Populus nigra L. is an ecologically important floodplain tree species whose declining and increasingly fragmented populations are exposed to the increased risk of inbreeding. This paper aimed to study mating processes that can occur in such populations. Offspring of mother trees with different levels of inbreeding and three types of pollination (inbred, outbred, and open pollination) were compared based on their vitality, assessed through seed germination and growth characteristics, over three consecutive years. Inbred crosses produced offspring that were the worst in most of the studied traits and in all observation years, demonstrating inbreeding depression. A negative association between inbreeding coefficients and the studied characteristics was confirmed in most cases. Parentage analysis of open-pollinated seedlings using eight microsatellite loci identified up to 49
The huge genome of coniferous trees and the extremely scarce validation genes lead to a long-term inefficiency in the exploration of stress-resistant genes. This study proposes the cross-species adaptive transfer learning framework CLAP-HMM v2, which systematically integrates domain adversarial (DANN), dynamic MMD regularization, and MAML few-shot meta-learning, successfully solving the negative transfer problem caused by the over 320 million years of evolutionary distance between poplar and pine trees. Across four representative pine species, including Pinus taeda, Pinus tabuliformis, Pinus albicaulis, and Pinus radiata, the model achieved an F1-score of 0.912 (improving by 14.1
The plant height is a critical characteristic that impacts rubber tree growth. In the previous study, we had developed a dwarf mutant MU73397 by mutagenesis of a rubber tree cultivar CATAS73397. In order to investigate the dwarf mechanism of MU73397, whole-genome resequencing was both conducted on MU73397 and the wild-type CATAS73397. After filtering the raw sequencing data, 180,428,852 and 181,551,617 clean reads were obtained for MU73397 and CATAS73397, respectively. The GC contents were 37.81
Malus genomic resources with improved quality are becoming an integral part of candidate gene identification and functional validation. Recently, we released a reference-based phased chromosome-level genome assembly of ‘Antonovka’ 172670B Malus domestica cultivar from the ‘Antonovka’ group known for its disease resistance and abiotic stress tolerance. However, reference-based assemblies have limited accuracy in candidate alleles identification along extended genomic loci, as these may contain contigs from different haplotypes. Here, we provide an improved high-quality version of the ‘Antonovka’ 172670B genome. This assembly is fully phased as it integrates chromosome conformation capture sequencing and parental SNP data binning for de novo scaffolding and post-assembly phasing of pseudochromosomes into haplotypes, respectively. It shows improved quality scores and completeness of 59.8 and 96.7
Common fig (Ficus carica L.), one of the earliest domesticated fruit trees, remains genetically underexplored, particularly regarding wild-cultivated relationships. We performed whole-genome resequencing of 50 accessions (15 wild from Hirkan National Park and 35 cultivated from Azerbaijan and diverse origins), identifying 4,818,956 high-quality single nucleotide polymorphisms (SNP). Overall, the dataset showed a moderate level of genetic diversity, with Ho = 0.338, He = 0.319, and PIC = 0.259. Pairwise genetic distances, calculated as nucleotide sequence divergences, ranged from 0.148 to 0.54 (mean = 0.436). The Hyrcanian gene pool harbored 395,398 group-specific SNPs, far exceeding the West Mediterranean pool (75,473) highlighting its distinct genomic composition. Population structure, neighbor-joining, and principle component analysis clearly separated wild Hyrcanian figs from cultivated germplasm. However, moderate differentiation (FST = 0.10; DR = 0.104) and evidence of admixture in some individuals suggest that Hyrcanian figs form a distinct and well-differentiated gene pool within the F. carica complex. Their limited genetic contribution to cultivars suggests minimal historical breeding use, preserving their distinct identity. No clear differentiation was observed between local and introduced cultivars; many Azerbaijani accessions showed strong affinity with West Mediterranean germplasm, reflecting historical introductions. These results provide a genomic framework for characterizing fig diversity and guiding their conservation and breeding.
