More than a century after two introduced pathogens killed billions of American chestnut trees, introgression of resistance alleles from Chinese chestnuts has contributed to the recovery of self-sustaining populations. However, progress has been slow because of the complex genetic architecture of resistance. To better understand blight resistance, we compared reference genomes, gene expression responses, and stem metabolite profiles of the resistant Chinese and susceptible American chestnut species. To accelerate resistance breeding, we conducted large-scale phenotyping and genotyping in hybrids of these species. Simulation and inoculation experiments suggest that significant resistance gains are possible through selectively breeding trees with an average of 70 to 85% American chestnut ancestry. The resources developed in this work are foundational for breeding to create diverse restoration populations with sufficient disease resistance and competitive growth.

If microbial traits are phylogenetically conserved, then variation in traits of plant hosts may influence rhizosphere microbiomes at higher taxonomic levels. To test this hypothesis and genotype-by-environment-by-microbiome (G x E x M) interactions in switchgrass (Panicum virgatum), we assessed rhizosphere bacterial composition using 128 host genotypes grown at three distinct field sites. First, we found that growing site was a substantial driver of bacterial composition and that specific bacterial taxa correlated with differences in disease incidence and yield across environments. Second, broad-sense heritability analyses revealed that host genetic effects on rhizosphere composition were strongest at the genus level, suggesting a conserved genetic basis for shaping beneficial or pathogenic taxa. Third, we identified shared host genetic variants associated with bacterial abundance and plant metabolism, indicating possible linkages between key microbial traits and agronomic performance. These findings underscore the importance of incorporating rhizosphere microbiomes into switchgrass breeding efforts and call for further investigation of G x E x M interactions to pinpoint microbial interventions that enhance yield and disease resistance.Copyright (c) 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Vachelia nilotica (L.) P. J. H. (Acacia nilotica (L.) Willd. ex Delile) ss a multi-purpose, fast-growing agroforestry species used by rural populations in livestock feed, construction, traditional pharmacopoeia, crafts, and as a source of fuel. We carried out a study on this species with the aim of characterizing its genetic variation in the Sudano-Sahelian zone of Cameroon and to guide future reforestation programs necessary in this zone which continues to lose cultivable areas due to the advance of the desert. Half-sib families from 20 trees were collected from 12 provenances and grown in the nursery for three months. At this age, morphological variables were measured from the young plants. Subsequently, five families were randomly selected for each provenance and used for analysis of genetic variation using microsatellite markers already tested on several related species belonging to the Acacia genus. Molecular data revealed that the samples were predominantly polyploid and thus the estimation of genetic diversity required the development of a binary matrix (0/1) indicating the presence or absence of each fragment. The results revealed 49 fragments for the 10 nuclear microsatellites (nSSRs) and two haplotypes for the one polymorphic chloroplast SSR (cpSSR). The characterization of the samples using cpSSRs and nSSRs highlighted two distinct genetic clusters with different ploidy levels and complete reproductive isolation, which suggested that they could be two different varieties. Several levels of ploidy (from diploid to hexaploid) were observed. At the level of morphological performance, there was no general trend in favor of polyploids for traits. For most morphological traits, no significant differences were observed between the two genetic clusters.

White oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. We report the first haplotype-resolved chromosome-scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data. Despite strongly conserved chromosome synteny and genome size across Quercus, certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species - as are the chromosomal locations of R gene clusters - but, gene number within clusters is more labile. We found that Q. alba has high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus. The white oak genome represents a major new resource for studying genome diversity and evolution in Quercus. Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution in Quercus.

Over a century after two introduced pathogens decimated American chestnut populations, breeding programs continue to incorporate resistance from Chinese chestnut to recover self-sustaining populations. Due to complex genetics of chestnut blight resistance, it is challenging to obtain trees with sufficient resistance and competitive growth. We developed high quality reference genomes for Chinese and American chestnut and leveraged large disease phenotype and genotype datasets to develop accurate genomic selection. Inoculation and simulation results indicate that resistance may be substantially increased in trees that inherited 70% to 100% of their genome from American chestnut. To facilitate gene editing, we integrated multiple lines of evidence to discover candidate alleles for blight resistance and susceptibility. These genomic resources provide a strong foundation to accelerate restoration of this iconic tree. ### Competing Interest Statement The authors have declared no competing interest.

