Michael Stoehr - Academia.edu (original) (raw)

Papers by Michael Stoehr

Research paper thumbnail of Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species

Research paper thumbnail of Patterns of Nucleotide Diversity and Association Mapping

Understanding the molecular basis of adaptive traits is a major interest in conservation and popu... more Understanding the molecular basis of adaptive traits is a major interest in conservation and population genetics. In commercial species, such as several conifers, it is also interesting for operational breeding. In this chapter, we provide a state-of-the-art view on candidate gene research, from general estimates of nucleotide diversity and recombination to new-generation neutrality tests and association genetics methodologies. Levels of nucleotide diversity in conifers are substantial, although lower than expected given their life-history traits. In addition, linkage disequilibrium seems to decay rapidly in this group of species, at least within genes that are not submitted to natural selection. These two facts makes genetic association studies appealing in conifers, as significant associations may correspond to the actual causal polymorphisms. Population genomic methods also seem appropriate in conifers, in particular for those species with accused population genetic structure and strong response to environmental gradients. New-generation neutrality tests, outlier loci detection methods and genotype/phenotype association studies have revealed various candidate genes and single nucleotide polymorphisms underlying different adaptive phenotypes, despite potential confounding effects of demographical and historical processes. Finally, perspectives about future genomic research in conifers are provided, including its application for conservation and breeding.

Research paper thumbnail of Effects of crown-pruning on seed and pollen cone production in two lodgepole pine seed orchards in British Columbia

Research paper thumbnail of Evaluating Supplemental Mass Pollination Efficacy in a Lodgepole Pine Orchard in British Columbia using Chloroplast DNA Markers

New Forest, 2006

Supplemental mass pollination (SMP) success in a grafted lodgepole pine (Pinus contorta Dougl. ex... more Supplemental mass pollination (SMP) success in a grafted lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) seed orchard in southern British Columbia was studied by employing four chloroplast DNA (cpDNA) markers to determine fertilization success of 10 pollen parents. SMP was conducted operationally with a bulked pollen mix twice during peak receptivity in the seed orchard. Fertilization success

Research paper thumbnail of Pollen contamination effects on progeny from an off-site Douglas-fir seed orchard

Research paper thumbnail of Anomalous Solitary Flowers on Anther-Derived Plants of Populus maximowiczii

American Journal of Botany, Apr 1, 1988

Research paper thumbnail of Levels of genetic diversity at different stages of the domestication cycle of interior spruce in British Columbia

Theoretical and Applied Genetics, 1997

Research paper thumbnail of High levels of chloroplast genetic variation differentiate coastal and interior Douglas-fir (Pseudotsuga menziesii) lineages in southern British Columbia

Research paper thumbnail of Protocols for Rating Seed Orchard Seedlots in British Columbia

Research paper thumbnail of Evaluating Pollen Competition in Douglas-Fir Using a Chloroplast Dna Marker

An experiment was conducted to test pollen competition as reflected in the reproductive success o... more An experiment was conducted to test pollen competition as reflected in the reproductive success of individual pollen lots in two polymixes in Douglas-fir (Pseudotsuga rnenziesii (Mirb.) Franco). One polymix contained six pollen lots in equal proportion by weight, the other polymix was formulated using the same six pollen lots but in inversely proportional amounts to their viability. Pollen lot viability was measured as respiration (oxygen uptake). Reproductive success of individual male parents (pollen lots) was determined following control pollinations using both polymixes separately on six female clones. The paternity analysis was carried out using a chloroplast DNA marker amplified by the polymerase chain reaction (PCR) in total DNA extracts of embryos dissected from mature seed, allowing the identification of the male parent in "polycrossed" seed. Average number of filled seed per cone was not affected by the two polymixes, but the reproductive success of individual ma...

Research paper thumbnail of Gwinorchards

Research paper thumbnail of Evaluating the Protocol for Quantifying Pollen Contamination on the Genetic Worth of Conifer Seed Orchards. Project Y051110

Research paper thumbnail of Challenges facing the forest industry in relation to seed dormancy and seed quality

Methods in molecular biology (Clifton, N.J.), 2011

Artificial regeneration of forests through planting requires high quantities of quality seeds for... more Artificial regeneration of forests through planting requires high quantities of quality seeds for growing vigorous seedlings. These seedlings are raised in nurseries, where germination capacity (GC) and speed are the most important germination parameters. Germination performance is enhanced by prescribing species-specific dormancy-breaking treatments to individual seedlots in bare-root and container nurseries. For most conifer species in British Columbia, the dormancy-breaking treatments and germination conditions have been worked out, but fine-tuning and optimization could improve germination capacity and speed of germination. Implications of inter- and intra-species variations in germination behaviour and seed quality and their influence on the development of unintentional directional selection of specific genotypes are discussed. The potential of molecular and genomics approaches to understand the underlying biology of seed germination-related problems is also discussed.

Research paper thumbnail of Quantifying safe seed transfer distance and impacts of tree breeding on adaptation

Forest Ecology and Management, 2014

ABSTRACT Tree seed zones that are too large can compromise forest plantation health and productiv... more ABSTRACT Tree seed zones that are too large can compromise forest plantation health and productivity due to maladaptation arising from some populations being transferred long distances, whereas tree seed zones that are too small can result in unwarranted seed collections or excessive numbers of breeding zones. There has been little discussion, however, regarding the development and use of transfer functions for quantifying critical (i.e., safe) seed transfer distance (CSTD) or how artificial selection might affect CSTD. Using data from a large, multi-site provenance test for Douglas-fir and Interior spruce containing both genetically selected and wildstand seed sources, we illustrate an approach to quantify CSTD using Euclidean climate transfer distance modeled with a half-normal transfer function. A wide range of CSTDs was calculated and most transfer functions showed that selected seed sources were considerably taller than wildstand seed sources when transferred short or medium climate distances. Contrarily, selected seed sources were shorter than wildstand seed sources when transferred long climate distances. CSTDs were shorter for Douglas-fir than for spruce, and shorter when calculated using height rather than survival as the transfer function response variable. These findings suggest that (1) unfavorable changes in adaptation due to artificial selection will be observable only when seed is transferred considerably beyond the CSTD; (2) differences in adaptation between selected and wildstand seed classes may not warrant separate seed transfer guidelines for these seed classes; (3) British Columbia’s Douglas-fir and Interior spruce breeding programs are generating significant height gain; (4) methods presented here produce logical transfer functions that can be used to calculate reliable site-specific CSTDs; (5) use of conservative (short) CSTDs may be advisable when tests are young; and (6) provenance tests should be located in disparate climates.

Research paper thumbnail of Inbreeding in mid-rotation coastal Douglas-fir: implications for breeding

Annals of Forest Science, 2014

Research paper thumbnail of Gain and diversity in advanced generation coastal Douglas-fir selections for seed production populations

Tree Genetics & Genomes, 2007

Research paper thumbnail of Ectomycorrhizal fungal maladaptation and growth reductions associated with assisted migration of Douglas-fir

The New phytologist, Jan 26, 2015

Climatic adaptations are the foundation of conifer genecology, but populations also display varia... more Climatic adaptations are the foundation of conifer genecology, but populations also display variation in traits for nitrogen (N) utilization, along with some heritable specificity for ectomycorrhizal fungi (EMF). We examined soil and EMF influences on assisted migration of Douglas-fir (Pseudotsuga menziesii var. menziesii) by comparing two contrasting maritime populations planted up to 400 km northward in southwestern British Columbia. Soil N availability and host N status (via δ(15) N) were assessed across 12 maritime test sites, whereas EMF on local and introduced hosts were quantified by morphotyping with molecular analysis. Climatic transfer effects were only significant with soil N concentrations of test sites as a covariate, and illustrated how height growth was compromised for populations originating from relatively dry or cool maritime environments. We also found evidence for EMF maladaptation, where height declined by up to 15% with the extent of dissimilarity in EMF commun...

Research paper thumbnail of Within and among family variation of orchard and wild-stand progeny of interior spruce in British Columbia

Tree Genetics & Genomes, 2005

Research paper thumbnail of Levels of genetic diversity at different stages of the domestication cycle of interior spruce in British Columbia

Theoretical and Applied Genetics, 1997

Research paper thumbnail of Evaluating Supplemental Mass Pollination Efficacy in a Lodgepole Pine Orchard in British Columbia using Chloroplast DNA Markers

New Forests, 2006

Supplemental mass pollination (SMP) success in a grafted lodgepole pine (Pinus contorta Dougl. ex... more Supplemental mass pollination (SMP) success in a grafted lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) seed orchard in southern British Columbia was studied by employing four chloroplast DNA (cpDNA) markers to determine fertilization success of 10 pollen parents. SMP was conducted operationally with a bulked pollen mix twice during peak receptivity in the seed orchard. Fertilization success

Research paper thumbnail of Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species

Research paper thumbnail of Patterns of Nucleotide Diversity and Association Mapping

Understanding the molecular basis of adaptive traits is a major interest in conservation and popu... more Understanding the molecular basis of adaptive traits is a major interest in conservation and population genetics. In commercial species, such as several conifers, it is also interesting for operational breeding. In this chapter, we provide a state-of-the-art view on candidate gene research, from general estimates of nucleotide diversity and recombination to new-generation neutrality tests and association genetics methodologies. Levels of nucleotide diversity in conifers are substantial, although lower than expected given their life-history traits. In addition, linkage disequilibrium seems to decay rapidly in this group of species, at least within genes that are not submitted to natural selection. These two facts makes genetic association studies appealing in conifers, as significant associations may correspond to the actual causal polymorphisms. Population genomic methods also seem appropriate in conifers, in particular for those species with accused population genetic structure and strong response to environmental gradients. New-generation neutrality tests, outlier loci detection methods and genotype/phenotype association studies have revealed various candidate genes and single nucleotide polymorphisms underlying different adaptive phenotypes, despite potential confounding effects of demographical and historical processes. Finally, perspectives about future genomic research in conifers are provided, including its application for conservation and breeding.

Research paper thumbnail of Effects of crown-pruning on seed and pollen cone production in two lodgepole pine seed orchards in British Columbia

Research paper thumbnail of Evaluating Supplemental Mass Pollination Efficacy in a Lodgepole Pine Orchard in British Columbia using Chloroplast DNA Markers

New Forest, 2006

Supplemental mass pollination (SMP) success in a grafted lodgepole pine (Pinus contorta Dougl. ex... more Supplemental mass pollination (SMP) success in a grafted lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) seed orchard in southern British Columbia was studied by employing four chloroplast DNA (cpDNA) markers to determine fertilization success of 10 pollen parents. SMP was conducted operationally with a bulked pollen mix twice during peak receptivity in the seed orchard. Fertilization success

Research paper thumbnail of Pollen contamination effects on progeny from an off-site Douglas-fir seed orchard

Research paper thumbnail of Anomalous Solitary Flowers on Anther-Derived Plants of Populus maximowiczii

American Journal of Botany, Apr 1, 1988

Research paper thumbnail of Levels of genetic diversity at different stages of the domestication cycle of interior spruce in British Columbia

Theoretical and Applied Genetics, 1997

Research paper thumbnail of High levels of chloroplast genetic variation differentiate coastal and interior Douglas-fir (Pseudotsuga menziesii) lineages in southern British Columbia

Research paper thumbnail of Protocols for Rating Seed Orchard Seedlots in British Columbia

Research paper thumbnail of Evaluating Pollen Competition in Douglas-Fir Using a Chloroplast Dna Marker

An experiment was conducted to test pollen competition as reflected in the reproductive success o... more An experiment was conducted to test pollen competition as reflected in the reproductive success of individual pollen lots in two polymixes in Douglas-fir (Pseudotsuga rnenziesii (Mirb.) Franco). One polymix contained six pollen lots in equal proportion by weight, the other polymix was formulated using the same six pollen lots but in inversely proportional amounts to their viability. Pollen lot viability was measured as respiration (oxygen uptake). Reproductive success of individual male parents (pollen lots) was determined following control pollinations using both polymixes separately on six female clones. The paternity analysis was carried out using a chloroplast DNA marker amplified by the polymerase chain reaction (PCR) in total DNA extracts of embryos dissected from mature seed, allowing the identification of the male parent in "polycrossed" seed. Average number of filled seed per cone was not affected by the two polymixes, but the reproductive success of individual ma...

Research paper thumbnail of Gwinorchards

Research paper thumbnail of Evaluating the Protocol for Quantifying Pollen Contamination on the Genetic Worth of Conifer Seed Orchards. Project Y051110

Research paper thumbnail of Challenges facing the forest industry in relation to seed dormancy and seed quality

Methods in molecular biology (Clifton, N.J.), 2011

Artificial regeneration of forests through planting requires high quantities of quality seeds for... more Artificial regeneration of forests through planting requires high quantities of quality seeds for growing vigorous seedlings. These seedlings are raised in nurseries, where germination capacity (GC) and speed are the most important germination parameters. Germination performance is enhanced by prescribing species-specific dormancy-breaking treatments to individual seedlots in bare-root and container nurseries. For most conifer species in British Columbia, the dormancy-breaking treatments and germination conditions have been worked out, but fine-tuning and optimization could improve germination capacity and speed of germination. Implications of inter- and intra-species variations in germination behaviour and seed quality and their influence on the development of unintentional directional selection of specific genotypes are discussed. The potential of molecular and genomics approaches to understand the underlying biology of seed germination-related problems is also discussed.