Fire blight, caused by the bacterial pathogen Erwinia amylovora, is a persistent problem for pear (Pyrus spp.) growers across most production regions around the world. Growing resistant cultivars is one of the best options for managing fire blight. The resistant P. communis cultivars ‘Potomac’ and ‘Old Home’, and the hybrid selection NJA2R59T69 were used in a previous study to identify quantitative trait loci (QTLs) linked to the resistance. The major chromosome 2 QTLs identified in the ‘Potomac’ and ‘Old Home’ sources overlap with QTLs that were previously identified in ‘Harrow Sweet’ and ‘Moonglow’, while that of NJA2R59T69 (through P. ussuriensis ‘Pai Li’) mapped to a nearby location on chromosome 2. In the current study, genes associated with disease resistance in the two chromosome 2 QTL regions were cloned in 23 accessions representing resistant and susceptible cultivars, and progeny from the three sources. Alleles unique to resistant cultivars in these genic regions were targeted by SeqSNP and used to genotype a diversity set of 382 pear accessions with known fire blight disease responses from multiple sources. Association mapping was conducted across subsets of the 382 accessions based on the shared fire blight resistance source. Association mapping identified a marker (Chr2_3601869) that was predictive with 88.0
Nucleotide-binding leucine-rich repeat (NLR) receptors play a central role in effector-triggered immunity, yet their diversity, regulation and evolutionary dynamics in conifers remain poorly understood. We investigated the NLR repertoire of Pinus pinaster during infection by the pathogen Fusarium circinatum, identifying 193 NB-ARC–containing genes expressed throughout infection. TIR-NLRs (TNLs) represented the largest subfamily, whereas helper-type RPW8-NLRs (RNLs) were comparatively rare. Most NLRs were transcriptionally repressed, but a subset displayed strong late induction, revealing four distinct temporal expression clusters. Phylogenetic analyses showed clear separation of major NLR clades but no correspondence between evolutionary relationships and transcriptional patterns, indicating extensive regulatory diversification. Among induced genes, on gene (PpRG) displayed exceptionally strong upregulation. Expression profiling across Pinus species showed conserved PpRG induction following F. circinatum infection, whereas lesion severity did not correlate with expression levels. In P. pinaster, PpRG responded specifically to stem-infecting pathogens (F. circinatum, Diplodia sapinea), but not to foliar pathogens, endophytic fungi, methyl jasmonate, or drought. Functional and phylogenetic analyses indicate that PpRG is related to NLR-like proteins, although its classification remains unresolved. Together, our results reveal a dynamically regulated NLR repertoire in P. pinaster and identify PpRG as a strongly induced, stem‑associated gene with potential value as a candidate biomarker associated with immune signalling during interactions with canker-causing pathogens. A dynamically regulated NLR network is revealed in Pinus pinaster, identifying a strongly inducible defence-related gene with NLR-like features.
In conifers, plastid DNA is inherited through the male lineage via the pollen grain. By contrast, mitochondrial DNA is maternally inherited in the well-studied Pinaceae, but is often paternally inherited in other conifer families. This paper examines the mode of inheritance of plastids and mitochondria in the rare Tasmanian podocarp Lagarostrobos franklinii. It is the first molecular genetic study of organelle inheritance in the Podocarpaceae family. Two intraspecific crosses were established with the same iconic father, which was cloned from a tree from a uniform clonal stand, estimated to be 11,000 years old. Genome skimming and subsequent bioinformatic analysis identified polymorphic positions in the parental genomes of one cross. Our Illumina reads were aligned to a published plastome and to newly assembled DNA contigs that represent the partial mitogenome of the father. We used PCR-based markers derived from these polymorphisms to genotype parents and offspring of both crosses. Both plastid DNA and mitochondrial DNA were paternally inherited in all five offspring examined. This study provides new insights into patterns of organelle inheritance in conifers and the evolution of this trait.
