Genetic analysis of Pinus strobus and Pinus monticola populations from Canada using ISSR and RAPD markers: development of genome-specific SCAR markers

Pinus is the largest genus of conifers, containing over 100 species and is also the most widespread genus in the Northern Hemisphere. Pinus monticola and P. strobus are two closely related and economically important species in Canada. Morphological and allometric characteristics have been used to assess genetic variation within these two species but these markers are not reliable due to ecological variations. The purpose of the present study was to determine the level of genetic diversity within and among Canadian populations from the two species using molecular markers and to identify and characterize genome-specific inter-simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) markers. The level of genetic variation among populations was much lower for P. monticola than P. strobus. For both species, the among population variation values were smaller than within population variation. The populations from P. monticola were more closely genetically related than populations from P. strobus based on ISSR and RAPD analyses. Six ISSR and four RAPD markers specific to either P. monticola or P. strobus were cloned and sequenced. Primer pairs flanking these specific sequences were designed and genome specific SCAR markers for P. monticola and P. strobus were developed and characterized.     

Host acceptance behavior of the red pine cone beetle (Conophthorus resinosae)

Adult female red pine cone beetles (Conophthorus resinosae Hopkins) (Coleoptera:Scolytidae) left cones of white pine (Pinus strobus L.) more readily than cones of red pine (Pinus resinosa Ait.) in the first 3 min after being placed on cones. Slices of white pine cones, however, did not elicit different beetle behavior than slices of red pine cones. Beetles bored into white pine as readily as into red pine. We conclude that beetles initially reject white pine due to structural traits, but eventually accept it during prolonged exposure and may utilize white pine in nature.

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Résumé C. resinosae Hopkins (Coleoptera, Scolytidae) s'alimente et pond sur les cônes de Pinus resinosa Ait.; il détruit souvent plus de la moitié des graines du pin dans la région des grands lacs aux USA. Cette espèce et les autres Conophthorus sont considérés comme des spécialistes très spécifiques. Nous avons voulu vérifier que les femelles de C. resinosae acceptent plus facilement comme hôtes les cônes de P. resinosae que ceux de P. strobus L. Au laboratoire, les scolytes ont abandonné les cônes de P. strobus plus rapidement que ceux de P. resinosae, au cours des 3 minutes qui ont suivi leur dépôt sur les cônes. Cependant des rondelles de P. resinosae n'ont pas été plus stimulantes que celles de P. strobus; les scolytes n'ont pas foré plus rapidement, ni n'ont plus séjourné sur P. resinosae que sur P. strobus au cours de 1, 2 ou 24 heures de l'expérience. Nous en concluons que les scolytes rejettent de prime abord P. strobus pour ses caractères structuraux, mais qu'ils l'acceptent éventuellement pendant expositions prolongées et peuvent le consommer dans la nature.

     

In situ regeneration of Pinus strobus and P. resinosa in the Great Lakes forest communities of Canada

Abstract. Two extensive forest vegetation survey datasets are explored, using ordination and classification, for evidence of in situ regeneration by Pinus strobus (Eastern white pine) and P. resinosa (Red pine). Ordination of tree species contributions to total basal area in 320 upland northern hardwood- conifer stands produced distinct stand groups for P.banksiana, P. resinosa, P. strobus and mesic hardwoods in an ascending sequence along the first axis. Quercus rubra (red oak), Q. alba (white oak) and tolerant conifer groups formed segregates from the hardwood complex along the second axis. P. strobus mixes with all other forest types, but P. resinosa is restricted to its own group. Seedlings and trees of P. strobus are more abundant than saplings, which are restricted to the pine and oak forests. Therefore, seed production, dispersal and seedling establishment seem to be less of a barrier to in situ regeneration by P. strobus than subsequent survival and growth. Canonical correspondence analysis of 170 pine-dominated stands from the Canadian Shield of Ontario, in which tree species variables are segmented into height-class pseudo- species, yielded no linear relationship between environmental features or stand structure and seedling densities of P. strobus. However, total tree basal area appears to impose an upper limit to seedling density on the forest floor. Strong correlations emerged between pine seedling density and understorey vegetation. Stand classification of the understorey vegetation, using constrained indicator species analysis, yielded distinct high and low seedling groups. Low pine seedling density was associated with abundant broadleaved shrubs, herbs and seedlings as well as feathermosses and tolerant conifers. High seedling density could not be ascribed to the presence of seedbed taxa, such as Polytrichum, but is ascribed to the absence of competition and other forms of inhibition in the understorey vegetation and down through the canopy profile. In situ regeneration of P. strobus does, therefore, occur but conditions over the forest landscape are largely restrictive.     

The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines

Accurately detecting signatures of local adaptation using genetic‐environment associations (GEAs) requires controlling for neutral patterns of population structure to reduce the risk of false positives. However, a high degree of collinearity between climatic gradients and neutral population structure can greatly reduce power, and the performance of GEA methods in such case is rarely evaluated in empirical studies. In this study, we attempted to disentangle the effects of local adaptation and isolation by environment (IBE) from those of isolation by distance (IBD) and isolation by colonization from glacial refugia (IBC) using range‐wide samples in two white pine species. For this, SNPs from 168 genes, including 52 candidate genes for growth and phenology, were genotyped in 133 and 61 populations of Pinus strobus and P. monticola, respectively. For P. strobus and using all 153 SNPs, climate (IBE) did not significantly explained among‐population variation when controlling for IBD and IBC in redundancy analyses (RDAs). However, 26 SNPs were significantly associated with climate in single‐locus GEA analyses (Bayenv2 and LFMM), suggesting that local adaptation took place in the presence of high gene flow. For P. monticola, we found no evidence of IBE using RDAs and weaker signatures of local adaptation using GEA and F_ST outlier tests, consistent with adaptation via phenotypic plasticity. In both species, the majority of the explained among‐population variation (69 to 96%) could not be partitioned between the effects of IBE, IBD, and IBC. GEA methods can account differently for this confounded variation, and this could explain the small overlap of SNPs detected between Bayenv2 and LFMM. Our study illustrates the inherent difficulty of taking into account neutral structure in natural populations and the importance of sampling designs that maximize climatic variation, while minimizing collinearity between climatic gradients and neutral structure.     

Transient gene expression in pine pollen tubes following particle bombardment

 A biolistic particle delivery system was used to genetically transform pollen tubes of three species of white pine (Pinus aristata, P. griffithii and P. monticola). The introduced plasmid DNA contained the GUS coding sequence flanked by the 35S CaMV promoter and NOS terminator sequences. Successful gene delivery was demonstrated by transient GUS expression as evaluated by standard histochemical assay. Distance of target specimens significantly influenced transient GUS expression in all three species of white pine. A target distance of 6 cm resulted in a significant number of transformed pollen tubes in P. aristata and P. griffithii, while distances of 6 and 9 cm resulted in a significant number of transformed pollen tubes in P. monticola. Generally, the number of pollen tubes expressing GUS activity was higher in P. aristata than in P. griffithii and P. monticola. The possibility of using GUS-transformed pollen tubes in conjunction with in vitro fertilization in conifers was examined. Gene expression in pollen tubes was also examined under electron microscopy where the X-glu reaction product occurred as large crystalline electron-dense precipitates in the cytoplasm. Received: 17 December 1998 / Revision received: 17 March 1999 / Accepted: 14 April 1999     

Development of leucine-rich repeat polymorphism, amplified fragment length polymorphism, and sequence characterized amplified region markers to the Cronartium ribicola resistance gene Cr2 in western white pine ( Pinus monticola )

White pine blister rust (WPBR), caused by Cronartium ribicola, is a devastating disease in Pinus monticola and other five-needle pines. Pyramiding a major resistance gene (Cr2) with other resistance genes is an important component of integrated strategies to control WPBR in P. monticola. To facilitate this strategy, the objective of the present study was to identify leucine-rich repeat (LRR) polymorphisms, amplified fragment length polymorphisms (AFLPs), and sequence characterized amplified region (SCAR) markers linked to the western white pine Cr2 (BSA) gene for precise gene mapping. Bulked segregant analysis and haploid segregation analysis allowed the identification of 11 LRR polymorphisms and five AFLP markers in the Cr2 linkage. The closest LRR markers were 0.53 Kosambi cM from Cr2 at either end. After marker cloning and sequencing, AFLP marker EacccMccgat-365 and random polymorphic DNA marker U570–843 were converted successfully into SCAR markers. For a potential application in marker-assisted selection (MAS), these two SCAR markers were verified in two western white pine families. This study represents the first report of LRR-related DNA markers linked to C. ribicola resistance in five-needle pines. These findings may help further candidate gene identification for disease resistance in a conifer species.     

A comparative cytogenetic analysis of five pine species from North America, Pinus banksiana, P. contorta, P. monticola, P. resinosa, and P. strobus

The genus Pinus comprises more than 100 species, which are widely distributed in the Northern hemisphere. Cytogenetic information on North American pines is very limited despite their economic importance. In the present study, a detailed comparative cytogenetic analysis is presented for five pine species from North America, P. resinosa, P. monticola, P. contorta, P. banksiana, and P. strobus. Morphometric analysis and physical mapping of rDNA probes were performed. The karyotype of P. monticola was considered ancestral with small difference in relative chromosome lengths. P. banksiana, P. contorta, and P. strobus karyotypes were considered semi-asymmetrical and less ancestral type. P. banksiana showed five secondary constrictions, P. strobus six, and P. contorta eight. P. resinosa karyotype was semi-asymmetrical and derived with 14 secondary constrictions identified on eight different chromosomes. Karyological data were consistent with molecular cytogenetic information. A significant association was observed between the number and locations of secondary constrictions and the 18S-5.8S-26S rDNA sites detected using fluorescence in situ hybridization. The two methods were used to establish a reliable comparative karyotype of the selected pines. In general, karyotype and chromosome evolution were not related to genetic relationships among pine species studied.     

The co-occurrence of ectomycorrhizal,arbuscular mycorrhizal,and dark septate fungi in seedlings of four members of the Pinaceae

Although roots of species in the Pinaceae are usually colonized by ectomycorrhizal (EM) fungi, there are increasing reports of the presence of arbuscular mycorrhizal (AM) and dark septate endophytic (DSE) fungi in these species. The objective of this study was to determine the colonization patterns in seedlings of three Pinus (pine) species (Pinus banksiana, Pinus strobus, Pinus contorta) and Picea glauca x Picea engelmannii (hybrid spruce) grown in soil collected from a disturbed forest site. Seedlings of all three pine species and hybrid spruce became colonized by EM, AM, and DSE fungi. The dominant EM morphotype belonged to the E-strain category; limited colonization by a Tuber sp. was found on roots of Pinus strobus and an unknown morphotype (cf. Suillus–Rhizopogon group) with thick, cottony white mycelium was present on short roots of all species. The three fungal categories tended to occupy different niches in a single root system. No correlation was found between the percent root colonized by EM and percent colonization by either AM or DSE, although there was a positive correlation between percent root length colonized by AM and DSE. Hyphae and vesicles were the only AM intracellular structures found in roots of all species; arbuscules were not observed in any roots.     

Compensatory growth in shoot populations of young white pine trees

Summary White pine (Pinus strobus L.) trees have shoot populations composed of subpopulations of terminal and lateral shoots. I tested whether the subpopulations would show compensatory (increased) growth when separated from each other. Ten-year-old white pine (Pinus strobus L.) trees growing under an oak (Quercus) overstory were untreated or treated in winter by removing either all terminal, or all lateral buds (10 trees per treatment). Growth was compared between control and treated shoot subpopulations. In the 1st year, shoot-length frequency distributions were similar between control and treated subpopulations. There was significant compensatory shoot elongation (mean of 1.5 cm per shoot) in both treated subpopulations. In the 2nd year each subpopulation produced both terminal and lateral shoots. Shoot-length frequency distributions were similar, but shifted toward longer shoots in treated populations. Shoot number, mean length and total shoot length were greater in treated populations. The increased growth in treated subpopulations was due both to differences in parent shoot length and to compensatory shoot production and elongation.     

Initiation of somatic embryogenesis in Pinus banksiana, P. strobus, P. pinaster, and P. sylvestris at three laboratories in Canada and France

During 2002–2004, three laboratories in Canada and France collaborated to improve initiation of somatic embryogenesis (SE) in jack pine (Pinus banksiana Lamb.), eastern white pine (P. strobus L.), maritime pine (P. pinaster Ait.), and Scots pine (P.␣sylvestris L.), giving particular attention to the effects of (1) N-(2-chloro-4-pyridyl)-N′-phenylurea (CPPU) versus various concentrations of 2,4-dichlorophenoxyacetic acid (2,4-D) and benzyladenine (BA), (2) differences in basal nutrient media, i.e., macro- and microelements, and (3) gelling agent concentration. The work was carried out separately at␣each laboratory, but the details of media compositions were shared and tested on their respective species. Results indicate that the developmental stage of the zygotic embryo (ZE) and genotype effects had a large influence on SE initiation, and that genetic effects were consistent over time. Different species responded differently to PGR types and concentration, basal nutrient media, trace elements, and their combinations. Currently, our best initiation rates based on a selected group of genotypes, optimal development stage of ZE, and medium are 3.9% for jack pine, 54.6% for eastern white pine, 76.2% for maritime pine, and 19.7% for Scots pine.     

The multivariate underpinnings of recruitment for three Pinus species in montane forests of the Sierra Nevada,USA

Recruitment success can have significant consequences on forest community dynamics. Seedlings and saplings were studied for 3 five-needled white pine species: sugar pine (Pinus lambertiana), western white pine (P. monticola), and whitebark pine (P. albicaulis) across an elevational gradient, representing three distinct forest types, in the Sierra Nevada. This study was designed to determine the importance of local environmental and biological conditions versus broad regional climate patterns influencing conifer recruitment. No relationships were found between recruitment and precipitation, but increasing nighttime temperature was positively correlated with sugar pine and western white pine recruitment and negatively correlated with whitebark pine recruitment. Recruitment pulses were found for sugar pine and western white pine from 1995 to 2006. Whitebark pine recruitment is low and relatively steady from 1970 to 2000 with no observed new recruits after 2001. Source strength was the most consistent predictor of white pine recruitment along with soil properties, climate, light, and the presence of non-conspecifics. Source, light, and soil explained 71 % of the variation in sugar pine recruitment. The presence of non-conspecifics, source, and climate explained 71 % of the variation in western white pine recruitment, and the presence of non-conspecifics and source explained 36 % of the variation for whitebark pine. Recruitment present in forest communities of the Sierra Nevada have successfully transitioned through critical stages (i.e., seed and germinant) and appear to be influenced by multiple factors at both local and regional scales.     

Linkage mapping and genome length in eastern white pine (Pinus strobus L.)

 Haploid linkage analysis of eastern white pine, Pinus strobus L., was carried out using mainly RAPD markers and microsatellite, or simple-sequence-repeat, markers. Ninety one loci mapped to 12 linkage groups of three or more markers. The resulting framework genome map, the first for a soft pine species, contained 69 markers. The map covered 58% of the estimated genome length of 2071 cM(K), with a 95% confidence interval of 1828–2242 cM(K). A systematic comparison of linkage data from eastern white pine, longleaf pine (P. palustris Mill.) and maritime pine (P. pinaster Ait.), gave genome-length estimates for all three species very close to either 2000 cM(K) or 2600 cM(H), depending on whether the Kosambi(K) or Haldane(H) map functions, respectively, were employed. Differences among previous pine genome-length estimates were attributed to the divergent criteria used in the methods of estimation, and indicate the need for the adoption of uniform criteria when performing genome-length estimates. Current data suggest that members of the two pine subgenera, which diverged during the late Mesozoic era, have highly conserved rates of recombination. Received: 5 January 1997/Accepted: 24 January 1997     

A Comparison of Phenolic Constituents of Pinus monticola Resistant and Susceptible to Cronartium ribicola

Polyphenols and simple phenols in Pinus monticola Dougl. foliage and hark were studied in relation to host resistance to Cronartium ribicola J. C. Fisch. ex Rabenh. More than 50 phenolic substances were detected but no qualitative differences were found between resistant and susceptible trees. Some evidence is given for a quantitative relationship between one polyphenol in white pine foliage and resistance to blister rust. This compound may be a guaiacyl derivative. Differences in phenolics due to tree-to-tree variation, needle age, tissue (foliage versus bark), and season of year are also reported.     

Genetic diversity and structure of western white pine (Pinus monticola) in North America: a baseline study for conservation, restoration, and addressing impacts of climate change

Western white pine (Pinus monticola) is an economically and ecologically important species in western North America that has declined in prominence over the past several decades, mainly due to the introduction of Cronartium ribicola (cause of white pine blister rust) and reduced opportunities for regeneration. Amplified fragment length polymorphism (AFLP) markers were used to assess the genetic diversity and structure among populations at 15 sites (e.g., provenances) across the native range of western white pine. The level of genetic diversity was different among 15 populations tested using 66 polymorphic AFLP loci. Nei’s gene diversity (H _E) at the population level ranged from 0.187 to 0.316. Genetic differentiation (G _ST) indicated that 20.1% of detected genetic variation was explained by differences among populations. In general, populations below 45^oN latitude exhibited a higher level of genetic diversity than higher latitude populations. Genetic distance analysis revealed two major clades between northern and southern populations, but other well-supported relationships are also apparent within each of the two clades. The complex relationships among populations are likely derived from multiple factors including migration, adaptation, and multiple glacial refugia, especially in higher latitudes. Genetic diversity and structure revealed by this study will aid recognition and selection of western white pine populations for species management and conservation programs, especially in consideration of current and future climate changes.     

Foliar nutrients shape fungal endophyte communities in Western white pine (Pinus monticola) with implications for white-tailed deer herbivory

Asymptomatic fungal endophytes colonize tissues of woody plants worldwide, with largely unknown ecological effects. Using culture-based methods and ITS1-5.8S-ITS2 rDNA sequence analysis, we investigated differences between foliar endophyte communities in disease-resistant hybrid and wild-type Pinus monticola (Western white pine) trees with observed variation in tree growth, vigor, and browsing damage by white-tailed deer (Odocoileus virginianus). We isolated 69 phylotypes of endophytic fungi in at least 39 genera, including 26 that have not previously been reported in P. monticola. Principal components analysis revealed that endophyte communities differed between browsed seedlings, unbrowsed seedlings, and unbrowsed adult trees. Sulfur, nitrate and calcium concentrations correlated with endophyte community differences among tree groups based on a distance-based redundancy analysis. Our results indicate that foliar nutrient variation influences endophyte community assembly and deer herbivory in P. monticola on a small landscape scale (80 hectares).     

Fungal endophytes in seeds and needles of Pinus monticola

Using a sequence-based approach, we investigated the transmission of diverse fungal endophytes in seed and needles of Pinus monticola, western white pine. We isolated 2003 fungal endophytes from 750 surface-sterilized needles. In contrast, only 16 endophytic isolates were obtained from 800 surface-sterilized seeds. The ITS region was sequenced from a representative selection of these endophytes. Isolates were then assigned to the most closely related taxa in GenBank. Although 95 % of the endophytes in needles from mature trees belonged to the Rhytismataceae, 82 unique ITS sequences were obtained from at least 21 genera and 10 different orders of fungi. Significantly, none of the endophytes in seed were rhytismataceous (χ² = 180; P < 0.001). Similarly, needles of greenhouse seedlings yielded only non-rhytismataceous isolates, whereas seedlings of the same age that had naturally regenerated near older white pines in roadless areas were colonized by rhytismataceous endophytes almost to the same extent as in mature trees. Only one of 17 rhytismataceous isolates were able to grow on a medium containing only 0.17 % nitrogen, whereas 25 of 31 non-rhytismataceous endophytes grew. Rhytismataceous endophytes are dominant in needles of P. monticola, but they appear to be absent in seed, and unlikely colonists of nitrogen-limiting host tissues such as the apoplast.     

Intergeneric pollen – megagametophyte relationships of conifers in vitro

 Germinating pollen from larch (Larix occidentalis), Sitka spruce (Picea sitchensis) and white pine (Pinus monticola) were co-cultured with megagametophytes dissected from cones of other genera (Pseudotsuga menziesii, Larix×eurolepis and Pinus monticola). Pollen was presented to megagametophytes possessing archegonia which were either alive, degenerating or dead. In addition, pollen was presented to fertilized megagametophytes and to megagametophytes that had been cut in half. Megagametophyte penetration by pollen tubes and male gamete release into archegonia were verified by serial sections of glycomethacrylate-embedded specimens. Pollen tubes penetrated through any part of the apex of the megagametophyte. Division of the body cell into the two gametes was regularly observed. Delivery of gametes was confirmed between spruce and larch. Pollen tubes also penetrated fertilized megagametophytes, dead or degenerating archegonia as well as wounded and/or cut surfaces. This demonstrates the inability of the male gametophyte to optimize its mating efforts, since it is unable to differentiate between healthy and unhealthy archegonia. The megagametophyte cells are unable to optimize male selection. They may produce secretions of a generally attractive nature, as pollen is attracted to the apex of the megagametophyte, but archegonia themselves do not produce pollen-specific signals of either a promotive or inhibitory nature. These results open new avenues for the development of novel breeding strategies where natural breeding barriers may be bypassed. Received: 19 March 1998 / Accepted: 29 April 1998