### Competing Interest Statement The authors have declared no competing interest.

Quercus alba L., also known as white oak, eastern white oak, or American white oak, is a quintessential North American species within the white oak section (Quercus) of the genus Quercus, subgenus Quercus. This species plays a vital role as a keystone species in eastern North American forests and plays a significant role in local and regional economies. As a long-lived woody perennial covering an extensive natural range, Q. alba’s biology is shaped by a myriad of adaptations accumulated throughout its natural history. Populations of Q. alba are crucial repositories of genetic, genomic, and evolutionary insights, capturing the essence of successful historical adaptations and ongoing responses to contemporary environmental challenges in the Anthropocene. This intersection offers an exceptional opportunity to integrate genomic knowledge with the discovery of climate-relevant traits, advancing tree improvement, forest ecology, and forest management strategies. This review provides a comprehensive examination of the current understanding of Q. alba’s biology, considering past, present, and future research perspectives. It encompasses aspects such as distribution, phylogeny, population structure, key adaptive traits to cyclical environmental conditions (including water use, reproduction, propagation, and growth), as well as the species’ resilience to biotic and abiotic stressors. Additionally, this review highlights the state-of-the-art research resources available for the Quercus genus, including Q. alba, showcasing developments in genetics, genomics, biotechnology, and phenomics tools. This overview lays the groundwork for exploring and elucidating the principles of longevity in plants, positioning Q. alba as an emerging model tree species, ideally suited for investigating the biology of climate-relevant traits.

Gene flow affects the genetic diversity and structure of tree species and can be influenced by stress related to changing climatic conditions. The study of tree species planted in locations outside their natural range, such as arboreta or botanical gardens, allows us to analyse the effect of severe fragmentation on patterns and distances of gene flow. Paternity analysis based on microsatellite marker genotyping was used to analyse how fragmentation affects gene flow among individuals of Quercus rubra L. distributed in a small isolated group of trees (15 trees) planted in the arboretum on the North Campus of the University of Göttingen. For paternity analysis, 365 seedlings from four seed parents were selected and genotyped using 16 microsatellites. The analysis revealed the majority of pollen (84.89

Summary White oak ( Quercus alba ) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. We report the first haplotype-resolved chromosome-scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. In addition, we probe the genetic diversity of this widespread species and investigate its phylogenetic relationships with other oaks using whole-genome data. Our genome assembly comprises two haplotypes each consisting of 12 chromosomes. We found that the species has high genetic diversity, much of which predates the divergence of Q. alba from other oak species and likely impacts divergence time estimation in Quercus . Our phylogenetic results highlight phylogenetic discordance across the genus and suggest different relationships among North American oaks than have been reported previously. Despite a high preservation of chromosome synteny and genome size across the Quercus phylogeny, certain gene families have undergone rapid changes in size including resistance genes (R genes). The white oak genome represents a major new resource for studying genome diversity and evolution in Quercus and forest trees more generally. Future research will continue to reveal the full scope of genomic diversity across the white oak clade.