Research paper thumbnail of Quantifying safe seed transfer distance and impacts of tree breeding on adaptation

Forest Ecology and Management, 2014

ABSTRACT Tree seed zones that are too large can compromise forest plantation health and productiv... more ABSTRACT Tree seed zones that are too large can compromise forest plantation health and productivity due to maladaptation arising from some populations being transferred long distances, whereas tree seed zones that are too small can result in unwarranted seed collections or excessive numbers of breeding zones. There has been little discussion, however, regarding the development and use of transfer functions for quantifying critical (i.e., safe) seed transfer distance (CSTD) or how artificial selection might affect CSTD. Using data from a large, multi-site provenance test for Douglas-fir and Interior spruce containing both genetically selected and wildstand seed sources, we illustrate an approach to quantify CSTD using Euclidean climate transfer distance modeled with a half-normal transfer function. A wide range of CSTDs was calculated and most transfer functions showed that selected seed sources were considerably taller than wildstand seed sources when transferred short or medium climate distances. Contrarily, selected seed sources were shorter than wildstand seed sources when transferred long climate distances. CSTDs were shorter for Douglas-fir than for spruce, and shorter when calculated using height rather than survival as the transfer function response variable. These findings suggest that (1) unfavorable changes in adaptation due to artificial selection will be observable only when seed is transferred considerably beyond the CSTD; (2) differences in adaptation between selected and wildstand seed classes may not warrant separate seed transfer guidelines for these seed classes; (3) British Columbia’s Douglas-fir and Interior spruce breeding programs are generating significant height gain; (4) methods presented here produce logical transfer functions that can be used to calculate reliable site-specific CSTDs; (5) use of conservative (short) CSTDs may be advisable when tests are young; and (6) provenance tests should be located in disparate climates.

Research paper thumbnail of Inbreeding in mid-rotation coastal Douglas-fir: implications for breeding

Annals of Forest Science, 2014

Research paper thumbnail of Gain and diversity in advanced generation coastal Douglas-fir selections for seed production populations

Tree Genetics & Genomes, 2007

Research paper thumbnail of Ectomycorrhizal fungal maladaptation and growth reductions associated with assisted migration of Douglas-fir

The New phytologist, Jan 26, 2015

Climatic adaptations are the foundation of conifer genecology, but populations also display varia... more Climatic adaptations are the foundation of conifer genecology, but populations also display variation in traits for nitrogen (N) utilization, along with some heritable specificity for ectomycorrhizal fungi (EMF). We examined soil and EMF influences on assisted migration of Douglas-fir (Pseudotsuga menziesii var. menziesii) by comparing two contrasting maritime populations planted up to 400 km northward in southwestern British Columbia. Soil N availability and host N status (via δ(15) N) were assessed across 12 maritime test sites, whereas EMF on local and introduced hosts were quantified by morphotyping with molecular analysis. Climatic transfer effects were only significant with soil N concentrations of test sites as a covariate, and illustrated how height growth was compromised for populations originating from relatively dry or cool maritime environments. We also found evidence for EMF maladaptation, where height declined by up to 15% with the extent of dissimilarity in EMF commun...

Research paper thumbnail of Within and among family variation of orchard and wild-stand progeny of interior spruce in British Columbia

Tree Genetics & Genomes, 2005

Research paper thumbnail of Levels of genetic diversity at different stages of the domestication cycle of interior spruce in British Columbia

Theoretical and Applied Genetics, 1997

Research paper thumbnail of Evaluating Supplemental Mass Pollination Efficacy in a Lodgepole Pine Orchard in British Columbia using Chloroplast DNA Markers

New Forests, 2006

Supplemental mass pollination (SMP) success in a grafted lodgepole pine (Pinus contorta Dougl. ex... more Supplemental mass pollination (SMP) success in a grafted lodgepole pine (Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) seed orchard in southern British Columbia was studied by employing four chloroplast DNA (cpDNA) markers to determine fertilization success of 10 pollen parents. SMP was conducted operationally with a bulked pollen mix twice during peak receptivity in the seed orchard. Fertilization success