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Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive 1 . Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 ( ARR17 ) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR–Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes. Populus has young sex chromosomes despite ancient dioecy. This study shows that the ARR17 gene functions as a sex switch, triggering female development when on and male development when off. This single-gene system enables dynamic evolution of poplar sex chromosomes.

In Germany, Douglas fir (Pseudotsuga menziesii Franco) is seen as a valuable species for future cultivation in times of climate change. Local seed production in seed stands and seed orchards may secure that local adaptation is transferred to the next generation, but small population sizes could lower genetic diversity and thus future adaptability. Here we analyse the transfer of genetic diversity from parent to offspring generation in four older German seed orchards. We detected low pollen contamination rates due to high levels of spatial isolation. Even with a relatively low number of 40 clones, seed orchard design with randomized and repeated planting of clones led to low selfing rates, and despite uneven parental contributions, the number of successful parents and the level of genetic intermixture were high enough to allow the transfer of an adequate part of the genetic diversity to the next generation. Larger numbers, however, might be needed to reliably conserve the entire genetic diversity over succeeding generations. Conclusions on the establishment of future seed orchards and regarding areas requiring further research are drawn at the end of the paper.

Key message This review gives a comprehensive overview on the genomics of sex determination in dioecious woody plants and plants with a tree-like habitus, in particular considering species where sex-linked regions and/or markers have been identified. Dioecious plant species are characterized by unisexual flowers located on separate male or female individuals. While only about 5–6% of angiosperm species are reported to be dioecious, tree species seem to show a higher percentage of dioecy. Generally, it is presumed that various different genetic and developmental mechanisms underlie unisexuality in different dioecious species. This review focusses on the genomics of sex determination in dioecious woody plant species like trees, shrubs and vines as well as other plant species with a tree-like habitus like papaya and the monocot date palm. Findings for different tree species, including Diospyros lotus and members of the Salicaceae family, are summarized including information on sex-linked markers that enable to identify the sex of a tree before the tree reaches sexual maturity.

100 SNP and one Indel markers were developed for Khaya using a combination of restriction associated DNA sequencing and low coverage MiSeq genome sequencing. The marker set was successfully used to genotype a set of 1919 individuals, representing 5 Khaya species from 18 African countries, using MassARRAY ® iPLEX™ genotyping.

In the course of the 4th German National Forest Inventory, samples of the two oak species Quercus robur and Quercus petraea were collected throughout Germany. Genetic analyses were performed based on 403 nuclear, 21 chloroplast and 7 mitochondrial markers. The analyses showed good differentiation between the two species based on genetic data. Both species are connected through hybridization and introgression, but only about 2% of the samples analysed were found to be potential first-generation hybrids. Identical chloroplast and mitochondrial haplotypes with lineage specific distribution patterns were identified in both species. Different haplo- and mitotypes showed a tight linkage. Analysis of nuclear SNPs revealed a clear genetic structure in Q. robur , which appears to be largely of natural origin and can be explained by the postglacial recolonization routes through which the species dispersed throughout Germany after the last glacial maximum. Environmental influences, most importantly continentality, also appear to have an impact on the genetic structure of Q. robur , possibly caused by preadaptation within the refugial source-populations. For Q. petraea , the situation seems more complicated and no clear genetic structure could be identified.

Adult individuals and seeds of two mixed stands of coastal and interior Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) were analysed for genetic differentiation between the two varieties and evidence of intervarietal pollination. Clear genetic discrimination between the two varieties was observed based on multilocus evaluation of nine microsatellite markers using other Douglas-fir stands of known variety composition for comparison. Analysis of pollination distances showed that 80% of pollinations took place within a distance of about 44–55 m. Analysis of stand structure showed clearly separated areas of mainly coastal or interior Douglas-fir within both stands. Together with short pollination distances this led to an apparent dominance of intravarietal pollinations. However, analysis of pollination partners of trees growing near the border of the variety specific areas, does not indicate the existence of reproductive barriers between trees of the two varieties growing in mixed stands. Therefore, commercial seed harvesting in mixed stands should be avoided if the production of seed lots of pure coastal or interior Douglas-fir is intended.

The Meliaceae family mainly consists of trees and shrubs with a pantropical distribution. In this study, the complete chloroplast genomes of four Meliaceae species were sequenced and compared with each other and with the previously published Azadirachta indica plastome. The five plastomes are circular and exhibit a quadripartite structure with high conservation of gene content and order. They include 130 genes encoding 85 proteins, 37 tRNAs and 8 rRNAs. Inverted repeat expansion resulted in a duplication of rps19 in the five Meliaceae species, which is consistent with that in many other Sapindales, but different from many other rosids. Compared to Azadirachta indica, the four newly sequenced Meliaceae individuals share several large deletions, which mainly contribute to the decreased genome sizes. A whole-plastome phylogeny supports previous findings that the four species form a monophyletic sister clade to Azadirachta indica within the Meliaceae. SNPs and indels identified in all complete Meliaceae plastomes might be suitable targets for the future development of genetic markers at different taxonomic levels. The extended analysis of SNPs in the matK gene led to the identification of four potential Meliaceae-specific SNPs as a basis for future validation and marker development.

A large number of simple sequence repeat (SSR) marker-containing genetic maps are available for several Populus species. For aspen however, no SSR-containing map has been published so far. In this study, genetic linkage mapping was carried out with an interspecific mapping pedigree of 61 full-sib hybrids of European x quaking aspen (Populus tremula L. x Populus tremuloides Michx.), using the two-way pseudo-testcross strategy. Amplified fragment-length polymorphism (AFLP) and SSR markers were used for mapping, resulting in the first SSR-containing genetic linkage maps for aspen. The maps allow comparisons with a Populus consensus map and other published genetic maps of the genus Populus. The maps showed good collinearity to each other and to the Populus consensus map and provide a direct link to the Populus trichocarpa genomic sequence. Sex as a morphological trait was assessed in the mapping population and mapped on a non-terminal position of linkage group XIX on the male P. tremuloides map.

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios.

The genus Khaya includes some of the highest-value timber species in natural forests in Africa, which are under heavy exploitation pressure. Genetic identification of Khaya species is important to confirm the taxonomic classification for biodiversity conservation purposes and as a forensic tool aiding law enforcement in the fight against illegal logging. We collected samples from a total of 2222 trees belonging to five or six (depending on classification) different Khaya species (K. ivorensis, K. anthotheca/K. nyasica, K. grandifoliola, K. senegalensis, K. madagascariensis). Representative sampling was conducted over the natural ranges of all sampled Khaya species, in humid tropical forest and savanna zones. We genotyped individuals based on 101 molecular markers (67 nuclear, 11 chloroplast and 22 mitochondrial SNPs, 1 chloroplast indel). Bayesian clustering produced three main genetic groups assigning all K. ivorensis and all K. senegalensis trees, respectively, in two different clusters and all remaining individuals in a third cluster. Genetic self-assignment tests with all 101 SNPs had success rates of 97–100% for all species except for K. nyasica and K. madagascariensis, which could not be clearly distinguished from each other. A success rate for species identification nearly as high was observed using a subset of 15 highly differentiated SNPs. There was only very little evidence for hybridization among species and the vast majority (> 97%) of individuals were assigned to the same species group as identified based on morphological characters.