Elie Raherison | Université Laval (original) (raw)

Papers by Elie Raherison

Research paper thumbnail of Supplemental Material for Raherison et al., 2020

Supplemental methods, figures and tables. <br>

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Research paper thumbnail of See Profile

Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organiza... more Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures

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Research paper thumbnail of Structure, dynamique et évolution du transcriptome chez les conifères

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Research paper thumbnail of Plant Biomass, Nutrient Concentration and Nutrient Storage in a Tropical Dry Forest in the South–west of Madagascar

Plant Ecology, 2005

Plant biomass, mineral composition and the amounts of nutrients in the different fractions of the... more Plant biomass, mineral composition and the amounts of nutrients in the different fractions of the vegetation were determined for a dense dry deciduous forest growing on light red sands in south-western Madagascar. Complete harvesting and soil coring were used to determine the above- and below-ground biomass respectively. The above-ground biomass, weighing 118 t ha−1 (dry matter), was mostly (96%) made up of

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Research paper thumbnail of Evidence for the Accumulation of Nonsynonymous Mutations and Favorable Pleiotropic Alleles During Wheat Breeding

G3 Genes|Genomes|Genetics, 2020

Plant breeding leads to the genetic improvement of target traits by selecting a small number of g... more Plant breeding leads to the genetic improvement of target traits by selecting a small number of genotypes from among typically large numbers of candidate genotypes after careful evaluation. In this study, we first investigated how mutations at conserved nucleotide sites normally viewed as deleterious, such as nonsynonymous sites, accumulated in a wheat, Triticum aestivum, breeding lineage. By comparing a 150 year old ancestral and modern cultivar, we found recent nucleotide polymorphisms altered amino acids and occurred within conserved genes at frequencies expected in the absence of purifying selection. Mutations that are deleterious in other contexts likely had very small or no effects on target traits within the breeding lineage. Second, we investigated if breeders selected alleles with favorable effects on some traits and unfavorable effects on others and used different alleles to compensate for the latter. An analysis of a segregating population derived from the ancestral and m...

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Research paper thumbnail of Genetic architecture of wood properties based on association analysis and co-expression networks in white spruce

The New phytologist, Jan 30, 2015

Association studies are widely utilized to analyze complex traits but their ability to disclose g... more Association studies are widely utilized to analyze complex traits but their ability to disclose genetic architectures is often limited by statistical constraints, and functional insights are usually minimal in nonmodel organisms like forest trees. We developed an approach to integrate association mapping results with co-expression networks. We tested single nucleotide polymorphisms (SNPs) in 2652 candidate genes for statistical associations with wood density, stiffness, microfibril angle and ring width in a population of 1694 white spruce trees (Picea glauca). Associations mapping identified 229-292 genes per wood trait using a statistical significance level of P < 0.05 to maximize discovery. Over-representation of genes associated for nearly all traits was found in a xylem preferential co-expression group developed in independent experiments. A xylem co-expression network was reconstructed with 180 wood associated genes and several known MYB and NAC regulators were identified as...

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Research paper thumbnail of Forest Tree Genomics: Review of Progress

Advances in Botanical Research, 2015

ABSTRACT Forest tree genomics is progressing at an accelerated pace owing to recent developments ... more ABSTRACT Forest tree genomics is progressing at an accelerated pace owing to recent developments in next-generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In the last few years, the first conifer genomes at a staggering size of 20e24 gigabases and the genomes of several hardwood trees have been sequenced and analyzed. Biological insights have resulted from these sequencing initiatives as well as from genetic mapping, gene expression profiling and gene discovery research over nearly two decades. This review emphasizes major areas of progress in forest tree genomics, including insights into genome evolution, genome function arising from large-scale gene expression profiling, the genomic architecture of quantitative traits and the population genomics of adaptation. We discuss future directions in these areas with potential inputs from NGS technologies and propose avenues for developing a more integrated understanding of genetic diversity and its impacts on genome function. These directions promise to sustain research aimed at addressing emerging challenges in forestry and produce applied outputs to preserve, enhance and responsibly use world forests.

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Research paper thumbnail of Evidence for the Accumulation of Nonsynonymous Mutations and Favorable Pleiotropic Alleles During Wheat Breeding

G3, 2020

Plant breeding leads to the genetic improvement of target traits by selecting a small number of g... more Plant breeding leads to the genetic improvement of target traits by selecting a small number of genotypes from among typically large numbers of candidate genotypes after careful evaluation. In this study, we first investigated how mutations at conserved nucleotide sites normally viewed as deleterious, such as nonsynonymous sites, accumulated in a wheat, Triticum aestivum, breeding lineage. By comparing a 150 year old ancestral and modern cultivar, we found recent nucleotide polymorphisms altered amino acids and occurred within conserved genes at frequencies expected in the absence of purifying selection. Mutations that are deleterious in other contexts likely had very small or no effects on target traits within the breeding lineage. Second, we investigated if breeders selected alleles with favorable effects on some traits and unfavorable effects on others and used different alleles to compensate for the latter. An analysis of a segregating population derived from the ancestral and modern parents provided one example of this phenomenon. The recent cultivar contains the Rht-B1b green revolution semi-dwarfing allele and compensatory alleles that reduce its negative effects. However, improvements in traits other than plant height were due to pleiotropic loci with favorable effects on traits and to favorable loci with no detectable pleiotropic effects. Wheat breeding appears to tolerate mutations at conserved nucleotide sites and to only select for alleles with both favorable and unfavorable effects on traits in exceptional situations.

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Research paper thumbnail of Forest Tree Genomics: Review of Progress

Advances in Botanical Research, 2015

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Research paper thumbnail of Forest Tree Genomics Review of Progress

Forest tree genomics is progressing at an accelerated pace owing to recent developments in next-g... more Forest tree genomics is progressing at an accelerated pace owing to recent developments in next-generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In the last few years, the first conifer genomes at a staggering size of 20e24 gigabases and the genomes of several hardwood trees have been sequenced and analyzed. Biological insights have resulted from these sequencing initiatives as well as from genetic mapping, gene expression profiling and gene discovery research over nearly two decades. This review emphasizes
major areas of progress in forest tree genomics, including insights into genome evolution, genome function arising from large-scale gene expression profiling, the genomic
architecture of quantitative traits and the population genomics of adaptation. We discuss future directions in these areas with potential inputs from NGS technologies and propose avenues for developing a more integrated understanding of genetic diversity and its impacts on genome function. These directions promise to sustain research aimed at addressing emerging challenges in forestry and produce applied outputs to preserve, enhance and responsibly use world forests.

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Research paper thumbnail of Modular organization of the white spruce ( Picea glauca ) transcriptome reveals functional organization and evolutionary signatures

New Phytologist, 2015

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Research paper thumbnail of Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression

BMC Genomics, 2012

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Research paper thumbnail of Exploring the White Spruce Genome: Gene Content, Evolution and Expression

Plant and Animal Genome XX Conference (January …, 2012

... QC, Canada. Elie Raherison , Université Laval, Québec, QC, Canada. Isabelle Giguère , Univers... more ... QC, Canada. Elie Raherison , Université Laval, Québec, QC, Canada. Isabelle Giguère , Université Laval, Québec, QC, Canada. Jukka-Pekka Verta , Université Laval, Québec, QC, Canada. Claude Bomal , Université Laval, Québec, QC, Canada. John MacKay , Université Laval ...

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Research paper thumbnail of Plant Biomass, Nutrient Concentration and Nutrient Storage in a Tropical Dry Forest in the South–west of Madagascar

Plant biomass, mineral composition and the amounts of nutrients in the different fractions of the... more Plant biomass, mineral composition and the amounts of nutrients in the different fractions of the vegetation were determined for a dense dry deciduous forest growing on light red sands in south-western Madagascar. Complete harvesting and soil coring were used to determine the above- and below-ground biomass respectively. The above-ground biomass, weighing 118 t ha−1 (dry matter), was mostly (96%) made up of phanerophytes (woody trees and shrubs >25 cm tall). Dead material (litter and dead wood on the soil surface) represented 13.8 t ha−1. These results fit well into the range of values reported for other tropical ecosystems. The below-ground biomass was 17.8 t ha−1 giving a root/shoot ratio of 0.15. Rooting is superficial. The nutrient concentration in this dry forest on light reddish-brown sands is, as in other dry forests, considerably higher than that usually found for humid forests. Calcium is the most abundant element. The plant biomass Ca/K ratio is much higher than that of humid tropical forests. In spite of its high originality, this Madagascan dry forest has the same behaviour as other dry forests of the world.

