Multiple-population versus hierarchical conifer breeding programs: a comparison of genetic diversity levels

Scanning SNPs from a large set of expressed genes to assess the impact of artificial selection on the undomesticated genetic diversity of white spruce

A scan involving 1134 single-nucleotide polymorphisms (SNPs) from 709 expressed genes was used to assess the potential impact of artificial selection for height growth on the genetic diversity of white spruce. Two case populations of different sizes simulating different family selection intensities (K = 13% and 5%, respectively) were delineated from the Quebec breeding program. Their genetic diversity and allele frequencies were compared with those of control populations of the same size and geographic origin to assess the effect of increasing the selection intensity. The two control populations were also compared to assess the effect of reducing the sampling size. On one hand, in all pairwise comparisons, genetic diversity parameters were comparable and no alleles were lost in the case populations compared with the control ones, except for few rare alleles in the large case population. Also, the distribution of allele frequencies did not change significantly (P ≤ 0.05) between the populations compared, but ten and nine SNPs (0.8%) exhibited significant differences in frequency (P ≤ 0.01) between case and control populations of large and small sizes, respectively. Results of association tests between breeding values for height at 15 years of age and these SNPs supported the hypothesis of a potential effect of selection on the genes harboring these SNPs. On the other hand, contrary to expectations, there was no evidence that selection induced an increase in linkage disequilibrium in genes potentially affected by selection. These results indicate that neither the reduction in the sampling size nor the increase in selection intensity was sufficient to induce a significant change in the genetic diversity of the selected populations. Apparently, no loci were under strong selection pressure, confirming that the genetic control of height growth in white spruce involves many genes with small effects. Hence, selection for height growth at the present intensities did not appear to compromise background genetic diversity but, as predicted by theory, effects were detected at a few gene SNPs harboring intermediate allele frequencies.

Positive assortative mating with selection restrictions on group coancestry enhances gain while conserving genetic diversity in long-term forest tree breeding

Selection and mating principles in a closed breeding population (BP) were studied by computer simulation. The BP was advanced, either by random assortment of mates (RAM), or by positive assortative mating (PAM). Selection was done with high precision using clonal testing. Selection considered both genetic gain and gene diversity by "group-merit selection", i.e. selection for breeding value weighted by group coancestry of the selected individuals. A range of weights on group coancestry was applied during selection to vary parent contributions and thereby adjust the balance between gain and diversity. This resulted in a series of scenarios with low to high effective population sizes measured by status effective number. Production populations (PP) were selected only for gain, as a subset of the BP. PAM improved gain in the PP substantially, by increasing the additive variance (i.e. the gain potential) of the BP. This effect was more pronounced under restricted selection when parent contributions to the next generation were more balanced with within-family selection as the extreme, i.e. when a higher status effective number was maintained in the BP. In that case, the additional gain over the BP mean for the clone PP and seed PPs was 32 and 84% higher, respectively, for PAM than for RAM in generation 5. PAM did not reduce gene diversity of the BP but increased inbreeding, and in that way caused a departure from Hardy-Weinberg equilibrium. The effect of inbreeding was eliminated by recombination during the production of seed orchard progeny. Also, for a given level of inbreeding in the seed orchard progeny or in a mixture of genotypes selected for clonal deployment, gain was higher for PAM than for RAM. After including inbreeding depression in the simulation, inbreeding was counteracted by selection, and the enhancement of PAM on production population gain was slightly reduced. In the presence of inbreeding depression the greatest PP gain was achieved at still higher levels of status effective number, i.e. when more gene diversity was conserved in the BP. Thus, the combination of precise selection and PAM resulted in close to maximal short-term PP gain, while conserving maximal gene diversity in the BP.

