Search

Genomic Selection (GS) in tree breeding optimizes genetic gains by leveraging genomic data to enable early selection of seedlings without phenotypic data reducing breeding cycle and increasing selection intensity. Traditional assessments of the potential of GS in forest trees have typically focused on model performance using cross-validation within the same generation but evaluating effectively realized predictive ability (RPA) across generations is crucial. This study estimated RPAs for volume growth (VOL), wood density (WD), and pulp yield (PY) across four generations breeding of Eucalyptus grandis. The training set spanned three generations, including 34,461 trees with three-year growth data, 6,014 trees with wood quality trait data, and 1,918 trees with 12,695 SNPs (single nucleotide polymorphisms) data. Employing single-step genomic BLUP, we compared the genomic predictions of breeding values (GEBVs) for 1,153 fourth-generation full-sib seedlings in the greenhouse with their later-collected phenotypic estimated breeding values (EBVs) at age three years. RPAs were estimated using three GS targets (individual trees, trees within families, and families), two selection criteria (single- and multiple-trait), and training populations of either all 1,918 genotyped trees or the 67 direct ancestors of the selection candidates. RPAs were higher for wood quality traits (0.33 to 0.59) compared to VOL (0.14 to 0.19) and improved for wood traits (0.42 to 0.75) but not for VOL when trained only with direct ancestors, highlighting the challenges in accurately predicting growth traits. GS was more effective at excluding bottom-ranked candidates than selecting top-ranked ones. The between-family GS approach outperformed individual-tree selection for VOL (0.11 to 0.16) and PY (0.72 to 0.75), but not for WD (0.43 vs. 0.42). Furthermore, higher levels of relatedness and lower genotype by environment (G × E) interaction between training and testing populations enhanced RPAs for VOL (0.39). In summary, despite limited effectiveness in ranking top VOL individuals, GS effectively identified low-performing individuals and families. These multi-generational findings underscore GS's potential in tree breeding, stressing the importance of considering relatedness and G × E interaction for optimal performance. [ABSTRACT FROM AUTHOR]

Cultivated cotton plants are the world's largest source of natural fibre, where yield and quality are key traits for this renewable and biodegradable commodity. The Gossypium hirsutum cotton genome contains ~80K protein-coding genes, making precision breeding of complex traits a challenge. This study tested approaches to improving the genomic prediction (GP) accuracy of valuable cotton fibre traits to help accelerate precision breeding. With a biology-informed basis, a novel approach was tested for improving GP for key cotton fibre traits with transcriptomics of key time points during fibre development, namely, fibre cells undergoing primary, transition, and secondary wall development. Three test approaches included weighting of SNPs in DE genes overall, in target DE gene lists informed by gene annotation, and in a novel approach of gene co-expression network (GCN) clusters created with partial correlation and information theory (PCIT) as the prior information in GP models. The GCN clusters were nucleated with known genes for fibre biomechanics, i.e., fasciclin-like arabinogalactan proteins, and cluster size effects were evaluated. The most promising improvements in GP accuracy were achieved by using GCN clusters for cotton fibre elongation by 4.6%, and strength by 4.7%, where cluster sizes of two and three neighbours proved most effective. Furthermore, the improvements in GP were due to only a small number of SNPs, in the order of 30 per trait using the GCN cluster approach. Non-trait-specific biological time points, and genes, were found to have neutral effects, or even reduced GP accuracy for certain traits. As the GCN clusters were generated based on known genes for fibre biomechanics, additional candidate genes were identified for fibre elongation and strength. These results demonstrate that GCN clusters make a specific and unique contribution in improving the GP of cotton fibre traits. The findings also indicate that there is room for incorporating biology-based GCNs into GP models of genomic selection pipelines for cotton breeding to help improve precision breeding of target traits. The PCIT-GCN cluster approach may also hold potential application in other crops and trees for enhancing breeding of complex traits. [ABSTRACT FROM AUTHOR]

Forests worldwide are under increasing pressure from climate change and emerging diseases, threatening their vital ecological and economic roles. Traditional breeding approaches, while valuable, are inherently slow and limited by the long generation times and existing genetic variation of trees. CRISPR technologies offer a transformative solution, enabling precise and efficient genome editing to accelerate the development of climate-resilient and productive forests. This review provides a comprehensive overview of CRISPR applications in forestry, exploring its potential for enhancing disease resistance, improving abiotic stress tolerance, modifying wood properties, and accelerating growth. We discuss the mechanisms and applications of various CRISPR systems, including base editing, prime editing, and multiplexing strategies. Additionally, we highlight recent advances in overcoming key challenges such as reagent delivery and plant regeneration, which are crucial for successful implementation of CRISPR in trees. We also delve into the potential and ethical considerations of using CRISPR gene drive for population-level genetic alterations, as well as the importance of genetic containment strategies for mitigating risks. This review emphasizes the need for continued research, technological advancements, extensive long-term field trials, public engagement, and responsible innovation to fully harness the power of CRISPR for shaping a sustainable future for forests. [ABSTRACT FROM AUTHOR]

Summary: Forests face many threats. While traditional breeding may be too slow to deliver well‐adapted trees, genomic selection (GS) can accelerate the process. We describe a comprehensive study of GS from proof of concept to operational application in western redcedar (WRC, Thuja plicata).Using genomic data, we developed models on a training population (TrP) of trees to predict breeding values (BVs) in a target seedling population (TaP) for growth, heartwood chemistry, and foliar chemistry traits. We used cross‐validation to assess prediction accuracy (PACC) in the TrP; we also validated models for early‐expressed foliar traits in the TaP.Prediction accuracy was high across generations, environments, and ages. PACC was not reduced to zero among unrelated individuals in TrP and was only slightly reduced in the TaP, confirming strong linkage disequilibrium and the ability of the model to generate accurate predictions across breeding generations. Genomic BV predictions were correlated with those from pedigree but displayed a wider range of within‐family variation due to the ability of GS to capture the Mendelian sampling term.Using predicted TaP BVs in multi‐trait selection, we functionally implemented and integrated GS into an operational tree‐breeding program. [ABSTRACT FROM AUTHOR]

Background: Larch is an important timber tree species. The traditional methods of tree genetic breeding have been progressing slowly. It is necessary to carry out gene function analysis and genetically modified breeding research. The NAC transcription factor family is a plant-specific transcription factor family with various biological functions, as shown in recent research. However, there are few studies on the NAC gene among gymnosperm coniferous species. Results: LoNAC3 with complete cds was identified and isolated from the cDNA of Larix olgensis based on transcriptome data. The cDNA length of LoNAC3 is 1185 bp, encoding 394 amino acids, with a conserved NAM domain located at the N-terminus, and subcellular localization in the nucleus. The results of real-time quantitative PCR analysis showed that at different growth stages and in different tissues of L. olgensis, the relative expression level of LoNAC3 was highest in the needles. After drought, salt, alkali stress and hormone treatment, expression was induced to different degrees. The expression level of LoNAC3 was significantly increased under drought and salt conditions. The relative expression level changed under methyl jasmonate (MeJA) and abscisic acid (ABA) treatment. By observing the phenotype of overexpressed LoNAC3 tobacco, it was found that overexpressed tobacco is shorter and blooms earlier than wild-type tobacco. Under abiotic stress, LoNAC3 overexpressed tobacco has lower germination rates and poorer growth status. Transgenic tobacco under stress treatment has a higher malondialdehyde (MDA) content than wild-type tobacco, while peroxidase (POD) activity is lower than wild-type tobacco. Conclusions: Through the analysis of LoNAC3 sequence and promoter expression, it can be concluded that LoNAC3 is involved in the drought and salt stress response processes of L. olgensis, and is induced by ABA and MeJA expression. Overexpression of LoNAC3 leads to stunted tobacco growth and negatively regulates its tolerance to drought and salt stress through the reactive oxygen species pathway. The preliminary analysis of the expression pattern and function of the LoNAC3 can provide a theoretical basis and high-quality materials for genetic improvement of larch in later stages. [ABSTRACT FROM AUTHOR]

