Association genetics in Pinus taeda L. II. Carbon isotope discrimination

González‐Martínez, Santiago C.; Huber, D. M.; Ersoz, Elhan S.; Davis, John M.; Neale, David B.

doi:10.1038/hdy.2008.21

Cited by 125 publications

(87 citation statements)

References 69 publications

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“…The SNP‐by‐SNP association approach has shown that the effect of each SNP on the total phenotypic variation is generally low, which is expected for multigenic control and may also suggest complex gene interaction effects (González‐Martínez et al ., 2008; Prunier et al ., 2013). …”

Section: Discussionmentioning

confidence: 99%

Genetic architecture of wood properties based on association analysis and co‐expression networks in white spruce

et al. 2015

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Summary 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 network hubs. The network revealed a link between the gene PgNAC8, wood stiffness and microfibril angle, as well as considerable within‐season variation for both genetic control of wood traits and gene expression. Trait associations were distributed throughout the network suggesting complex interactions and pleiotropic effects.Our findings indicate that integration of association mapping and co‐expression networks enhances our understanding of complex wood traits.

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Section: Discussionmentioning

confidence: 99%

Genetic architecture of wood properties based on association analysis and co‐expression networks in white spruce

et al. 2015

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“…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%

“…This trend indicates that larger sets of genes should be analyzed in conifers to get a more complete picture of LD of the gene space. The information obtained should contribute to build more efficient gene SNP arrays for use in association studies (González-Martínez et al, 2008) and for outlier detection among natural populations or environments (Namroud et al, 2008;Prunier et al, 2011). Accordingly, we sequenced a large number of genes in natural populations of white spruce to assess LD and its contributing factors more completely, and to compare with results obtained for other conifers.…”

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

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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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“…In P. pinaster it was validated that δ 13 C may be used as a surrogate for WUE (Fernandez et al, 2006), is linked to other hydraulic traits in Pinaceae (Martinez-Villalta et al, 2004) and might have higher heritability than other measures of WUE (McKay et al, 2003). On the other hand, the trait shows a remarkable environmental influence, and consequently needs to be tested in a wide range of environments with a rigorous environmental control, and the complexity of the trait, which involve several functional candidate gene types, might complicate validation of genotype/phenotype associations for WUE (Gonzalez et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Phenotypic plasticity in Pinus pinaster δ13C: environment modulates genetic variation

Corcuera¹,

Gil‐Pelegrín²,

Notivol³

2010

Ann. For. Sci.

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Keywords:carbon isotope / phenotypic plasticity / genetic variation / environmental interaction / water use efficiency Abstract • Carbon isotope composition (δ 13 C) is a complex trait involved in acclimation, adaptive processes and related to water use efficiency (WUE) and/or productivity.• To estimate the genetic variation in δ 13 C and growth (h), their relationship, and the genotype by environment interaction effect in both variables, we analyzed three Pinus pinaster populations and six to ten families per population, in two experimental trial sites and in two consecutive years.• δ 13 C increased in the drier site (from -27.15 ± 0.18 to -24.53 ± 0.22) and was more affected by environment (62% of variance) than by genotype.• All populations and families exhibited a high phenotypic plasticity in δ 13 C and increased WUE in the xeric site.• As expected, significant height differences between sites, years, populations and families were displayed. Smaller trees were associated to higher water use efficiency (δ 13 C) in both, mesic and xeric trial sites.• Aridity and continentality enhanced population differences in δ 13 C, therefore, in afforestation programs of arid and continental zones, the selection at the population level would be more efficient than at the family level. In the mesic site, the presence of a high genetic variation in δ 13 C and h between families allows the possibility of a selection for growth and water use efficiency within populations in sub-humid sites.

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Association genetics in Pinus taeda L. II. Carbon isotope discrimination

Cited by 125 publications

References 69 publications

Genetic architecture of wood properties based on association analysis and co‐expression networks in white spruce

Genetic architecture of wood properties based on association analysis and co‐expression networks in white spruce

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

Phenotypic plasticity in Pinus pinaster δ13C: environment modulates genetic variation

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