An overall picture comparing the repetitive components of the genomes of three Quercus species was obtained by genome skimming with Illumina sequence reads. Read sets of Q. lobata, Q. robur, and Q. suber species were subjected to hybrid clustering in order to assemble a repeatome of the Quercus genus and to annotate it. The repeatome was composed of 8573 clusters. The abundance of repeated sequences in the three species was assessed by mapping Illumina reads of each species onto the repeatome. The repetitive portion of the genome was similar among the three species. The most abundant repetitive sequences were long terminal repeat-retrotransposons. Copia elements were overrepresented when compared with Gypsy ones. The most abundant retrotransposon lineages were SIRE for the Copia superfamily and Ogre/TAT for the Gypsy superfamily. Some of the clusters belonging to these lineages showed different transpositional time profiles among the three species. Ribosomal DNAs accounted for 3.64–6.75% of the repetitive component. Satellite DNAs were much more abundant in Q. lobata (8.68% of the genome) than in the two other species. However, different satellite DNAs showed large variations in their abundances. Overall, the composition of the repetitive portion of the genome showed some differences among oak species, suggesting a possible role of repeats for Quercus species differentiation. In the cases of Q. lobata and Q. robur, both of which belong to the Quercus section of the Quercus genus, such differences may be related to the different geographical origins of the species.

High numbers of endemic plants exist in subtropical China, but there have been few investigations of the phylogeography and dynamic history for endemic tree species in this region. In this study, we explored the phylogeographic pattern of Quercus fabri, an endemic oak species in subtropical China, to assess the effects of past geographical and climatic changes on the evolutionary history of this deciduous species using three chloroplast DNA (cpDNA) fragments and the internal transcribed spacer region (ITS) and ecological niche modeling (ENM). The cpDNA fragments differentiated three phylogeographical groups among Q. fabri populations. A BEAST-derived chronogram based on the cpDNA haplotypes indicated that the initial divergence of Q. fabri probably occurred during the late Miocene (12.33 Ma), whereas haplotype divergence time could date back to the late Pliocene to early Pleistocene. ENM showed that the suitable areas contracted during the last glacial maximum (LGM) and expanded in the warm period during the Pleistocene. Consistently, both the cpDNA and ITS datasets suggested that population expansion occurred after the LGM period (ca. 13–14 kyr) for Q. fabri. Demographical analyses based on multiple genetic datasets and a coalescent-based method also suggested a shrinkage–expansion trend for the effective population sizes of Q. fabri during the glacial–interglacial periods in the Quaternary. Our results suggest that the Neogene and Pleistocene were important periods for triggering species differentiation and intraspecific diversification in Q. fabri, thereby providing insights into the effects of environmental changes in the Quaternary on the population dynamics of endemic tree species in subtropical China.

Forest trees exhibit strong patterns of local adaptation in phenological traits along latitudinal gradients. Previous studies in spruce have shown that variation at genes from the photoperiodic pathway and the circadian clock are associated to these clines but it has been difficult to find solid evidence of selection for some of these genes. Here, we used growth cessation, gene expression, and single nucleotide polymorphism (SNP) data at two major candidate loci, FLOWERING LOCUS T/TERMINAL FLOWER1-Like2 (FTL2) and GIGANTEA (GI), as well as at background loci from a latitudinal gradient in Siberian spruce (Picea obovata) populations along the Ob River to test for clinal variation in growth cessation and at the two candidate genes. As in previous studies, there was a strong latitudinal cline in growth cessation that was accompanied by a significant cline in the expression of FTL2. Expression of FTL2 was significantly associated with allele frequencies at some of the GI’s SNPs. However, the cline in allele frequency at candidate genes was not as steep as in a Norway spruce cline and in a parallel Siberian spruce cline studied previously and nonsignificant when a correction for population structure was applied. A McDonald-Kreitman test did not detect decisive evidence of selection on GI (p value = 0.07) and could not be applied to FTL2 because of limited polymorphism. Nonetheless, polymorphisms contributed more to the increased neutrality index of PoGI than to that of control loci. Finally, comparing the results of two previously published studies to our new dataset led to the identification of strong candidate SNPs for local adaptation in FTL2 promoter and GI.