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Research paper thumbnail of Supplemental Material for Raherison et al., 2020

Supplemental methods, figures and tables. <br>

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Research paper thumbnail of See Profile

Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organiza... more Modular organization of the white spruce (Picea glauca) transcriptome reveals functional organization and evolutionary signatures

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Research paper thumbnail of Structure, dynamique et évolution du transcriptome chez les conifères

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Plant Biomass, Nutrient Concentration and Nutrient Storage in a Tropical Dry Forest in the South–west of Madagascar

Plant Ecology, 2005

Plant biomass, mineral composition and the amounts of nutrients in the different fractions of the... more Plant biomass, mineral composition and the amounts of nutrients in the different fractions of the vegetation were determined for a dense dry deciduous forest growing on light red sands in south-western Madagascar. Complete harvesting and soil coring were used to determine the above- and below-ground biomass respectively. The above-ground biomass, weighing 118 t ha−1 (dry matter), was mostly (96%) made up of

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Evidence for the Accumulation of Nonsynonymous Mutations and Favorable Pleiotropic Alleles During Wheat Breeding

G3 Genes|Genomes|Genetics, 2020

Plant breeding leads to the genetic improvement of target traits by selecting a small number of g... more Plant breeding leads to the genetic improvement of target traits by selecting a small number of genotypes from among typically large numbers of candidate genotypes after careful evaluation. In this study, we first investigated how mutations at conserved nucleotide sites normally viewed as deleterious, such as nonsynonymous sites, accumulated in a wheat, Triticum aestivum, breeding lineage. By comparing a 150 year old ancestral and modern cultivar, we found recent nucleotide polymorphisms altered amino acids and occurred within conserved genes at frequencies expected in the absence of purifying selection. Mutations that are deleterious in other contexts likely had very small or no effects on target traits within the breeding lineage. Second, we investigated if breeders selected alleles with favorable effects on some traits and unfavorable effects on others and used different alleles to compensate for the latter. An analysis of a segregating population derived from the ancestral and m...

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Research paper thumbnail of Genetic architecture of wood properties based on association analysis and co-expression networks in white spruce

The New phytologist, Jan 30, 2015

Association studies are widely utilized to analyze complex traits but their ability to disclose g... more Association studies are widely utilized to analyze complex traits but their ability to disclose genetic architectures is often limited by statistical constraints, and functional insights are usually minimal in nonmodel organisms like forest trees. We developed an approach to integrate association mapping results with co-expression networks. We tested single nucleotide polymorphisms (SNPs) in 2652 candidate genes for statistical associations with wood density, stiffness, microfibril angle and ring width in a population of 1694 white spruce trees (Picea glauca). Associations mapping identified 229-292 genes per wood trait using a statistical significance level of P < 0.05 to maximize discovery. Over-representation of genes associated for nearly all traits was found in a xylem preferential co-expression group developed in independent experiments. A xylem co-expression network was reconstructed with 180 wood associated genes and several known MYB and NAC regulators were identified as...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Forest Tree Genomics: Review of Progress

Advances in Botanical Research, 2015

ABSTRACT Forest tree genomics is progressing at an accelerated pace owing to recent developments ... more ABSTRACT Forest tree genomics is progressing at an accelerated pace owing to recent developments in next-generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In the last few years, the first conifer genomes at a staggering size of 20e24 gigabases and the genomes of several hardwood trees have been sequenced and analyzed. Biological insights have resulted from these sequencing initiatives as well as from genetic mapping, gene expression profiling and gene discovery research over nearly two decades. This review emphasizes major areas of progress in forest tree genomics, including insights into genome evolution, genome function arising from large-scale gene expression profiling, the genomic architecture of quantitative traits and the population genomics of adaptation. We discuss future directions in these areas with potential inputs from NGS technologies and propose avenues for developing a more integrated understanding of genetic diversity and its impacts on genome function. These directions promise to sustain research aimed at addressing emerging challenges in forestry and produce applied outputs to preserve, enhance and responsibly use world forests.

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Research paper thumbnail of Evidence for the Accumulation of Nonsynonymous Mutations and Favorable Pleiotropic Alleles During Wheat Breeding

G3, 2020

Plant breeding leads to the genetic improvement of target traits by selecting a small number of g... more Plant breeding leads to the genetic improvement of target traits by selecting a small number of genotypes from among typically large numbers of candidate genotypes after careful evaluation. In this study, we first investigated how mutations at conserved nucleotide sites normally viewed as deleterious, such as nonsynonymous sites, accumulated in a wheat, Triticum aestivum, breeding lineage. By comparing a 150 year old ancestral and modern cultivar, we found recent nucleotide polymorphisms altered amino acids and occurred within conserved genes at frequencies expected in the absence of purifying selection. Mutations that are deleterious in other contexts likely had very small or no effects on target traits within the breeding lineage. Second, we investigated if breeders selected alleles with favorable effects on some traits and unfavorable effects on others and used different alleles to compensate for the latter. An analysis of a segregating population derived from the ancestral and modern parents provided one example of this phenomenon. The recent cultivar contains the Rht-B1b green revolution semi-dwarfing allele and compensatory alleles that reduce its negative effects. However, improvements in traits other than plant height were due to pleiotropic loci with favorable effects on traits and to favorable loci with no detectable pleiotropic effects. Wheat breeding appears to tolerate mutations at conserved nucleotide sites and to only select for alleles with both favorable and unfavorable effects on traits in exceptional situations.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Forest Tree Genomics: Review of Progress

Advances in Botanical Research, 2015

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Forest Tree Genomics Review of Progress

Forest tree genomics is progressing at an accelerated pace owing to recent developments in next-g... more Forest tree genomics is progressing at an accelerated pace owing to recent developments in next-generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In the last few years, the first conifer genomes at a staggering size of 20e24 gigabases and the genomes of several hardwood trees have been sequenced and analyzed. Biological insights have resulted from these sequencing initiatives as well as from genetic mapping, gene expression profiling and gene discovery research over nearly two decades. This review emphasizes
major areas of progress in forest tree genomics, including insights into genome evolution, genome function arising from large-scale gene expression profiling, the genomic
architecture of quantitative traits and the population genomics of adaptation. We discuss future directions in these areas with potential inputs from NGS technologies and propose avenues for developing a more integrated understanding of genetic diversity and its impacts on genome function. These directions promise to sustain research aimed at addressing emerging challenges in forestry and produce applied outputs to preserve, enhance and responsibly use world forests.

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Research paper thumbnail of Modular organization of the white spruce ( Picea glauca ) transcriptome reveals functional organization and evolutionary signatures

New Phytologist, 2015

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression

BMC Genomics, 2012

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Exploring the White Spruce Genome: Gene Content, Evolution and Expression

Plant and Animal Genome XX Conference (January …, 2012

... QC, Canada. Elie Raherison , Université Laval, Québec, QC, Canada. Isabelle Giguère , Univers... more ... QC, Canada. Elie Raherison , Université Laval, Québec, QC, Canada. Isabelle Giguère , Université Laval, Québec, QC, Canada. Jukka-Pekka Verta , Université Laval, Québec, QC, Canada. Claude Bomal , Université Laval, Québec, QC, Canada. John MacKay , Université Laval ...

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Research paper thumbnail of Plant Biomass, Nutrient Concentration and Nutrient Storage in a Tropical Dry Forest in the South–west of Madagascar

Plant biomass, mineral composition and the amounts of nutrients in the different fractions of the... more Plant biomass, mineral composition and the amounts of nutrients in the different fractions of the vegetation were determined for a dense dry deciduous forest growing on light red sands in south-western Madagascar. Complete harvesting and soil coring were used to determine the above- and below-ground biomass respectively. The above-ground biomass, weighing 118 t ha−1 (dry matter), was mostly (96%) made up of phanerophytes (woody trees and shrubs >25 cm tall). Dead material (litter and dead wood on the soil surface) represented 13.8 t ha−1. These results fit well into the range of values reported for other tropical ecosystems. The below-ground biomass was 17.8 t ha−1 giving a root/shoot ratio of 0.15. Rooting is superficial. The nutrient concentration in this dry forest on light reddish-brown sands is, as in other dry forests, considerably higher than that usually found for humid forests. Calcium is the most abundant element. The plant biomass Ca/K ratio is much higher than that of humid tropical forests. In spite of its high originality, this Madagascan dry forest has the same behaviour as other dry forests of the world.

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