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Forest trees are affected by climate change, anthropogenic pressure, as well as abiotic and biotic stresses. Conventional tree breeding has so far been limited to enhance overall productivity, and our understanding of the genetic basis of quantitative traits is still inadequate. Quantum leaps in next-generation sequencing technologies and bioinformatics have permitted the exploration and identification of various non-coding regions of the genome other than protein coding genes. These genomic regions produce various types of non-coding RNAs and regulate myriads of biological functions at epigenetic, transcriptional and translational levels. Recently, long non-coding RNAs (lncRNAs) which act as molecular switch have been identified to be pivotal molecules in forest trees. This review focuses on progress made in regulatory mechanisms in various developmental phases like wood formation, adventitious rooting and flowering and stress responses. It was predicted that complex regulatory interactions among lncRNA, miRNA and gene exist. LncRNAs can function as a sponge for miRNAs, reducing the suppressive effect of miRNAs on target mRNAs and perhaps adding a new layer of regulatory interactions among non-coding RNA classes in trees. Furthermore, network analysis revealed the interactions of lncRNA and genes during the expression of several important genes. The insights generated about lncRNAs in forest trees would enable improvement of economically important traits including the devastating abiotic and biotic stresses. In addition, solid understanding on the wide range of regulatory functions of lncRNAs on traits influencing biomass productivity and adaptation would aid the applications of biotechnology in genetic improvement of forest trees.

Scots pine (Pinus sylvestris L.) seeds have variable levels of primary dormancy which reflect within-species adaptation to local environments. The objective of this study was to use a thermal time approach to determine whether primary dormancy levels in seeds were correlated with mean ambient temperature during temperature-sensitive phases of the reproductive cycle. Seedlots were obtained from a single open-pollinated clonal seed orchard in five crop years and germinated over a wide temperature range (7–35 °C) to calculate base temperature for germination with and without pre-chills (4 and 8 weeks). Primary dormancy levels varied amongst seedlots collected in different crop years (CY). Unchilled seeds were the most dormant for CY2007 (Tb = 10.9 °C) and least dormant for CY2012 (Tb = 5.6 °C). Base temperatures for germination were correlated with mean ambient temperature during different phases of the reproductive cycle. There was a strong positive correlation between base temperature for germination of unchilled seeds and mean temperature during pollination and early pollen tube growth. This suggests that maternal environmental effects during this phase could potentially select for dormant or non-dormant seeds, which has implications for tree breeding and seedling production in forest nurseries.

In multisite forest genetic experiments, the presence of genotype × environment interaction (GEI) is common. GEI may negatively affect the estimates of genetic variance and hamper selection decisions in tree breeding programs. Several measures exist to evaluate the stability of tested genotypes’ performance across environments with a choice of the method likely affecting breeders’ decisions. In this study, we evaluated variation in diameter and height growth performance in the progeny test established at 4 sites with 80 open-pollinated half-sib families of Scots pine. We found significant variation among examined progeny at age 10, reaching up to 31% for diameter and 20% for height depending on site, and significant GEI in both traits. We estimated contribution of each family to GEI using various methods and tools of GEI analysis—AMMI, GGE biplots, heterogeneity of regression coefficients (bi’s), the deviation mean squares from regression (s2di) and Kang’s yield-stability index (YSi). Despite the presence of the cross-over interaction, family ranks did not vary much among sites. The selections based on the phenotype, YSi and restricted bi corresponded well to each other leading to the expected response to selection up to 7.8% on diameter and 4.4% on height, whereas those based on the AMMI stability variance were different and lead to a slight loss in both traits. We discuss our results in the context of the usefulness of those measures of genotype stability for tree breeding programs and propose the procedure to follow for making selection decisions in forest experiments with GEI.

The study of vegetative phenology is important to understand adaptation to different environments and potential trade-offs with growth traits. Crown leaf-out and leaf-fall phenology was evaluated on 168 open-pollinated families from 19 Cedrela odorata provenances in an eleven-year-old provenance/progeny trial established in the state of Veracruz, Eastern coast of Mexico. The objectives were: (a) to evaluate the extent of inter- and intra-population genetic variation of leaf phenology traits; (b) to examine the relationship between leaf phenology traits and climate variables at the population level; (c) to estimate the genetic relationships between leaf phenology and growth traits; and (d) to evaluate the accuracy, in terms of genetic control, of using alternative methods to measure leaf phenology in broadleaf trees. The study revealed significant genetic variation in leaf phenology traits both among and within populations. Leaf-out traits showed higher genetic variation than leaf-fall traits. A moderate to large genetic differentiation among Cedrela odorata populations was found; Qst values for leaf-out were 2–6 times higher than those for leaf-fall. Leaf-fall was primarily associated with mean annual temperature, while leaf-out and length of the leafless period were related to annual precipitation and the aridity index of the site of origin. Leaf phenology traits showed moderate to high genetic control (h2i = 0.12–0.67; h2f = 0.27–0.72). However, it was higher for leaf-out traits, so they might play a more important adaptive role. Genetic correlations between leaf phenology and growth traits allow selecting early flushing genotypes within populations to increase adaptation and growth, but caution should be taken when selecting among populations.

Genomic selection based on the single-step genomic best linear unbiased prediction (ssGBLUP) approach is becoming an important tool in forest tree breeding. The quality of the variance components and the predictive ability of the estimated breeding values (GEBV) depends on how well marker-based genomic relationships describe the actual genetic relationships at unobserved causal loci. We investigated the performance of GEBV obtained when fitting models with genomic covariance matrices based on two identity-by-descent (IBD) and two identity-by-state (IBS) relationship measures. Multiple-trait multiple-site ssGBLUP models were fitted to diameter and stem straightness in five open-pollinated progeny trials of Eucalyptus dunnii, genotyped using the EUChip60K. We also fitted the conventional ABLUP model with a pedigree-based covariance matrix. Estimated relationships from the IBD estimators displayed consistently lower standard deviations than those from the IBS approaches. Although ssGBLUP based in IBS estimators resulted in higher trait-site heritabilities, the gain in accuracy of the relationships using IBD estimators has resulted in higher predictive ability and lower bias of GEBV, especially for low-heritability trait-site. ssGBLUP based on IBS and IBD approaches performed considerably better than the traditional ABLUP. In summary, our results advocate the use of the ssGBLUP approach jointly with the IBD relationship matrix in open-pollinated forest tree evaluation.

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook), a fast-growing and economically important timber tree species in China, is widely used in construction, furniture, and paper manufacture but has a long breeding cycle. Chemical mutagens, such as ethyl methane sulfonate (EMS) and sodium azide (SA), are widely used in crops such as rice, wheat, cotton, soybean and sugarcane but their utility for tree breeding is unknown. In this study we examined the effects of EMS and SA on Chinese fir seed germination and growth. Chinese fir seeds were treated with the two chemical mutagens; were planted in Jiangle County, Fujian Province, China; and their heights were measured from 2011 to 2017. The concentrations and durations of treatment with the two chemical mutagens were significantly associated with the Chinese fir seedling and mortality rates, as well as with the heights of trees from the seedling stage to 3 years old. We also generated 127 mutants with abnormal branches and reproductive growth. We report here the effects of two chemical mutagens on Chinese fir breeding; our data will contribute to knowledge of the utility of EMS and SA in forestry.

Through stochastic simulations, accuracies of breeding values and response to selection were assessed under traditional pedigree- (BLUP) and genomic-based evaluation methods (GBLUP) in forest tree breeding. The latter provides a methodological foundation for genomic selection. We evaluated the impact of clonal replication in progeny testing on the response to selection realized in seed orchards under variable marker density and target effective population sizes. We found that clonal replication in progeny trials boosted selection accuracy, thus provided additional genetic gains under BLUP. While a similar trend was observed for GBLUP, however, the added gains did not surpass those under BLUP. Therefore, breeding programs deploying extensive progeny testing with clonal propagation might not benefit from the deployment of genomic information. These findings could be helpful in the context of operational breeding programs.

