Genetic Diversity Maximization as a Strategy for Resilient Forest Ecosystems: A Case Study on Norway Spruce

Norway spruce, economically and ecologically one of the most important European forest tree species, rapidly declines due to massive bark beetle outbreaks across many countries. As a prerequisite of ecosystem stability facing climate changes of uncertain predictions, the reforestation management promoting locally adapted resources of broad genetic diversity should be prioritized, especially in nature conservation areas. In our case study carried out in the national park, Krkonoše Mountains (the Giant Mountains, the Czech Republic), we demonstrated a tree breeding strategy aiming at maximizing genetic diversity. More than four hundred unique Norway spruce accessions were genotyped on 15 microsatellite loci (Ne = 5.764, I = 1.713 and He = 0.685). Two core collection selection approaches were proposed to establish a new deployment population providing local gene sources of high genetic diversity. Namely, the Core Hunter selection algorithm, with average entry-to-nearest-entry distance (EN) optimization, was applied to identify the most diverse core collection set with the highest genetic diversity parameters obtained for 57 selected individuals (Ne = 6.507, I = 1.807, and He = 0.731). The latter core collection method proposed is innovative, based on choosing appropriate genotypes from a clustered heatmap. For simplicity, we demonstrated the principle of selection strategy on a reduced dataset. It is vital to promote panmixia of a newly established production population from a core collection to complete the conservation breeding effort. Thus, we demonstrated the utilization of the Optimum Neighborhood Algorithm (ONA) deployment that outperformed other deployment algorithms, especially in the case of balanced clone representation and uneven shapes of planting plots. We believe that the case study presented can be generalized and considered as a guideline for analogical tree breeding intentions.

Mating System in a Native Norway Spruce (Picea abies [L.] KARST.) Stand-Relatedness and Effective Pollen Population Size Show an Association with the Germination Percentage of Single Tree Progenies

Norway spruce differs little in neutral genetic markers among populations and provenances often reported, but in terms of putative adaptive traits and their candidate genes, some clear differences have been observed. This has previously been shown for crown morphotypes. Stands with mostly narrow crown shapes are adapted to high elevation conditions, but these stands are scattered, and the forest area is often occupied by planted stands with predominantly broad crowned morphotypes. This raises questions on whether this differentiation can remain despite gene flow, and on the level of gene flow between natural and planted stands growing in close neighbourhood. The locally adapted stands are a valuable seed source, the progeny of which is expected to have high genetic quality and germination ability. The presented case study is useful for spruce plantation by demonstrating evaluation of these expectations. Immigrant pollen and seeds from planted trees could be maladaptive and may alter the genetic composition of the progeny. This motivated us to study single tree progenies in a locally adapted stand with narrow crowned trees in a partial mast year at nuclear genomic simple sequence repeat (SSR) markers. Spruce is a typical open-pollinated conifer tree species with very low selfing rates, which were also observed in our study (s = 0.3–2.1%) and could be explained by efficient cross-pollination and postzygotic early embryo abortion, common in conifers. The estimated high amount of immigrant pollen found in the pooled seed lot (70.2–91.5%) is likely to influence the genetic composition of the seedlings. Notably, for individual mother trees located in the centre of the stand, up to 50% of the pollen was characterised as local. Seeds from these trees are therefore considered to retain most of the adaptive variance of the stand. Germination percentage varied greatly between half-sib families (3.6–61.9%) and was negatively correlated with relatedness and positively with effective pollen population size of the respective families. As pollen mostly originated from outside the stand and no family structures in the stand itself were found, germination differences can likely be explained by diversity differences in the individual pollen cloud.

Genetic Structure of Norway Spruce Ecotypes Studied by SSR Markers

Norway spruce is a widespread and economically highly important tree species in Central Europe which occurs there in different morphotypic forms (also known as ecotypes). Previously established common garden experiments indicated that the morphological differentiation is most likely genetically determined. The genetic structure of Norway spruce morphological variants might be an indicator (marker) of specific sustainability in forest ecosystems. In this study, we investigated 436 individuals from autochthonous populations belonging to three different ecotypes. The main aim was to evaluate a level of genetic intra and interpopulation diversity among the low, medium and high-elevation ecotypes using both expressed sequence tag simple sequence repeats (EST – SSR) and genomic SSR markers. Sixteen highly polymorphic microsatellite loci folded in two newly designed multiplexes were used to depicture the genetic structure of targeted trees. Important allele frequency parameters, such as the mean expected (0.722, SE = 0.061) and observed (0.585, SE = 0.062) heterozygosity and mean effective number of alleles (Ne = 5.943, SE = 1.279), were estimated. The low genetic differentiation detected among different ecotypes (Fst = 0.008) was further discussed and clarified.