Apple (Malus domestica Borkh.) is one of Europe’s most significant fruit crops, and preserving its genetic diversity is critical for breeding and adaptation to climate change. This study presents a comprehensive molecular characterisation of apple germplasm collections from Ukraine, Sweden, and Estonia using 16 SSR markers to assess genetic identity, diversity, and structure. Genotyping data were harmonised using the Malus UNiQue genotype (MUNQ) system, enabling accurate cross-collection comparisons and clarification of mislabelled or synonymous accessions. In total, 422 unique diploid genotypes were analysed, representing both historical heirloom and modern cultivars from three national collections with diverse geographic and breeding origins. Structure analysis demonstrated clear genetic separation between Ukrainian and Northern European germplasm, with Swedish and Estonian cultivars clustering together, reflecting their shared breeding history and regional adaptation. Ukrainian heirloom cultivars formed a distinct genetic subgroup, whilst modern Ukrainian cultivars showed admixture with foreign germplasm, highlighting the underutilisation of the native gene pool in breeding programmes. These findings underscore the importance of preserving Ukrainian heirloom cultivars as valuable genetic resources for future breeding and conservation efforts, contribute to the global understanding of apple genetic resources, and demonstrate the utility of MUNQ harmonisation for curation and diversity studies in fruit tree collections.
This study presents SST (Species Selection Tool), a climate-based framework designed to support species selection across geographic regions and climate scenarios. The tool was developed to enable breeders to examine species selection scenarios across countries and climate horizons. Beyond identifying promising species for testing, SST prioritizes candidate species, highlights opportunities for germplasm exchange, anticipates climate-driven shifts, and maps environmental clusters and adapted genetic resources to guide near- and long-term breeding strategies. Built with the Shiny framework in R, SST allows users to upload tabular data in CSV format for flexible analyses. We demonstrate its application for a Eucalyptus breeding example in Brazil, using occurrence data from GBIF and environmental covariates from TerraClimate and CHIRPS, and complemented by CMIP6 future climate projections. Temperature and precipitation data were used to compute 19 bioclimatic variables (BIO1–BIO19) for macroenvironmental classification and species suitability assessment. SST integrates five analytical indices, scaled from 0 to 1, producing an overall suitability index and ranking species accordingly. The tool identified E. urophylla, E. brassiana, E. deglupta, and E. pellita as the most suitable for the study area in the Maranhão State, Brazil. Open-source and user-friendly, SST accelerates breeding decisions, supports climate-adaptive planning, and provides access to advanced analytical tools. The tool is a useful contribution to forest management and forest tree breeding, supporting data-driven strategies for sustainable forestry under changing climates.
Hazelnuts are a valuable source of nutrients and have health-promoting properties including beneficial fatty acids, vitamins and antioxidant compounds. In this work, a core collection of 96 hazelnut accessions including cultivars, landraces and wild materials was evaluated for total oil, fatty acids, α-tocopherol, oil stability, phenolics and mineral contents. Genomic loci controlling these traits were identified using genome-wide association analysis. Multivariate analysis indicated that separation of the accessions for nutritional traits was mainly attributed to oleic acid, linoleic acid and α-tocopherol contents. Some landraces and wild accessions possessed exceptional levels of these beneficial compounds suggesting that they can be used for trait improvement. Association mapping using a Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) approach detected linkage between 98 single nucleotide polymorphisms (SNPs) and 15 traits with four genomic regions associated with more than one parameter. Based on SNP location, candidate genes and loci with effects on more than one trait were identified providing potential targets for breeding for improved nutritional quality. It was also found that favorable alleles for some loci were under-represented in cultivars. Thus, introgression of these alleles via marker-assisted selection could further improve cultivar quality providing a needed boost to Turkish hazelnut breeding.
Complex chromosome pairing and separation occur in triploid individuals during meiosis, which affect the genetic composition and fertility of gametes. In the present study, compared with the diploid control Populus ‘84 K’ that exhibited regular and synchronous meiosis with normal microspore formation, the triploid hybrid clone ‘Beilinxiongzhu 1#’ displayed numerous meiotic abnormalities, such as univalents, premature chromosome migration, lagging chromosomes, chromosome bridges, asymmetric segregation, and premature cytokinesis. These abnormalities contributed to the unbalanced allocation of genetic material, which seriously affected gamete fertility. A total of 393 progeny were generated by crossing ‘Beilinxiongzhu 1#’ with diploid Populus ‘YXY 7#’, suggesting that not all gametes produced by triploid Populus were aborted. Nineteen SSR polymorphic primers distributed on 19 chromosomes were screened to analyze the parental heterozygosity transmitted to 393 progeny. The transmitted paternal heterozygosity values for the hyper-diploids, hypo-triploids, hyper-triploids, and hypo-tetraploids were 0.627, 0.677, 0.825, and 0.905, respectively, indicating that the viable pollen grains of ‘Beilinxiongzhu 1#’ transmitted higher heterozygosity to progeny. Our findings confirm that aneuploids will play an important role in the genetic improvement of Populus.