Biotechnological tools such as clonal propagation, haploid production, protoplast fusion, marker-assisted selection, and quantitative trait loci mapping are the age-old approaches in commercial forestry. Biotechnology has shown immense guarantee for the subsequent generation of plant breeders to alleviate the rising demand for food, fiber, and wood. The probable social and environmental impacts of the release of transgenic trees become a progressively more debatable issue and call more considerations. The present review is an attempt to summarize how advances in molecular biology i.e., comparative genomics and genome assembly approaches identify numerous polymorphic molecular markers like microsatellite, simple sequence repeats, single-nucleotide polymorphism (SNP), random amplified polymorphic DNA etc. and revolutionize the science of forest tree biotechnology during the last decade. The advent of next-generation sequencing technology identified many microsatellite loci in forest trees. Microsatellite markers play an important role in population genetics, conservation ecology, and phylogenetic analysis. SNP markers provide novel opportunities for the discovery of regulatory elements in the genome and eventually accelerate forest tree breeding.

Spanish red cedar, Cedrela odorata L. (Meliaceae), is a valuable timber tree in tropical American forests. Existing demand for elite individuals endangers the conservation of interesting germplasm, prompting the development of efficient protocols for the establishment of orchards for tree breeding. Based on previous work regarding grafting adult individuals onto young rootstocks, superior trees from Calakmul Biosphere Reserve in Campeche, Mexico were employed as a source of explants for plant regeneration after successive rounds of grafting and micrografting onto juvenile rootstocks. The results showed that root length and appearance, internode distance, leaf length and number, and plant height values for trees derived from successive rounds of grafting and micrografting were similar to those obtained from juvenile trees derived from seeds, suggesting that developmental traits associated with reinvigoration were partially induced following the reported procedure. This protocol may be useful for the propagation of mature elite trees belonging to the Meliaceae family.

Liriodendron plants have been cultivated in many regions of the world for both wood production and landscape ornamentation. Hybrid Liriodendron varieties show obvious growth and resistance heterosis; thus, interspecies hybridization and heterosis utilization constitute the major breeding strategy for Liriodendron plants. Choosing superior crossing parents/combinations and predicting the heterosis of potential hybrid combinations will greatly improve breeding efficiency and accelerate the breeding process. To explore the relationships between genetic parameters and heterosis, we investigated dynamic changes in the genetic parameters of growth traits with age by testing 57 progeny combinations derived from six cross types in Liriodendron. Tree height (H) and diameter at breast height (DBH) were under intermediate to strong genetic control and varied among combinations, indicating that parent-pair selection or combination selection is feasible. Both heritability and combining ability (general combining ability, GCA; specific combining ability, SCA) changed with age, with narrow-sense heritability fluctuating greatly in the early stage and increasing in the late stage, and the combining abilities varied among combinations. Additionally, the GCA of Liriodendron chinense parents was higher than that of Liriodendron tulipifera and hybrid Liriodendron parents, and the SCA of L. tulipifera × L. chinense combinations fluctuated less than that of other combinations. Further, midparent heterosis (MPH) and SCA were significantly positively correlated, suggesting that SCA could be a suitable criterion for predicting growth heterosis. Our findings provide useful clues for selecting parent pairs/combinations and predicting heterosis, which will accelerate Liriodendron tree breeding and shed light on cross-breeding in other plants.

International audience; Key message: A novel multi-environment competition individual-tree mixed model resulted in better fit, and greater individual narrow- and broad-sense heritabilities than the model without competition, notably for traits showing competition. In multi-environment tests, the proposed model would allow tree breeders to select genotypes with the best performance in both additive direct and competition breeding values, increasing forest productivity. Context: Genetic merit of trees is known to be affected and interact with local competition effects as well as changes across environmental conditions. Recent studies showed that competition genetic effects can affect the genetic variance and bias the tree breeding values, and its covariance with direct breeding values has been variable across traits. Aims: The present paper extends a mixed-model methodology to the problem of accounting for competition in a multi-environment set of forest genetic trials and exploring its impact on genetic variances as well as the multi-environment genetic correlation. Methods: The proposed model is illustrated using data from two full-sib trials of Pinus elliottii var. elliottii × Pinus caribaea var. hondurensis F1. Dispersion parameters and (co)variance of total breeding values were estimated for diameter at breast height, total tree height, and stem straightness at age 10. Results: For traits showing competition effects (diameter at breast height and total tree height), the proposed multi-environment competition model gave better fit than the simpler model. Accounting for competition increased the direct additive variance, reduced the residual variances, and did not change significantly the across-site additive genetic correlation. However, for diameter at breast height, top 5% best genetic rankings showed differences. Conclusion: When traits are strongly affected by inter-tree competition, the use of the proposed model in multi-environment analyses can efficiently identify the phenomenon with general benefits in the fitting of genetic components and open the door to select on the basis of competitiveness.

BackgroundGenomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine (Pinus sylvestrisL.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers.ResultsGenomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143% higher than the traditional pedigree-based selection.ConclusionsAlthough prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50%.

Pedigree reconstruction via DNA markers and subsequent quantitative genetic analyses in production stands of trees is an alternative to traditional forest tree breeding. The method requires variable DNA markers; preferably cost-efficient to genotype. We tested the approach in breeding for Christmas tree traits in a Danish landrace of Abies procera. Initial analysis with simple sequence repeats (SSRs) revealed a substantial reduction in genetic diversity of Danish A. procera compared with direct imports from the USA, indicating a genetic bottleneck. Due to the reduced genetic variation, the SSRs were not variable enough for pedigree reconstruction, and 145 single nucleotide polymorphisms (SNPs) were therefore identified and genotyped via high-throughput targeted sequencing. In the field, we phenotypically selected 674 superior trees, based on criteria for good Christmas trees, among 21,000 trees in three Christmas tree plantations originating from an A. procera clonal seed orchard. By SNP-genotyping and parentage analysis, pedigree was reconstructed for the selected individuals, and genetic predictions for the Christmas tree traits were estimated. A final selection of 45 trees out of the 674 genotyped, based on an index of predicted values for different traits, foresees a gain in the Christmas tree score and branch angle score of 16% and 10%, respectively. The study clearly demonstrated the benefits of pedigree reconstruction, even though mass selection seemed to give similar gain. Primarily, the possibilities to control the level of inbreeding, and to check whether the production stands, from where we select trees, actually originate from the declared and desired parent pool.

Genomic selection (GS) can substantially reduce breeding cycle times in forest trees compared to traditional breeding cycles. Practical implementation of GS in tree breeding requires an assessment of significant drivers of genetic gains over time, which may differ among species and breeding objectives. We present results of a GS study of growth and wood quality traits in an operational Eucalyptus grandis breeding program in South Africa. The training population consisted of 1575 full and half-sib individuals, genotyped with the Eucalyptus (EUChip60K) SNP chip resulting in 15,040 informative SNP markers. The accuracy of the GS models ranged from 0.47 (diameter) to 0.67 (fibre width). We compared a 4-year GS breeding cycle equivalent to half of a traditional 8-year E. grandis breeding cycle and obtained GS efficiencies ranging from 1.20 (wood density) to 1.62 (fibre length). Simulated over 17 years, the ratio of the accumulated genetic gains between three GS cycles and two traditional breeding cycles ranged from 1.53 (diameter) to 3.35 (wood density). To realise these genetic gains per unit time in E. grandis breeding, we show that significant adjustments have to be made to integrate GS into operational breeding steps.