Acacia crassicarpa is a fast-growing leguminous tree that is widely cultivated in tropical areas such as Indonesia, Malaysia, Australia, and southern China. This tree has versatile utility in timber, furniture, and pulp production. Illumina sequencing of A. crassicarpa was conducted, and the raw data of 124,410,892 reads were filtered and assembled de novo into 93,317 unigenes, with a total of 84,411,793 bases. Blast2GO annotation, Benchmark Universal Single-Copy Ortholog evaluation, and GO-term classification produced a catalogue of unigenes for studying primary metabolism, phytohormone signaling, and transcription factors. Massive transcriptomic analysis has identified microsatellites composed of simple sequence repeat (SSR) loci representing di-, tri-, and tetranucleotide repeat units in the predicted open reading frames. Polymorphism was induced by PCR amplification of microsatellite loci located in several genes encoding auxin response factors and other transcription factors, which successfully distinguished 16 local trees of A. crassicarpa tested, representing potentially exploitable molecular markers for efficient tree breeding for plantation and biomass exploitation. [ABSTRACT FROM AUTHOR]

The Belgian Salpingidae are small elongated or long-oval beetles measuring 1,5 to 5,2 mm. They are usually glossy black or brown, sometimes with a reddish-brown head and pronotum. Larvae, as well as imagos, live behind the bark of dead deciduous and coniferous trees and in the galleries of bark beetles. This small beetle family counts about 350 species worldwide. In Europe, 19 species are known. In this article, the 11 Belgian species are discussed with attention to their breeding trees and their distribution. Not much is known about their way of life. [ABSTRACT FROM AUTHOR]

The European beech (Fagus sylvatica L.) is one of the most important tree species in Europe. In order to understand the breeding and biological aspects of the species, the Institute of Forest Genetics and Forest Tree Breeding (Großhansdorf, Germany) has carried out several series of provenance trials in collaboration with researchers throughout Europe. The most extensive series was the International Beech Provenance Trial 1993/95 (established in 1995). One of the provenance trials, Bu19_19 (Roztochja), involving 70 provenances from 10 European countries, was established in Ukraine at the north-eastern edge of the species' natural range. We investigated survival and DBH at this site in May 2023. The average survival rate was 38% (57 trees per provenance), while the number of surviving trees per provenance ranged from 37 to 76. The average DBH was 11.2 centimeters, with the DBH of some individual trees exceeding 30 centimeters. The Bu19_19 provenance trial remains a valuable resource for studying the performance of European beech populations and can provide important insights into their resilience and adaptation. [ABSTRACT FROM AUTHOR]

The current planting of economically important timber species, such as Douglas-fir, mainly relies on genetically improved seeds from seed orchards. However, published research on the effects of climate change has largely focused on natural populations. To bridge this gap, data from 80 cooperative second-cycle coastal Douglas-fir progeny tests across eight breeding zones in western Washington and Oregon were analyzed. Climate transfer functions for age-12 growth were derived, showing significant results for the US Pacific Northwest. Region-specific transfer functions (Coast, Inland, and Cascade) displayed stronger correlations. Mean annual temperature and mean coldest month temperature were the most important climatic variables explaining growth. The study found that populations from slightly warmer areas tended to grow better but moving populations from colder to warmer areas by 2 °C (analogous to projected global warming) would result in an 8% genetic loss in age-12 height and a 25% genetic loss in age-12 volume. However, substantial diversity in climatic response was found among full-sib families within large breeding zones, suggesting that breeding and selecting suitable families for future climatic conditions within breeding zones is feasible. The study discusses potential strategies to adapt current breeding programs to address the impacts of future climate change while maintaining high population growth rates in Douglas-fir breeding programs. [ABSTRACT FROM AUTHOR]

The growth characteristics (stem diameter at 1.3 m above the ground and tree height) and stress-wave velocity of the stem were determined for three species from natural stands in four provenances in Mongolia (Populus laurifolia from Arkhangai, Populus suaveolens from Bulgan and Ulaanbaatar, and Populus × sibirica from Ulaanbaatar) to compare the characteristics among species and to clarify the correlations between the characteristics. The mean stem diameter and tree height values were 25.5 cm and 11.8 m, 20.4 cm and 10.1 m, and 21.8 cm and 9.9 m in P. laurifolia, P. suaveolens, and Populus × sibirica, respectively. The stress-wave velocity of the stems in P. laurifolia (3.30 km s−1) showed a significantly lower value than that of the stems in the other two species, suggesting that the Young’s modulus in P. laurifolia might be low. Although the growth characteristics of P. suaveolens in the Bulgan and Ulaanbaatar were similar, a lower p-value in the t-test was found in the stress-wave velocity of the stems. Furthermore, there were no significant or lower correlation coefficients between the growth characteristics and the stress-wave velocity of the stems in P. laurifolia and P. suaveolens. Based on the results, it is concluded that tree breeding for wood quality can be established for three Populus species in Mongolia.

Abstract Understanding the genotype-by-environment interaction (GEI) and considering it in the selection process is a sine qua non condition for the expansion of Brazilian eucalyptus silviculture. This study’s objective is to select high-performance and stable eucalyptus clones based on a novel selection index that considers the Factor Analytic Selection Tools (FAST) and the clone’s reliability. The investigation explores the nuances interplay of GEI and extends its insights by scrutinizing the relationship between latent factors and real environmental features. The analysis, conducted across seven trials in five Brazilian states involving 78 clones, employs FAST. The clonal selection was performed using an extended FAST index weighted by the clone’s reliability. Further insights about GEI emerge from the integration of factor loadings with 25 environmental features through a principal component analysis. Ten clones, distinguished by high performance, stability, and reliability, have been selected across the target population of environments. The environmental features most closely associated with factor loadings, encompassing air temperature, radiation, and soil characteristics, emerge as pivotal drivers of GEI within this dataset. This study contributes insights to eucalyptus breeders, equipping them to enhance decision-making by harnessing a holistic understanding-from the genotypes under evaluation to the diverse environments anticipated in commercial plantations.

Understanding the genotype-by-environment interaction (GEI) and considering it in the selection process is a sine qua non condition for the expansion of Brazilian eucalyptus silviculture. This study's objective is to select high-performance and stable eucalyptus clones based on a novel selection index that considers the Factor Analytic Selection Tools (FAST) and the clone's reliability. The investigation explores the nuances interplay of GEI and extends its insights by scrutinizing the relationship between latent factors and real environmental features. The analysis, conducted across seven trials in five Brazilian states involving 78 clones, employs FAST. The clonal selection was performed using an extended FAST index weighted by the clone's reliability. Further insights about GEI emerge from the integration of factor loadings with 25 environmental features through a principal component analysis. Ten clones, distinguished by high performance, stability, and reliability, have been selected across the target population of environments. The environmental features most closely associated with factor loadings, encompassing air temperature, radiation, and soil characteristics, emerge as pivotal drivers of GEI within this dataset. This study contributes insights to eucalyptus breeders, equipping them to enhance decision-making by harnessing a holistic understanding-from the genotypes under evaluation to the diverse environments anticipated in commercial plantations. [ABSTRACT FROM AUTHOR]

Summary: Forests make immense contributions to societies in the form of ecological services and sustainable industrial products. However, they face major challenges to their viability and economic use due to climate change and growing biotic and economic threats, for which recombinant DNA (rDNA) technology can sometimes provide solutions. But the application of rDNA technologies to forest trees faces major social and biological obstacles that make its societal acceptance a 'wicked' problem without straightforward solutions. We discuss the nature of these problems, and the social and biological innovations that we consider essential for progress. As case studies of biological challenges, we focus on studies of modifications in wood chemistry and transformation efficiency. We call for major innovations in regulations, and the dissolution of method‐based market barriers, that together could lead to greater research investments, enable wide use of field studies, and facilitate the integration of rDNA‐modified trees into conventional breeding programs. Without near‐term adoption of such innovations, rDNA‐based solutions will be largely unavailable to help forests adapt to the growing stresses from climate change and the proliferation of forest pests, nor will they be available to provide economic and environmental benefits from expanded use of wood and related bioproducts as part of an expanding bioeconomy. [ABSTRACT FROM AUTHOR]

