New sequencing technologies allow development of genome-wide markers for any genus of ecological interest, including plant genera such as Betula (birch) that have previously proved difficult to study due to widespread polyploidy and hybridization. We present a de novo reference genome sequence assembly, from 66× short read coverage, of Betula nana (dwarf birch) - a diploid that is the keystone woody species of subarctic scrub communities but of conservation concern in Britain. We also present 100 bp PstI RAD markers for B. nana and closely related Betula tree species. Assembly of RAD markers in 15 individuals by alignment to the reference B. nana genome yielded 44-86k RAD loci per individual, whereas de novo RAD assembly yielded 64-121k loci per individual. Of the loci assembled by the de novo method, 3k homologous loci were found in all 15 individuals studied, and 35k in 10 or more individuals. Matching of RAD loci to RAD locus catalogues from the B. nana individual used for the reference genome showed similar numbers of matches from both methods of RAD locus assembly but indicated that the de novo RAD assembly method may overassemble some paralogous loci. In 12 individuals hetero-specific to B. nana 37-47k RAD loci matched a catalogue of RAD loci from the B. nana individual used for the reference genome, whereas 44-60k RAD loci aligned to the B. nana reference genome itself. We present a preliminary study of allele sharing among species, demonstrating the utility of the data for introgression studies and for the identification of species-specific alleles.

Past reproductive interactions among incompletely isolated species may leave behind a trail of introgressed alleles, shedding light on historical range movements. Betula pubescens is a widespread native tetraploid tree species in Britain, occupying habitats intermediate to those of its native diploid relatives, B. pendula and B. nana. Genotyping 1134 trees from the three species at 12 microsatellite loci, we found evidence of introgression from both diploid species into B. pubescens, despite the ploidy difference. Surprisingly, introgression from B. nana, a dwarf species whose present range is highly restricted in northern, high-altitude peat bogs, was greater than introgression from B. pendula, which is morphologically similar to B. pubescens and has a substantially overlapping range. A cline of introgression from B. nana was found extending into B. pubescens populations far to the south of the current B. nana range. We suggest that this genetic pattern is a footprint of a historical decline and/or northwards shift in the range of B. nana populations due to climate warming in the Holocene. This is consistent with pollen records that show a broader, more southerly distribution of B. nana in the past. Ecological niche modelling predicts that B. nana is adapted to a larger range than it currently occupies, suggesting additional factors such as grazing and hybridization may have exacerbated its decline. We found very little introgression between B. nana and B. pendula, despite both being diploid, perhaps because their distributions in the past have rarely overlapped. Future conservation of B. nana may partly depend on minimization of hybridization with B. pubescens, and avoidance of planting B. pendula near B. nana populations.

Armillaria causes problems of root rot, kill trees and decay wood in the forests of Serbia and Montenegro, but the species involved have not hitherto been identified. The aim of this study was to identify field isolates collected on 25 localities. Identification was based on restriction fragment length polymorphism (RFLP) analysis of intergenic spacer 1 (IGS1) region and comparisons of IGS1 sequence with those available on NCBI database. Phylogenetic analysis was performed on sequence information from selected isolates to determine possible interrelationships between isolates with different banding patterns and previously identified tester isolates of five European Armillaria species. Five Armillaria species were identified in 90 isolates obtained from forests in Serbia and Montenegro. Armillaria gallica was most frequently isolated, followed by A. cepistipes, A. mellea, A. ostoyae and A. tabescens; two isolates remained unidentified. Restriction digestion of IGS1 amplification products with AluI produced 10 RFLP patterns. Patterns G4 (400, 250, 180) for A. gallica and pattern X (400, 180, 140) for isolates 74 and 79 are reported for the first time in European isolates. Eight RFLP patterns were observed after restriction with TaqI. Two patterns each were observed for A. ostoyae and A. gallica, and one each for A. cepistipes, A. mellea, A. tabescens and isolates 74 and 79. Parsimony analyses based on the IGS1 region placed the isolates into four clades: one including A. mellea, the second containing A. gallica-A. cepistipes isolates, while isolates of A. ostoyae and A. borealis were in the third clade. Armillaria tabescens differed from all annulate species. Phylogenetic analysis supported the conclusion that European Armillaria species are closely related and separated from a common ancestor in the near past. According to this survey five European Armillaria species are present in the forests of Serbia and Montenegro, while A. borealis is not present in the studied ecosystems.

A quantitative multiplex real-time polymerase chain reaction (PCR) procedure was developed to assess the extent of Heterobasidion annosum (Fr.) Bref. growth in Sitka spruce (Picea sitchensis (Bong.) Carr.) bark and wood and to determine correlations between lesion length and fungal colonization. Based on lesion length and real-time PCR, the responses of four 3-year-old Sitka spruce clones to inoculation with H. annosum were characterized as showing either resistance or susceptibility to the pathogen. In susceptible clones, the extent of bark colonization did not differ from the visible length of the bark lesion, whereas lesions were longer than the extent of fungal colonization in resistant clones. The resistant clones contained considerably less fungal DNA than the susceptible clones, relative to the amount of host DNA in both the bark and the wood, indicating less resistance and more host cell death in the susceptible clones following inoculation. In both resistant and susceptible clones, fungal colonization in the wood extended beyond the visible necrotic lesion in the bark, indicating that host defense responses are weaker in wood than in bark. The spread of the pathogen in both bark and wood was less in the resistant clones than in the susceptible clones, indicating that defenses in both bark and wood of the resistant clones were superior to those in the susceptible clones.

Three genetically distinct groups of Sitka spruce, open-pollinated Queen Charlotte Island provenance, A13 selected seed and M0044 half-sib mixture, were wounded alone or wounded and inoculated with Heterobasidion annosum sensu stricto on the lower stems. Growth of the pathogen and lesion formation was compared in the three genetic groups after treatment. No differences in the rate of colonization of the three genetic groups were observed over a 40 day period; lesion lengths in the bark and sapwood correlated closely. Moreover, lesions were considerably longer in inoculated plants than in those which were wounded only. No correlations were found within or between host genetic groups in the numbers or total areas of resin canals present in the first 18 mm from the wound in bark tissues for the three host genetic groups. Formation of the ligno-suberized boundary zone (LSZ), however, was inhibited in the bark of inoculated plants, being first detected later and at a greater distance from the wound/inoculation point in the presence of H. annosum than in plants that were wounded only. Thickness of the suberin cell layers within the LSZ of M0044 plants was greater in wounded and inoculated, than in wounded only plants. The significance of these findings in relation to detecting spruce genotypes potentially resistant to H. annosum is discussed.