Reaction norms fitted through random regression models are a powerful tool to identify and quantify the genotype × environment (G × E) interaction and they represent a promising alternative in forest tree breeding for analysis of multi-environment trials. Thus, the objective of this study was to compare random regression models with the compound symmetry model in Eucalyptus breeding for analysis of multi-environment trials. To this end, a data set with 215 Eucalyptus clones of different species and hybrids evaluated in four environments for diameter at breast height and Pilodyn penetration was used. The random regression models provided a better fit for both traits. Results showed that there was genotypic variability among Eucalyptus clones and that the reaction norms over the environmental gradients identified the G × E interaction. The compound symmetry model and the random regression models are highly correlated in terms of genotype ranking for both traits. The main advantage of random regression models over the compound symmetry model is the ability to predict genotypic performance in environments where a genotype has not been evaluated. Thus, our results suggest that reaction norms fitted through random regression models can be successfully used in forest tree breeding for analysis of multi-environment trials.

Random k-fold cross-validation in genome-wide selection (GWS) can help to estimate predictive ability ( $$ {r}_{y\hat{y}} $$ ). Predictive ability tends to be higher when training, and validation sets present a high degree of kinship. However, many tree breeding populations are less genetically related to the training sets and have different levels of phenotypic diversity. Therefore, this study proposes methods of splitting k-fold cross-validation sets to optimize $$ {r}_{y\hat{y}} $$ estimates that are consistent with the breeding population and verify the impact of phenotypic and genotypic distribution on GWS. Using a simulated Eucalyptus trait (h2=0.5) and Pinus taeda L. data for diameter at breast height (h2=0.31), six methods were developed based on mutual information (I) and entropy (H) for measuring genetic similarity and phenotypic dissimilarity, respectively. All methods were evaluated for $$ {r}_{y\hat{y}} $$ , bias, minimum squared error of prediction, and genomic heritability. The Pearson correlations of these parameters with the kinship coefficient, and I and H between and within training and validation sets were also estimated. Our results show that closer genetic similarity did not significantly increase $$ {r}_{y\hat{y}} $$ and that a lower H reduced $$ {r}_{y\hat{y}} $$ and overestimated genomic breeding values. Consequently, phenotypic diversity (high H) should be added to tree breeding populations to increase genetic gain and reduce bias. The new methods accurately fitted models according to the entropy of tree breeding populations and their genetic relationship to the training sets. Therefore, these methods provided usable estimates of genetic gain to produce consistent success of long-term tree breeding programs.

Intensive plantation forestry is a potent strategy for forest managers to increase wood production on a smaller forest land acreage, especially with the use of genetically improved reforestation stock. The main drawback with conventional conifer improvement is the several decades it takes before stock deployment, which is particularly acute in the context of climate change and evolving wood markets. Use of genomic selection allows to drastically shorten breeding cycles, resulting in more flexibility and potentially increasing benefits. This study compares the financial performance of five white spruce (Picea glauca) breeding and deployment scenarios, from conventional breeding to genomic selection in conjunction with top-grafting or the use of somatic embryogenesis, in the context of plantations established by the Quebec government on public lands with banned herbicide use. We estimated the land expectation value (LEV) for the five scenarios applied to eight site productivity indices, and considered costs and revenues from breeding, plantation establishment, silviculture, and harvest. LEVs at 4% discount rate were positive for all scenarios on all site indices, and varied from $197 to $2015 ha−1assuming mechanical brushing of the plantations. The scenarios integrating genomic selection resulted in the highest LEVs, which increased with site index. We also conducted sensitivity analyses with 3% and 5% discount rates, with a range of costs and benefits, and with herbicide control of competing vegetation. These results should help orientate public investment decisions regarding the integration of genomic selection at the operational level in tree breeding and reforestation programs on public lands.

The laticifer density in callus of young tissue is positively correlated with the rubber yields of adult trees and can serve as an early selection marker to accelerate rubber tree breeding. The rubber tree (Hevea brasiliensis Muell. Arg.) is a perennial crop with a breeding cycle of approximately 30 years in the conventional breeding practices. The lack of suitable parameters linking the juvenile and adult trees has made the early selection attempts inefficient. We performed comparative morphology of laticifer cells in callus induced from young shoots and the primary and secondary laticifers in the trunk of adult trees, and investigated their relationships to rubber yields. Results indicate that the secondary laticifers have smooth lateral walls and perforated end walls and belong to articulated anastomosing laticifers. The primary laticifers are unbranched, non-articulated, and anastomosing, and have bumpy lateral walls when matured. The callus-derived laticifers are morphologically similar to the secondary laticifers with smooth lateral walls and the existence of end walls, and similar relative cell wall thickness. The laticifer density in callus and the laticifer ring number in bark are both genotype-dependent, and they are both highly correlated with the rubber yields with correlation coefficients R = 0.846 (P

Non-spatial and spatial analyses were carried out to estimate genetic parameters for growth and stem straightness traits between ages 4 and 7 in two series of eight progeny trials of Pinus elliottii Engelm. var. elliottii (PEE) established in 2004 and 2008, comprising 429 open-pollinated families from Instituto Nacional de Tecnología Agropecuaria (INTA) tree breeding population in Argentina. A first-order autoregressive spatial mixed model was found to significantly improve the fit of the model, compared with the standard non-spatial mixed model approach, due to substantial spatial heterogeneity within sites. The average individual-tree narrow-sense heritability estimates based on this spatial analysis were 0.49 for diameter at breast height, 0.36 for total height, and 0.48 for volume, with stem straightness being low to moderate (average = 0.11). The additive genetic correlation estimates between growth traits were positive (0.51 ≤ r^ a ≤ 0.99) and statistically significant from zero. In contrast, the genetic correlations between growth traits and stem straightness although in general also positive were not significantly different from zero (− 0.22 ≤ r^ a ≤ 0.59). Age-to-age genetic correlations were consistently higher for growth traits (r^ a ≥ 0.81) than for stem straightness (r^ a ≥ 0.33). The average additive genetic correlation estimated between sites within test series was high for all traits evaluated (average > 0.72). In contrast, average additive genetic correlation estimated between sites across series was slightly lower (average < 0.63). Implications of all these parameter estimates for genetic improvement of PEE in Argentina are discussed. Fil: Belaber, Ector C.. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Misiones. Estación Experimental Agropecuaria Montecarlo; Argentina Fil: Gauchat Funes, Maria Elena. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Misiones. Estación Experimental Agropecuaria Montecarlo; Argentina Fil: Rodriguez, Horacio Gustavo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Misiones. Estación Experimental Agropecuaria Montecarlo; Argentina Fil: Borralho, Nuno M.. Universidad de Lisboa; Portugal Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina

Forty-one E. bosistoana families were evaluated for the production of heartwood quantity and quality in two sites. High estimated heritabilities of heartwood diameter (HWD) were found in both sites (0.66 and 0.71). The estimated heritabilities of extractives content (EC) were lower with 0.16 and 0.25. Weak genetic correlations between HWD and EC were found in one site, but highly negative (− 0.86) genetic correlations were observed in the other. The G × E interaction had no significant influence on growth traits but a small-level influence on the EC. Five families were selected for tree breeding as they produced both large HWD and high EC in both sites. It was suggested that genetic breeding selection could improve the heartwood quantity and quality of E. bosistoana plantations.