We estimated genetic parameters of two Pinus caribaea var. caribaea progeny tests based on growth traits aiming at the identification of the best selection strategy. This study was conducted in two progeny tests located in Selvíria (MS), Brazil. Tests were set up in block design, one with 76 progenies (area 1) and the other with 99 progenies (area 2). Genetic parameters were estimated using the SELEGEN software through REML/BLUP method. To estimate the genetic gain through selection, four selection methods and ten selection intensities were tested. The intensity of selection that maximizes genetic gain and genetic diversity was calculated by the optimization point. Significant variation was observed between and with progeny for all traits in area 2 and only within plots for height in area 1. Higher values of heritability were observed in area 1. Considering the optimization of selection, the best selection method for both areas was the individual. [ABSTRACT FROM AUTHOR]

The Rawa Kidang Restoration is an area designated to plant tree species that rhinos like. Food is planted at the Rawa Kidang Restoration to maintain the rhino population. Knowledge of the importance of tree health is necessary because this can be a guide for rejuvenating or breeding trees attacked by disease or pests. To know the quality of rhino food, you need information about the health of rhino food trees. This research aims to investigate the health of rhino food trees in the Rawa Kidang Restoration. This research uses the Cluster Plot Level Index (CLI) formula to observe and examine canopy conditions and tree damage. The canopy condition parameters consist of five parameters: live crown ratio, density, transparency, diameter, and dieback. The parameters for the tree damage condition are the damage's location, the type I feel, and the level of tree damage. The research results show that the tree health value in cluster plot 1 is 2.35; in plot cluster 2, 2.50; in plot cluster 3, 3.70; and in plot cluster 4, 2.92. So, it can be concluded that the average tree health value in the four plot clusters is in the medium category. The severity of canopy conditions and tree damage can be influenced by surrounding conditions such as sunshine, growing conditions, water, and growing space. [ABSTRACT FROM AUTHOR]

The risk of predation directly affects the physiology, behavior, and fitness of wild birds. Strong social connections with conspecifics could help individuals recover from a stressful experience such as a predation event; however, competitive interactions also have the potential to exacerbate stress. Few studies have investigated the interaction between environmental stressors and the social landscape in wild bird populations. In 2 years of field studies, we experimentally simulated predation attempts on breeding female tree swallows (Tachicyneta bicolor). At the same time, we manipulated female breast plumage color, a key social signal. Simulated predation events on tree swallows early in the nestling period reduced young nestlings' mass by approximately 20% and shortened telomere lengths. Ultimately, only 31% of nestlings in the predation group fledged compared with 70% of control nestlings. However, the effects of experimental manipulations were timing dependent: the following year when we swapped the order of the experimental manipulations and simulated predation during incubation, there were no significant effects of predation on nestling condition or fledging success. Contrary to our expectations, manipulation of the social environment did not affect the response of tree swallows to simulated predation. However, manipulating female plumage during the nestling period did reduce nestling skeletal size and mass, although the effects depended on original plumage brightness. Our data demonstrate that transient stressors on female birds can have carry‐over effects on their nestlings if they occur during critical periods in the breeding season. [ABSTRACT FROM AUTHOR]

Genetically improved forest reproductive materials are now widely accessible in many European countries due to decades of continuous breeding efforts. Tree breeding does not only contribute to higher-value end products but allows an increase in the rate of carbon capture and sequestration, helping to mitigate the effects of climate change. The usefulness of breeding programmes depends on (i) the relevance of the set of selected traits and their relative weights (growth, drought tolerance, phenology, etc.); (ii) the explicit management of targeted and “neutral” diversity; (iii) the genetic gain achieved; and (iv) the efficiency of transferring diversity and gain to the plantation. Several biological factors limit both operational breeding and mass reproduction. To fully realise the potential of tree breeding, the introduction of new technologies and concepts is pivotal for overcoming these constraints. We reviewed several European breeding programmes, examining their current status and factors that are likely to influence tree breeding in the coming decades. The synthesis was based on case studies developed for the European Union-funded B4EST project, which focused on eight economically important tree species with breeding histories and intensities ranging from low-input breeding (stone pine, Douglas-fir and ash) to more complex programmes (eucalyptus, maritime pine, Norway spruce, poplar, and Scots pine). Tree breeding for these species is managed in a variety of ways due to differences in species’ biology, breeding objectives, and economic value. Most programmes are managed by governmental institutes with full or partial public support because of the relatively late return on investment. Eucalyptus is the only tree species whose breeding is entirely sponsored and managed by a private company. Several new technologies have emerged for both phenotyping and genotyping. They have the potential to speed up breeding processes and make genetic evaluations more accurate, thereby reducing costs and increasing genetic gains per unit of time. In addition, genotyping has allowed the explicit control of genetic diversity in selected populations with great precision. The continuing advances in tree genomics are expected to revolutionise tree breeding by moving it towards genomic-based selection, a perspective that requires new types of skills that are not always available in the institutions hosting the programmes. We therefore recognise the importance of promoting coordination and collaboration between the many groups involved in breeding. Climate change is expected to bring in new pests and diseases and increase the frequency of extreme weather events such as late frosts and prolonged droughts. Such stresses will cause slow growth and mortality, reducing forest productivity and resilience. Most of these threats are difficult to predict, and the time-consuming nature of conventional breeding does not allow for an adequate and timely reaction. We anticipate that most breeding programmes will need to revise their selection criteria and objectives to place greater emphasis on adaptive performance, tolerance to multiple environmental stresses, stability in different environments, and conservation of genetic diversity. Testing breeding materials in a variety of environments, including potentially contrasting climates, will become increasingly important. Climate change may also force the incorporation of new genetic resources that provide new useful adaptations, which may involve the use of new, previously unexplored gene pools or hybridisation, with the enormous challenge of incorporating useful alleles without adding along an unfavourable genetic background. Decision-support tools to help landowners and foresters select the best-performing forest reproductive material in each specific environment could also help reduce the impact of climate change.

Silver birch, a widely distributed deciduous tree native to Europe, is valued for its wood applications in construction, furniture making, and paper production. In Lithuania, silver birch ranks as the third most common forest-tree species, comprising 22% of the forested areas, and is an important species for tree breeding due to its potential and adaptability. This study was focused on assessing the mechanical properties of wood (sample and log hardness, wood density, dynamic modulus of elasticity (MOEdyn), static modulus of elasticity (MOE) and bending strength (MOR)) in silver birch (Betula pendula L. Roth.) trees from different half-sibling families. Two experimental plantations of the progenies of Lithuanian populations (half-sib families) of silver birch from different regions were analysed. From these plantations, four genetic families were selected for mechanical properties evaluation. The study findings revealed significant variability in various wood properties among different genetic families, although the static modulus of elasticity did not exhibit significant differences between the chosen genetic families. All measured wood properties decreased from the bottom to the top of the model trees. Wood hardness displayed a moderately negative correlation for wood density and weak correlations for MOE and MOR. Given the weak correlations between wood hardness and other wood mechanical properties, it is suggested that MOEdyn would be a more suitable trait for genetic studies. [ABSTRACT FROM AUTHOR]

Russet formation in apple (Malus domestica Borkh.) is a superficial skin disorder that detracts from fruit appearance and is likely controlled by many small-effect quantitative trait loci (QTLs). Genomewide prediction has been reported to be an effective breeding approach when targeting highly quantitative traits in apple. Our objective was to investigate the utility of genomewide prediction for russet formation within an apple breeding program. Germplasm included 1,009 unselected offspring from 13 full-sib families derived from 14 breeding parents. 'Honeycrisp' and 'Minneiska', two breeding parents prone to moderate levels of russet, were highly represented. High-quality single nucleotide polymorphism data (947 SNPs) and three years of shoulder and lenticel russet formation data were leveraged in this study. Moderate predictive abilities (r = 0.28−0.35) were observed across training-testing set scenarios and models. In this germplasm, the inclusion of previously detected QTLs as fixed effects in the model did not have significant effects on predictive abilities. Postdiction (retrospective) analyses demonstrated that genomewide predictions and phenotypic observations agreed for 54% of advanced selections. Genomewide prediction is a promising approach when targeting russet formation, a trait that cannot be phenotypically observed in offspring in apple breeding programs until they are past their juvenile phase.