Comparison of Genetic Diversity in Naturally Regenerated Norway Spruce Stands and Seed Orchard Progeny Trials

Forest ecosystems in Europe are expected to experience changes in temperature and water regimes associated with increased risks of extreme environmental events and disasters. Genetic diversity and relatedness has been linked to resilience of forest stands and landscapes. Genetic diversity indicators were compared between a Norway spruce population naturally regenerated after extensive windthrow and Norway spruce progeny populations derived from two seed orchards. In addition, genetic diversity in an undisturbed stand in a long established national park and a spruce genetic resource stand were analyzed. Populations were genotyped at 11 simple sequence repeat (SSR) loci. Average genetic diversity indicators were similar across populations. However, the total number of alleles, average number of alleles over all loci, effective number of alleles, average gene diversity, and average allelic richness were highest in the naturally regenerated population and lowest in one of the seed orchard progeny populations. The genetic diversity in progeny from seed orchards used for stand renewal is comparable to the genetic diversity in naturally regenerated stands. However, fluctuations in seed production between years can have a large impact on genetic diversity in seed orchard progeny. The use of improved Norway spruce germplasm deployed via clonal seed orchards for forest renewal can maintain similar levels of genetic diversity compared to naturally regenerated stands, while also increasing production and timber quality.

High Morphological Differentiation in Crown Architecture Contrasts with Low Population Genetic Structure of German Norway Spruce Stands

High elevation sites in the low mountain ranges in Germany are naturally covered by Norway spruce (Picea abies (Karst.) L.) stands. Historically, large scale anthropogenic range expansion starting in the mid to late 18th century had a huge impact on the forest composition throughout Germany. Utilisation and exploitation often led to artificial regeneration, mostly carried out using seeds from allochthonous provenances. Usually, autochthonous (natural) high elevation Norway spruce trees have narrow crown phenotypes, whereas lowland trees have broader crowns. Narrow crown phenotypes are likely the result of adaptation to heavy snow loads combined with high wind speeds. In the present study, neighbouring stand pairs of putative autochthonous and allochthonous origin with contrasting phenotypes in high elevation sites were investigated with 200 samples each. These stands are located in the Ore Mountains, the Thuringian Forest, and the Harz Mountains. Additionally, a relict population with the typical narrow high elevation phenotypes was sampled in Thuringia, known as “Schlossbergfichte”. The objective of the study was to quantify supposedly adaptive phenotypic differences in crown architecture and the genetic differentiation of 11 putatively neutral nuclear microsatellite markers (i.e., simple sequence repeats (nSSRs)). The high differentiation of morphological traits (PST = 0.952–0.989) between the neighbouring autochthonous and allochthonous stands of similar age contrasts with the very low neutral genetic differentiation (FST = 0.002–0.007; G″ST = 0.002–0.030), suggesting that directional selection at adaptive gene loci was involved in phenotypic differentiation. Comparing the regions, a small isolation by distance effect for the Harz Mountains was detected, suggesting landscape resistance restricting gene flow. Finally, the differentiation of the very old autochthonous (up to 250 years) stand “Schlossbergfichte” with typical high elevation phenotypes could cohere with the sampling of a relict genepool.

Distinctions in Fine-Scale Spatial Genetic Structure Between Growth Stages of Picea jezoensis Carr