Biomass production is traditionally an important goal in forest tree breeding programs. However, progress in classical tree breeding is limited because of long generation cycles of many forest tree species. Due to this limitation, genetic engineering, and also the quite recently developed genome editing technique, are very attractive tools to improve tree characteristics in a relatively short time. As a proof-of-concept approach, the GIBBERELLIC ACID 20 OXIDASE (GA20-OXIDASE) gene was constitutively overexpressed in poplar leading to significantly higher plants. Unfortunately, deleterious side-effects were also observed, like longer and thinner shoots leading to plants with unstable stems unable to grow without external stabilization. In the literature, polyploidization was reported to increase stem thickness relatively to plant height in several plant species. Therefore, polyploidization of GA20-OXIDASE overexpressing transgenic poplar lines was attempted. Mixoploid (ploidy chimeric: diploid and tetraploid nuclei) plants were obtained and assessed for several years for ploidy status and growth performance (stem height and diameter, bud set) in climate chamber and glasshouse. The results indicate that mixoploid GA20-OXIDASE overexpressing transgenic poplar still reveal increased growth but also showed a lower height-to-stem ratio compared to the diploid GA20-OXIDASE transgenic poplar, enabling the mixoploid transgenic plants to grow without external stabilization.

RAPD (randomly amplified polymorphic DNA) markers were employed to characterize polymorphisms among 5 provenances of Acacia leucophloea and to detect genetic relatedness of the species with 6 other acacias (A. holosericea, A. auriculiformis, A. mangium, A. dealbata, A. ferruginea, and A. nilotica) widely grown in India. Of 194 markers scored for the provenances, 29.38% exhibited polymorphism. Also, 326 markers were generated among 7 species of Acacia, accounting for 55.82% of the polymorphisms. The fifteen 10-mer primers employed were capable of producing 1–8 polymorphic bands for the provenances, and 6–17 for all seven species of Acacia. The genetic similarity coefficient based on Jaccard’s coefficient revealed that provenances Thirumangalam and Dharmapuri were closely related. The dendrogram based on a sequential agglomerative hierarchical non-overlapping (SAHN) clustering analysis grouped 4 provenances of A. leucophloea (Dharapuram, Thirumangalam, Pudukottai and Dharmapuri) into one cluster and the other provenance, Sendurai, into a separate cluster. The genetic similarity matrix for 7 Acacia species showed that A. nilotica and A. dealbata were distantly related, while A. holosericea and A. ferruginea were very closely related. Cluster analysis grouped the species of Acacias into 3 major groups of which A. dealbata alone formed a separate group. The RAPD markers generated 36 provenance-specific markers and 162 species-specific markers that could have strong applications for species identification and tree breeding programs for A. leucophloea and for other Acacia species included in this study.

We investigated genetic parameters for juvenile to mature growth and stem forking in black spruce [Picea mariana (Mill.) B.S.P.] in order to obtain reliable estimates for supporting eastern Canadian tree breeding strategies. The study was based on data collected from two series of progeny tests of black spruce in New Brunswick (NB) including 285 open-pollinated families and more than 57,000 individual trees. Height (HT), diameter at breast height (DBH), and stem forking (SF) were periodically measured between ages 5 and 35 years. Results showed that tree volume (V), HT and DBH were highly genetically controlled, with average individual narrow-sense heritability ( $$h_{i}^{2}$$ ) estimates of 0.29, 0.29 and 0.21, and family mean heritability ( $$h_{F}^{2}$$ ) estimates of 0.82, 0.85 and 0.77, respectively. SF had low $$h_{i}^{2}$$ (= 0.06 on average) but had moderate $$h_{F}^{2}$$ (= 0.56), indicating family selection might effectively reduce SF. Both $$h_{i}^{2}$$ and $$h_{F}^{2}$$ increased with age and then stabilized or declined, being the highest around ages 15–20 years for all traits. The type-B genetic correlation ( $$r_{B}$$ ) estimates were moderate to high for all the traits, suggesting negligible genotype × environment interactions. Strong age–age genetic correlation estimates were found for growth traits, implying the potential for practicing early selection. Age–age genetic correlation estimates were moderate for SF (= 0.72). Trait–trait genetic correlation estimates were strong and positive among growth traits, but between growth traits and SF they were mostly negligible albeit positive. Overall, results suggest that genetic selection will be effective for growth traits but much less so for reducing stem forking in New Brunswick’s black spruce.

Financial performance of the P. patula × P. tecunumanii, P. greggii × P. tecunumanii, P. taeda × P. tecunumanii hybrids and their parental species was studied for South Africa. A model was developed for use in determining the profitability of a tree-breeding program (TBP) with pine hybrids in commercial plantations. Growth measurement data were collected in four, 12-year-old genetic trials on Mondi and Sappi land holdings in South Africa. Growth models developed for P. patula and P. taeda in South Africa were used to infer models for the other taxa and to calculate the optimal financial rotation age at discount rates of 6 and 8%. Financial data on pine plantations were collected from different sources in South Africa. Optimal rotation lengths in this study were found to be between 12 and 16 years for pulpwood and 17 years for sawtimber. The model output shows the net present value (NPV), the internal rate of return, and the minimum area that a tree grower has to plant every year in order to justify the investment in a TBP. A stochastic approach with Monte Carlo simulation showed that the sensitivity of NPV to uncertainty in the wood price was greater than that for the planting, harvesting, and transport costs.

Understanding genetic variation is important for efficiently selecting excellent clones and utilizing genetic resources during tree breeding. We investigated 16 growth traits of 50 32-year-old Pinus koraiensis clones. Analyses of variance showed that all the test traits differed significantly among clones. Average height, diameter at breast height (DBH), and volume of all clones were 10.41 m, 21.30 cm, and 0.148 m3, respectively. Phenotypic coefficients of variation and repeatabilities of traits ranged from 4.37 to 48.03% and from 0.013 to 0.900, respectively. There exists significant positive correlations among heights, diameter at different heights (1.3, 3.0, 5.0 m), and volumes; genetic correlation was close to phenotype correlation. Using four growth traits (height, DBH, volume, average crown width) as indices for a comprehensive evaluation, five clones (PK 11, PK 19, PK 04, PK 14, and PK 28), whose traits scored in the top 10%, were selected as elite clones. For these clones, genetic gains in height, DBH, volume and crown height were 8.58, 13.02, 32.72 and 3.83%, respectively. These results provide important information for improving P. koraiensis breeding programs.

We report a genomic selection (GS) study of growth and wood quality traits in an outbred F2 hybrid Eucalyptus population (n=768) using high-density single-nucleotide polymorphism (SNP) genotyping. Going beyond previous reports in forest trees, models were developed for different selection targets, namely, families, individuals within families and individuals across the entire population using a genomic model including dominance. To provide a more breeder-intelligible assessment of the performance of GS we calculated the expected response as the percentage gain over the population average expected genetic value (EGV) for different proportions of genomically selected individuals, using a rigorous cross-validation (CV) scheme that removed relatedness between training and validation sets. Predictive abilities (PAs) were 0.40–0.57 for individual selection and 0.56–0.75 for family selection. PAs under an additive+dominance model improved predictions by 5 to 14% for growth depending on the selection target, but no improvement was seen for wood traits. The good performance of GS with no relatedness in CV suggested that our average SNP density (~25 kb) captured some short-range linkage disequilibrium. Truncation GS successfully selected individuals with an average EGV significantly higher than the population average. Response to GS on a per year basis was ~100% more efficient than by phenotypic selection and more so with higher selection intensities. These results contribute further experimental data supporting the positive prospects of GS in forest trees. Because generation times are long, traits are complex and costs of DNA genotyping are plummeting, genomic prediction has good perspectives of adoption in tree breeding practice.