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

Black walnut (Juglans nigra L.) nut production stands on the brink of potentially great market expansion that can only be realized with significant genetic and horticultural improvement, such that commercial production becomes feasible. The goal of this study was to incorporate microsatellite/simple sequence repeat (SSR) markers to genotype 11 cultivars and selections, and establish a mapping population from a cross of two cultivars, “Football” × “Sparrow.” Morphology of these two cultivars coupled with phylogenetic analysis supports the notion that a cross between them may yield desirable hybrids. Of the 51 SSR markers amplified, 23 were polymorphic and useful for genotyping. A selection mislabeled as “Mintyle” was definitively identified as “Mintle”; therefore, the number of cultivars was reduced to 10. Furthermore, seven of the 23 markers were used to identify 91 intraspecific hybrids (“Football” × “Sparrow”) resulting from open pollination, thereby establishing the first mapping population of black walnut using SSR markers.

Salix purpurea is a woody perennial that is bred as a high-yielding bioenergy crop in North America. To gain an understanding of the genotypic variation associated with phenotypic diversity, this study characterized the population structure and genetic diversity of S. purpurea from its native range of Europe and naturalized range of the Northeastern United States (US). A total of 273 genotypes of S. purpurea were analyzed, which included 95 naturalized accessions and 19 horticultural cultivars from the US and 159 accessions collected from the native range of four European countries. All individuals were evaluated using a filtered set of 2287 genotyping-by-sequencing (GBS) single nucleotide polymorphism (SNP) markers. Using five clustering techniques (PCA, neighbor joining, STRUCTURE, DAPC, and affinity propagation), population structure was resolved into three broadly classified groups. Further analysis revealed seven to eight subpopulations which corresponded to geographical collection sites, where performance of the DAPC and affinity propagation methods was superior to STRUCTURE analysis for the purposes of characterizing population structure and performing population assignment. The native European accessions exhibited greater diversity and subpopulation structure than the US naturalized accessions, where there was a clear geographical delineation between the alpine/subalpine collections and the lowland collections at the Baltic Sea and Oder River. We also show that a subset of the horticultural cultivars had a higher likelihood of similarity to US naturalized populations which display hybrid ancestry, where both naturalized and cultivated genotypes appear to share a common ancestor. Additionally, several accessions collected from different sites were found to be clonal. Ongoing and future conservation and association studies will benefit from these known substructures and diversity assessments.

Species of Populus section Leuce are distributed throughout most parts of the Northern Hemisphere and have important economic and ecological significance. However, due to frequent hybridization within Leuce, the phylogenetic relationship between species has not been clarified. The chloroplast (cp) genome is characterized by maternal inheritance and relatively conservative mutation rates; thus, it is a powerful tool for building phylogenetic trees. In this study, we used the PacBio SEQUEL software to determine that the cp genome of Populus tomentosa has a length of 156,558 bp including a long single-copy region (84,717 bp), a small single-copy region (16,555 bp), and a pair of inverted repeat regions (27,643 bp). The cp genome contains 131 unique genes, including 37 transfer RNAs, 8 ribosomal RNAs, and 86 protein-coding genes. We compared the cp genomes of seven species of section Leuce and identified five cp DNA markers with > 1% variable sites. Phylogenetic analyses revealed two evolutionary branches for section Leuce. The species with the closest relationship with P. tomenstosa was P. adenopoda, followed by P. alba. These cp genome data will help to determine the cp evolution of section Leuce and further elucidate the origin of P. tomentosa.