Butternut (Juglans cinerea L.) is a rapidly declining tree species threatened by Ophiognomonia clavigignenti-juglandacearum (Oc-j), the causal agent of butternut canker. The introduction of Japanese walnut (Juglans ailantifolia Carrière), which hybridizes with butternut and exhibits greater resistance to the disease, presents both a conservation challenge and a potential avenue for genetic improvement. Identifying non-admixed butternuts is critical for conservation efforts and breeding programs aimed at preserving the species’ genetic integrity while exploring resistance strategies. However, morphological identification of first and advanced generation hybrids is unreliable, necessitating the development of efficient detection tools. In this study, we developed and validated a cost-effective, high-throughput SNP genotyping tool using the MassARRAY platform to distinguish between J. cinerea, J. ailantifolia, and their hybrids. The panel consists of 28 nuclear SNPs and two chloroplast SNPs and demonstrates strong concordance with genotyping-by-sequencing (GBS) results using nearly 12,000 SNPs (R² = 0.98), indicating high predictive accuracy. Field testing this genotyping tool to 1,269 trees from natural stands and breeding programs in Canada and the U.S. revealed substantial hybridization, particularly in U.S. plantations, where hybrids comprised up to 18
Coffee is among the most widely consumed beverages worldwide, with diverse Coffea species displaying a broad spectrum of flavors and important agronomic traits. Despite recent advances in genomics and the availability of assembled coffee genomes, comparative genomic analyses remain underutilized for crop improvement. In this study, we conducted comprehensive orthology and orthogroup evolution analyses across 24 plant species–four Gentianales, including three Coffea species (Coffea arabica, Coffea canephora, and Coffea eugenioides), twelve Lamiales, and eight Solanales–to identify lineage-specific genomic features associated with adaptation and coffee quality traits. Using OrthoFinder in conjunction with gene family evolution models (CAFE5 and COUNT), we identified 1,552 orthogroups that are either specific to Coffea or have undergone significant expansion or contraction. Disease‑resistance genes were the most prominent among rapidly expanded orthogroups, reflecting an ongoing evolutionary arms race with pathogens. We also observed asymmetric patterns of orthogroup evolution, including contraction of light and ethylene signaling orthogroups in C. canephora, contrasted by their expansion in C. arabica and C. eugenioides, which may contribute to their adaptation to shaded, high-altitude environments. Further analysis using COUNT identified twelve Coffea-specific orthogroup expansions associated with secondary metabolite biosynthesis, including key enzymes for caffeine and chlorogenic acid production. Our comprehensive catalog of lineage-specific orthogroups, supported by functional enrichment and phylogenetic analyses, provides a valuable genomic resource to support breeding programs focused on enhancing stress resilience, disease resistance, and cup quality in cultivated coffee.
Camellia impressinervis and Camellia indochinensis are two narrow endemic species with especial yellow flowers, which grows in the karst limestone mountains in Guangxi, China. They are endangered requiring information on genetic structure and diversity to inform conservation efforts. In this study, the chloroplast analysis was based on 10 individuals per population, while the microsatellite analysis included all 203 individuals from eight populations of C. impressinervis and all 277 individuals from 10 populations of C. indochinensis. Our results showed that despite their narrow geographic range, significant population structure was detected in both species, with each population constituting a distinct genetic cluster. Both species maintained relatively high genetic diversity (C. impressinervis: Ho = 0.593, He = 0.631; C. indochinensis: Ho = 0.686, He = 0.693). These findings emphasize the need for population-level conservation strategies to preserve the unique genetic resources of these ecologically specialized species.