Acacia hybrids offer a great potential for paper industry in Southeast Asia due to their fast growth and ability to grow on abandoned or marginal lands. Breeding Acacia hybrids with desirable traits can be achieved through marker assisted selection (MAS) breeding. To develop a MAS program requires development of linkage maps and QTL analysis. Two mapping populations were developed through interspecific hybridization for linkage mapping and QTL analysis. All seeds per pod were cultured initially to improve hybrid yield as quality and density of linkage mapping is affected by the size of the mapping population. Progenies from two mapping populations were field planted for phenotypic and genotypic evaluation at three locations in Malaysia, (1) Forest Research Institute Malaysia field station at Segamat, Johor, (2) Borneo Tree Seeds and Seedlings Supplies Sdn, Bhd. (BTS) field trial site at Bintulu, Sarawak, and (3) Asiaprima RCF field trial site at Lancang, Pahang. During field planting, mislabeling was reported at Segamat, Johor, and a similar problem was suspected for Bintulu, Sarawak. Early screening with two isozymes effectively selected hybrid progenies, and these hybrids were subsequently further confirmed by using species-specific SNPs. During field planting, clonal mislabeling was reported and later confirmed by using a small set of STMS markers. A large set of SNPs were also used to screen all ramets in both populations. A total of 65.36% mislabeled ramets were encountered in the wood density population and 60.34% in the fibre length mapping population. No interpopulation pollen contamination was detected because all ramets found their match within the same population in question. However, mislabeling was detected among ramets of the same population. Mislabeled individuals were identified and grouped as they originated from 93 pods for wood density and 53 pods for fibre length mapping populations. On average 2 meiotically unique seeds per pod (179 seeds/93 pods) for wood density and 3 meiotically unique seeds per pod (174 seeds/53 pods) for fibre length mapping population were found. A single step statistical method was used to evaluate the most informative set of SNPs that could subsequently be used for routine checks for mislabeling in multi-location field trials and for labelling superior clones to protect breeder’s rights. A preliminary set of SNPs with a high degree of informativeness was selected for the mislabeling analysis in conjunction with an assignment test. Two subsets were successfully identified, i.e., 51 SNPs for wood density and 64 SNPs for fibre length mapping populations to identify all mislabeled ramets which had been previously identified. Mislabeling seems to be a common problem due to the complexity involved in the production of mapping populations. Therefore, checking for mislabeling is imperative for breeding activities and for analyses such as linkage mapping in which a correlation between genotypic and phenotypic data is determined.

Tree planters of the Yucatan peninsula in Mexico are mostly first-generation small-scale forest owners. As a consequence of the lack of a management plan, trees employed for plantations are currently produced without any traceability or genetic improvement protocol, resulting in the reduced quality and heterogeneity of established materials. Recently, the Mexican government published a law to force planters to reverse this situation through the initiation and operation of germplasm management and traceability programs within each physiographic sub-province. Thus, planters located in the “Campeche Karts sub-provenance” now need to select superior trees for plant production, provenance assays, and orchard establishment. As a reference for the improvement goals in this work, we developed a model ideotype tree and qualification tool based on a weight-free selection index to compare trees in established plantations to enable the effective selection of superior trees to be used as seed sources and as a starting population for genetic improvement programs. The tool presented here is easy to use by planters, requiring a very basic computer or smartphone to run a spreadsheet where simple morphometric evaluation are captured, trees are qualified in comparison to the ideotypic values of each parameter with the aid of common field equipment. When this tool was applied to individuals from two different plantations, the qualification methodology ranked the individuals, allowing for the selection of superior trees in a more robust way, in contrast to the use of parameters mostly based on price and driven by wood volume.

There has been an increased interest in tree breeding for resistance to exotic pests and pathogens, however relatively little research has focused on the reintroduction of these tree species. Understanding the durability of resistance in field settings and the field performance of improved trees is critical for successful species reintroduction. To evaluate methods for reintroducing American chestnut [Castanea dentata (Marsh.) Borkh] to managed forests on the Cumberland Plateau, we quantified four-year survival and growth and three-year competitive ability of chestnut seedlings planted on the Daniel Boone National Forest in southeastern Kentucky, USA. We used a split-plot design to compare chestnut response among three silvicultural treatments spanning a gradient of light levels; midstory removal, thinning, and shelterwood with reserves (2, 24, and 65% available photosynthetically active radiation, respectively) and three chestnut breeding types; American, Chinese (C. mollissima Blume.), and BC2F3 hybrid. One of two hybrid families planted had similar survival to American chestnuts, 21 and 27% survival, respectively, while the other had better survival, 57%. Chinese chestnut survival was better than the other breeding generations (90%). High mortality among American and hybrid chestnut seedlings was likely caused by infection from Phytophthora cinnamomi Rands. Incidence of blight infection was low. While chestnut seedling growth was greatest in the high-light treatment, competitive ability of chestnut, evaluated by comparing planted seedling height to height of understory competitors, was maximized in the intermediate light treatment. These results demonstrate the importance of evaluating competition pressure from co-occurring vegetation and field performance of resistant genotypes when assessing methods for reintroducing tree species to forested settings.

Tree breeders must almost always address multiple traits. That entails choosing selection methods and weighing up known or assumed economic-worth functions for traits. Classically, selection methods include independent culling levels, sequential culling for traits within generations, culling for different traits in successive generations (tandem selection), and selection indices, but elements of individual methods can be used in combination. Adverse genetic correlations among economic traits create a need to know the comparative economic worth of gains in different traits and can severely constrain feasible breeding goals. A traditionally cited optimal method is the Smith-Hazel selection index (and more generalised variants) based on good genetic-parameter information and known, linear economic-worth functions. The theoretical optimality, however, depends on various assumptions which are often tacit and unrecognised, and violated. Optimally cost-efficient selection will also depend on evaluation costs and ages of expression for different traits and may need to go well beyond selection indices. More complex criteria of optimality may also arise, making true optimisation very challenging and often unachievable. Where the genetic gain is delivered as mixes of segregants produced by seed propagation, non-linearities of economic-worth functions may not be readily exploited. However, non-linearities that include intermediate optima for trait values, or optima that are conditional on values for other traits (namely restricted domains in ‘multi-dimensional space’), might be exploited much better in clonal forestry systems. With adverse genetic correlations and differences among environments in the expression of genetic variation in individual traits, optimal solutions may entail selection for specific environments or production systems, on a finer scale for deployment than in breeding populations. Genomic selection offers accelerated genetic gains, and may mitigate effects of adverse genetic correlations, but depends strongly on high-quality phenotypic information on the expression of different traits at different ages in specific environments. This technology and its potential combination with gene editing promise enhancements of multi-trait selection. Remote-sensing technologies can now yield huge volumes of field data and much expanded candidate populations, but in some trade-off with effective heritabilities of remote-sensed phenotypes.

Avocado (Persea americana) is an important tropical and subtropical fruit tree crop. Traditional tree breeding programs face the challenges of long generation times and significant expense in land and personnel resources. Avocado selection and breeding can be more efficient and less expensive through the development and application of molecular markers. A total of 1524 individuals were genotyped with 384 SNPs creating the largest SNP genotype database for avocado. These individuals correspond to four extensive germplasm collections including two housed in Florida and two in California. In addition, hybrids and selections from two rootstock breeding programs have been genotyped. Genotype data were analyzed using an affinity propagation method to define 155 groups. The 384 SNP markers provided accurate genotype data for individuals from different Persea species as well as half-siblings. Therefore, the majority of the genetic diversity of the avocado germplasm and related species that were genotyped has been captured. A simple visual method can also be used to identify self-pollinated individuals among the half-siblings of known maternal parents and, in some cases, to infer likely candidates for the paternal parent. Finally, this dataset is unambiguous so breeders can determine the genetic diversity of their breeding stock to optimize avocado breeding and selection programs by identifying outcrossed individuals at the seedling stage, thus increasing the efficiency of avocado genetic improvement.

