Eric J. Jokela

Accuracy of Genomic Selection Methods in a Standard Data Set of Loblolly Pine (Pinus taeda L.)

Genomic selection can increase genetic gain per generation through early selection. Genomic selection is expected to be particularly valuable for traits that are costly to phenotype and expressed late in the life cycle of long-lived species. Alternative approaches to genomic selection prediction models may perform differently for traits with distinct genetic properties. Here the performance of four different original methods of genomic selection that differ with respect to assumptions regarding distribution of marker effects, including (i) ridge regression–best linear unbiased prediction (RR–BLUP), (ii) Bayes A, (iii) Bayes Cπ, and (iv) Bayesian LASSO are presented. In addition, a modified RR–BLUP (RR–BLUP B) that utilizes a selected subset of markers was evaluated. The accuracy of these methods was compared across 17 traits with distinct heritabilities and genetic architectures, including growth, development, and disease-resistance properties, measured in a Pinus taeda (loblolly pine) training population of 951 individuals genotyped with 4853 SNPs. The predictive ability of the methods was evaluated using a 10-fold, cross-validation approach, and differed only marginally for most method/trait combinations. Interestingly, for fusiform rust disease-resistance traits, Bayes Cπ, Bayes A, and RR–BLUB B had higher predictive ability than RR–BLUP and Bayesian LASSO. Fusiform rust is controlled by few genes of large effect. A limitation of RR–BLUP is the assumption of equal contribution of all markers to the observed variation. However, RR-BLUP B performed equally well as the Bayesian approaches.The genotypic and phenotypic data used in this study are publically available for comparative analysis of genomic selection prediction models.

DEVELOPMENTAL PATTERNS AND NUTRITION IMPACT RADIATION USE EFFICIENCY COMPONENTS IN SOUTHERN PINE STANDS

A number of contemporary forest productivity models use some variation of a growth efficiency (e) approach. Typically, these models predict production (aboveground net primary production, ANPP, in units of dry mass biomass per unit of area per unit of time) as the product of two terms: radiation use efficiency (e, in units of dry mass biomass per megajoule of photosynthetically active radiation [PAR] intercepted or absorbed by the plant canopy) and the sum of PAR intercepted or absorbed by the canopy (Φpar, in units of megajoules per unit of radiation area per unit of time). Predicting productivity in a biologically realistic manner requires an understanding of how model components are affected by natural and anthropogenic environmental factors, as well as other influences such as aging or stand development. We measured or calculated all components of the e model (aboveground woody biomass increment, IWB; foliage biomass increment, IFB; aboveground net primary production, ANPP; leaf area index, LAI; Φpar;...

BAAD: a biomass and allometry database for woody plants

Understanding how plants are constructed—i.e., how key size dimensions and the amount of mass invested in different tissues varies among individuals—is essential for modeling plant growth, carbon stocks, and energy fluxes in the terrestrial biosphere. Allocation patterns can differ through ontogeny, but also among coexisting species and among species adapted to different environments. While a variety of models dealing with biomass allocation exist, we lack a synthetic understanding of the underlying processes. This is partly due to the lack of suitable data sets for validating and parameterizing models. To that end, we present the Biomass And Allometry Database (BAAD) for woody plants. The BAAD contains 259 634 measurements collected in 176 different studies, from 21 084 individuals across 678 species. Most of these data come from existing publications. However, raw data were rarely made public at the time of publication. Thus, the BAAD contains data from different studies, transformed into standard units and variable names. The transformations were achieved using a common workflow for all raw data files. Other features that distinguish the BAAD are: (i) measurements were for individual plants rather than stand averages; (ii) individuals spanning a range of sizes were measured; (iii) plants from 0.01–100 m in height were included; and (iv) biomass was estimated directly, i.e., not indirectly via allometric equations (except in very large trees where biomass was estimated from detailed sub-sampling). We included both wild and artificially grown plants. The data set contains the following size metrics: total leaf area; area of stem cross-section including sapwood, heartwood, and bark; height of plant and crown base, crown area, and surface area; and the dry mass of leaf, stem, branches, sapwood, heartwood, bark, coarse roots, and fine root tissues. We also report other properties of individuals (age, leaf size, leaf mass per area, wood density, nitrogen content of leaves and wood), as well as information about the growing environment (location, light, experimental treatment, vegetation type) where available. It is our hope that making these data available will improve our ability to understand plant growth, ecosystem dynamics, and carbon cycling in the worlds vegetation.

Fertilization of Southern Pines at Establishment

Fertilization is a silvicultural practice used for increasing forestland productivity in the southern U.S. Effective operational use of fertilizers requires diagnostic systems, used individually or in combination, that accurately identify site nutrient status, needs, and potential responsiveness. Interactions of fertilization with other silvicultural practices such as site preparation and genetic tree improvement, and impacts of fertilization on pests, wood quality, and the environment, must be accounted for if fertilizer prescriptions are to be biologically effective and economically justified. This chapter introduces important concepts of forest nutrition and provides guidelines for fertilizing young, intensively managed southern pine plantations.

