Porth, Charles Chen, B Jaquish, Yousry A. El-kassabyAbstract:Genomic selection (GS) potentially offers an unparalleled advantage over traditional pedigree-based selection (TS) methods by reducing the time commitment required to carry out a single cycle of tree improvement. This quality is particularly appealing to tree breeders, where lengthy improvement cycles are the norm. We explored the prospect of implementing GS for interior spruce ( Picea engelmannii × glauca ) utilizing a genotyped population of 769 trees belonging to 25 open-pollinated families. A series of repeated tree height measurements through ages 3–40 years permitted the testing of GS methods temporally. The genotyping-by-sequencing (GBS) platform was used for single nucleotide polymorphism (SNP) discovery in conjunction with three unordered imputation methods applied to a data set with 60% missing information. Further, three diverse GS models were evaluated based on predictive accuracy (PA), and their marker effects. Moderate levels of PA (0.31–0.55) were observed and were of sufficient capacity to deliver improved selection response over TS. Additionally, PA varied substantially through time accordingly with spatial competition among trees. As expected, temporal PA was well correlated with age-age genetic correlation ( r =0.99), and decreased substantially with increasing difference in age between the training and validation populations (0.04–0.47). Moreover, our imputation comparisons indicate that k-nearest neighbor and singular value decomposition yielded a greater number of SNPs and gave higher predictive accuracies than imputing with the mean. Furthermore, the ridge regression (rrBLUP) and BayesCπ (BCπ) models both yielded equal, and better PA than the generalized ridge regression heteroscedastic effect model for the traits evaluated.
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A comparison of genomic selection models across time in interior spruce ( Picea engelmannii × glauca ) using unordered SNP imputation methods
Heredity, 2015Co-Authors: Blaise Ratcliffe, Omnia Gamal El-dien, Jaroslav Klápště, Ilga Porth, Charles Chen, B Jaquish, Yousry A. El-kassabyAbstract:A comparison of genomic selection models across time in interior spruce ( Picea engelmannii × glauca ) using unordered SNP imputation methods
D. F. Greene - One of the best experts on this subject based on the ideXlab platform.
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a method for studying dead bole dynamics in pinus contorta var latifolia Picea engelmannii forests
Journal of Vegetation Science, 1991Co-Authors: Edward A. Johnson, D. F. GreeneAbstract:. Rates of decomposition were determined for the boles of Pinus contorta var. latifolia Engelm. and Picea engelmannii Parry ex. Engelm. in five lower subalpine forest stands in the Southern Canadian Rocky Mountains. Stands ranged in age from 58 to 222 yr since last fire. The date of death of standing dead and fallen boles was determined by cross-dating their ring-width patterns to stand master ring- width chronologies. Boles could be dated which had been dead for up to 35 years in a 58-yr old stand and 100 yr in a 222-yr old stand. An empirical relationship between mass density and diameter of live trees was used to predict the mass density at death for trees already dead. The falling rate of dead standing boles was estimated from the dead bole's time of death and whether it was standing or on the ground at the time of observation. The falling rates for both Pinus contorta and Picea engelmannii ranged from 0.020 to 0.064/yr falling with most stands in the 0.050 range. No effect of size was found on the falling rate probably as a result of the small size of the boles (< 20 cm). Because of their dry condition standing dead boles do not decompose. An equation was developed which estimates the time a dead bole has been on the ground, given that it would have stood for some time before falling over and been subject to little decomposition during this time. Decomposition rates, using a negative exponential model, gave only marginally better r2 than linear models. Pinus contorta had exponential decay rates from 0.0299 and 0.0171 mass density loss/yr for the most recent 15 and 25 yr in stands 58 yr old, to 0.0045 and 0.0035 mass loss/yr for the most recent 65 and 80 yr in stands 215 and 222 yr old. Picea engelmannii had exponential decay rates of 0.0054 and 0.0025 mass loss/yr for the most recent 20 and 65 yr in stands 99 and 215 yr old.
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A method for studying dead bole dynamics in Pinus contorta var. latifolia ‐ Picea engelmannii forests
Journal of Vegetation Science, 1991Co-Authors: Edward A. Johnson, D. F. GreeneAbstract:. Rates of decomposition were determined for the boles of Pinus contorta var. latifolia Engelm. and Picea engelmannii Parry ex. Engelm. in five lower subalpine forest stands in the Southern Canadian Rocky Mountains. Stands ranged in age from 58 to 222 yr since last fire. The date of death of standing dead and fallen boles was determined by cross-dating their ring-width patterns to stand master ring- width chronologies. Boles could be dated which had been dead for up to 35 years in a 58-yr old stand and 100 yr in a 222-yr old stand. An empirical relationship between mass density and diameter of live trees was used to predict the mass density at death for trees already dead. The falling rate of dead standing boles was estimated from the dead bole's time of death and whether it was standing or on the ground at the time of observation. The falling rates for both Pinus contorta and Picea engelmannii ranged from 0.020 to 0.064/yr falling with most stands in the 0.050 range. No effect of size was found on the falling rate probably as a result of the small size of the boles (< 20 cm). Because of their dry condition standing dead boles do not decompose. An equation was developed which estimates the time a dead bole has been on the ground, given that it would have stood for some time before falling over and been subject to little decomposition during this time. Decomposition rates, using a negative exponential model, gave only marginally better r2 than linear models. Pinus contorta had exponential decay rates from 0.0299 and 0.0171 mass density loss/yr for the most recent 15 and 25 yr in stands 58 yr old, to 0.0045 and 0.0035 mass loss/yr for the most recent 65 and 80 yr in stands 215 and 222 yr old. Picea engelmannii had exponential decay rates of 0.0054 and 0.0025 mass loss/yr for the most recent 20 and 65 yr in stands 99 and 215 yr old.