Cloned progeny tests in forest tree breeding provide the ability to assess the same genotypes across multiple environments and partition observed phenotypic variance into additive and non-additive genetic effects. In this study, 2362 clones from 53 crosses of loblolly pine (Pinus taeda L.) were tested across eight locations in the Southern US. Alpha cyclic incomplete row-column design was used to accommodate a large number of clones in a replication. Tree stem volume (cubic decimeter) was assessed at age 6 using various variance-covariance structures of mixed models. Models with factor analytic additive genetic structures and spatially correlated residuals or polynomial fixed row and column effects efficiently captured heterogeneity in the data. The narrow-sense clone mean heritability estimate for stem volume was 0.41 for the simple compound symmetry additive genetic structure. The estimates were higher for more complex models, ranging from 0.56 to 0.61. Non-additive genetic variance for stem volume was about a fraction of the additive genetic variance, suggesting that the trait is mainly controlled by large number of genes each with small effect. The results suggested that for forest trees genetic field tests with large number of genetic entries, breeders should consider incomplete row-column designs to model micro-site heterogeneity in two directions. These designs allow spatial modeling using row and column information, which can efficiently account for heterogeneity in the environment, resulting in higher heritability estimates and more reliable ranking of varieties for selection.

Genetic variance includes both additive and non-additive components, and the latter can be partitioned into dominance and epistatic variance. Additive genetic variance has been the main source of genetic improvement in most tree breeding programs and the genetic gain achieved has mostly been deployed through open-pollinated seed orchards. However, non-additive effects could be exploited in alternative deployment programs and provide additional genetic gain. Thus, knowledge of non-additive effects is essential for constructing robust genetic models and evaluating vegetative deployment systems, particularly for clonal forestry. In this study, we used data drawn from seven Norway spruce full-sib and three half-sib clonal trials to test and compare different models partitioning genetic effects into additive, dominance, and epistatic components for height and diameter. Simpler models provided more robust estimates of additive and non-additive effects, whereas more complex models provided more detail and insight in performance at single sites and G × E patterns, but with less reliable estimates. In this study, we cannot clearly distinguish the size and importance of dominance and epistatic effects. However, the total non-additive effects seem to be substantial, being around 80–90% of the additive, and were of the magnitude required to consider clonal forestry as an alternative to current deployment systems. Additive correlations largely followed the expected patterns based on seed zones and late spring frost incidence. Clonal correlations were generally lower than the additive implying that G × E interactions were stronger for non-additive effects.

International audience; AbstractKey messageTo inform emerging initiatives, we explored five programmes that aimed to develop trees resistant to specific pests or pathogens. These case studies show resistant tree programmes are a medium to long-term approach requiring sustained investment, and can encounter substantial difficulties in developing and maintaining resistance. Equally, adequately resourced and well-planned programmes have resulted in operational deployment of resistant trees.ContextDeveloping trees that are resistant to specific pests and pathogens is an increasingly prominent strategy for responding to this escalating threat. It is therefore important to ensure decisions to use resistant trees and approaches to development are well-informed.AimsWe aimed to provide insights for newer or proposed resistant tree breeding programmes by identifying key lessons from earlier programmes, some of which date back several decades.MethodsWe selected five mature programmes as case studies, and in each case synthesised information from key publications and by following citations to original sources. We examined the objectives, methods, problems, successes and timescales in each programme.ResultsResistant tree breeding is generally a medium to long-term approach requiring sustained investment and co-ordination, although culturally valued species can attract considerable support from volunteers. Deployment of resistant trees often recommends maintaining genetic variation and mixing with other tree species. Substantial costs and loss of confidence in future material can arise if resistance breaks down or resistant material is susceptible to other threats.ConclusionThe case studies illustrate success is not guaranteed, but also provide evidence that adequately resourced and well-planned resistant tree programmes can contribute to strategies to mitigate impacts from pests and pathogens.

Myrtle rust, caused by the pathogen Austropuccinia psidii, is a disease affecting numerous species of Myrtaceae around the globe. Many Australian ecosystems are dominated by Myrtaceae, making them, along with the industries that rely on them, particularly vulnerable to this disease. With over 800 endemic species, Eucalyptus is a major genus within the Myrtaceae in Australia. Wide variation in response to A. psidii infection, from extreme susceptibility to resistance, has been reported among Eucalyptus species in which any pre-formed resistance to this invasive pathogen is unexpected. This study aims to define and contrast geographical patterns of variation in rust susceptibility within the overlapping, natural ranges of Eucalyptus globulus and Eucalyptus obliqua, two commercially and ecologically important species from different Eucalyptus subgenera. Phenotypic disease screening of seedlings of E. globulus races and E. obliqua forest districts (defined geographically) showed E. obliqua to be more susceptible than E. globulus with significant differences in disease susceptibility and symptomatic trait expression. Eucalyptus globulus showed a trend for decreased susceptibility to A. psidii from south- to north-eastern Tasmania, eastwards along the Otway Ranges and southward from the Strzelecki Ranges to the Wilson Promontory Lighthouse in Victoria, but no such geographical patterns were observed within E. obliqua. No significant correlations were found between climatic conditions (i.e. rainfall, temperature and elevation) and rust susceptibility at provenance levels in either species. Taken together, these results support a hypothesis that population divergence in resistance to A. psidii has not been driven by climate.

Background Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species. Results Targeted sequencing was achieved by capturing P. abies exome with probes previously designed from the sequenced transcriptome of white spruce (Picea glauca (Moench) Voss). Capture efficiency was high (74.5%) given a high level of exome conservation between the two species. Using stringent criteria, we delimited a set of 61,771 high-confidence SNPs across 13,543 genes. To validate SNPs, a high-throughput genotyping array was developed for a subset of 5571 predicted SNPs representing as many different gene loci, and was used to genotype over 1000 trees. The estimated true positive rate of the resource was 84.2%, which was comparable with the genotyping success rate obtained for P. abies control SNPs recycled from previous genotyping efforts. We also analyzed SNP abundance across various gene functional categories. Several GO terms and gene families involved in stress response were found over-represented in highly polymorphic genes. Conclusion The annotated high-confidence SNP catalog developed herein represents a valuable genomic resource, being representative of over 13 K genes distributed across the P. abies genome. This resource should serve a variety of population genomics and breeding applications in Norway spruce. Electronic supplementary material The online version of this article (10.1186/s12864-018-5247-z) contains supplementary material, which is available to authorized users.

We used spatial, global trend and post-blocking analysis to examine the effectiveness of a progeny trial in a tree breeding program for Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) on a hilly site with an environmental gradient from hill top to bottom. Diameter at breast height (DBH) and tree height data had significant spatial auto-correlations among rows and columns. Adding a first-order separable autoregressive term more effectively modelled the spatial variation than did the incomplete block (IB) model used for the experimental design. The spatial model also accounted for effects of experimental design factors and greatly reduced residual variances. The spatial analysis relative to the IB analysis improved estimation of genetic parameters with the residual variance reduced 13 and 19% for DBH and tree height, respectively; heritability increased 35 and 51% for DBH and tree height, respectively; and genetic gain improved 3–5%. Fitting global trend and post-blocking did not improve the analyses under IB model. The use of a spatial model or combined with a design model is recommended for forest genetic trials, particularly with global trend and local spatial variation of hilly sites.