Betula lenta (sweet birch, cherry birch) belongs to an early-branching lineage within the genus Betula and is native to North America, with distinct ecological and biochemical traits. Despite its importance, genomic resources for this species have been lacking, limiting comparative and evolutionary studies across the genus. Here, we present a scaffold-level reference genome for B. lenta, assembled using 10X Genomics linked-read sequencing. The assembly spans 456 Mb with a scaffold N50 of 2.99 Mb. A total of 21,639 protein-coding genes were predicted using a combination of transcriptome, homology-based, and ab initio annotation approaches. Genome completeness assessment using BUSCO (embryophyta_odb10) revealed 96.7
The Atlantic Forest is a biodiversity hotspot facing severe habitat loss and fragmentation, with most of its remnants experiencing biomass and biodiversity declines. Butia eriospatha, an endangered palm species endemic to this biome, is threatened with extinction by habitat loss, poaching, and lack of regeneration. Despite its ecological and cultural importance, genetic studies have focused only on open grassland populations, leaving the rare forest populations unexplored. Here, we compared genetic diversity aspects of a forest (FOR) and a grassland (GRA) B. eriospatha population to inform seed collection guidelines and further expand our knowledge on the genetic conservation of this important species. Using nine microsatellite loci, we assessed genetic diversity, mating system, and spatial genetic structure (SGS) of both populations. We found that both FOR and GRA had moderate genetic diversity but were significantly differentiated from each other, despite the short geographic distance. Allogamy predominated in both populations, with a small proportion of mating among relatives detected in the forest population. SGS was weak but extended over longer distances in FOR (up to 60 m) compared to GRA (up to 30 m), suggesting differences in mortality dynamics. To maximize genetic diversity in long-term conservation strategies, seeds should be collected from 132 to 139 seed-trees, respecting SGS distances. Our findings highlight the need to conserve both grassland and forest populations to safeguard B. eriospatha’s genetic diversity.
As genome sequencing becomes more accessible to non-model species, it is key to ensure high-quality genome annotations exist. These efforts include the re-annotation of important genomes when newer data and software are available. Here, we present a re-annotation of the ‘Bartlett’ doubled haploid (DH) genome, which has served as the reference genome for European pear research. We employed a newly developed annotation pipeline that incorporated a polished version of the DH genome, an Iso-Seq RNA-seq dataset developed by sampling eleven different tissue types from adult trees and in vitro treelets, and RNA-seq evidence from nine publicly available transcriptomes encompassing ten tissue types. The resulting re-annotation exhibited improved BUSCO and OMArk scores, increased gene capture, and improved gene model accuracy. Further, we saw increases in the number of orthogroups represented, as well as improved completeness of those orthogroups, based on Core Orthogroup similarity to recent high-quality pome annotations. Together, the improvements generated from this annotation will enable efficient use for molecular biology, genetic evolution studies, and other downstream applications.
Picea crassifolia is a unique evergreen tree species native to China and plays a crucial role in regulating the regional ecological balance. However, the extent of variation in key traits and the genetic mechanisms underlying this variation remain unclear, limiting the development of P. crassifolia seed orchards. In this study, we evaluated essential wood, needle and growth traits and conducted a genome-wide association analysis to elucidate the genetic basis of these traits using clonal means from 106 clones of P. crassifolia collected from the Qilian Mountains, ensuring the representativeness of the germplasm. Substantial phenotypic variation was observed among clones for wood and needle properties, with an average coefficient of variation of 20.79
Recent advances in third-generation sequencing have enabled high-quality genome assemblies of complex plant genomes. Existing reference genomes of Prunus avium L. (sweet cherry) may not adequately represent the genetic diversity of the self-incompatible cultivars that are widely grown in Chile. We report chromosome-scale consensus and phased genome assemblies of two of the most cultivated varieties in Chile, ’Santina’ and ‘Regina’. This was achieved using a multi-platform strategy that combines PacBio HiFi, Nanopore, Hi-C, and a genetic map of sweet cherry. The assemblies span 354 Mbp (Santina) and 357.5 Mbp (Regina) and have contig N50 values of 22.7 Mbp and 19.2 Mbp, respectively. Chromosome anchoring covered 301 Mbp (85