Microsatellite analysis of Pinus taeda L. in Zimbabwe

Deducing the origin of early 20th century introductions of Pinus taeda into Zimbabwe is possible given microsatellite markers and clear population differentiation in ancestral U.S. populations. This study was designed to determine whether P. taeda introductions into Zimbabwe came from one U.S. region or whether the present-day population is an admixture of introductions from east and west of the Mississippi River Valley. Principal components analysis, Cavalli-Sforza and Edwards' chord distances and presence of diagnostic alleles each indicate that the Zimbabwe population is an admixture. There were five novel alleles in the Zimbabwe population not represented in the indigenous U.S. populations, possibly because of de novo mutation, introgression with other introduced North American pines or sampling error.

THE SCIENTIFIC BASIS OF FORESTRY

A sufficiently wise and flexible silvicultural art can be developed on the ground only by practitioners who understand the forest as a biological entity.

     F. S. Baker ( 10 )

…the existing level of knowledge about forests is inadequate to develop sound forest management policies.

     National Research Council ( 114 )

▪ Abstract  Over the past two decades forestry in the United States has diverged into two approaches with quite different objectives and scientific priorities. The management focus of most industrial lands is on increasing productivity of wood fiber via plantations and various cultural tools, especially genetic selection, fertilization, and control of noncrop vegetation. Federal forest management has shifted from a similar focus to greater emphasis on protecting diversity and water. Issues of long-term sustainability are important regardless of ownership. Science has played and continues to play a fundamental role in all aspects. Selection for fast-growing genotypes has increased yields on the order of 10% to 20% depending on species. Fertilization often increases growth significantly but responses are variable and difficult to predict. Significant questions remain concerning the sustainability of intensive forestry, particularly when practiced over wide areas. Soils are heavily impacted by some harvesting practices, and the degree to which damage can be repaired by fertilizers is an important scientific issue. Intensive forestry often results in increased pest problems. In at least one case (fusiform rust in southern pines), a pest has been contained by selecting resistant cultivars, a situation that may or may not be evolutionarily stable. Species diversity is clearly reduced under intensive management, raising questions about the functional role of species with no commercial value. Many of the questions facing forestry science—particularly those dealing with the relation between complexity and function—are precisely the ones confronting basic ecology. Over the past decade scientists have labored to develop ecosystem-based management approaches that maintain system complexity and function, and scientists have increasingly played nontraditional roles at the interface between biology, sociology, and policy.

Levels of genetic diversity at different stages of the domestication cycle of interior spruce in British Columbia

Concerns over the reductionist nature of the domestication of forest-tree species focus on the possibility of potential genetic erosion during this process. To address these concerns, genetic diversity assessments in a breeding zone the Province of British Columbia "interior" spruce (Picea glauca x engelmanni) program was conducted using allozyme markers. Genetic-variation comparisons were made between natural and production (seed orchard) populations as well as seed and seedling crops produced from the same breeding zone's seed orchard. The natural population sample consisted of a total of 360 trees representing three stands within each of three watersheds present in the Shuswap-Adams low-elevation zone of interior British Columbia. Small amounts of genetic differentiation were observed among the nine natural populations (4%) and this was attributable to extensive gene flow (N(m) = 7). Consequently, the sum of these nine populations was considered as a baseline for the genetic variation present in the breeding zone. The comparisons between the seed orchard and the breeding zone produced a similar percentage of polymorphic loci (%P = 64.7%) while the expected hetrozygosity (H(e)) (0.207 vs 0.210) and the average number of alleles per locus (2.7 vs 2.4) were slightly lower in the seed orchard. A total of seven natural populations' rare alleles (P < 0.007) were not present in the orchard population, while one allele was unique to the orchard. The %P increased to 70.6% in the seedlot, but dropped to the natural populations level (64.7%) in the plantation. The observed increase in %P was a result of pollen contamination in the orchard. It is suspected that the reduction in the plantation was caused by an unintentional selection in the nursery. Simulated roguing in the orchard did not drastically reduce H(e) even if up to 50% of the orchard's clones were rogued. However, roguing was associated with a reduction in the average number of alleles per locus (i.e., sampling effect).