Changes in the pattern of genetic variability over time in American sycamore and the implication for early selection

1992 ◽  
Vol 22 (5) ◽  
pp. 713-717 ◽  
Author(s):  
T.A. Greene ◽  
W.J. Lowe
Keyword(s):  
Volume Growth ◽  
Stem Canker ◽  
Early Selection ◽  
Phenotypic Variance ◽  
Additive Variance ◽  
Individual Tree ◽  
Genetic Prediction ◽  
Family Effects ◽  
Error Terms ◽  
Over Time

Height, volume, and stem canker symptom data were collected at ages 3, 5, 7, 10, 13, and 15 years in three genetic tests of American sycamore (Platanusoccidentalis L.) planted in Texas and Louisiana. Five provenances from Texas, Arkansas, and Louisiana were represented in the tests. Data were subjected to analysis of variance; heritabilities, coefficients of genetic prediction, and variance components were calculated. Provenance had no significant effect on height and volume; however, northern provenances tended to be more susceptible to stem canker. Significant family effects occurred for height and volume at all ages, and family heritabilities were moderate to high for all traits. Coefficients of genetic prediction between age 3 height and age 15 volume and canker rating were large and positive, suggesting that early selection to improve 15-year volume and canker resistance in sycamore would be possible. Over the course of this study, the additive variance for height and volume growth gradually increased. The variance attributed to the plantation x family interaction was generally small and nonsignificant. Changes in height and volume individual tree heritabilities over time were due to changes in the magnitude of the between-plot and within-plot error terms and their impact on phenotypic variance. This appeared to be caused by differential timing and severity of stem canker infection in the tests.

scholarly journals Direct and Competition Additive Effects in Tree Breeding: Bayesian Estimation From an Individual Tree Mixed Model

2008 ◽  
Vol 57 (1-6) ◽  
pp. 45-56 ◽  
Author(s):  
E. P. Cappa ◽  
R. J. C. Cantet
Keyword(s):  
Environmental Effects ◽  
Fixed Effects ◽  
Mixed Model ◽  
Phenotypic Variance ◽  
Tree Model ◽  
Data Set ◽  
Additive Variance ◽  
Individual Tree ◽  
Breeding Values ◽  
Competition Effects

Abstract An individual tree model with additive direct and competition effects is introduced to account for competitive effects in forest genetics evaluation. The mixed linear model includes fixed effects as well as direct and competition breeding values plus permanent environmental effects. Competition effects, either additive or environmental, are identified in the phenotype of a competitor tree by means of ‘intensity of competition’ elements (IC), which are non-zero elements of the incidence matrix of the additive competition effects. The ICs are inverse function of the distance and the number of competing individuals, either row-column wise or diagonally. The ICs allow standardization of the variance of competition effects in the phenotypic variance of any individual tree, so that the model accounts for unequal number of neighbors. Expressions are obtained for the bias in estimating additive variance using the covariance between half-sibs, when ignoring competition effects for row-plot designs and for single-tree plot designs. A data set of loblolly pines on growth at breast height is used to estimate the additive variances of direct and competition effects, the covariance between both effects, and the variance of permanent environmental effects using a Bayesian method via Gibbs sampling and Restricted Maximum Likelihood procedures (REML) via the Expectation- Maximization (EM) algorithm. No problem of convergence was detected with the model and ICs used when compared to what has been reported in the animal breeding literature for such models. Posterior means (standard error) of the estimated parameters were σ̂2Ad = 12.553 (1.447), σ̂2Ac = 1.259 (0.259), σ̂AdAc = -3.126 (0.492), σ̂2 p = 1.186 (0.289), and σ̂2e = 5.819 (1.07). Leaving permanent environmental competition effects out of the model may bias the predictions of direct breeding values. Results suggest that selection for increasing direct growth while keeping a low level of competition is feasible.

Trends in variances and heritabilities with stand development of tropical pines

1996 ◽  
Vol 26 (8) ◽  
pp. 1473-1480 ◽  
Author(s):  
J. Vásquez ◽  
W.S. Dvorak
Keyword(s):  
Phenotypic Trait ◽  
Phenotypic Variance ◽  
Narrow Sense ◽  
Ontogenetic Changes ◽  
Narrow Sense Heritability ◽  
Additive Variance ◽  
Genetic Variances ◽  
Rate Of Increase ◽  
The Individual ◽  
Over Time

Phenotypic and additive genetic variances as well as narrow-sense heritability for cumulative height were determined from assessments of tropical pine (Pinuscaribaea Morelet, Pinuschiapensis (Mart.) Andresen, and Pinustecunumanii (Schw.) Eguiluz et Perry) trials established in South America and South Africa by the Central America and Mexico Coniferous Resources (CAMCORE) Cooperative. Cumulative stem height was analyzed from 1-, 3-, 5-, and 8-year data collected on open-pollinated families to determine additive genetic and phenotypic variances. Variances based on arithmetic as well as log-transformed values are presented. Phenotypic and genetic variances of log-transformed values decreased over time, probably reflecting the onset of intergenotypic competition. Absolute variances increased over time as the trials became older, but the rate of increase for phenotypic variance was greater than that for additive variance. Individual narrow-sense heritabiiities changed over time but without showing any definite trend by species. It appeared that variance trends reflected the varying ontogenetic changes during the development of the stands, which could be indicated by size of the trees rather than by their age. Breeding strategies in tropical pines should consider the increasing intensity of environmental effects as a stand matures, since they cause a decline of genetic variances at a higher rate than phenotypic variances. Furthermore, it is hypothesized that a phenotypic trait at a given ontogenetic stage of the individual is under temporal control of a set of genes that changes as the temporal environmental conditions change.

scholarly journals Fluctuating selection: the perpetual renewal of adaptation in variable environments

2010 ◽  
Vol 365 (1537) ◽  
pp. 87-97 ◽  
Author(s):  
Graham Bell
Keyword(s):  
Natural Selection ◽  
Evolutionary Biology ◽  
Natural Populations ◽  
Phenotypic Variance ◽  
Weak Selection ◽  
Fluctuating Selection ◽  
Environmental Variance ◽  
Strong Selection ◽  
Genomic Studies ◽  
Over Time

Darwin insisted that evolutionary change occurs very slowly over long periods of time, and this gradualist view was accepted by his supporters and incorporated into the infinitesimal model of quantitative genetics developed by R. A. Fisher and others. It dominated the first century of evolutionary biology, but has been challenged in more recent years both by field surveys demonstrating strong selection in natural populations and by quantitative trait loci and genomic studies, indicating that adaptation is often attributable to mutations in a few genes. The prevalence of strong selection seems inconsistent, however, with the high heritability often observed in natural populations, and with the claim that the amount of morphological change in contemporary and fossil lineages is independent of elapsed time. I argue that these discrepancies are resolved by realistic accounts of environmental and evolutionary changes. First, the physical and biotic environment varies on all time-scales, leading to an indefinite increase in environmental variance over time. Secondly, the intensity and direction of natural selection are also likely to fluctuate over time, leading to an indefinite increase in phenotypic variance in any given evolving lineage. Finally, detailed long-term studies of selection in natural populations demonstrate that selection often changes in direction. I conclude that the traditional gradualist scheme of weak selection acting on polygenic variation should be supplemented by the view that adaptation is often based on oligogenic variation exposed to commonplace, strong, fluctuating natural selection.

scholarly journals Early Selection of Douglas-Fir across South Central Coastal Oregon, USA

2006 ◽  
Vol 55 (1-6) ◽  
pp. 135-141 ◽  
Author(s):  
C. A. Dean ◽  
R. W. Stonecypher
Keyword(s):  
Genetic Correlations ◽  
Volume Growth ◽  
Douglas Fir ◽  
Early Selection ◽  
Stem Volume ◽  
Direct Selection ◽  
South Central ◽  
Coos Bay ◽  
The Individual ◽  
Age Range