Natural populations or landraces contains a high level of genetic variation that can be used for the selection of plus trees in Faidherbia albida agroforestry parklands in the Sudano-Sahelian zone of Cameroon. With the high rate of deforestation and overpopulation in recent times, there is the danger of losing these naturally adapted landraces of trees. This study investigates the influence of environmental conditions (altitude, human activity, rainfall and soil types) on four (Kodex, Mambang, Dinao and Parkine) Faidherbia albida agroforestry parklands in Cameroon. A forest inventory sampling method with a set of 33 plots 200 m in diameter was established in the parklands to collect data. Phenotypic measurements (height, diameter at breast height, number of branches, crown diameter and calculated biovolume) were taken and leaf phenology was observed on 156 trees in addition to environmental conditions of the parklands. Species diversity was recorded only in the transects of Kodek and Parkine agroforestry parklands during the inventory. Significant differences were observed among the agroforestry parklands, the soil types, altitude, and human activities on the morphological parameters measured. The inverse phenology of Faidherbia albida was observed in three of the parklands with Mambang still conserving its leaves in the rainy season. A total of 1904 trees (1233 from Kodek and 671 from Parkine) were recorded during the species diversity inventory process from 63 species with Parkine parkland being the most diverse in species types with Shannon H = 2,058 index at Kodek and Shannon H = 2.53 index at Parkine. The results of this study indicated that diverse environmental conditions do exist in these parklands and have influenced the measured parameters. This information can aid in the selection of plus-trees for breeding, conservation and management of the species while the information on species diversity will assist in monitoring the dynamic of the parklands.

Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to the northeastern United States. We present a chromosome-scale, haplotype-resolved genome of Q. rubra, a representative red oak species, generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Megabases (Mb) with 95.27% of the genome sequences scaffolded into 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Q. lobata and Q. mongolica reveal high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other oak and rosid tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubra genome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the nine species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfamily, similar to Q. robur. Single major QTL regions were identified for vegetative bud break and marcescence which contain candidate genes for further research, including a putative ortholog of the circadian clock constituent cryptochrome (CRY2) and a family of eight tandemly duplicated genes for serine protease inhibitors, respectively. Genome-environment associations across natural populations identified candidate abiotic stress tolerance genes and predicted performance in a common garden. This high-quality red oak genome represents an essential resource to the oak genomics community which will further supplement the knowledge of Quercus genomics.

Tree peony is a unique traditional flower in China, with large, fragrant, and colorful flowers. However, a relatively short and concentrated flowering period limits the applications and production of tree peony. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of flowering phenology traits and ornamental phenotypes in tree peony. A diverse panel of 451 tree peony accessions was phenotyped for 23 flowering phenology traits and 4 floral agronomic traits over 3 years. Genotyping by sequencing (GBS) was used to obtain a large number of genome-wide single-nucleotide polymorphisms (SNPs) (107 050) for the panel genotypes, and 1047 candidate genes were identified by association mapping. Eighty-two related genes were observed during at least 2 years for flowering, and seven SNPs repeatedly identified for multiple flowering phenology traits over multiple years were highly significantly associated with five genes known to regulate flowering time. We validated the temporal expression profiles of these candidate genes and highlighted their possible roles in the regulation of flower bud differentiation and flowering time in tree peony. This study shows that GWAS based on GBS can be used to identify the genetic determinants of complex traits in tree peony. The results expand our understanding of flowering time control in perennial woody plants. Identification of markers closely related to these flowering phenology traits can be used in tree peony breeding programs for important agronomic traits.

Summary Since microbial traits are conserved at different taxonomic levels, plant hosts may influence microbiome composition differently at different levels to broadly promote or resist microbiota with traits that impact host fitness. We tested this hypothesis by assessing signals of host genetic influence on bacterial composition in the switchgrass rhizosphere using 128 genotypes in dissimilar growing sites. We employed three common gardens, combined with host genetic mapping, 16S rRNA gene sequence analysis, hierarchical modeling, tests of phylogenetic conservation of host influence, and genome-wide association analyses to determine the contributions of host genetics in shaping rhizosphere bacterial composition at different taxonomic levels. Modeling bacterial assembly showed that growing site was a strong factor shaping bacterial composition in the rhizosphere, though host genetic influence played a significant role. The heritability of bacterial abundance was strongest at the genus level. Phylogenetic signal for heritability was detected within the bacterial phylogeny but conserved clades differed between common gardens. We identified shared host genetic variants associated with bacterial abundance and host traits related to plant metabolism. Our results suggest further investigation is required regarding the genotype-by-environment-by-microbiome relationship to elucidate the factors shaping rhizosphere microbiome composition and the agroecological dynamics shaping plant phenotype.

Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Quercus lobata and Quercus mongolica revealed high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubra genome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the 9 species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfamily, similar to Quercus robur. Phylogenetic analysis also identified 4 subfamilies of the IGT/LAZY gene family in Q. rubra important for plant structure. Single major QTL regions were identified for vegetative bud break and marcescence, which contain candidate genes for further research, including a putative ortholog of the circadian clock constituent cryptochrome (CRY2) and 8 tandemly duplicated genes for serine protease inhibitors, respectively. Genome-environment associations across natural populations identified candidate abiotic stress tolerance genes and predicted performance in a common garden. This high-quality red oak genome represents an essential resource to the oak genomic community, which will expedite comparative genomics and biological studies in Quercus species.

As a candidate national flower of China, tree peony has extremely high ornamental, medicinal and oil value. However, the short florescence and rarity of early-flowering and late-flowering varieties restrict further improvement of the economic value of tree peony. Specific miRNAs and their target genes engaged in tree peony floral florescence, development and senescence remain unknown. This report presents the integrated analysis of the miRNAome, transcriptome and degradome of tree peony petals collected from blooming, initial flowering, full blooming and decay stages in early-flowering variety Paeonia ostii 'Fengdan', an early-flowering mutant line of Paeonia ostii 'Fengdan' and late-flowering variety Paeonia suffruticosa 'Lianhe'. Transcriptome analysis revealed a transcript ('psu.G.00014095') which was annotated as a xyloglucan endotransglycosylase/hydrolase precursor XTH-25 and found to be differentially expressed across flower developmental stages in Paeonia ostii 'Fengdan' and Paeonia suffruticosa 'Lianhe'. The miRNA-mRNA modules were presented significant enrichment in various pathways such as plant hormone signal transduction, indole alkaloid biosynthesis, arachidonic acid metabolism, folate biosynthesis, fatty acid elongation, and the MAPK signaling pathway. Multiple miRNA-mRNA-TF modules demonstrated the potential functions of MYB-related, bHLH, Trihelix, NAC, GRAS and HD-ZIP TF families in floral florescence, development, and senescence of tree peony. Comparative spatio-temporal expression investigation of eight floral-favored miRNA-target modules suggested that transcript 'psu.T.00024044' and microRNA mtr-miR166g-5p are involved in the floral florescence, development and senescence associated agronomic traits of tree peony. The results might accelerate the understanding of the potential regulation mechanism in regards to floral florescence, development and abscission, and supply guidance for tree peony breeding of varieties with later and longer florescence characteristics.

Host genetic variation can shape the diversity and composition of associated microbiomes, which may reciprocally influence host traits and performance. While the genetic basis of phenotypic diversity of plant populations in nature has been studied, comparatively little research has investigated the genetics of host effects on their associated microbiomes. Switchgrass (Panicum virgatum) is a highly outcrossing, perennial, grass species with substantial locally adaptive diversity across its native North American range. Here, we compared 383 switchgrass accessions in a common garden to determine the host genotypic influence on rhizosphere bacterial composition. We hypothesized that the composition and diversity of rhizosphere bacterial assemblages would differentiate due to genotypic differences between hosts (potentially due to root phenotypes and associated life history variation). We observed higher alpha diversity of bacteria associated with upland ecotypes and tetraploids, compared to lowland ecotypes and octoploids, respectively. Alpha diversity correlated negatively with flowering time and plant height, indicating that bacterial composition varies along switchgrass life history axes. Narrow-sense heritability (h2 ) of the relative abundance of 21 core bacterial families was observed. Overall compositional differences among tetraploids, due to genetic variation, supports widespread genotypic influence on the rhizosphere microbiome. Tetraploids were only considered due to complexities associated with the octoploid genomes. Lastly, a genome-wide association study identified 1861 single-nucleotide polymorphisms associated with 110 families and genes containing them related to potential regulatory functions. Our findings suggest that switchgrass genomic and life-history variation influences bacterial composition in the rhizosphere, potentially due to host adaptation to local environments.

Eastern black walnut (Juglans nigra L.), one of the most valuable timber and veneer trees in North America, provides nut shells with unique industrial uses and nut kernels with distinctive culinary attributes. A mature F-1 full-sib progeny orchard of 248 individuals from the cross of two eastern black walnut cultivars provides a long-term resource for discovering genetic mechanisms controlling life history, quality traits, and stress resistance. The genetic linkage map, constructed with 356 single nucleotide polymorphism (SNP) markers and 62 expressed sequence tag simple sequence repeats (EST-SSRs), is 1645.7 cM in length, distributed across the expected 16 linkage groups. In this first application of QTL mapping in J. nigra, we report QTL for budbreak, peak pistillate bloom, peak staminate bloom, and heterodichogamy. A dominant major QTL for heterodichogamy is reported, the sequence for which is syntenic with the heterodichogamy QTL on chromosome 11 of Persian walnut (J. regia L.). The mapping population parents are both protogynous, and segregation suggests a Mendelian component, with a 3:1-like inheritance pattern from heterozygous parents. Mapping the sequenced EST-SSR markers to the J. regia "Chandler " V2.0 genome sequence revealed evidence for collinearity and structural changes on two of the sixteen chromosomes. The inclusion of sequenced EST-SSR markers enables the direct comparison of this and subsequent J. nigra maps and other Juglandaceae genetic maps. This investigation initiates long-term QTL detection studies for quality and stress resistance traits in black walnut.

Buffalo nut (Cervantesiaceae; Pyrularia pubera Michx.) is a unique facultative hemiparasitic species that can reproduce clonally or sexually. Fragmented population stands of buffalo nut in Pennsylvania, USA, represent the northern-most range of distribution of the species. These leading-edge populations could be the originators for new stands expected to arise as climate change shifts this species' native range further north. When observing an isolated stand of buffalo nut, it is impossible to be sure if individual trees are clones of a common parental plant or the product of sexual reproduction. Our study represents the first attempt to use population genetic methodologies to determine the genetic relatedness of individual plants in fragmented stands, and to assess the genetic diversity of native buffalo nut populations in North America. Our study used microsatellite markers to compare genetic variation in samples from populations in Pennsylvania to samples collected in other populations in the northern end of its range (i.e., West Virginia, Kentucky, and Virginia). We found 1) that trees could not be located at most sites, and 2) that Pennsylvania populations are largely clonal with little genetic diversity among locations within the state (similar to 200 km(2)) relative to populations sampled in Kentucky and Virginia. We provide best practice suggestions for conservation of this species.

Adaptive divergence is widely accepted as a contributor to speciation and the maintenance of species integrity. However, the mechanisms leading to reproductive isolation, the genes involved in adaptive divergence, and the traits that shape the adaptation of wild species to changes in climate are still largely unknown. In studying the role of ecological interactions and environment-driven selection, trees have emerged as potential model organisms because of their longevity and large genetic diversity, especially in natural habitats. Due to recurrent gene flow among species with different ecological preferences, oaks arose as early as the 1970s as a model for understanding how speciation can occur in the face of interspecific gene flow, and what we mean by "species" when geographically and genomically heterogeneous introgression seems to undermine species' genetic coherence. In this review, we provide an overview of recent research into the genomic underpinnings of adaptive divergence and maintenance of species integrity in oaks in the face of gene flow. We review genomic and analytical tools instrumental to better understanding mechanisms leading to reproductive isolation and environment-driven adaptive introgression in oaks. We review evidence that oak species are genomically coherent entities, focusing on sympatric populations with ongoing gene flow, and discuss evidence for and hypotheses regarding genetic mechanisms linking adaptive divergence and reproductive isolation. As the evolution of drought- and freezing-tolerance have been key to the parallel diversification of oaks, we investigate the question of whether the same or a similar set of genes are involved in adaptive divergence for drought and stress tolerance across different taxa and sections. Finally, we propose potential future research directions on the role of hybridization and adaptive introgression in adaptation to climate change.