The MADS box genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) and FRUITFULL (FUL) are widely known to be involved in the determination of flowering time and the transition from vegetative to reproductive meristem identity in A. thaliana and many other plant species. Analog to the induction of SOC1 and FUL, double mutants in Arabidopsis revealed both secondary cell wall and wood formation. We tested a putative influence of the overexpression of both genes onto growth and plant habitus in the perennial genus Populus. Two different poplar hybrid clones were transformed with SOC1 from A. thaliana (AtSOC1) and FUL from Sinapis alba (SaFUL). Both genes were under the control of the CaMV-35S promoter to induce constitutive overexpression. Regenerated single and double transgenic lines were transferred to the glasshouse and cultivated for up to two vegetation periods. Parallel overexpression of both genes led to plants with a significantly restricted plant growth compared to both untransformed controls and single transgenic plants. Extreme phenotypes also exhibit a different overall habitus of plants and leaf morphology. Thus, both genes seem to be involved in plant habitus and biomass formation in poplar. This study confirms the hypothesis that the two MADS box genes SOC1 and FUL are not only part of reproductive meristem regulation but also involved in vegetative meristem growth. In the next step, downregulation of all SOC1 and FUL genes in poplar by genome editing could lead to increased plant growth and biomass formation.

Little information is available on the Citrus genus and its relatives with regard to their ability to tolerate oxygen deficiency, establishing physiological and structural modifications. In order to gain insight into how citrus rootstocks respond to low-oxygen stress, a transcriptomic analysis (using a custom microarray) was performed on Carrizo citrange (CC) seedlings. These seedlings were transformed with OsMybleu transcription factor (TF), known for inducing tolerance to oxygen deficiency, and compared with CC wildtype. They were flushed for 24 h with N2 and microarray, carrying out expressed sequence tags of Citrus and relatives isolated from the roots, was hybridized with RNA of roots before and after hypoxia treatment. The genes involved in fermentation, Krebs cycle, sugar metabolism, cell wall metabolism, hormones, and TFs all resulted significantly altered in response to hypoxia in both samples. Quantitative expression analysis was performed on 42 selected genes to validate microarray results. The outcome was that most of them were confirmed. The main results lead to the conclusion that CC is naturally tolerant to oxygen limitation. Transformed CC responded to hypoxia by activating the main genes which are known in other plants to be responsible for this type of tolerance such as pyruvate decarboxylase and alcohol dehydrogenase. Among TFs, several were also induced, such as an HDZipIII homologous to AtHB15, target of mir166, itself overexpressed exclusively in transformed CC under hypoxia compared with all other samples. The present manuscript represents one of the very few investigative works focused on hypoxia-responsive transcriptional networks in citrus.

Walnut (Juglans regia L.) is one of the most important nut tree species. Simple sequence repeat (SSR)-based genetic linkage maps are valuable and effective tools for studies on integrative and comparative mapping. The data available in literature on walnut is inadequate for linkage mapping. Therefore, in the present study, we aimed to construct the first SSR-based genetic linkage map using the ‘Chandler’ × ‘Kaplan-86’ F1 population and to identify QTL (Quantitative Trait Loci) for leafing time in walnut. A total of 386 SSRs were mapped to 16 linkage groups (LGs) after screening 1437 SSR primer pairs. Among the mapped markers, 166 SSRs (43.0%) were heterozygous in both the parents, whereas 113 (29.3%) and 107 (27.7%) markers were from one of the parents that were integrated into the female and male maps, respectively. The total length of the consensus map was 1568.2 cM, with an average length of 98.0 cM. It included an average of 24.1 markers per LG, and the mean distance between SSR markers was 4.3 cM. The Chandler maternal linkage map included 279 SSR markers of total map length 1285.8 cM, whereas the Kaplan-86 male genetic map contained 273 SSRs of total map length 1574.4 cM. The SSR-based linkage maps presented in this study are moderately dense and can be considered as a fundamental genetic linkage map for further genetic and molecular studies in walnut, as well as in other Juglans species. A major QTL was identified for leafing time on LG4 explaining 52.0–68.8% of the phenotypic variation at similar positions in parental and consensus maps. The identified QTL region with associate markers can be potential for marker-assisted selection in the future for walnut breeding programs.