Abstract Details are given of three first-generation progeny tests (CB1, CB2 and CB3) of coastal Douglas-fir (Pseudotsuga menziesii [MIRB.] FRANCO var. menziesii) planted in the Coos Bay region of south-central coastal Oregon in 1973. The three tests included 15 polymix families based on a 10-pollen mix, and 27 families openpollinated on the ortet. The present study gives heritabilities and additive genetic correlations for growth measured between two and 17 years after planting. Correlated responses are estimated for volume at 17 years from early selection for height and diameter. Between four and 17 years after planting the individual heritability (h2) of height of coastal Douglas-fir across the Coos Bay tests was quite stable between h2 = 0.18 and 0.22. The heritability of stem diameter age-forage was consistently much lower than for height. In the critical age range for early selection between five and 10 years the individual heritability of diameter ranged from h2 = 0.07 to 0.10. The additive genetic correlations involving volume-17 and height or diameter increased to high values of rA = 0.80 to 0.84 between eight to 10 years after planting. Before seven years the absolute values of juvenilemature correlations were much lower. The higher heritability of height made this trait the best criterion for early indirect selection to improve mature stem volume growth. Across these Coos Bay tests, early selection on stem height measured at 5-8 years after planting was estimated to produce almost 40% more gain per year in volume-17 compared with direct selection at 17 years on volume-17 itself. The recommendation for maximizing gain per year in mature volume of coastal Douglas-fir at Coos Bay is to select on height at 7-8 years when the mean height of trees in tests should be around 4.5 to 5.5 meters.

What contributes to differences in phenotypic variation between generations?

2009 ◽  
Vol 2009 ◽  
pp. 200-200
Author(s):  
A Wolc ◽  
I White ◽  
M Lisowski ◽  
W G Hill
Keyword(s):  
Animal Model ◽  
Environmental Effects ◽  
Environmental Conditions ◽  
Phenotypic Variation ◽  
Variance Components ◽  
Genetic Variance ◽  
Phenotypic Variance ◽  
Base Population ◽  
Substantial Heterogeneity ◽  
Over Time

Under the animal model genetic variance is estimated in the base population taking into account inbreeding and is otherwise assumed to remain unchanged over generations. In practice, phenotypic variation differs randomly or systematically over time. Intuitively, such changes would be attributed mostly to environmental effects, and so lower heritability would be expected when variation is inflated. Studies in dairy cattle show contradictory results (e.g. Boldman and Freeman, 1990). Laying hens are kept under environmental conditions intended to be constant, but show substantial heterogeneity in phenotypic variance (VP) over generations. The aim was to investigate how variance components change.

scholarly journals Increased Individual Tree Growth Maintains Stand Volume Growth after B-Level Thinning and Crop-Tree Management in Mature Oak Stands

2019 ◽  
Vol 65 (6) ◽  
pp. 784-795
Author(s):  
Jeffrey S Ward ◽  
Jessica Wikle
Keyword(s):  
Tree Growth ◽  
Growth Response ◽  
Volume Growth ◽  
Diameter Growth ◽  
Red Oak ◽  
Individual Tree ◽  
Stand Volume ◽  
Tree Management ◽  
Individual Tree Growth ◽  
Partial Release

AbstractSix study areas were established in 80–125-year-old upland oak stands on average sites to compare stand and individual tree growth response following two active treatments (B-level thinning, crop tree) with an unmanaged control. Initial stocking of 104 percent was reduced to 62 percent and 60 percent on the B-level and crop-tree-management plots, respectively. Approximately 7,200 board feet per acre (International ¼) were harvested on the actively managed plots with upland oaks accounting for 81 percent of pre- and 86 percent of residual stand. Eleven-year diameter and volume growth of oak sawtimber trees was greater on actively managed plots. Growth response increased with degree of release and was maintained for the length of the study. Because of the increased individual tree growth of oaks in response to release, stand volume growth of oak sawtimber did not differ between treatments. In contrast to an 11-year decline of poletimber stocking on unmanaged plots, poletimber stocking increased on managed plots as diameter growth increased in response to partial release. This may increase difficulty of regenerating oak in the future. For those mature red oak stands where traditional regeneration prescriptions will not be implemented or will be delayed, commercial harvests can be conducted without compromising stand volume growth of oak.

scholarly journals Growth of Black Spruce Trees Following Fertilization on Drained Peatland

1989 ◽  
Vol 65 (2) ◽  
pp. 102-106 ◽  
Author(s):  
Bijan Payandeh
Keyword(s):  
Black Spruce ◽  
Linear Regression Analysis ◽  
Volume Growth ◽  
Average Diameter ◽  
Multiple Linear Regression Analysis ◽  
Stepwise Multiple Linear Regression ◽  
Individual Tree ◽  
Individual Trees ◽  
Volume Equations ◽  
Tree Characteristics

Stem analyse of 67 peatland black spruce trees from previously drained experimental areas in northeastern Ontario that had been fertilized was used to examine effects on growth of individual trees. Stepwise multiple linear regression analysis was used to express pre- and post-fertilization diameter and volume growth as a function of site, stand and individual tree characteristics and amelioration treatments.Results indicated that, on average, diameter growth increased by 4% after fertilization. Standard volume equations, in comparison with sectional volume summation underestimated both inside- and outside-bark tree volumes by about 3%.