Casuarina equisetifolia, the most commonly grown species of Casuarina in India, is mainly used for pulpwood, scaffolding, poles, fuelwood and stakes for banana crop. It is most suited for agrarian ecosystems due to many favourable characteristics like desirable stem form and fast growth. It is one among the non-leguminous nitrogen fixing tree species also. In India, tremendous variations are documented for tree species in different states. Wide variations were observed when 23 international provenances of C. equisetifolia infused from CSIRO, Australia were subjected to multi-location field testing. Among the three primary characters which contribute directly towards volume growth, diameter at breast height showed higher degree of variation than total height in all the provenances. Volume index recorded the maximum genotypic coefficient of variation followed by frustum volume in all the provenances at 3 years of age. Tree height registered the lowest value for GCV and PCV. Among the various characters studied, frustum volume recorded the maximum heritability (0.24) followed by diameter at breast height, basal diameter and volume index (0.20). The lowest value was for tree height (0.05). Mahalanobis’ D2 statistics followed by Tocher’s clustering method grouped the 23 provenances of C. equisetifolia into 9 clusters with cluster strength varying from one (clusters 8 and 9) to eight (cluster 4). Clusters 4,5,7 and 9 registered higher mean values for frustum volume and volume index. Based on the genetic variability studies, it is concluded that provenances 18141 Kenya, 18378 QLD, 18298 Thailand, 18344 Malaysia, Mixed Seedlot India, 18586 China and 18355 Benin could be the potential candidates for future breeding programmes.

The GRAS (GAI\RGA\SCL) gene family encodes plant-specific transcription factors that play crucial roles in plant growth and development, stress tolerance, and hormone network regulation. Plant dwarfing symptom is mainly regulated by DELLA proteins of the GRAS gene subfamily. In this study, the association between the GRAS gene family and Paulownia witches' broom (PaWB) was investigated. A total of 79 PfGRAS genes were identified using bioinformatics methods and categorized into 11 groups based on amino acid sequences. Tandem duplication and fragment duplication were found to be the main modes of amplification of the PfGRAS gene family. Gene structure analysis showed that more than 72.1% of the PfGRASs had no introns. The genes PfGRAS12/18/58 also contained unique DELLA structural domains; only PfGRAS12, which showed significant response to PaWB phytoplasma infection in stems, showed significant tissue specificity and responded to gibberellin (GA3) in PaWB-infected plants. We found that the internodes were significantly elongated under 100 µmol·L−1 GA3 treatment for 30 days. The subcellular localization analysis indicated that PfGRAS12 is located in the nucleus and cell membrane. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays confirmed that PfGRAS12 interacted with PfJAZ3 in the nucleus. Our results will lay a foundation for further research on the functions of the PfGRAS gene family and for genetic improvement and breeding of PaWB-resistant trees. [ABSTRACT FROM AUTHOR]

Light is one of the most important environmental factors for plant growth. In the production process of tung oil tree cultivation, due to the inappropriate growth of shading conditions, the lower branches are often dry and dead, which seriously affects the yield of tung oil trees. However, little is known about the key factors of light-induced tree photomorphogenesis. In this study, a total of 22 VfBBX family members were identified to provide a reference for candidate genes in tung tree seedlings. All members of the VfBBX family have different numbers of highly conserved B-box domains or CCT domains. Phylogenetic evolution clustered the VfBBX genes into four categories, and the highest density of members was on chromosome 6. Interspecific collinearity analysis suggested that there were six pairs of duplicate genes in VfBBX members, but the expression levels of all family members in different growth and development stages of the tung tree were significantly divergent. After different degrees of shading treatment and physiological data determination of tung tree seedlings, the differential expression level and chlorophyll synthesis genes correlation analysis revealed that VfBBX9 was a typical candidate nuclear localization transcription factor that was significantly differentially expressed in light response. This study systematically identified the VfBBX gene family and provided a reference for studying its molecular function, enhanced the theoretical basis for tung tree breeding, and identified excellent varieties. [ABSTRACT FROM AUTHOR]

Background: Early selection in tree breeding could be achieved by addressing the longevity of tree improvement activities. Genetic parameter changes and age–age correlations are essential for determining the optimal timing of early selection. Practical tracking of genetic parameters of Pinus koraiensis, a major timber species with economic and ecological value, has become feasible as its progeny testing has entered the mid-term age in Korea. However, research on the age−age correlation of P. koraiensis as progeny trials approach rotation age is limited. This study aimed to investigate genetic parameter trends and age−age correlations in P. koraiensis progeny. P. koraiensis progeny were assessed at two sites using a linear mixed-effects model with two-dimensional spatial autoregressive structure. Height, diameter, and volume growth were measured in 11 assessments over 40 years. Results: Genetic parameters, such as height and diameter, showed different patterns of change. The heritability ranged for the three growth traits in 0.083–0.710, 0.288–0.781, and 0.299–0.755 across the sites and age. Height heritability and its coefficient of variance decreased, whereas the diameter and volume estimates remained relatively constant. Correlations with Age 40 for phenotypic, genetic, and rank of breeding values ranged between 0.16 and 0.92, 0.594 and 0.988, and 0.412 and 0.965, respectively. These correlations generally increased as the age approached Age 40, with particularly high levels observed at Age 26 and Age 30. Conclusion: The observed genetic trends in P. koraiensis progeny testing offer valuable insights for early and precise selection. Notably, selecting superior genotypes at Ages 26–30 is supported by discernible genetic gains and robust correlations. Future research should integrate unbalanced data for selecting mother trees or families and conduct a comprehensive economic analysis of early selection to validate its practical benefits. [ABSTRACT FROM AUTHOR]

Families of 38 month-old Calycophyllum spruceanum planted at three locations in the Peruvian Amazon were analyzed for breeding purpose. Significant differences were detected among families, sites and combined sites for the traits trunk diameter (D), height (H), number of nodes (NN), number of branches (NB) and survival rate (SUR), except for NN at site 2 and SUR at site 3 and combined sites. The correlation of the genotype-environment interaction was simple for D, H, NN, and SUR (0.77-0.89). Heritability was generally highest for D, H, NN, and NB (0.12-0.7), and the genotypic coefficient of variation ranged from 8.6-27.4%. Genetic correlations between these traits within and among sites ranged from 0.35-1.0. The selection of 75 trees from different families, within blocks and locations, suggested the possibility of genetic gains (6.1-29.8%) for D, H, NN, and NB, and that the remaining effective population size can be exploited in future selection cycles. [ABSTRACT FROM AUTHOR]

Forest tree breeding is new and more difficult, time-consuming, and expensive than crop breeding. Forest trees breed every 20–40 years. Genomic and molecular biology advances have revolutionized plant breeding based on phenotypes. Molecular markers make genotype selection possible. Marker-assisted breeding can speed up breeding, however, it is not effective for selecting complicated features in forest trees. The genomic estimated breeding value of an individual can be determined using this unique genomic selection method, which studies all impacts of quantitative trait loci using a large number of genetic markers across the genome. This method should improve forest trees better than conventional breeding. This article reviews genomic selection's current advancements in forest tree improvement and discusses genotyping and phenotyping methods. We also evaluate genomic prediction algorithms and stress the importance of cost–benefit analysis before genomic selection. This technique of forest breeding can be improved by boosting species diversity, favorable traits, and epigenetic variation. [ABSTRACT FROM AUTHOR]

