SNP Markers and Evaluation of Duplicate Holdings of Brassica oleracea in Two European Genebanks.

Around the world, there are more than 1500 genebanks storing plant genetic resources to be used in breeding and research. Such resources are essential for future food security, but many genebanks experience backlogs in their conservation work, often combined with limited budgets. Therefore, avoiding duplicate holdings is on the agenda. A process of coordination has started, aiming at sharing the responsibility of maintaining the unique accessions while allowing access according to the international treaty for plant genetic resources. Identifying duplicate holdings based on passport data has been one component of this. In the past, and especially in vegetables, different selections within the same varieties were common and the naming practices of cultivars/selections were flexible. Here, we examined 10 accession pairs/groups of cabbage (Brassica oleracea var. capitata) with similar names maintained in the Russian and Nordic genebanks. The accessions were analyzed for 11 morphological traits and with a SNP (Single Nucleotide Polymorphism) array developed for B. napus. Both proved to be useful tools for understanding the genetic structure among the accessions and for identifying duplicates, and a subset of 500 SNP markers are suggested for future Brassica oleracea genetic characterization. Within five out of 10 pairs/groups, we detected clear genetic differences among the accessions, and three of these were confirmed by significant differences in one or several morphological traits. In one case, a white cabbage and a red cabbage had similar accession names. The study highlights the necessity to be careful when identifying duplicate accessions based solely on the name, especially in older cross-pollinated species such as cabbage.

Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems.

Both mating system and population history can have large impacts on genetic diversity and population structure. Here, we use multilocus sequence data to investigate how these factors impact two closely related Brassicaceae species: the selfing Capsella rubella and the outcrossing C. grandiflora. To do this, we have sequenced 16 loci in approximately 70 individuals from 7 populations of each species. Patterns of population structure differ strongly between the two species. In C. grandiflora, we observe an isolation-by-distance pattern and identify three clearly delineated genetic groups. In C. rubella, where we estimate the selfing rate to be 0.90-0.94, the pattern is less clear with some sampling populations forming separate genetic clusters while others are highly mixed. The two species also have divergent histories. Our analysis gives support for a bottleneck approximately 73 kya (20-139 kya) in C. rubella, which most likely represents speciation from C. grandiflora. In C. grandiflora, there is moderate support for the standard neutral model in 2 of 3 genetic clusters, while the third cluster and the total data set show evidence of expansion. It is clear that mating system has an impact on these two species, for example affecting the level of genetic variation and the genetic structure. However, our results also clearly show that a combination of past and present processes, some of which are not affected by mating system, is needed to explain the differences between C. rubella and C. grandiflora.

Speciation history of three closely related pines Pinus mugo (T.), P. uliginosa (N.) and P. sylvestris (L.).

Nucleotide polymorphisms at genomic regions including 17 nuclear loci, two chloroplast and one mitochondrial DNA fragments were used to study the speciation history of three pine species: dwarf mountain pine (Pinus mugo), peat-bog pine (P. uliginosa) and Scots pine (P. sylvestris). We set out to investigate three specific speciation scenarios: (I) P. uliginosa is a homoploid hybrid between the other two, (II) the species have evolved without gene flow after divergence and (III) there has been substantial gene flow between the species since their divergence. Overall, the genetic data suggest that P. mugo and P. uliginosa share the same gene pool (average net divergence of 0.0001) and that the phenotypic differences (e.g. growth form) are most likely due to very limited areas of the genome. P. mugo and P. uliginosa are more diverged from P. sylvestris than from each other (average net divergence of 0.0027 and 0.0026, respectively). The nucleotide patterns can best be explained by the divergence with migration speciation scenario, although the hybrid speciation scenario with small genomic contribution from P. sylvestris cannot be completely ruled out. We suggest that the large amount of shared polymorphisms between the pine taxa and the lack of monophyly at all loci studied between P. sylvestris and P. mugo-P. uliginosa can largely be explained by relatively recent speciation history and large effective population sizes but also by interspecific gene flow. These closely related pine taxa form an excellent system for searching for loci involved in adaptive variation as they are differentiated in phenotype and ecology but have very similar genetic background.

Patterns of divergence among conifer ESTs and polymorphism in Pinus sylvestris identify putative selective sweeps.

Finding genes that are under positive selection is a difficult task, especially in non-model organisms. Here, we have analyzed expressed sequence tag (EST) data from 4 species (Pinus pinaster, Pinus taeda, Picea glauca, and Pseudotsuga menziesii) to investigate selection patterns during their evolution and to identify genes likely to be under positive selection. To confirm selection, population samples of these genes have been sequenced in Pinus sylvestris, a species that was not included in the EST data set. The estimates of branch-specific Ka/Ks (nonsynonymous/synonymous substitution rates) across all genes in the EST data set were similar or smaller than estimates from other higher plant species. There was no evidence for the traditional indication of positive selection, Ka/Ks above 1. However, several lines of evidence based on polymorphism patterns suggest that genes with high Ka/Ks (0.20-0.52) in the EST data set are in fact more affected by positive selection in P. sylvestris than genes with low Ka/Ks (0.01-0.04). The high Ka/Ks genes have a lower level of polymorphism and more negative Tajima's D than the low Ka/Ks genes. Further, in the high Ka/Ks group, the Hudson-Kreitman-Aguade test is significant. This suggests that the EST data set is a good starting point for finding genes under positive selection in conifers and that even moderate Ka/Ks values could be indicative of selection. A group of 5 genes with high Ka/Ks collectively show evidence for positive selection within P. sylvestris.

Impact of Ice Ages on the genetic structure of trees and shrubs.

Data on the genetic structure of tree and shrub populations on the continental scale have accumulated dramatically over the past decade. However, our ability to make inferences on the impact of the last ice age still depends crucially on the availability of informative palaeoecological data. This is well illustrated by the results from a recent project, during which new pollen fossil maps were established and the variation in chloroplast DNA was studied in 22 European species of trees and shrubs. Species exhibit very different levels of genetic variation between and within populations, and obviously went through very different histories after Ice Ages. However, when palaeoecological data are non-informative, inferences on past history are difficult to draw from entirely genetic data. On the other hand, as illustrated by a study in ponderosa pine, when we can infer the species' history with some certainty, coalescent simulations can be used and new hypotheses can be tested.