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

Genomic selection in forest tree breeding - basic principles, problems and future prospects

All tree breeders cope with the same challenge of the very long time interval of a single breeding cycle. What is more, trees are long−lived, with desirable breeding traits expressing late during their life cycle. Increasing problems with climate change, globalization or economic growth have forced us to accelerate tree breeding and improve selection precision, both of which can be achieved by genomic selection (GS). The idea of GS was introduced nearly 20 years ago as an extension of marker−assisted selection (MAS) in order to advance breeding technologies using genetic markers. Unlike MAS, which exploits only a set of marker−trait associations, GS relies on a high number of genetic markers that are spread throughout the entire length of the genome. All markers effects are assessed simultaneously in order to build a precise model that allows prediction of genetic estimated breeding value of a particular individual using genetic data only. GS has already revolutionized dairy cattle breeding resulting in remarkable improvements across multiple traits and is becoming more and more common in crop production. We now know that genetic architecture of quantitative traits is complex, but recent advances in genomics have made it possible to deal with this problem in an unprecedented way. There are certain concerns regarding GS in forest tree species that include genotype−environment (G×E) interaction and the usefulness of the predictive model built up by GS in the next generation of trees. Nevertheless, experimental results obtained so far have shown that the genetic gain per unit time as well as selection precision can be substantially increased. Here we present the basic principles of GS for forest tree species, giving examples of studies carried out so far and discussing problems and future possibilities that GS may soon open up for forest tree breeders

Cross-amplification and multiplexing of cpSSRs and nSSRs in two closely related pine species (Pinus sylvestris L. and P. mugo Turra)

Background: Simple sequence repeats (SSRs) are widespread molecular markers commonly used in population genetic studies. Nowadays, next-generation sequencing (NGS) methods allow identifying thousands of SSRs in one sequencing run, which greatly facilitates isolation and development of new SSRs. However, their usefulness as molecular markers still must be tested empirically on a number of populations to select SSRs with best parameters for future population genetic research. An alternative approach, cheaper and faster than isolation and characterization of new SSRs, involves cross-amplification of SSRs in closely related species. Aims: Our goal was to develop multiplex PCR protocols that will be useful in population genetic studies of Scots pine (Pinus sylvestris L.) and dwarf mountain pine (P. mugo Turra), and possibly other pine species. Methods: We tested 14 chloroplast (cpSSRs) and 22 nuclear (nSSRs) microsatellite markers originally designed for Japanese black pine (P. thunbergii Parl.), P. sylvestris and loblolly pine (P. taeda L.) in four populations of P. sylvestris and P. mugo across different locations in Europe. We designed six multiplex PCRs, which were subsequently screened for their ability to provide repeatable and high quality amplification products using capillary electrophoresis. Results: The transfer rate in our study was similar in both pine species, and it was very high for cpSSRs (93% and 86% for P. sylvestris and P. mugo, respectively) and moderate for nSSRs (59% for both species). We managed to design five well-performing multiplex reactions out of six initially tested. Most of the tested loci were polymorphic. Moreover, the allelic patterns detected at some cpSSRs were species-specific. Conclusions: We provide a set of five multiplexes which can be used in genetic studies of both P. sylvestris and P. mugo. Chloroplast marker PCP30277 is a good candidate for a cheap species diagnostic marker suitable for tracking interspecific gene flow between hybridizing species of P. sylvestris and P. mugo

Determination of the origin of the rychtal Scots pine (Pinus sylvestris L.) seed tree stands using microsatellite markers

The rychtal pine is one of the most valuable ecotypes of Scots pine (Pinus sylvestris L.) approved for the breeding purposes in Poland. However, it occupies stands typical for oaks and beeches as shown by the compatibility analysis of species composition in relation to the habitat type in which they occur. Such result raises some doubts in terms of the naturalness of the rychtal pine and calls its history and origin into question. In the present study, we used the set of nuclear microsatellite markers to characterize and compare the gene pool composition of the selected seed tree stands of the rychtal pine with 200−year−old pine trees which grow at the Syców Forest District (SW Poland). We aimed to know to what extent the set of alleles specified for the group of the oldest trees from natural habitats is represented in the younger forest tree stands of the rychtal pine. The analysis of molecular variance (AMOVA) and clustering analysis showed that the gene pool of the studied pine populations was homogenous (FST=0,02%, K=1). The parameters of genetic variation were similar for all populations except for the mean number of alleles. On average, 25 new alleles were found in two rychtal pine seed tree stands as compared to the set of alleles found in the group of old pine trees. However, all alleles defined for old pines were also present in the gene pool of younger rychtal pine forest stands. The differences in the gene pool richness result most likely from quite high differences in the number of individuals analyzed from each population. In conclusion, our results indicate the common origin of the studied Scots pine populations