Salix psammophila is an important tree species adapted to sand-fixing afforestation in arid areas, and its different plant type characteristics can have different ecological functions. To identify the genes affecting the plant type of S. psammophila, this study used RT-qPCR and RNA-seq technology to establish a method for screening the candidate genes of the S. psammophila plant type based on the correlation coefficient of the crown–height ratio. We then screened out the gene combination that can best control the expression of the S. psammophila plant type. The results show the following: (1) The expression levels of the FHY1 and TAC2 genes were positively correlated with the crown–height ratio, whereas those of the ATX1, RFK1, PYL1, ABF2, SPA2, TB1, ZFP4, and LAZY1b genes were negatively correlated with the crown–height ratio. (2) The ATX1 + FHY1 gene combination had the greatest influence on the plant type traits of S. psammophila, and the correlation between the gene combination and the crown–height ratio reached 0.74. (3) The double- gene combination screening method improved the screening efficiency and accuracy, as well as the sensitivity and specificity, indicating certain universality. This strategy can be used for the determination of other plants or other traits, providing a theoretical basis for the directional breeding of forest trees. [ABSTRACT FROM AUTHOR]

In the Baltics, warming is expected to burden the growth of Norway spruce Picea abies, with weather anomalies/extremes having strong triggering effects, which can be mitigated by tree breeding. Within the region, breeding programmes have been aiming for productivity, yet being conservative, their sustainability depends on the adaptability of native genotypes, which is unclear. The adaptability of genotypes can be assessed through local adaptations and phenotypic plasticity, with the sensitivity of increment depicting the conformity of genotypes and environments. To assess the adaptability of native populations to anticipated climates, local genetic adaptation and phenotypic plasticity of the weather sensitivity of the radial increment were assessed by the methods of time series analysis and quantitative genetics based on three clonal trials (low-density single-tree plot plantations of grafted clones of native plus trees) representing the local climatic gradient in Latvia. The growth of trees was sensitive to the moisture availability in summer and the thermal regime in winter, yet coinciding anomalies in both were associated with abrupt changes in tree ring width. These environmental effects differed among the clones, indicating genetic controls over the sensitivity of increment, which, however, decreased under a warmer climate, suggesting a limited adaptability of local populations to warming. Still, the weather-growth relationships showed moderate phenotypic plasticity, suggesting some mid-term adaptability. Accordingly, supplementation of breeding populations via assisted gene transfer with the genotypes that are adapted to warmer and drier climates appears crucial. [ABSTRACT FROM AUTHOR]

Background: Light-harvesting chlorophyll a/b binding proteins (Lhcb) play crucial roles in plant growth, development, and the response to abiotic stress in higher plants. Previous studies have reported that Lhcb genes were involved in the phytochrome regulation and responded to different light and temperature conditions in Poaceae (such as maize). However, the evolution and functions of Lhcb genes remains poorly characterized in important Rosaceae species. Results: In this investigation, we conducted a genome-wide analysis and identified a total of 212 Lhcb genes across nine Rosaceae species. Specifically, we found 23 Lhcb genes in Fragaria vesca, 20 in Prunus armeniaca, 33 in Malus domestica 'Gala', 21 in Prunus persica, 33 in Rosa chinensis, 29 in Pyrus bretschneideri, 18 in Rubus occidentalis, 20 in Prunus mume, and 15 in Prunus salicina. Phylogenetic analysis revealed that the Lhcb gene family could be classified into seven major subfamilies, with members of each subfamily sharing similar conserved motifs. And, the functions of each subfamily was predicted based on the previous reports from other species. The Lhcb proteins were highly conserved within their respective subfamilies, suggesting similar functions. Interestingly, we observed similar peaks in Ks values (0.1–0.2) for Lhcb genes in apple and pear, indicating a recent whole genome duplication event (about 30 to 45 million years ago). Additionally, a few Lhcb genes underwent tandem duplication and were located across all chromosomes of nine species of Rosaceae. Furthermore, the analysis of the cis-acting elements in the 2000 bp promoter region upstream of the pear Lhcb gene revealed four main categories: light response correlation, stress response correlation, hormone response correlation, and plant growth. Quantitative expression analysis demonstrated that Lhcb genes exhibited tissue-specific expression patterns and responded differently to low-temperature stress in Rosaceae species. Conclusions: These findings shed light on the evolution and phylogeny of Lhcb genes in Rosaceae and highlight the critical role of Lhcb in pear's response to low temperatures. The results obtained provide valuable insights for further investigations into the functions of Lhcb genes in Rosaceae, and these functional genes will be used for further fruit tree breeding and improvement to cope with the current climate changes. [ABSTRACT FROM AUTHOR]

CRISPR (short for "Clustered Regularly Interspaced Short Palindromic Repeats") is a technology that research scientists use to selectively modify the DNA of living organisms. CRISPR was adapted for use in the laboratory from the naturally occurring genome-editing systems found in bacteria. In this work, we reviewed the methods used to introduce CRISPR/Cas-mediated genome editing into fruit species, as well as the impacts of the application of this technology to activate and knock out target genes in different fruit tree species, including on tree development, yield, fruit quality, and tolerance to biotic and abiotic stresses. The application of this gene-editing technology could allow the development of new generations of fruit crops with improved traits by targeting different genetic segments or even could facilitate the introduction of traits into elite cultivars without changing other traits. However, currently, the scarcity of efficient regeneration and transformation protocols in some species, the fact that many of those procedures are genotype-dependent, and the convenience of segregating the transgenic parts of the CRISPR system represent the main handicaps limiting the potential of genetic editing techniques for fruit trees. Finally, the latest news on the legislation and regulations about the use of plants modified using CRISPR/Cas systems has been also discussed. [ABSTRACT FROM AUTHOR]

Forest trees are beleaguered by the ever-increasing onslaught of invasive pests and pathogens, with some species in danger of functional extinction. Recent successes in developing resistant populations using traditional tree breeding assures that some of the affected species will persist in future forests. However, the sheer number of threatened species requires increases in breeding efficiency. The time is right to consider how the use of genomic resources might aid breeding efforts in the next 20 years. Any operational benefit of genomic resources will be minimal without closer collaboration between tree breeders, forest managers, and genomic researchers. We reflect here on what attributes were responsible for the success of traditional resistance breeding programs and whether advances in genomics can realistically accelerate breeding. We conclude that the use of genomics to directly advance resistance breeding efforts in the next 20 years will be limited. Major obstacles will include factors such as the undomesticated nature of most tree species, the quantitative genetic nature of resistance in many species, and the lack of adequate funding to accelerate and more fully develop genomic resources. Despite these limitations, genomic tools have potential to help increase our understanding of the nature of resistance, and the genetic variability in the host, which can aid in the deployment of resistant populations and may assist in marker-assisted selection, particularly for major gene resistance. [ABSTRACT FROM AUTHOR]

AbstractThe breeding program for Acacia mangium has entered advanced-generation breeding cycles through adopting a recurrent selection system and a sub-lining breeding population. Genetic variation changes along the successive generations could affect its genetic stability on wide ranges of sites. The aim of this study is to observe genetic stability in third-generation progeny trials of A. mangium established at three different sites in Indonesia. Analysis was conducted, including single-site and multi-sites analyses for height, diameter, and stem forking that were grouped into two sets of analysis based on the genetic background of the trial: SET01 for the single sub-line and SET02 for the composite sub-lines. Index selection for multiple-traits was then used to identify the family changing ranks for multiple-traits and genetic gain prediction. The results showed that the recurrent selection system adopted in the breeding strategy for single-site analysis could maintain sufficient genetic variance of A. mangium in the third-generation progeny trial. Family heritability was moderate to high for almost all traits. However, a strong genetic-environment interaction (G × E) exists in multi-sites analysis for the single sub-line population (SET01), indicating a less sufficient genetic variation and a low Type B genetic correlation in anticipating a wider range of environment. On the contrary, compositing selected family from several sub-lines (SET02) could diminish the strength of G × E and increase Type B correlation. Selection and genetic gain prediction could be more effective in multi-sites analysis for SET02, but it was less effective for SET01. The results imply that adopting a recurrent selection system in advanced-generation breeding of A. mangium should consider structuring the breeding population. It could be practiced by compositing selected superior families from several sub-lines into one breeding population to maintain high genetic stability, while increasing genetic diversity and productivity.

Introduction: Shorea macrophylla is a commercially important tropical tree species grown for timber and oil. It is amenable to plantation forestry due to its fast initial growth. Genomic selection (GS) has been used in tree breeding studies to shorten long breeding cycles but has not previously been applied to S. macrophylla. Methods: To build genomic prediction models for GS, leaves and growth trait data were collected from a half-sib progeny population of S. macrophylla in Sari Bumi Kusuma forest concession, central Kalimantan, Indonesia. 18037 SNP markers were identified in two ddRAD-seq libraries. Genomic prediction models based on these SNPs were then generated for diameter at breast height and total height in the 7th year from planting (D7 and H7). Results and discussion: These traits were chosen because of their relatively high narrow-sense genomic heritability and because seven years was considered long enough to assess initial growth. Genomic prediction models were built using 6 methods and their derivatives with the full set of identified SNPs and subsets of 48, 96, and 192 SNPs selected based on the results of a genome-wide association study (GWAS). The GBLUP and RKHS methods gave the highest predictive ability for D7 and H7 with the sets of selected SNPs and showed that D7 has an additive genetic architecture while H7 has an epistatic genetic architecture. LightGBM and CNN1D also achieved high predictive abilities for D7 with 48 and 96 selected SNPs, and for H7 with 96 and 192 selected SNPs, showing that gradient boosting decision trees and deep learning can be useful in genomic prediction. Predictive abilities were higher in H7 when smaller number of SNP subsets selected by GWAS p-value was used, However, D7 showed the contrary tendency, which might have originated from the difference in genetic architecture between primary and secondary growth of the species. This study suggests that GS with GWAS-based SNP selection can be used in breeding for non-cultivated tree species to improve initial growth and reduce genotyping costs for next-generation seedlings. [ABSTRACT FROM AUTHOR]

Introduction: Genomic selection (GS) experiments in forest trees have largely reported estimates of predictive abilities from cross-validation among individuals in the same breeding generation. In such conditions, no effects of recombination, selection, drift, and environmental changes are accounted for. Here, we assessed the effectively realized predictive ability (RPA) for volume growth at harvest age by GS across generations in an operational reciprocal recurrent selection (RRS) program of hybrid Eucalyptus. Methods: Genomic best linear unbiased prediction with additive (GBLUP_G), additive plus dominance (GBLUP_G+D), and additive single-step (HBLUP) models were trained with different combinations of growth data of hybrids and pure species individuals (N = 17,462) of the G1 generation, 1,944 of which were genotyped with ~16,000 SNPs from SNP arrays. The hybrid G2 progeny trial (HPT267) was the GS target, with 1,400 selection candidates, 197 of which were genotyped still at the seedling stage, and genomically predicted for their breeding and genotypic values at the operational harvest age (6 years). Seedlings were then grown to harvest and measured, and their pedigree-based breeding and genotypic values were compared to their originally predicted genomic counterparts. Results: Genomic RPAs ≥0.80 were obtained as the genetic relatedness between G1 and G2 increased, especially when the direct parents of selection candidates were used in training. GBLUP_G+D reached RPAs ≥0.70 only when hybrid or pure species data of G1 were included in training. HBLUP was only marginally better than GBLUP. Correlations ≥0.80 were obtained between pedigree and genomic individual ranks. Rank coincidence of the top 2.5% selections was the highest for GBLUP_G (45% to 60%) compared to GBLUP_G+D. To advance the pure species RRS populations, GS models were best when trained on pure species than hybrid data, and HBLUP yielded ~20% higher predictive abilities than GBLUP, but was not better than ABLUP for ungenotyped trees. Discussion: We demonstrate that genomic data effectively enable accurate ranking of eucalypt hybrid seedlings for their yet-to-be observed volume growth at harvest age. Our results support a two-stage GS approach involving family selection by average genomic breeding value, followed by within-top-families individual GS, significantly increasing selection intensity, optimizing genotyping costs, and accelerating RRS breeding. [ABSTRACT FROM AUTHOR]

Background: Global climate change poses a grave threat to biodiversity and underscores the importance of identifying the genes and corresponding environmental factors involved in the adaptation of tree species for the purposes of conservation and forestry. This holds particularly true for spruce species, given their pivotal role as key constituents of the montane, boreal, and sub-alpine forests in the Northern Hemisphere. Results: Here, we used transcriptomes, species occurrence records, and environmental data to investigate the spatial genetic distribution of and the climate-associated genetic variation in Picea crassifolia. Our comprehensive analysis employing ADMIXTURE, principal component analysis (PCA) and phylogenetic methodologies showed that the species has a complex population structure with obvious differentiation among populations in different regions. Concurrently, our investigations into isolation by distance (IBD), isolation by environment (IBE), and niche differentiation among populations collectively suggests that local adaptations are driven by environmental heterogeneity. By integrating population genomics and environmental data using redundancy analysis (RDA), we identified a set of climate-associated single-nucleotide polymorphisms (SNPs) and showed that environmental isolation had a more significant impact than geographic isolation in promoting genetic differentiation. We also found that the candidate genes associated with altitude, temperature seasonality (Bio4) and precipitation in the wettest month (Bio13) may be useful for forest tree breeding. Conclusions: Our findings deepen our understanding of how species respond to climate change and highlight the importance of integrating genomic and environmental data in untangling local adaptations. [ABSTRACT FROM AUTHOR]

The increasing demand for climate-adapted seeds and planting material poses a challenge due to the limited availability, particularly for tree species such as oaks. National parks, known for their large-standing diversity and a wide range of habitats, can serve as valuable sources for identifying trees suitable for both the initiation of tree breeding and conservation strategies. This study aimed to identify valuable forest genetic resources of the Thayatal National Park in Austria by selecting potentially drought-tolerant phenotypes. For this purpose, we selected 404 mature trees of Quercus petraea (Matt.) Liebl. from eight populations growing on medium to dry sites in eight populations. Further, we characterized them for autochthony, genetic structure, genetic diversity using genetic markers (plastid- and nuclear-SSRs) and estimated their age. Finally, we applied wood core analysis to estimate tree response to historical drought events to identify the possible drought-tolerant phenotypes. The age of the trees ranged from 29 to 245 years (as of the year 2023). All Q. petraea trees were inhabiting a plastid haplotype 17a, autochthonous for this area. Nevertheless, the genetic structure estimated by ten nuSSRs revealed a pronounced structure in the dataset, largely caused by young trees exhibiting lower genetic diversity. A total of 85 elite potentially drought-tolerant trees were finally selected based on their morphological response (resistance, recovery ability, resilience, and relative resilience) to three historical drought events (1992–1994, 1947, 1917). The intrinsic water use efficiency and its difference (iWUE and DWiWUE), estimated by isotope analysis of δ13C of latewood in wet (1987) and dry (1994) years, did not correlate with any of the drought response traits (Rt, Rc, Rs, rRs). We discuss the further use of the selected oak trees for the establishment of seed stands and orchards to enhance seed production and the integration of other omics approaches, such as large-scale high-throughput plant phenotyping (HTPP) and transcriptomics, for in-depth analyses of drought tolerance of selected phenotypes. [ABSTRACT FROM AUTHOR]

The utilization of genotyping has gained significant popularity in tree improvement programs, aiding in enhancing the precision of breeding values, removing pedigree errors, the assessment of genetic diversity, and evaluating pollen contamination. Our study explores the impact of utilizing 5308 SNP markers to genotype seed orchard parents (166), progeny in progeny trials (667), and seedlot orchard seedlings (780), to simultaneously enhance variance components, breeding values, genetic diversity estimates, and pollen flow in the Region I white spruce (Picea glauca) breeding program in central Alberta (Canada). We compared different individual tree mixed models, including pedigree-based (ABLUP), genomic-based (GBLUP), and single-step pedigree-genomic-based (ssGBLUP) models, to estimate variance components and predict breeding values for the height and diameter at breast height traits. The highest heritability estimates were achieved using the ssGBLUP approach, resulting in improved breeding value accuracy compared to the ABLUP and GBLUP models for the studied growth traits. In the six orchard seedlots tested, the genetic diversity of the seedlings remained stable, characterized by an average of approximately 2.00 alleles per SNP, a Shannon Index of approximately 0.44, and an expected and observed heterozygosity of approximately 0.29. The pedigree reconstruction of seed orchard seedlings successfully identified consistent parental contributions and equal genotype contributions in different years. Pollen contamination levels varied between 11% and 70% using SNP markers and 8% to 81% using pollen traps, with traps both over- and under-estimating contamination. Overall, integrating genomic information from parents and offspring empowers forest geneticists and breeders in the Region I white spruce breeding program to correct errors, conduct backward and forward selections with greater precision, gain a deeper understanding of the orchard's genetic structure, select superior seedlots, and accurately estimate the genetic worth of each orchard lot, which can ultimately result in increased and more precise estimates of genetic gain in the studied growth traits. [ABSTRACT FROM AUTHOR]