Conifers in northern forests, such as fir and spruce, preferably regenerate on coarse woody debris, including fallen logs, stumps, and snags. In northern Japan, the sub-boreal conifer species Picea jezoensis is completely dependent on coarse woody debris for seedling establishment. To understand the fine-scale spatial genetic structure (FSGS) of this species, a 5-ha plot was established in central Hokkaido, and 531 individual trees were categorized into four life-stages (seedling, sapling, juvenile, and mature) on the basis of age and size. The FSGS of the established seedlings and later growth stages was investigated using 11 nuclear simple sequence repeat loci. A STRUCTURE analysis of seedlings and saplings established on fallen logs revealed that genetically related individuals were spatially localized between adjacent logs. We also found a significant FSGS in early life-stages based on a decline in the kinship coefficient calculated between individuals over shorter to longer spatial distances. Furthermore, the estimation of dispersal kernels indicated the frequent occurrence of short-distance seed dispersal. These results indicated that genetically related seedlings and saplings regenerated on the same or nearby fallen logs. In contrast to the results for the early stages, mature-stage trees showed no significant FSGS. We ran a simulation to examine the hypothesis that the FSGS could be eliminated by demographic thinning during life history processes. We calculated values for simulated offspring generated under three sets of conditions; i.e., by removing (i) inbred individuals, (ii) randomly chosen individuals, and (iii) all individuals on the specific fallen logs. However, the results for the FSGS were significant for all simulated data sets. This indicated that inbreeding depression, stochastic loss, or eradication of establishment sites by local disturbances alone could not explain the lack of FSGS among mature-stage trees. Therefore, it is possible that the colonization history of mature trees present on the study site might differ from that of the current offspring.

DNA from processed and unprocessed wood: factors influencing the isolation success

Molecular genetic markers have numerous potential applications in environmental forensics if DNA can be isolated from 'difficult' non-human biological material such as hairs, feathers, or wood. The identification of the origin of wood is particularly important in order to identify illegally harvested and traded timber and wood products. We describe success rates of DNA isolation from wood based on a simple, previously published extraction protocol. The protocol was used to isolate DNA from a total of 406 wood samples, mainly of the important tropical tree family Dipterocarpaceae. The reliability of the extraction method was confirmed by comparing fragment sizes and sequences after isolation of DNA from leaves and wood of the same trees. We observed the success of amplification of chloroplast DNA (cpDNA) fragments of different lengths by means of PCR, investigated key factors influencing PCR, and conducted inhibitor tests for a subset of the samples. The average rate of successful PCR amplification was 75.7%. Main factors influencing the success of PCR amplification were the size of the amplified fragment and the processing status of the wood. Short fragments and unprocessed wood resulted in higher success rates. The success rate was also dependent on the age (storage duration) of the wood probe and on the investigated species. Amplification success was higher if DNA was isolated from outer sapwood (without cambium) in comparison to DNA isolated from the transition zone between sapwood and heartwood and the inner heartwood. However, inhibitor tests also indicated more PCR inhibitory substances in the outer sapwood in comparison to transition wood and heartwood. The addition of polyvinylpyrolidone (PVP) to the lysis buffer proved to be highly efficient to improve the amplification success if inhibitory substances were present.

The molecular ecologist's guide to expressed sequence tags

Genomics and bioinformatics have great potential to help address numerous topics in ecology and evolution. Expressed sequence tags (ESTs) can bridge genomics and molecular ecology because they can provide a means of accessing the gene space of almost any organism. We review how ESTs have been used in molecular ecology research in the last several years by providing sequence data for the design of molecular markers, genome-wide studies of gene expression and selection, the identification of candidate genes underlying adaptation, and the basis for studies of gene family and genome evolution. Given the tremendous recent advances in inexpensive sequencing technologies, we predict that molecular ecologists will increasingly be developing and using EST collections in the years to come. With this in mind, we close our review by discussing aspects of EST resource development of particular relevance for molecular ecologists.

Comparative genome mapping among Picea glauca, P. mariana x P. rubens and P. abies, and correspondence with other Pinaceae

A composite linkage map was constructed from four individual maps for the conifer Picea glauca (Moench) Voss, from anonymous and gene-specific markfers (714 AFLPs, 38 SSRs, and 53 ESTPs). A total of 12 linkage groups were delineated with an average marker density of 2.7 cM. Macro-synteny and macro-colinearity comparisons with two other composite linkage maps developed for the species complex P. mariana (Mill.) B.S.P. x P. rubens Sarg., and for P. abies (L.) Karst. revealed an identical number of linkage groups and a remarkable conservation of the gene content and gene order of linkage groups over the million years since the split between these taxa. Identical gene order among taxa was observed for 10 of the 12 assembled composite linkage groups. The discovery of one breakdown in synteny between P. glauca and the other two taxa indicated the occurrence of an inter-chromosomal rearrangement involving an insertional translocation. Analysis of marker colinearity also revealed a putative segmental duplication. The combined information from these three Picea genomes validated and improved large-scale genome comparisons at the inter-generic level in the family Pinaceae by allowing for the identification of 11 homoeologous linkage groups between Picea and Pinus, and nine such groups between Picea and Pseudotsuga menziesii. Notably, the analysis of synteny among the three genera revealed a putative case of chromosomal fission and an inter-chromosomal rearrangement in the genome of P. menziesii. Both of these changes are inter-connected, indicating much instability in this part of the P. menziesii genome. Overall, the macro-structure of the Pinaceae genome was well conserved, which is notable given the Cretaceous origin of its main lineages.