Hybridization experiments among fir (Abies) species contribute to clarification of both crossability and evolutionary relationships of organisms at least from the second half of the nineteenth century. The main aim of our study was to find possible effects of hybridization on survival rate and two growth parameters (height and diameter at the breast height) of fir trees at various levels of complexity in the Czech Republic. We compared (1) pure species consisting of seven fir taxa, (2) open pollinated hybrids comprising of twenty-one hybrid progenies of Greek Fir (A. cephalonica), Cilician Fir (A. cilicica) and Algerian Fir (A. numidica) and (3) artificial complex hybrids of Korean Fir (A. koreana) × (A. cilicica × A. cephalonica). For our analyses, we used combination of so-called traditional statistical methods and spatial modelling. Our results revealed that a higher level of hybridization and introgression may lead to a higher survival rate and furthermore, that neglecting of spatial autocorrelation in randomized complete block design might lead to wrong conclusions—because our analyses on height showed contrasting results between traditional and spatial modelling. The results of this study appear to be a good message for scientists dealing with forest tree breeding and facing a lack of confidence by practice. They might be also a good news for forestry practice, where foresters face high mortality during afforestation, e.g. in extreme environmental conditions. Our study highlighted that neglecting spatial autocorrelation could possibly lead to wrong conclusions in studies of similar spatial scale level.

International audience; AbstractKey messageAccurate evaluation of genetic performances of trees is crucial in order to improve the efficiency of forest tree breeding. We revealed that spatial analysis is effective for predicting individual tree breeding values at the forward selection stage ofCryptomeria japonicaD. Don (sugi) breeding program by using a novel validation approach.ContextIn the process of selecting genetically superior trees for breeding, appropriate handling of environmental effects is important in order to precisely evaluate candidate trees. Spatial analysis has been an effective statistical approach for genetic evaluation at sites with heterogeneous microenvironments. However, the efficiency of spatial analysis on forward selection has not been validated on a practical scale to date.AimsThis study aimed to reveal the effectiveness of spatial analysis, which incorporates spatially autocorrelated residuals into mixed models, for the prediction of breeding values at the forward selection stage by validation using progeny or clonal tests of forward-selected individuals.MethodsTree height was analyzed by ordinary randomized complete block design models and spatial models incorporating spatially autocorrelated residuals in a linear mixed model framework, and model selection was conducted at thirty Cryptomeria japonica D. Don breeding population sites having various topographical ruggedness. For validation, three clonal tests and one progeny test of individuals selected from three and four breeding populations, respectively, were used. The effectiveness of forward selection using the two models was evaluated based on the correlation between individual breeding values at the stage of forward selection and genotypic and breeding values that were estimated by clonal and progeny tests.ResultsSpatial models were more predictive than ordinary models in all cases. Spatial correlation parameters tend to increase with the topographical ruggedness index of each site. The correlation coefficients between breeding values at the time of forward selection and genotypic or breeding values evaluated in succeeding clonal and progeny tests were significantly higher in spatial models than in ordinary models in six out of nine cases.ConclusionValidation using progeny and clonal tests of forward-selected individual trees revealed that spatial analysis is more effective for the evaluation of genetic performance of individuals at the stage of forward selection in Cryptomeria japonica.

Through stochastic simulations, estimates of breeding values accuracies and response to selection were assessed under traditional pedigree-based and genomic-based evaluation methods. More specifically, several key parameters such as the trait’s heritability (0.2 and 0.6), the number of QTLs underlying the trait (100 to 200), and the marker density (1 to 10 SNPs/cM) were evaluated. Additionally, impact of two contrasting mating designs (partial diallel vs. single-pair mating) was investigated. Response to selection was then assessed in a seed production population (seed orchard consisting of unrelated selections) for different effective population sizes (Ne = 5 to 25). The simulated candidate population comprised a fixed size of 2050 individuals with fast linkage disequilibrium decay, generally found in forest tree populations. Following the genetic/genomic evaluation, top-ranked individuals were selected to meeting the predetermined effective population size in target production population. The combination of low h2, high Ne, and dense marker coverage resulted at maximum relative genomic prediction efficiency and the most efficient exploitation of the Mendelian sampling term (within-family additive genetic variance). Since genomic prediction of breeding values constitutes the methodological foundation of genomic selection, our results can be used to address important questions when similar scenarios are considered.

Quasi-field trials (QFTs) using offspring from first-generation plus trees of Abies bornmulleriana were established on two sites in Denmark via DNA markers and parentage analysis. The aim of this study was to demonstrate an example of ad hoc breeding to make better genetic material available for Christmas tree production. Assessments of several important Christmas tree quality-associated phenotypic traits were made for all offspring individuals in delineated areas of the production stands, and moreover the best individuals in the whole production stands were identified. Postharvest needle retention was evaluated in the parent population in both 2016 and 2017. The results showed that by combining available methodology and pre-selected material, substantial genetic gain in relation to Christmas tree production in A. bornmulleriana could be achieved. Backward selection seems tempting due to its shorter time horizon for delivering improved genetic material. Postharvest needle retention evaluation can be a cheap but important last step in modifying the backward selection. We propose to combine the results based on QFTs with selective seed harvest and paternity tests to give the best possible starting point for production of clonal A. bornmulleriana plants using somatic embryogenesis (SE).

Key message In Chile, breeding radiata pine for growth has led to drifts in the degree of drought tolerance of the seedlings. Interior provenances gained a larger tolerance to drought after three breeding generations as shown by larger survival and root/shoot ratio under water shortage, while coastal provenance displayed an opposite trend. • Context Given that rainfall is predicted to decrease and to affect establishment and early survival of radiata pine (Pinus radiata D. Don) in Chile, there is a need to identify more drought tolerant genotypes at seedling stage. • Aims The aim of this study was to test whether provenances of P. radiata originating from interior or from coastal provenances, displayed different responses to short-term water shortage, and whether these responses differed from the first to the third breeding generation. • Methods Three generations of breeding families from two sites in Central Chile were compared. The seedlings were grown during 100 days and subjected to two watering regimes for 45 days. Survival, growth, and biomass allocation to roots and shoots were recorded. • Results The two provenances displayed different responses to drought. Biomass allocation to shoots and survival were significantly reduced by water shortage. The first generation seedlings from the coastal provenance displayed a larger survival rate when exposed to water shortage (i.e., 60 %); this rate decreased in the following breeding generations. On the contrary, the survival rate increased from the first to the third generation in the interior provenance. • Conclusions We observed an important local adaptation to water shortage in the interior provenance. This response may be due to the fact that parent tree populations of the interior provenance have successfully adapted to sites with periodic drought.

Wood volume growth per unit evapotranspiration was calculated from water balance and growth measurements in irrigated and water-limited Eucalyptus globulus and E. nitens plantations in the 3rd, 4th and 5th year of growth. Wood volume growth per unit evapotranspiration (plantation water productivity) was increased by irrigation for both species in the 3rd and 4th growing year but only in E. nitens in the 5th year. Irrigated trees required significantly less water than water-limited trees to produce 1 m3 of wood. At the same site, stomatal conductance was significantly greater in irrigated compared to water stressed trees through spring, summer and early autumn of each year. These data provide indirect evidence that leaf-scale measures of water-use efficiency are not well correlated with stand-scale measures of plantation water productivity. This was probably due to increased proportional allocation of assimilated carbon to stem wood in the irrigated compared to the water-limited stands. These results are consistent with recent studies in Brazil and Australia and suggest that plantation management systems, inclusive of tree breeding, that maximise growth rather than leaf-scale water-use efficiency, will also maximise the amount of wood produced from each unit of water used by the stand.

Turkey ranked third place in the world for chestnut production after China and South Korea and the country has unique chestnut forests including valuable and diverse chestnut genotypes. This study was conducted to select superior chestnut genotypes within seedling populations found in natural wild grown chestnut forest located in Isparta province in Turkey during 2010–2011 years. A total of 2500 wild grown chestnut trees were examined on the field first year and among them the most promising 22 genotypes were chosen according to relatively high yield capacity, earliness, tolerance to chestnut blight (Cryphonectria parasitica), ink disease (Phytopthora cambivora), and fruit quality characteristics. The selected 22 genotypes were evaluated for their detailed morphological, phenological and pomological traits in 2010 and 2011. According to average of 2 years, nut weight, the number of nut per kilogram, nut width, nut length, nut height and nut shell thickness of 22 promising genotypes ranged from 10.26 to 22.32 g, 97.47 to 44.80/kg, 26.80 to 42.47, 16.92 to 25.91, 27.74 to 39.73, and 0.26 to 1.01 mm, respectively. The ash, crude protein, and total fat content of kernels were between 0.85 to 1.94, 3.69 to 7.06 and 1.32 to 4.52, respectively. The genotypes were evaluated with weighted ranking method and the highest general quality score was observed in genotypes of IY17, IY01, IY42, IY43 and IY12.

