Patterns of mtDNA variation reveal complex evolutionary history of relict and endangered peat bog pine (Pinus uliginosa)

Molecular Insight into Genetic Structure and Diversity of Putative Hybrid Swarms of Pinus sylvestris × P. mugo in Slovakia

The genetic structures of the four putative hybrid swarms of Pinus sylvestris × P. mugo in Slovakia were analyzed in terms of individual admixture proportions calculated via inter-primer binding site (iPBS) marker loci. This work aimed to reevaluate the hybrid swarms’ differentiation status as postulated in the previous studies at both population and genomic levels. The study confirmed intermediate divergence of each of the swarms examined. Based on 80-loci hybrid index scores, we have revealed the presence of introgressive and intermediate hybrids with frequencies corresponding to differentiation estimates. Surprisingly, irrespective of individual phenotypes, the most frequent intermediates were found in Sucha Hora (29.5%) and Obsivanka (28.6%) populations, which resemble rather pure P. mugo and were previously considered as bimodal hybrid zones with a negligible amount of hybrids. The remaining hybrid zone population Zuberec seems to be highly introgressed to P. sylvestris, while Tisovnica is clearly inclined to P. mugo. The results and different methodologies are discussed.

Genetic Consequences of Hybridization in Relict Isolated Trees Pinus sylvestris and the Pinus mugo Complex

Scots pine (Pinus sylvestris L.) and the taxa from the P. mugo complex can hybridize in the contact zones and produce fertile hybrids. A unique example of an early Holocene relict population of P. sylvestris and P. uliginosa (a taxon from the P. mugo complex) growing on the tops of Jurassic sandstone rocks is located in Błędne Skały (Sudetes). Phenotypically, there are trees resembling P. sylvestris, P. uliginosa and intermediate forms between them. We expected that some of P. sylvestris and/or P. uliginosa-like trees could be in fact cryptic hybrids resembling one of the parental phenotypes. To address this question, we examined randomly sampled individuals, using a set of plastid (cpDNA), nuclear (nDNA) and mitochondrial (mtDNA) markers as well as biometric characteristics of needles and cones. The results were compared to the same measurements of allopatric reference populations of the P. sylvestris and the P. mugo complex (Pinus mugo s.s, P. uncinata and P. uliginosa). We detected cpDNA barcodes of the P. mugo complex in most individuals with the P. sylvestris phenotype, while we did not detect cpDNA diagnostic of P. sylvestris within P. uliginosa-like trees. These results indicate the presence of cryptic hybrids of the P. sylvestris phenotype. We found only three typical P. sylvestris individuals that were clustered with the species reference populations based on needle and cone characteristics. Most trees showed intermediate characteristics between P. sylvestris and P. uliginosa-like trees, indicating intensive and probably long-lasting hybridization of the taxa at this area and subsequent gene erosion of parental species.

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.