Key message: The range-wide level of genetic variation of Scots pine (Pinus sylvestris L.) is geographically structured. High admixture and low genetic structure of populations in Central Europe and Fennoscandia suggest past recolonization from multiple sources and the influence of human-mediated gene transfer. Gene pools of marginal and isolated stands require active conservation. Some areas of Scots pine distribution need further genetic studies. Context: Scots pine (Pinus sylvestris L.) seems to be a species of low conservation priority because it has a very wide Eurasian distribution and plays a leading role in many forest tree breeding programs. Nevertheless, considering its economic value, long breeding history, range fragmentation, and increased mortality, which is also projected in the future, it requires a more detailed description of its genetic resources. Aims: Our goal was to compare patterns of genetic variation found in biparentally inherited nuclear DNA with previous research carried out with mitochondrial and chloroplast DNA due to their different modes of transmission. Methods: We analyzed the genetic variation and relationships of 60 populations across the distribution of Scots pine in Eurasia (1262 individuals) using a set of nuclear DNA markers. Results: We confirmed the high genetic variation and low genetic differentiation of Scots pine spanning large geographical areas. Nevertheless, there was a clear division between European and Asian gene pools. The genetic variation of Asian populations was lower than in Europe. Spain, Turkey, and the Apennines constituted separate gene pools, the latter showing the lowest values of all genetic variation parameters. The analyses showed that most populations experienced genetic bottlenecks in the distant past. Ongoing admixture was found in Fennoscandia. Conclusions: Our results suggest a much simpler recolonization history of the Asian than European part of the Scots pine distribution, with migration from limited sources and possible founder effects. Eastern European stands seem to have descended from the Urals refugium. It appears that Central Europe and Fennoscandia share at least one glacial refugium in the Balkans and migrants from higher latitudes, as well as from south-eastern regions. The low genetic structure between Central Europe and Fennoscandia, along with their high genetic admixture, may result at least partially from past human activities related to the transfer of germplasm in the nineteenth and early twentieth centuries. In light of ongoing climate changes and projected range shifts of Scots pine, conservation strategies are especially needed for marginal and isolated stands of this species. Genetic research should also be complemented in parts of the species distribution that have thus far been poorly studied. [ABSTRACT FROM AUTHOR]

The aim of this study was to evaluate the genetic diversity among 36 wild strawberry tree (Arbutus unedo L.) genotypes belonging to different altitude and geographical origins, using 16 ISSR (Inter Simple Sequence Repeats) markers. Results revealed that ISSR primers produced a total of 344 bands, of which 94.1% were polymorphic, indicating a high level of genetic variation among the studied populations. The mean values of polymorphism information content (PIC), efective multiplex ratio (EMR), resolving power (Rp) and marker index (MI) were 0.34, 19.13, 23.46 and 6.45, respectively. The total gene diversity (Ht), gene diversity within populations (Hs) and total genetic differentiation coefficient among the populations (Gst) values were 0.33, 0.15 and 0.50, respectively. The genetic distance between all pairwise combinations of the genotypes ranged from 0.113 to 0.512. The cluster analysis revealed three main groups and which are subdivided into eight subgroups and a two independant branches. Therefore, the grouping of strawberry tree genotypes was independent of their geographical origins and altitude with exception for the genotypes belonging to Bin El-ouidane and Laanoucer populations. The results showed that ISSR markers are suitable tools for the evaluation of genetic diversity among strawberry tree genotypes. The data of this work will be useful for strawberry tree breeding programs and conservation strategies. [ABSTRACT FROM AUTHOR]

SUMMARY: Olive tree (Olea europaea L. subsp. europaea var. europaea) is one of the most important species of the Mediterranean region and one of the most ancient species domesticated. The availability of whole genome assemblies and annotations of olive tree cultivars and oleaster (O. europaea subsp. europaea var. sylvestris) has contributed to a better understanding of genetic and genomic differences between olive tree cultivars. However, compared to other plant species there is still a lack of genomic resources for olive tree populations that span the entire Mediterranean region. In the present study we developed the most complete genomic variation map and the most comprehensive catalog/resource of molecular variation to date for 89 olive tree genotypes originating from the entire Mediterranean basin, revealing the genetic diversity of this commercially significant crop tree and explaining the divergence/similarity among different variants. Additionally, the monumental ancient tree 'Throuba Naxos' was studied to characterize the potential origin or routes of olive tree domestication. Several candidate genes known to be associated with key agronomic traits, including olive oil quality and fruit yield, were uncovered by a selective sweep scan to be under selection pressure on all olive tree chromosomes. To further exploit the genomic and phenotypic resources obtained from the current work, genome‐wide association analyses were performed for 23 morphological and two agronomic traits. Significant associations were detected for eight traits that provide valuable candidates for fruit tree breeding and for deeper understanding of olive tree biology. Significance Statement: The most comprehensive genomic variation map to date has been developed for olive trees (Olea europaea L. subsp. europaea var. europaea) originating from the entire Mediterranean basin, providing insights into the complex olive tree domestication and biology, and through a selective sweep scan and genome‐wide association approaches candidate genes controlling important agronomic traits in olive tree have been identified. [ABSTRACT FROM AUTHOR]

Tamil Nadu, in southern India, has the second-largest number of neem trees in the country. The oil from the seeds has high economic significance for cottage industries in the region. This paper examines 28 Candidate Plus Trees (CPTs) selected from six agroclimatic zones in Tamil Nadu which exhibit exceptional traits such as superior growth and other desirable characteristics. We aimed to understand seed morphology variations and physicochemical properties in the oil across different regions. Significant differences were observed for morphometric traits. Fruit production correlated negatively with rainfall. 100-seed kernel weight and seed length correlated with oil percentage. Rainfall influenced seed breadth and pericarp weight. Clustering using morphological characters did not group genotypes from the same region; while soil type could distinguish them. Correlation helped us determine the prominent features which influence the traits of interest, which can be useful for breeding programs, cultivation practices, and the development of neem-based products in Tamil Nadu and beyond. [ABSTRACT FROM AUTHOR]

Advances in DNA sequencing technologies allow the sequencing of whole genomes of thousands of individuals and provide several million single nucleotide polymorphisms (SNPs) per individual. These data combined with precise and high-throughput phenotyping enable genome-wide association studies (GWAS) and the identification of SNPs underlying traits with complex genetic architectures. The identified causal SNPs and estimated allelic effects could then be used for advanced marker-assisted selection (MAS) in breeding programs. But could such MAS compete with the broadly used genomic selection (GS)? This question is of particular interest for the lengthy tree breeding strategies. Here, with our new software "SNPscan breeder," we simulated a simple tree breeding program and compared the impact of different selection criteria on genetic gain and inbreeding. Further, we assessed different genetic architectures and different levels of kinship among individuals of the breeding population. Interestingly, apart from progeny testing, GS using gBLUP performed best under almost all simulated scenarios. MAS based on GWAS results outperformed GS only if the allelic effects were estimated in large populations (ca. 10,000 individuals) of unrelated individuals. Notably, GWAS using 3,000 extreme phenotypes performed as good as the use of 10,000 phenotypes. GS increased inbreeding and thus reduced genetic diversity more strongly compared to progeny testing and GWAS-based selection. We discuss the practical implications for tree breeding programs. In conclusion, our analyses further support the potential of GS for forest tree breeding and improvement, although MAS may gain relevance with decreasing sequencing costs in the future. [ABSTRACT FROM AUTHOR]

Key message: Forest tree breeding must undergo significant revisions to adapt to the evolving challenges posed by climate change. Addressing the shifts in environmental conditions requires a comprehensive multidisciplinary approach that includes theoretical work and practical application. Specifically, there is a need to focus on developing new breeding strategies that are theoretically sound and practically feasible, considering the economic constraints of actual tree breeding programs. We present a novel concept utilizing genetic evaluation of multiple traits in forest stands of successive ages across wide ecological ranges. Incorporating genomics allows for detailed genetic evaluation, making use of high-density SNP markers and sophisticated algorithms like GBLUP for genetic parameter estimates. High-throughput phenotyping is conducted using drone-borne lidar technology to capture tree height and survival data across various forest stands. Assisted migration is considered to strategically position genotypes across predicted environmental climatic gradients, thereby accommodating the dynamic nature of ecological shifts. Mathematical optimization acts as an essential component for logistics, guiding the spatial allocation and timely substitution of genotypes to ensure a continually adaptive breeding program. The concept replaces distinct breeding cycles with continuous evaluation and selection, enhancing the rate of genetic response over time. [ABSTRACT FROM AUTHOR]

Breeding long-lived trees is challenging, but it has been shown that genomic information can be used to improve efficiency. In this study, genomic prediction (GP) was tested on selected individuals of a two-generation breeding population of Cryptomeria japonica, the most common plantation tree in Japan. In the 1980s, the second-generation plus trees (101 clones) were selected from about 8500 individuals obtained by cross-mating the first-generation plus trees (47 clones). RAD-seq based on 8664 SNPs was used to perform GP for three important traits in this population: tree height, wood stiffness, and male flower quantity. The association between traits and genotypes was modeled using five Bayesian models whose predictive accuracy was evaluated by cross-validation, revealing that the best model differed for each trait (BRR for tree height, BayesA for wood stiffness, and BayesB for male flower quantity). GP was 1.2–16.0 times more accurate than traditional pedigree-based methods, attributed to its ability to model Mendelian sampling. However, an analysis of the effects of intergenerational kinship showed that parent–offspring relationships reduce the predictive accuracy of GP for traits strongly affected by selection pressure. Overall, these results show that GP could significantly expedite tree breeding when supported by a deep understanding of the targeted population's genetic background. [ABSTRACT FROM AUTHOR]

Parrots are among the most diverse and widely distributed groups of birds and one of the most threatened bird orders mainly due to habitat loss and illegal poaching. Most parrots are obligate cavity nesters, so the logging of mature trees and the transformation of natural cliffs represent important threats to their conservation. Here, we report novel observations of Neotropical parrots nesting in previously unrecorded substrates. We show the first documented case of the cliff‐nesting burrowing parrots trying to breed at ground level in an abandoned burrowing owl cavity. Additionally, we provide the first documented observations of this species attempting to nest in building cavities in three urbanized areas of Argentina. Moreover, we report data from four countries of 148 pairs of eight species typically breeding in tree cavity using palm tree bracts as nest sites. Behavioral plasticity in nest sites may allow parrots to maximize their nesting success by exploiting alternative breeding substrates. Moreover, these novelties could contribute to cope with habitat loss and further transformation. However, further research is needed to assess the consequences of these nesting innovations in terms of individual fitness and population dynamics as well as potential factors promoting their appearance. [ABSTRACT FROM AUTHOR]

Breeding perennial tree crops often requires prediction of mature performance from juvenile data. To assess the utility of juvenile screens to predict salinity tolerance of mature pistachio trees, we compared performance of 3-month ungrafted seedlings and 4-year-old grafted rootstocks under salinity stress. The QTL allele associated with higher salt exclusion from seedling leaves conferred lower growth in saline field conditions, suggesting that mapping QTL in seedlings may be easier than discerning the optimal allele for field performance. [ABSTRACT FROM AUTHOR]

Eucalyptus is an economically important genus comprising more than 890 species in different subgenera and sections. Approximately twenty species of subgenus Symphyomyrtus account for 95% of the world's planted eucalypts. Discrimination of closely related eucalypt taxa is challenging, consistent with their recent phylogenetic divergence and occasional hybridization in nature. Admixture, misclassification or mislabeling of Eucalyptus germplasm resources maintained as exotics have been suggested, although no reports are available. Moreover, hybrids with increased productivity and traits complementarity are planted worldwide, but little is known about their actual genomic ancestry. In this study we examined a set of 440 trees of 16 different Eucalyptus species and 44 interspecific hybrids of multi-species origin conserved in germplasm banks in Brazil. We used genome-wide SNP data to evaluate the agreement between the alleged phylogenetic classification of species and provenances as registered in their historical records, and their observed genetic clustering derived from SNP data. Genetic structure analyses correctly assigned each of the 16 species to a different cluster although the PCA positioning of E. longirostrata was inconsistent with its current taxonomy. Admixture was present for closely related species' materials derived from local germplasm banks, indicating unintended hybridization following germplasm introduction. Provenances could be discriminated for some species, indicating that SNP-based discrimination was directly proportional to geographical distance, consistent with an isolation-by-distance model. SNP-based genomic ancestry analysis showed that the majority of the hybrids displayed realized genomic composition deviating from the expected ones based on their pedigree records, consistent with admixture in their parents and pervasive genome-wide directional selection toward the fast-growing E. grandis genome. SNP data in support of tree breeding provide precise germplasm identity verification, and allow breeders to objectively recognize the actual ancestral origin of superior hybrids to more realistically guide the program toward the development of the desired genetic combinations. [ABSTRACT FROM AUTHOR]

Tree peonies are an economically important crop with flowers of high ornamental value. Most tree peony cultivars in gardens are once-flowering, and the continuous flowering (CF) trait has been revealed only in a few tree peony cultivars, such as 'High Noon' ('HN'). However, the molecular mechanism underlying its CF remains unclear. Here, we demonstrated that PsTFL1 functions as a floral inhibitor via the ectopic expression of PsTFL1 in transgenic Arabidopsis thaliana plants. Our findings suggest that PsFT and PsTFL1 interact with PsFD, and the detected interactions may occur in the nucleus. Compared with the non-CF variety, the gene expression patterns of PsFT, PsTFL1, and PsFD during the flower development indicate that these three genes may be related to the CF habit in tree peony 'HN'. These findings will aid future investigations of CF behavior and promote the breeding of tree peonies and other perennial woody plants. [ABSTRACT FROM AUTHOR]

A study was conducted to identify balsam fir (Abies balsamea) for use in Christmas tree breeding programs in Northeastern North America. A total of sixty-four phenotypically good trees were identified from a provincial clonal seed orchard in New Brunswick, a multi-aged natural seed production area in Nova Scotia, and an operational plantation in Quebec, Canada. Trees were selected for good growth and form, numbers, and vigour of internodal branches, acceptable crown taper, needle colour, age class, branch angle, needle configuration, and freedom from insects and diseases or deformities, all traits deemed desirable in a Christmas tree. Three branches from each tree were collected at two harvest dates each year, one early and one late during the normal harvesting season in 2020, 2021, and 2022. Qualitative assessments of colour and branch pliability were performed weekly in conjunction with needle loss rub tests. A quantitative assessment of moisture loss was conducted weekly by measuring branch weights. The combination of qualitative and quantitative assessments was used to identify 7 of the 64 trees for which one or more tested branches consistently remained green and pliable, retained the majority of their needles, and lost moisture at a significantly reduced rate in all six testing periods. Grafts of the seven 'Select' trees are currently being integrated into seed orchards in the three participating provinces. These second-generation seed orchards are part of breeding programs designed to develop Christmas trees that will perform well under warm fall conditions, an outcome of climate change. The results from this study combined with the progeny testing of the 'Select' trees will be used to test for the heritability of needle retention, a key trait for the next generation of Christmas trees in the Northeast. [ABSTRACT FROM AUTHOR]