Comparison of duration and method of herbaceous weed control on loblolly pine response through midrotation

1993 ◽  
Vol 23 (10) ◽  
pp. 2116-2125 ◽  
Author(s):  
Dwight K. Lauer ◽  
Glenn R. Glover ◽  
Dean H. Gjerstad
Keyword(s):  
Weed Control ◽  
Loblolly Pine ◽  
Volume Growth ◽  
Tree Height ◽  
Control Treatment ◽  
Control Individual ◽  
First Year ◽  
Individual Tree ◽  
Stem Infection ◽  
Herbaceous Weed Control

Herbaceous weed control studies installed by the Auburn University Silvicultural Herbicide Cooperative to examine response to methods and duration of herbaceous weed control in eight loblolly pine (Pinustaeda L.) plantations were analyzed to determine stand response through age 9. Studies were designed to compare weed control treatments with an untreated check, weed control methods (band vs. broadcast), and weed control duration (first year vs. first 2 years). Pine growth was increased by weed control on all sites. Growth was increased by an additional year of weed control (duration) on about one-half of the sites, but did not differ between band and broadcast treatments (method). Age 9 volume response above the check averaged 27.3 m3/ha for first-year weed control and 42.9 m3/ha for the first 2 years of weed control. Individual-tree height growth between ages 7 and 9 did not differ by treatment at most sites, but stand volume growth was higher with weed control at six of the eight sites. Uniformity of individual tree size, as represented by the standard deviation of DBH adjusted for dominant height, was more dependent on survival, hardwood encroachment, and level of fusiform rust stem infection, which varied by treatment and site, than on the result of herbaceous weed control per se. Growth projections made with the least intensive weed control treatment at each site indicated that on average, merchantable volume at age 22 with weed control will equal that of an age 25 stand without weed control. Largest gains were on sites where weed control increased survival.

scholarly journals A model for the regulation of the timing of cell division by the circadian clock in the cyanobacterium Synechococcus elongatus

2019 ◽  
Author(s):  
Po-Yi Ho ◽  
Bruno M.C. Martins ◽  
Ariel Amir
Keyword(s):  
Circadian Clock ◽  
Time Window ◽  
Volume Growth ◽  
Synechococcus Elongatus ◽  
Clock Signal ◽  
Cell Divisions ◽  
Activity Peak ◽  
Period 2 ◽  
Clock Proteins ◽  
Over Time

1SummaryCells of the cyanobacterium Synechococcus elongatus possess a circadian clock in the form of three core clock proteins (the Kai proteins) whose concentrations and phosphorylation states oscillate with daily periodicity under constant conditions [1]. The circadian clock regulates the cell cycle such that the timing of cell divisions is biased towards certain times during the circadian period [2, 3, 4, 5], but the mechanism underlying how the clock regulates division timing remains unclear. Here, we propose a mechanism in which a protein limiting for division accumulates at a rate proportional to cell volume growth and modulated by the clock. This “modulated rates” model, in which the clock signal is integrated over time to affect division timing, differs fundamentally from the previously proposed “gating” concept, in which the clock is assumed to suppress divisions during a specific time window [2, 3]. We found that while both models can capture the single-cell statistics of division timing in S. elongatus, only the modulated rates model robustly places divisions away from darkness during changes in the environment. Moreover, within the framework of the modulated rates model, existing experiments on S. elongatus are consistent with the simple mechanism that division timing is regulated by the accumulation of a division limiting protein in phase with genes whose activity peak at dusk.

scholarly journals Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
João Vitor Maldonado dos Santos ◽  
Everton Geraldo Capote Ferreira ◽  
André Luiz de Lima Passianotto ◽  
Bruna Bley Brumer ◽  
Adriana Brombini Dos Santos ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Allelic Variation ◽  
Major Gene ◽  
Cost Effective ◽  
Stem Canker ◽  
Snp Marker ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
A Genome ◽  
Marker Assay

Abstract Background Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs. Results We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency. Conclusions Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression.

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