A composite linkage map from two crosses for the species complex Picea mariana x Picea rubens and analysis of synteny with other Pinaceae

Four individual linkage maps were constructed from two crosses for the species complex Picea mariana (Mill.) B.S.P. x Picea rubens Sarg in order to integrate their information into a composite map and to compare with other Pinaceae. For all individual linkage maps, 12 major linkage groups were recovered with 306 markers per map on average. Before building the composite linkage map, the common male parent between the two crosses made it possible to construct a reference linkage map to validate the relative position of homologous markers. The final composite map had a length of 2,319 cM (Haldane) and contained a total of 1,124 positioned markers, including 1,014 AFLPs, 3 RAPDs, 53 SSRs, and 54 ESTPs, assembled into 12 major linkage groups. Marker density of the composite map was statistically homogenous and was much higher (one marker every 2.1 cM) than that of the individual linkage maps (one marker every 5.7 to 7.1 cM). Synteny was well conserved between individual, reference, and composite linkage maps and 94% of homologous markers were colinear between the reference and composite maps. The combined information from the two crosses increased by about 24% the number of anchor markers compared to the information from any single cross. With a total number of 107 anchor markers (SSRs and ESTPs), the composite linkage map is a useful starting point for large-scale genome comparisons at the intergeneric level in the Pinaceae. Comparisons of this map with those in Pinus and Pseudotsuga allowed the identification of one breakdown in synteny where one linkage group homologous to both Picea and Pinus corresponded to two linkage groups in Pseudotsuga. Implications for the evolution of the Pinaceae genome are discussed.

Genomic organization of molecular differentiation in Norway spruce (Picea abies)

Diversity and differentiation among three populations representing the geographical domains commonly recognized within the natural distribution area of Picea abies were analysed by using a set of 292 AFLP (amplified fragment length polymorphism), SSR (single sequence repeat) and ESTP (expressed sequence tags polymorphism) markers. As usually observed in forest trees, results showed high within-population diversity (H(S) reaching 0.79) and low among-population differentiation (G(ST) approximately 2%). The genomic organization of differentiation was then investigated on the basis of a subsample of 150 AFLP, SSR and ESTP mapped markers. The number of the loci differentiating the Baltico-Nordic from the central European populations (25 loci) and, within the central European populations, the Alpine from the Hercyno-Carpathian populations (12 loci), were different. These 37 differentiated loci, with individual G(ST) values ranging from 0.008 to 0.20, were evenly distributed on all linkage groups and mostly followed the neutral expectations, suggesting genome-wide effects on differentiation. Nine of them however behave as 'outlier' loci indicating possible locus-specific selective effects. Contribution of ongoing evolutionary forces and historical effects to the geographical differentiation of the species are discussed.

Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags

Traditionally, simple sequence repeat (SSR)markers have been developed from libraries of genomic DNA. However, the large, repetitive nature of conifer genomes makes development of robust, single-copy SSR markers from genomic DNA difficult. Expressed sequence tags (ESTs), or sequences of messenger RNA, offer the opportunity to exploit single, low-copy, conserved sequence motifs for SSR development. From a 20,275-unigene spruce EST set, we identified 44 candidate EST-SSR markers. Of these, 25 amplified and were polymorphic in white, Sitka, and black spruce; 20 amplified in all 3 spruce species tested; the remaining five amplified in all except one species. In addition, 101 previously described spruce SSRs (mostly developed from genomic DNA), were tested. Of these, 17 amplified across white,Sitka, and black spruce. The 25 EST-SSRs had approximately 9% less heterozygosity than the 17 genomic-derived SSRs (mean H=0.65 vs 0.72), but appeared to have less null alleles, as evidenced by much lower apparent inbreeding (mean F=0.046 vs 0.126). These robust SSRs are of particular use in comparative studies,and as the EST-SSRs are within the expressed portion of the genome, they are more likely to be associated with a particular gene of interest, improving their utility for quantitative trait loci mapping and allowing detection of selective sweeps at specific genes.