The selected germplasm of Ficus carica established in a gene bank collection will be useful for conservation and management and important for fig tree breeding programs. Advancement in plant breeding is assisted by accurate information on genetic diversity and structure. A collection of ninety fig tree (Ficus carica L.) cultivars originating from the Mediterranean basin and conserved in an ex situ gene bank collection was genotyped using seven microsatellite markers. A total of 91 alleles were detected presenting an average of 13 alleles per locus. The gene bank fig tree collection preserved a high level of genetic diversity. The mean expected and observed heterozygosities over the seven single locus microsatellites averaged 0.747 and 0.784, respectively. The total value of the probability of identity was 2 × 10−6. The 90 fig tree accessions formed four clusters in the unweighted pair group method using arithmetic averages (UPGMA) dendrogram, although the clustering did not indicate any clear division among the fig tree accessions based on their geographical origin. Moreover, the 90 fig tree accessions could be divided into two clusters based on STRUCTURE analysis. Additionally, microsatellites coupled with high-resolution melting analysis enabled both the distinction, identification and authentication of the ‘Kymis’ fig tree Protected Designation of Origin cultivar and its products. In conclusion, results presented here are significant for the management of gene bank collections, breeding programs and authentication of fig tree cultivars.

Radiata pine plantation resources in Australia and New Zealand are a highly productive source of solid-wood and pulp products for domestic consumption and export. This has largely been achieved through long-term investments in tree breeding programs that select the best-performing genotypes for varied regional environments. However, climate change could threaten the realisation of genetic improvement in plantations due to suboptimal matching of improved planting stock to new climate conditions. Here, we investigate how information from genetic field tests could be utilised under anticipated climate change. We use principal component analysis and Mahalanobis distance measures to find the closest match between climate of plantation regions in the future and current climate of field test sites. By 2050, future climates of some important plantation regions are expected to match climates currently present in different regions. For example, future climates of Green Triangle, a key plantation region in Australia, will better match current climate of Western Australia. The Central North Island of New Zealand will shift to warmer and wetter climate with no current analogue, and Western Australia, to warmer and drier no-analogue climate. The latter is also likely to fall outside the climate niche where radiata pine can be grown in the future. Nevertheless, for the majority of radiata pine plantation regions in Australia and New Zealand our analysis provides a framework of how anticipated climate change can be addressed in tree improvement programs using existing field tests.

The emerald ash borer (EAB; Agrilus planipennis Fairmaire) is a bark and wood boring beetle native to east Asia that was first discovered in North America in 2002. Since then, entire stands of highly susceptible green ash (Fraxinus pennsylvanica Mar- shall) have been killed within a few years of infestation. We have identified a small number of mature green ash trees which have been attacked by EAB, yet survived the peak EAB infestation that resulted in mortality of the rest of the ash cohort. Adult landing and feeding preference bioassays, leaf volatile quantification and EAB egg bioassay experiments were used to characterize potential differences in responses of these select ''lingering'' green ash trees relative to known EAB susceptible controls. Three selections were identified as being significantly less preferred for adult feeding, but no specific leaf volatile profile was associated with this reduced preference. Egg bioassays identified two ash selections that had significant differences in larval survival and development; one having a higher number of larvae killed by apparent host tree defenses and the other having lower larval weight. Correlation and validation of the bioassay results in replicated plantings to assess EAB resistance in the field is still necessary. However, the differences between lingering ash selections and susceptible controls measured by these bioassays indicate that more than one mechanism is responsible for the increased resistance to EAB that resulted in these selections surviving longer than their counterparts. Efforts to further increase ash resistance to EAB through use of these selections in a breeding program are underway.

Woody biomass feedstock produced from hybrid poplar can be converted into bioenergy via thermochemical and biochemical processes. To better understand the genetic control of key properties (biomass production, extractives, holocellulose, lignin, and higher heating value) that relate to the quality of biomass feedstock in triploid hybrid clones of Populus tomentosa, genetic relationships among selected traits were examined in 5-year-old clonal field trials located in Yanzhou, Gaotang, Xiangfen, Zhengzhou, and Taiyuan, northern China. In total, 270 trees from nine clones were sampled from the five sites. Site had a highly significant (P

Mutational witches’ broom clones show a growth redistribution compared with normal clones. The main factor affecting the variations in mutant clone morphology is the strength of the mutation. Mutational witches’ broom is a fragment of the tree crown with abnormally dense branching and slower shoot growth, compared with those of a normal crown. Thousands of dwarf ornamental cultivars widely used in landscape design have been developed from mutational witches’ broom. In this study, crown morphology was compared between grafted clones of witches’ broom and normal clones from the same trees. The results quantify variations in crown structure between the mutants and normal clones. The sample materials were 10 pairs of grafted witches’ broom and normal crown clones of Pinus sibirica. The mutant and normal clones were discrete sets. Many morphological traits were affected in the mutants. Compared with the normal-crown clones, the mutants showed male sterility, decreased apical dominance, reduced shoot and needle length, and increased branching and seed cone bearing. In terms of morphogenic changes induced by the mutation, the shoots of the witches’ broom clones were bicyclic, generated seed cones that were much shorter than those of normal clones, and had acquired the ability to form lateral buds. The extent of interclonal variation was significantly greater among witches’ broom clones than among normal clones. Compared with the morphological traits of normal clones, those of the mutants were shifted in the same direction but to different extents. Therefore, mutational witches’ broom is the expression of a mutation that can be weak, medium, or strong. These results will be useful for unraveling the genetic basis of witches’ broom in conifers and for breeding new dwarf cultivars.

Most Argentinean forests have been lost by over exploitation and expansion of agricultural areas. The National breeding program for the native species Prosopis alba is still in its initial phase with only a few progeny trials installed from material collected in the wild and the first genetic studies are underway. Breeding value (BV) estimates based on pedigree data from a progeny trial were first compared to those derived by using microsatellite based kinship estimates to confirm the potential accuracy of g-best linear unbiased predictions (G-BLUP) when pedigree information is lacking. Afterwards, the possible genetic effects of alternative selection strategies to collect improved seeds from a wild population were evaluated. To achieve this goal the relationship among average genetic gain (predicted by G-BLUP), inbreeding and sampling size of the collected materials were weighed in a wild population consisting of trees of similar ages. The results obtained suggest that kinship estimates based on molecular data and breeding value predictions BV used for the selection of elite trees in wild populations may contribute to improve the genetic properties of the founder population. Controlling kinship allows reducing sampling size from 20 to 10 individuals per origin with no significant increase of inbreeding or loss of genetic gain. For a selected group of only ten top individuals per origin, the replacement of two strongly reduces the average group coancestry with minimal gain loss. Simultaneous selection for two traits by selection index might produce a gain of near 6 % in height and 2 % in diameter. The use of molecular marker information may contribute to reduce the time needed in a P. alba improvement program. Fil: Bessega, Cecilia Fabiana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina Fil: Pometti, Carolina Luciana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina Fil: Ewens, Mauricio. Universidad Católica de Santiago del Estero. Estación Experimental Fernández; Argentina Fil: Saidman, Beatriz Ofelia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina Fil: Vilardi, Juan Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina