Interspecific gene flow and ecological selection in a pine (Pinus sp.) contact zone

Nucleotide polymorphisms in a set of nuclear genes were studied in a sympatric population of pines Pinus mugo and Pinus sylvestris that includes trees classified as pure species and polycormic (multi-stemmed)individuals of potentially hybrid origin. Patterns of genetic diversity were compared between those groups of samples and to the reference allopatric populations of the species in Europe. Polymorphisms at the gene loci clearly distinguished pure parental species as measured by conventional frequency-based statistics and Bayesian assignment of samples into separate genetic clusters. Most individuals classified based on phenotypic assessments as putative hybrids were genetically very similar to P. mugo showing no existing average net divergence and genetic assignment to the same genetic cluster. On the other hand, individuals of P. sylvestris showed homogenous genetic background to the reference populations of the species from Central and Northern Europe. Ten individuals of admixed genetic composition were found in all three groups of samples; however, the majority of hybrids except one individual were identified across the samples classified as P. mugo and polycormic pines. Those trees that contained a mixture of nuclear gene haplotypes observed in the reference populations of pure species and cpDNA from P. mugo, most likely represent the first generation of hybrids. Analysis of the allelic frequency spectra and compound neutrality tests identified deviations from neutrality at several genes. This contact zone seems suitable for selection of a mapping population both in hybrid and parental species for admixture mapping to effectively search for polymorphisms that may play role in species adaptive variation and speciation

Among population differentiation at nuclear genes in native Scots pine (Pinus sylvestris L.) in Scotland

In the Scottish Highlands, Scots pine is at the north-western extreme of its wide natural distribution. Here, the remaining native populations are patchily distributed in highly variable environments, from the more continental, drier eastern Highlands to the milder, wetter Atlantic Ocean coast. As these pinewoods are the remnants of a naturally established forest, they form a valuable system for analysis of genetic and adaptive variation in heterogeneous environments. Using samples from across the Scottish population, we analysed data from nuclear and mitochondrial genes to assess patterns of within and between population genetic variation. Within population diversity levels were high, and significant genetic differentiation among pairs of Scottish populations at relatively small spatial scales was present at several nuclear loci. At these loci, no differentiation had been found among continental populations, even those separated by large geographic distances. Overall, no clear clustering of Scottish samples was found in population structure analysis suggesting that geographically distant populations with high intra-population nucleotide diversity are not strongly isolated and diverged from each other. Scottish populations lacked a mitotype that is widespread in eastern and north-eastern Europe, indicating that pines from that area may not have participated in the most recent colonisation of the British Isles

Development of a single nucleotide polymorphism array for population genomic studies in four European pine species

Pines are some of the most ecologically and economically important tree species in the world, and many have enormous natural distributions or have been extensively planted. However, a lack of rapid genotyping capability is hampering progress in understanding the molecular basis of genetic variation in these species. Here, we deliver an efficient tool for genotyping thousands of single nucleotide polymorphism (SNP) markers across the genome that can be applied to genetic studies in pines. Polymorphisms from resequenced candidate genes and transcriptome sequences of P. sylvestris, P. mugo, P. uncinata, P. uliginosa and P. radiata were used to design a 49,829 SNP array (Axiom_PineGAP, Thermo Fisher). Over a third (34.68%) of the unigenes identified from the P. sylvestris transcriptome were represented on the array, which was used to screen samples of four pine species. The conversion rate for the array on all samples was 42% (N = 20,795 SNPs) and was similar for SNPs sourced from resequenced candidate gene and transcriptome sequences. The broad representation of gene ontology terms by unigenes containing converted SNPs reflected their coverage across the full transcriptome. Over a quarter of successfully converted SNPs were polymorphic among all species, and the data were successful in discriminating among the species and some individual populations. The SNP array provides a valuable new tool to advance genetic studies in these species and demonstrates the effectiveness of the technology for rapid genotyping in species with large and complex genomes

Long-term growth performance and productivity of Scots pine (Pinus sylvestris L.) populations

The phenotypic differentiation of 16 provenances of Scots pine originating from a wide variety of habitats that range from lowland to southern highland locations in Poland was assessed during 47 years of their growth and development in the Carpathian Mountains. The traits, including height, diameter at breast height, stem straightness, and crown width, were used to evaluate the differentiation of the provenances in their juvenile period and at maturity and were examined for patterns of local adaptation. The populations from northern Poland were characterized by the best growth and productivity, whereas provenances from central Poland had the best stem quality. There were some changes in growth between provenances observed during the experiment, but the stand volume (m3/ha) in juvenile trees was closely correlated with that in mature trees (r = 0.979). There was a positive relationship between the productivity and the environmental conditions of the geographical origin of provenances with increasing values for the trees’ productivity from south to north. Additionally, the elevation above sea level of the original populations was inversely correlated with the growth achieved by the progeny. In general, most populations from the species distribution range in Poland tested in the severe climate conditions of the Carpathian Mountains showed good growth performance under that environment, characterized by low temperatures and short growing periods. Provenances from climatic zones outside mountain regions demonstrated great growth and productivity, which proved to be the most important for competitively outperforming the local populations. Our study demonstrates good adaptive potential of the tested provenances, as selection will favor fast-growing genotypes under the predicted environmental change scenario

Hybridization in contact zone between temperate European pine species

Hybridization studies are important to advance our understanding of the interspecific gene flow and its evolutionary consequences in closely related species. Hybridization and admixture patterns were assessed in a contact zone and reference populations of European pine species using sequence data from 26 nuclear genes and a species-diagnostic cpDNA marker. Reference populations formed three distinct genetic clusters comprising Pinus sylvestris, Pinus mugo/Pinus uliginosa, and Pinus uncinata. Evidence of population structure was found only in P. uliginosa. Based on phenotypic characteristics and molecular data, we identified five groups of individuals in the contact zone in Poland, comprising forms of the parental species and intermediates that were most probably the result of interspecific crosses. A combination of nuclear gene sequence data and a diagnostic organelle marker were used to show that hybridization is frequent in the contact zone and results in hybrid trees with distinct phenotypic identity. The influence of selection in maintaining hybrid phenotypes in environments unsuited to parental species was inferred from nucleotide polymorphism data. A lack of admixture in reference populations suggests that hybridization has not occurred during post-glacial migration and so the contact zone represents a distinct, active example of ongoing evolution. Pine populations in this zone will be a valuable system for studying the genetic basis of hybrid advantage in environmental conditions untypical of pure parental species

Identifying and testing marker–trait associations for growth and phenology in three pine species:Implications for genomic prediction

In tree species, genomic prediction offers the potential to forecast mature trait values in early growth stages, if robust marker-trait associations can be identified. Here we apply a novel multispecies approach using genotypes from a new genotyping array, based on 20,795 SNPs from three closely related pine species (Pinus sylvestris, Pinus uncinata and Pinus mugo), to test for associations with growth and phenology data from a common garden study. Predictive models constructed using significantly associated SNPs were then tested and applied to an independent multisite field trial of P. sylvestris and the capability to predict trait values was evaluated. One hundred and eighteen SNPs showed significant associations with the traits in the pine species. Common SNPs (MAF > 0.05) associated with bud set were only found in genes putatively involved in growth and development, whereas those associated with growth and budburst were also located in genes putatively involved in response to environment and, to a lesser extent, reproduction. At one of the two independent sites, the model we developed produced highly significant correlations between predicted values and observed height data (YA, height 2020: r = 0.376, p < 0.001). Predicted values estimated with our budburst model were weakly but positively correlated with duration of budburst at one of the sites (GS, 2015: r = 0.204, p = 0.034; 2018: r = 0.205, p = 0.034-0.037) and negatively associated with budburst timing at the other (YA: r = -0.202, p = 0.046). Genomic prediction resulted in the selection of sets of trees whose mean height was taller than the average for each site. Our results provide tentative support for the capability of prediction models to forecast trait values in trees, while highlighting the need for caution in applying them to trees grown in different environments

Evolutionary targets of gene expression divergence in a complex of closely related pine species

The environment is a powerful selective pressure for sessile organisms, such as plants, and adaptation to the environment is particularly important for long-lived species, like trees. Despite the importance of adaptive trait variation to the survival and success of trees, the molecular basis of adaptation is still poorly understood. Gene expression patterns in three closely related, but phenotypically and ecologically divergent, pine species were analyzed to detect differentiation that may be associated with their adaptation to distinct environments. Total RNA of Pinus mugo, Pinus uncinata, and Pinus sylvestris samples grown under common garden conditions was used for de novo transcriptome assembly, providing a new reference dataset that includes species from the taxonomically challenging P. mugo complex. Gene expression profiles were found to be very similar with only 121 genes significantly diverged in any of the pairwise species comparisons. Functional annotation of these genes revealed major categories of distinctly expressed transcripts, including wood trait properties, oxidative stress response, and response to abiotic factors such as salinity, drought, and temperature. We discuss putative associations between gene expression profiles and adaptation to different environments, for example, the upregulation of genes involved in lignin biosynthesis in the species, which have adapted to mountainous regions characterized by strong winds and thick snow cover. Our study provides valid candidates for verification of the importance of the gene expression role, in addition to evidence for selection within genomic regions, in the process of ecological divergence and adaptation to higher altitudes in pine taxa

Candidate genes for the high-altitude adaptations of two mountain pine taxa

Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism