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David B Neale - One of the best experts on this subject based on the ideXlab platform.
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Assessing the gene content of the megagenome: Sugar pine (Pinus lambertiana)
G3 (Bethesda Md.), 2016Co-Authors: Daniel Gonzalez-ibeas, Carol Loopstra, David B Neale, Annette Delfino-mix, Pedro J. Martínez-garcía, Randi A. Famula, Kristian Stevens, Charles H. Langley, Jill L. WegrzynAbstract:Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers.
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Patterns of neutral and adaptive genetic diversity across the natural range of sugar pine (Pinus lambertiana Dougl.)
Tree Genetics & Genomes, 2016Co-Authors: Carl Vangestel, Jill L. Wegrzyn, Pedro J. Martínez-garcía, Alejandra Vázquez-lobo, Irina Ćalić, David B NealeAbstract:Demographic and environmental forces shape geographical patterns of genetic diversity. Knowledge thereof is not only important for evolutionary ecologists but, in light of future climate change, will be of interest to conservation biologists as well. Sugar pine (Pinus lambertiana Dougl.) is an ecologically important species found in mixed conifer forests across western North America. We applied a candidate-gene-based environmental study to infer spatial patterns in neutral genetic variation and to identify genetic variants associated with local adaptation to drought. Using a panel of 186 candidate gene single nucleotide polymorphisms (SNP), we genotyped 313 individual trees sampled across the entire state of California, USA. We found evidence for a large-scale subdivision into two genetic clusters along the latitudinal axis and increased genetic similarity among sugar pines within a 200–300-km boundary. Associating allelic to environmental variation indicated nine putative SNPs related to local adaptation to drought. These results provide insights into neutral population structure across the natural range of sugar pine and further substantiated a key role of the mitochondrial import inner membrane machinery in enhanced tolerance to drought and constitute important steps into unravelling the eco-evolutionary dynamics in sugar pine.
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Eckert_et_al_pairwise_alignments
2016Co-Authors: Andrew J Eckert, Kathleen D. Jermstad, Jill L. Wegrzyn, Andrew D. Bower, Brian J. Knaus, John V. Syring, David B NealeAbstract:The file named Eckert_et_al_pairwise_alignments.zip contains 11 directories corresponding to pairwise alignments between loblolly pine and one of the eleven focal species. Within each directory are 192 fasta formatted alignment files (except for Pinus strobiformis which contains 191 alignment files). Alignment files are named by locus as defined in the manuscript associated with this Dryad entry. Within each alignment file are aligned sequences for the focal species and Pinus taeda (= loblolly pine). Sequences are identified to species using the following codes: Pial: Pinus albicaulis, Piar: Pinus aristata, Piay: Pinus ayacahuite, Pibf: Pinus balfouriana, Pifl: Pinus flexilis, Pila: Pinus lambertiana, Pilo: Pinus longaeva, Pimn: Pinus monticola, Pimo: Pinus monophylla, Pisb: Pinus strobiformis, Pist: Pinus strobus, Pita: Pinus taeda. Please note that a subset of 167 alignments was used in the final analysis. These can be identified using the online supplemental file available at the journal website
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Local adaptation at fine spatial scales: an example from sugar pine (Pinus lambertiana, Pinaceae)
Tree Genetics and Genomes, 2015Co-Authors: Andrew J Eckert, Annette Delfino Mix, Patricia E Maloney, Camille E Jensen, Detlev R Vogler, David B NealeAbstract:The forest environment can be heterogeneous over short physical distances, so that local adaptation by conifers, especially when selection is strong or gene flow restricted, may occur at fine spatial scales. Here, we examine patterns of genetic diversity across ten sugar pine (Pinus lambertiana Dougl.) populations located within the Lake Tahoe Basin of California and Nevada, USA. This region covers an area of only 1300 km2 but is heterogeneous with respect to local environmental conditions. We associated 475 single nucleotide polymorphisms (SNPs) with five phenotypic traits, as well as with 11 environmental variables that describe the maternal tree environments. Phenotypes were measured in a common garden established from offspring of 108 maternal trees sampled from eight populations. Genetic, phenotypic, and environmental variation was pronounced among populations. Association genetic analysis identified six associations between SNPs and phenotypic traits, as well as 31 associations between SNPs and environmental principal components (PCs). Only two SNPs were shared among these sets of results. One of these two SNPs was associated with carbon isotope ratios that were correlated to an environmental PC representing soil and climate variables involved with water availability. Utilization of this three-pronged approach established conceptual links between genotypes and phenotypes in an ecological context.
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Population biology of sugar pine (Pinus lambertiana Dougl.) with reference to historical disturbances in the Lake Tahoe Basin: Implications for restoration
Forest Ecology and Management, 2011Co-Authors: Patricia E Maloney, Camille E Jensen, Detlev R Vogler, Andrew J Eckert, David B NealeAbstract:Abstract Historical logging, fire suppression, and an invasive pathogen, Cronartium ribicola , the cause of white pine blister rust (WPBR), are assumed to have dramatically affected sugar pine ( Pinus lambertiana ) populations in the Lake Tahoe Basin. We examined population- and genetic-level consequences of these disturbances within 10 sugar pine populations by assessing current population structure and trends for 1129 individuals, genetic diversity for 250 individuals, and frequency of WPBR-resistance for 102 families. Logging had occurred in 9 of 10 sites and fire suppression was evident in all stands. High density of white fir ( Abies concolor ) is often an indicator of fire suppression and we found a negative relationship between sugar pine survivorship and white fir basal area ( r 2 = 0.31). C. ribicola was present in 90% of stands (incidence range: 0–48%) and we found a significant relationship between mean host survivorship and disease incidence ( r 2 = 0.46). We estimated population growth rates ( λ ) from size-based transition matrices. For six of 10 sugar pine populations λ was ⩾1.0, indicating that these populations appear to be stable; for four populations, λ was c i , which is a measure of genetic differentiation in allele frequencies relative to an ancestral population, ranged from 0.009 to 0.048. Higher values of c i indicate greater genetic drift, possibly due to a bottleneck caused by historical logging, other agents of mortality or much older events affecting population sizes. Effects of drift are known to be greater in small populations and we found a negative relationship between sugar pine density and c i ( r 2 = 0.36). Allele frequency of the Cr1 gene, responsible for WPBR-resistance in sugar pine, averaged 0.068 for all populations sampled; no WPBR infection was found in one population in which the Cr1 frequency was 0.112. Historical disturbances and their interactions have likely influenced the population biology of sugar pine in the Tahoe Basin; for some populations this has meant reduced population size, higher genetic drift, and poor survival of small- and intermediate-sized individuals. Possible management strategies include restoring population numbers, deploying WPBR-resistance, treating stands to promote natural sugar pine regeneration, and enhancing genetic diversity.
Andrew J Eckert - One of the best experts on this subject based on the ideXlab platform.
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Effect of fire and thinning on fine-scale genetic structure and gene flow in fire-suppressed populations of sugar pine (Pinus lambertiana Dougl.)
Forest Ecology and Management, 2019Co-Authors: Brandon M. Lind, Patricia E Maloney, Malcolm P. North, Andrew J EckertAbstract:Historically, frequent, low-severity fires in dry western North American forests were a major driver of ecological patterns and processes, creating resilient ecosystems dominated by widely-spaced pine species. However, a century of fire-suppression has caused overcrowding, altering forest composition to shade-tolerant species, while increasing competition and leaving trees stressed and susceptible to pathogens, insects, and high-severity fire. Exacerbating the issue, fire incidence is expected to increase with changing climate, while fire season has been observed to begin earlier and last longer than historic trends. Forest thinning and prescribed fire have been identified as important management tools to mitigate these risks. Yet little is known of how thinning, fire, or their interaction affect contemporary evolutionary processes of constituent pine species that influence fitness and play an important role in the opportunity for selection and population persistence. We assessed the impact of widely used fuel reduction treatments on fine-scale gene flow on an ecologically important and historically dominant shade-intolerant pine species of the Sierra Nevada, Pinus lambertiana Dougl. Treatment prescription (no-thin-no-fire, thin-no-fire, and fire-and-thin) was found to differentially affect both fine-scale spatial and genetic structure as well as effective gene flow in this species. Specifically, the thin-no-fire prescription increases genetic structure (spatial autocorrelation of relatives) between adults and seedlings, while seed and pollen dispersal increase and decrease, respectively, as a function of increasing disturbance intensity. While these results may be specific to the stands at our study site, they indicate how assumptions relating to genetic effects based on spatial structure can be misleading (for instance, in many stands the presence or absence of spatial structure was not indicative the presence or absence of genetic structure). It is likely that these disequilibrated systems will continue to evolve on unknown evolutionary trajectories. The long-term impacts of management practices on reduced fitness from inbreeding depression should be continually monitored to ensure resilience to increasingly frequent and severe fire, drought, and pest stresses.
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Effect of fire and thinning on fine-scale genetic structure and gene flow in fire-suppressed populations of sugar pine (Pinus lambertiana Douglas)
2018Co-Authors: Brandon M. Lind, Patricia E Maloney, Malcolm P. North, Andrew J EckertAbstract:Historically, frequent, low-severity fires in dry western North American forests were a major driver of ecological patterns and processes, creating resilient ecosystems dominated by widely spaced pine species. However, a century of fire-suppression has caused overcrowding, altering forest composition to shade-tolerant species, while increasing competition and leaving trees stressed and susceptible to pathogens, insects, and high-severity fire. Exacerbating the issue, fire incidence is expected to increase with changing climate, while fire season has been observed to begin earlier and last longer than historic trends. Forest thinning and prescribed fire have been identified as important management tools to mitigate these risks. Yet little is known of how thinning, fire, or their interaction affect contemporary evolutionary processes of constituent pine species that influence fitness and play an important role in the opportunity for selection and population persistence. We assessed the impact of widely used fuel reduction treatments and prescribed fire on fine-scale gene flow on an ecologically important and historically dominant shade-intolerant pine species of the Sierra Nevada, Pinus lambertiana Dougl. Treatment prescription (no-thin-no-fire, thin-no-fire, and fire-and-thin) was found to differentially affect both fine-scale spatial and genetic structure as well as effective gene flow in this species. Specifically, the thin-no-fire prescription increases genetic structure (spatial autocorrelation of relatives) between adults and seedlings, while seed and pollen dispersal increase and decrease, respectively, as a function of increasing disturbance intensity. While these results may be specific to the stands at our study site, they indicate how assumptions relating to genetic effects based on spatial structure can be misleading. It is likely that these disequilibrated systems will continue to evolve on unknown evolutionary trajectories. The long-term impacts of management practices on reduced fitness from inbreeding depression should be continually monitored to ensure resilience to increasingly frequent and severe fire, drought, and pest stresses.
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Eckert_et_al_pairwise_alignments
2016Co-Authors: Andrew J Eckert, Kathleen D. Jermstad, Jill L. Wegrzyn, Andrew D. Bower, Brian J. Knaus, John V. Syring, David B NealeAbstract:The file named Eckert_et_al_pairwise_alignments.zip contains 11 directories corresponding to pairwise alignments between loblolly pine and one of the eleven focal species. Within each directory are 192 fasta formatted alignment files (except for Pinus strobiformis which contains 191 alignment files). Alignment files are named by locus as defined in the manuscript associated with this Dryad entry. Within each alignment file are aligned sequences for the focal species and Pinus taeda (= loblolly pine). Sequences are identified to species using the following codes: Pial: Pinus albicaulis, Piar: Pinus aristata, Piay: Pinus ayacahuite, Pibf: Pinus balfouriana, Pifl: Pinus flexilis, Pila: Pinus lambertiana, Pilo: Pinus longaeva, Pimn: Pinus monticola, Pimo: Pinus monophylla, Pisb: Pinus strobiformis, Pist: Pinus strobus, Pita: Pinus taeda. Please note that a subset of 167 alignments was used in the final analysis. These can be identified using the online supplemental file available at the journal website
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Local adaptation at fine spatial scales: an example from sugar pine (Pinus lambertiana, Pinaceae)
Tree Genetics and Genomes, 2015Co-Authors: Andrew J Eckert, Annette Delfino Mix, Patricia E Maloney, Camille E Jensen, Detlev R Vogler, David B NealeAbstract:The forest environment can be heterogeneous over short physical distances, so that local adaptation by conifers, especially when selection is strong or gene flow restricted, may occur at fine spatial scales. Here, we examine patterns of genetic diversity across ten sugar pine (Pinus lambertiana Dougl.) populations located within the Lake Tahoe Basin of California and Nevada, USA. This region covers an area of only 1300 km2 but is heterogeneous with respect to local environmental conditions. We associated 475 single nucleotide polymorphisms (SNPs) with five phenotypic traits, as well as with 11 environmental variables that describe the maternal tree environments. Phenotypes were measured in a common garden established from offspring of 108 maternal trees sampled from eight populations. Genetic, phenotypic, and environmental variation was pronounced among populations. Association genetic analysis identified six associations between SNPs and phenotypic traits, as well as 31 associations between SNPs and environmental principal components (PCs). Only two SNPs were shared among these sets of results. One of these two SNPs was associated with carbon isotope ratios that were correlated to an environmental PC representing soil and climate variables involved with water availability. Utilization of this three-pronged approach established conceptual links between genotypes and phenotypes in an ecological context.
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Population biology of sugar pine (Pinus lambertiana Dougl.) with reference to historical disturbances in the Lake Tahoe Basin: Implications for restoration
Forest Ecology and Management, 2011Co-Authors: Patricia E Maloney, Camille E Jensen, Detlev R Vogler, Andrew J Eckert, David B NealeAbstract:Abstract Historical logging, fire suppression, and an invasive pathogen, Cronartium ribicola , the cause of white pine blister rust (WPBR), are assumed to have dramatically affected sugar pine ( Pinus lambertiana ) populations in the Lake Tahoe Basin. We examined population- and genetic-level consequences of these disturbances within 10 sugar pine populations by assessing current population structure and trends for 1129 individuals, genetic diversity for 250 individuals, and frequency of WPBR-resistance for 102 families. Logging had occurred in 9 of 10 sites and fire suppression was evident in all stands. High density of white fir ( Abies concolor ) is often an indicator of fire suppression and we found a negative relationship between sugar pine survivorship and white fir basal area ( r 2 = 0.31). C. ribicola was present in 90% of stands (incidence range: 0–48%) and we found a significant relationship between mean host survivorship and disease incidence ( r 2 = 0.46). We estimated population growth rates ( λ ) from size-based transition matrices. For six of 10 sugar pine populations λ was ⩾1.0, indicating that these populations appear to be stable; for four populations, λ was c i , which is a measure of genetic differentiation in allele frequencies relative to an ancestral population, ranged from 0.009 to 0.048. Higher values of c i indicate greater genetic drift, possibly due to a bottleneck caused by historical logging, other agents of mortality or much older events affecting population sizes. Effects of drift are known to be greater in small populations and we found a negative relationship between sugar pine density and c i ( r 2 = 0.36). Allele frequency of the Cr1 gene, responsible for WPBR-resistance in sugar pine, averaged 0.068 for all populations sampled; no WPBR infection was found in one population in which the Cr1 frequency was 0.112. Historical disturbances and their interactions have likely influenced the population biology of sugar pine in the Tahoe Basin; for some populations this has meant reduced population size, higher genetic drift, and poor survival of small- and intermediate-sized individuals. Possible management strategies include restoring population numbers, deploying WPBR-resistance, treating stands to promote natural sugar pine regeneration, and enhancing genetic diversity.
Alejandra Vazquezlobo - One of the best experts on this subject based on the ideXlab platform.
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finding loci associated to partial resistance to white pine blister rust in sugar pine Pinus lambertiana dougl
Tree Genetics & Genomes, 2017Co-Authors: Dean A. Davis, Deems Burton, Alejandra Vazquezlobo, Amanda R De La Torre, Pedro J Martinezgarcia, Carl Vangestel, Jill L Wegzryn, Irina Calic, Bohun B. KinlochAbstract:White pine blister rust (WPBR) is an exotic disease threatening five-needle pines in North America. In spite of its relatively recent introduction, some five-needle pines such as sugar pine (Pinus lambertiana) have developed both complete (major) gene resistance and partial (quantitative) resistance to WPBR. While significant effort has been dedicated to clone and locate the position of the major gene of WPBR resistance in sugar pine, the genetic basis of quantitative resistance remains largely unknown in all Strobus pines. In this work, we took a preliminary approach to identify potential genotype × phenotype associations using the results of long-term survival and symptoms of infection in both experimental and applied breeding populations. Our study found significant associations between several genes and WPBR disease symptoms such as normal active cankers and blights, important symptoms in the development of partial resistance. No significant associations were found with percentage of survival, probably due to the complex inheritance of the disease and long time to infection. With this study, we hope to lay the ground for further genome-wide association studies using large phenotypic data sets in sugar pine and other Strobus pines.
Bohun B. Kinloch - One of the best experts on this subject based on the ideXlab platform.
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finding loci associated to partial resistance to white pine blister rust in sugar pine Pinus lambertiana dougl
Tree Genetics & Genomes, 2017Co-Authors: Dean A. Davis, Deems Burton, Alejandra Vazquezlobo, Amanda R De La Torre, Pedro J Martinezgarcia, Carl Vangestel, Jill L Wegzryn, Irina Calic, Bohun B. KinlochAbstract:White pine blister rust (WPBR) is an exotic disease threatening five-needle pines in North America. In spite of its relatively recent introduction, some five-needle pines such as sugar pine (Pinus lambertiana) have developed both complete (major) gene resistance and partial (quantitative) resistance to WPBR. While significant effort has been dedicated to clone and locate the position of the major gene of WPBR resistance in sugar pine, the genetic basis of quantitative resistance remains largely unknown in all Strobus pines. In this work, we took a preliminary approach to identify potential genotype × phenotype associations using the results of long-term survival and symptoms of infection in both experimental and applied breeding populations. Our study found significant associations between several genes and WPBR disease symptoms such as normal active cankers and blights, important symptoms in the development of partial resistance. No significant associations were found with percentage of survival, probably due to the complex inheritance of the disease and long time to infection. With this study, we hope to lay the ground for further genome-wide association studies using large phenotypic data sets in sugar pine and other Strobus pines.
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Triadimefon controls white pine blister rust on sugar pine in a greenhouse test.
1992Co-Authors: David R. Johnson, Bohun B. Kinloch, Arthur H. MccainAbstract:Seven systemic fungicides were applied to sugar pine (Pinus lambertiana Dougl.) seedlings, as foliar sprays, to determine their efficacy against white pine blister rust-the major limiting factor in regenerating sugar pine. Benodanil and triadimefon showed strong protection after the initial inoculation, with triadimefon showing residual protection for up to 6 months. This protection was verified by a followup test. Tree Planters' Notes 43(1):7-10;1992. Sugar pine (Pinus lambertiana Dougl.) is one of the most important and valuable timber species in California. However, it is highly susceptible to white pine blister rust, caused by Cronartium ribicola J. C. Fisch. in Rabenh. Since its
Richard A. Sniezko - One of the best experts on this subject based on the ideXlab platform.
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Sexual reproduction and crossing barriers in white pines: the case between Pinus lambertiana (sugar pine) and P. monticola (western white pine)
Tree Genetics & Genomes, 2005Co-Authors: Danilo D. Fernando, Sally M. Long, Richard A. SniezkoAbstract:The sexual reproductive process in Pinus lambertiana has not been completely described, and previous attempts to generate hybrids with Pinus monticola and other North American pines have not been successful. The nature of incompatibility barriers between P. lambertiana and P. monticola is unknown. This needs to be understood if strategies are to be developed to overcome the said barriers. In this paper, development on interspecific crosses is compared with that on intraspecific crosses on the same parent trees. Pollen grains of both species germinated on the nucellus of both species within a week after pollination. Seed cone receptivity in P. lambertiana came approximately 2 weeks after receptivity in P. monticola , and this delay was perpetuated throughout ovule development in the first year of the reproductive process. Development of the second-year seed cones proceeded more gradually in P. lambertiana. However, seed cones reached maturity only for P. monticola x P. lambertiana . In both crosses, the barriers to hybridization occurred during the second year of the reproductive process. With the P. lambertiana as the seed parent, it was manifested through the failure of the megaspores at the free-nuclear stage to resume development. When P. monticola was used as the seed parent, the male and female gametes failed to fuse. Our results clearly show that the barriers to hybridization in these species occur before or at fertilization. However, the exact mechanisms behind these are still unknown. Based on the results of this study, we present several strategies to bypass the developmental barriers and possibly produce hybrid progenies.
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A Comparison of Early Field Results of White Pine Blister Rust Resistance in Sugar Pine and Western White Pine
HortTechnology, 2000Co-Authors: Richard A. Sniezko, Andrew Bower, Jude DanielsonAbstract:The cooperation of USDA Forest Service’s Region 5 (Pacific Southwest Region) for use of their Happy Camp test site and the input given by Dean Davis and Deems Burton to the planting and with the first assessment are gratefully acknowledged. Input from B.B. Kinloch and Westfall from USDA Forest Service’s Pacific Southwest Research Station was also valuable for this young trial. Establishment of this planting was made possible through funding from the USDA Forest Service, Forest Health and Protection Program, with special assistance from the Pacific Northwest Region. Thanks are also due to Lee Riley and other personnel at DGRC who organized the seedling culture and transport of plants. Robert Danchok, Sally Long, and Ann Willyard provided vital help with the rust assessment in summer of 1999. The cost of publishing this paper was defrayed in part by the payment of page charges. Under postal regulations, this paper therefore must be hereby marked advertisement solely to indicate this fact. ADDITIONAL INDEX WORDS. white pine blister rust, Cronartium ribicola, western white pine, Pinus monticola, sugar pine, Pinus lambertiana, resistance, bark reaction