Association Genetics of Coastal Douglas Fir (<i>Pseudotsuga menziesii</i> var. <i>menziesii</i>, Pinaceae). I. Cold-Hardiness Related Traits

Eckert, Andrew J.; Bower, Andrew D.; Wegrzyn, Jill L.; Pande, B. N.; Jermstad, K. D.; Krutovsky, Konstantin V.; Clair, J. Bradley St.; Neale, David B.

doi:10.1534/genetics.109.102350

Cited by 197 publications

(190 citation statements)

References 84 publications

(105 reference statements)

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“…The excess of negative Tajima's D, Fay and Wu's H, as well as Fu's F s values noted in this study was also observed in other temperate or boreal species being largely displaced during the Holocene, such as P. abies (Heuertz et al, 2006;Namroud et al, 2010), P. sylvestris (Pyhäjärvi et al, 2007), P. menziesii var. menziesii (Eckert et al, 2009b) and Picea mariana (Namroud et al, 2010). In other conifer species less displaced during the Holocene, the excess of negative Tajima's D values is not the rule.…”

Section: Ld and Selectionmentioning

confidence: 96%

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The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

Pavy

Gagnon

et al. 2011

Heredity

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In plants, knowledge about linkage disequilibrium (LD) is relevant for the design of efficient single-nucleotide polymorphism arrays in relation to their use in population and association genomics studies. Previous studies of conifer genes have shown LD to decay rapidly within gene limits, but exceptions have been reported. To evaluate the extent of heterogeneity of LD among conifer genes and its potential causes, we examined LD in 105 genes of white spruce (Picea glauca) by sequencing a panel of 48 haploid megagametophytes from natural populations and further compared it with LD in other conifer species. The average pairwise r 2 value was 0.19 (s.d.¼0.19), and LD dropped quickly with a half-decay being reached at a distance of 65 nucleotides between sites. However, LD was significantly heterogeneous among genes. A first group of 29 genes had stronger LD (mean r 2 ¼0.28), and a second group of 38 genes had weaker LD (mean r 2 ¼0.12). While a strong relationship was found with the recombination rate, there was no obvious relationship between LD and functional classification. The level of nucleotide diversity, which was highly heterogeneous across genes, was also not significantly correlated with LD. A search for selection signatures highlighted significant deviations from the standard neutral model, which could be mostly attributed to recent demographic changes. Little evidence was seen for hitchhiking and clear relationships with LD. When compared among conifer species, on average, levels of LD were similar in genes from white spruce, Norway spruce and Scots pine, whereas loblolly pine and Douglas fir genes exhibited a significantly higher LD.

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Section: Ld and Selectionmentioning

confidence: 96%

“…Association studies involving candidate genes have been successful to detect genetic polymorphisms associated with phenotypic variation in loblolly pine (González-Martínez et al, 2008), Douglas fir (Eckert et al, 2009b), Sitka spruce (Holliday et al, 2010) and white spruce .…”

Section: Introductionmentioning

confidence: 99%

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

Pavy

Gagnon

et al. 2011

Heredity

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“…The set of associations in loblolly pine, therefore, is comprehensive with regard to phenotypic trait diversity. This includes both explicitly and implicitly measured phenotypic traits, as environmental associations are expected to reflect unmeasured phenotypic traits since phenotypic traits are selected upon in natural populations (see Eckert et al 2009a for an example).Loblolly pine is an ecologically and economically important tree species of southeastern North America. Its range extends from eastern Texas throughout the southeastern United States and north into Delaware and thus is distributed across diverse environmental gradients ( Figure 1).…”

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confidence: 99%

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confidence: 99%

The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae)

et al. 2013

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A primary goal of evolutionary genetics is to discover and explain the genetic basis of fitness-related traits and how this genetic basis evolves within natural populations. Unprecedented technological advances have fueled the discovery of genetic variants associated with ecologically relevant phenotypes in many different life forms, as well as the ability to scan genomes for deviations from selectively neutral models of evolution. Theoretically, the degree of overlap between lists of genomic regions identified using each approach is related to the genetic architecture of fitness-related traits and the strength and type of natural selection molding variation at these traits within natural populations. Here we address for the first time in a plant the degree of overlap between these lists, using patterns of nucleotide diversity and divergence for .7000 unique amplicons described from the extensive expressed sequence tag libraries generated for loblolly pine (Pinus taeda L.) in combination with the .1000 published genetic associations. We show that loci associated with phenotypic traits are distinct with regard to neutral expectations. Phenotypes measured at the whole plant level (e.g., disease resistance) exhibit an approximately twofold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were apparent only when loci were considered at the level of functional sets. The ramifications of this result are discussed in light of the continued efforts to dissect the genetic basis of quantitative traits.A primary goal of population and quantitative genetics is to understand the genetic architecture of ecologically relevant traits (Stinchcombe and Hoekstra 2008; Barrett and Hoekstra 2011;Neale and Kremer 2011). A primary step on the path to this goal is to link genetic with phenotypic variation, either through linkage mapping of quantitative trait loci using pedigrees or through linkage disequilibrium mapping in natural populations (Lander and Schork 1994), with the latter currently being the most utilized. A multitude of studies ranging across a diverse set of taxa have discovered myriad genotype-phenotype correlations (Hindorff et al. 2009;Ingvarsson and Street 2011;Neale and Kremer 2011). Each discovered variant, however, often explains only a small fraction of the heritable phenotypic variance, thus being consistent with a polygenic model for the genetic architecture of complex traits (Lynch and Walsh 1998). Concomitant with the discovery of these associations are population genomic scans documenting deviations from expectations derived using the neutral theory (Nielsen 2005). Such scans have also discovered large numbers of loci putatively underlying phenotypic traits in many different taxa (e.g., Pollinger et al. 2005;Pritchard et al. 2010;Hufford et al. 2012), but in this case the link between genotype and phenotype is not explicit. A natural question thus arises about how much overlap exists between the lists gen...

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“…Similarly, Holliday et al (2010) found associations between 28 genes and phenotypic variance in two dormancy-related traits, autumn cold hardiness and budset timing, for Stika spruce, across its range. Eckert et al (2009) identified associations between genes and cold-hardiness related traits for coastal Douglas fir.…”

Section: Introductionmentioning

confidence: 99%

CartograTree: Enabling landscape genomics for forest trees

Herndon

Grau

Batra

et al. 2016

Preprint

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Forest trees cover just over 30% of the earth's surface and are studied by researchers around the world for both their conservation and economic value. With the onset of high throughput technologies, tremendous phenotypic and genomic data sets have been generated for hundreds of species. These long-lived and immobile individuals serve as ideal models to assess population structure and adaptation to environment. Despite the availability of comprehensive data, researchers are challenged to integrate genotype, phenotype, and environment in one place. Towards this goal, CartograTree was designed and implemented as an open repository and open-source analytic framework for genomic, phenotypic, and environmental data for forest trees. One of its key components, the integration of geospatial data, allows the display of environmental layers and acquisition of environmental metrics relative to the positions of georeferenced individuals. Currently, CartograTree uses the Google Maps API to load environmental data. Limitations inherent to this API are driving new development with a focus on functionality to provide efficient queries of numerous environmental metrics.

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Association Genetics of Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-Hardiness Related Traits

Cited by 197 publications

References 84 publications

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae)

CartograTree: Enabling landscape genomics for forest trees

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