Long-term effects of weed control and fertilization on the carbon and nitrogen pools of a slash and loblolly pine forest in north-central Florida

The effects of fertilization, weed control, and fertilization plus weed control on vegetation and soil C and N pools were examined for a loblolly pine (Pinus taeda L.) and slash pine (Pinus elliottii var. elliottii Engelm.) forest at ages 18 and 26 years (at the end of rotation). The total C accumulated in fertilized forests without weed control was 20% (slash pine) and 40% (loblolly pine) greater than in the control forests at the end of rotation. Weed control increased pine C pools at 18 years, but by the end of rotation, weed control effectively resulted in no gain in ecosystem C. When the two treatments were combined, weed control slightly subtracted from the net C benefit produced by fertilization. This result occurred because of decreased forest floor and soil C in the weed control plots. Fertilization significantly increased stem, foliage, forest floor, and soil N pools, and N retention was 63% and 103% of the applied N in the slash and loblolly pine forests, respectively. Weed control with fertilization reduced ecosystem N retention efficiency, but weed control alone did not negatively affect ecosystem N accumulation. These results suggest that the optimal treatment for increasing C accumu- lation and N retention in these ecosystems is fertilization without weed control.

Growth and leaf nutrient responses of loblolly and slash pine families to intensive silvicultural management

Intra-specific variation in foliar nutrient response to fertilization treatments and associated growth performance is largely unknown in southern pines. Sixteen open-pollinated families from each of three pine taxa—genetically improved loblolly pine (PTI; Pinus taeda), improved slash pine (PEI; Pinus elliottii var. elliottii), and unimproved slash pine (PEU)—were planted in two locations under a common split–split plot experimental design in north Florida. At each site, two levels of silvicultural treatments (low intensity—no fertilization; high intensity—fertilization and weed control) were implemented. Vector analysis suggested that N, P, and K were nutrients mostly commonly limiting growth, while Mg and Ca were generally not deficient for the three taxa over four different sampling periods during the growing season. The period of highest nutrient demand occurred during the growing season from June to September, with deficiencies easing throughout the remainder of the year. Differential family responses in foliar nutrient levels (especially N and P) were closely associated with current-year foliage biomass production and annual height growth for the three taxa. PTI and PEI families with constant, but minor, foliar N and P deficiencies during the growing season had higher foliage biomass production and height increments than those exhibiting excess, dilution, or severe deficiency. PEU families generally had lower nutrient requirements than PTI and PEI families. Differences in nutrient demand for growth existed between PEU and PEI. Differences between PEI and PEU in foliar nutrient response to intensive management from this study, along with findings in growth performance and crown structure, suggested that PEI had growth strategies more closely aligned with PTA than with PEU. Significant intra-specific differences in growth and nutritional characteristics also indicated that family forestry could be a viable option suited for intensive plantation management because family-specific fertilizer prescriptions may be needed to further improve stand growth.

Competition dynamics in pure- versus mixed-family stands of loblolly and slash pine in the southeastern United States

Few studies within the native range of loblolly (Pinus taeda L.) and slash pine (Pinus elliottii Engelm. var. elliot- tii) have compared yield and stand dynamics in pure-family block versus mixed-family block plantings under a range of sil- vicultural treatments. Understanding intergenotypic competitive interactions is important for predicting phenotypic performance, defining growth strategies and ideotypes, and deploying the correct mix of families that possess complemen- tary characteristics for enhanced yield and pest resistance. In 2000, replicated experimental trials were installed in the south- eastern United States, controlling for genotype (pure- and mixed-family plantings; consisting of seven full-sibling loblolly and six full-sibling slash pine families), planting density (1334 vs. 2990 trees/ha), and levels of silvicultural treatment inten- sity (operational vs. intensive). We measured four installations of these trials. There were numerous examples of differential family performance in mixed versus pure plots manifested as significant deploymentfamily interactions for diameter at breast height, height, basal area, volume, survival, disease, and damage traits. Significant and consistent interactions of sev- eral families with mixed versus pure deployment led to the identification of putative crop and competition ideotypes in both loblolly and slash pine. Tree-level crown architectural traits and an index of growth efficiency for the identified families were consistent with the hypothesized ideotypes.

Silviculture in the United States: An Amazing Period of Change over the Past 30 Years

The practice of silviculture is continually evolving in response to a multitude of social, economic, and ecological factors. In 1986, the Journal of Forestry published a series of papers that reflected on changes in silviculture in the United States from the 1950s to 1980s and predicted how silviculture might develop in the next 30 years. We revisit the fundamental changes influencing the practice of silviculture since 1986; we explore how contemporary silviculture may evolve in the coming years in response to changing ownership structures on industry lands, declining research investments, and an increasing suite of stressors affecting forests, including invasive species and climate change. Many of the changes in management context and forest conditions occurring over the last 30 years were not anticipated and have resulted in an increase in silvicultural systems that integrate ecological and noneconomic social values on public lands. Many advances reflect a legacy of investment in silvicultural research and development in the 1970s and 1980s.