Identification of Genes Differentially Expressed in Shoot Apical Meristems and in Mature Xylem of Populus tomentosa

Yang, Xiaohui; Li, Xinguo; Li, Bai-Lian; Zhang, Deqiang

doi:10.1007/s11105-013-0660-6

Cited by 8 publications

(5 citation statements)

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“…In addition to master regulators of secondary cell wall formation such as MYB46 and MYB103 [ 7 ], it integrated genes for cellulose synthase, for hemicellulose formation as well as laccases and peroxidases required for lignification. Moreover, complex 3 encompassed about one-third of the genes denominated as “core xylem gene set” in Arabidopsis [ 53 ] and contained various genes found to be preferentially expressed during secondary wall formation in wood of P. tomentosa [ 54 ]. In contrast to the remarkable overlap with the genes for secondary cell wall formation, we found only one common gene between complex 3 and the N-regulated genes earlier identified in the developing xylem of Populus trichocarpa × deltoides ([ 36 ], Additional file 5 : Table S4).…”

Section: Discussionmentioning

confidence: 99%

Nitrogen-driven stem elongation in poplar is linked with wood modification and gene clusters for stress, photosynthesis and cell wall formation

et al. 2014

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BackgroundNitrogen is an important nutrient, often limiting plant productivity and yield. In poplars, woody crops used as feedstock for renewable resources and bioenergy, nitrogen fertilization accelerates growth of the young, expanding stem internodes. The underlying molecular mechanisms of nitrogen use for extension growth in poplars are not well understood. The aim of this study was to dissect the nitrogen-responsive transcriptional network in the elongation zone of Populus trichocarpa in relation to extension growth and cell wall properties.ResultsTranscriptome analyses in the first two internodes of P. trichocarpa stems grown without or with nitrogen fertilization (5 mM NH4NO3) revealed 1037 more than 2-fold differentially expressed genes (DEGs). Co-expression analysis extracted a network containing about one-third of the DEGs with three main complexes of strongly clustered genes. These complexes represented three main processes that were responsive to N-driven growth: Complex 1 integrated growth processes and stress suggesting that genes with established functions in abiotic and biotic stress are also recruited to coordinate growth. Complex 2 was enriched in genes with decreased transcript abundance and functionally annotated as photosynthetic hub. Complex 3 was a hub for secondary cell wall formation connecting well-known transcription factors that control secondary cell walls with genes for the formation of cellulose, hemicelluloses, and lignin. Anatomical and biochemical analysis supported that N-driven growth resulted in early secondary cell wall formation in the elongation zone with thicker cell walls and increased lignin. These alterations contrasted the N influence on the secondary xylem, where thinner cell walls with lower lignin contents than in unfertilized trees were formed.ConclusionThis study uncovered that nitrogen-responsive elongation growth of poplar internodes is linked with abiotic stress, suppression of photosynthetic genes and stimulation of genes for cell wall formation. Anatomical and biochemical analysis supported increased accumulation of cell walls and secondary metabolites in the elongation zone. The finding of a nitrogen-responsive cell wall hub may have wider implications for the improvement of tree nitrogen use efficiency and opens new perspectives on the enhancement of wood composition as a feedstock for biofuels.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0391-3) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Nitrogen-driven stem elongation in poplar is linked with wood modification and gene clusters for stress, photosynthesis and cell wall formation

et al. 2014

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“…In P. trichocarpa, this gene had moderate expression in pre-, early and late dormant buds, young and immature and first fully expanded leaves, and stem nodes and internodes (Goodstein et al, 2012). Another gene, Potri.010G102300, encodes a xyloglucan endotransglucosylase that is a member of the Glycoside Hydrolase Family 16 and which is also expected to affect cell wall properties (Nishikubo et al, 2011;Yang et al, 2014).…”

Section: New Phytologistmentioning

confidence: 99%

Multitrait genome‐wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits

et al. 2019

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Summary Genome‐wide association studies (GWAS) have great promise for identifying the loci that contribute to adaptive variation, but the complex genetic architecture of many quantitative traits presents a substantial challenge. We measured 14 morphological and physiological traits and identified single nucleotide polymorphism (SNP)‐phenotype associations in a Populus trichocarpa population distributed from California, USA to British Columbia, Canada. We used whole‐genome resequencing data of 882 trees with more than 6.78 million SNPs, coupled with multitrait association to detect polymorphisms with potentially pleiotropic effects. Candidate genes were validated with functional data. Broad‐sense heritability (H2) ranged from 0.30 to 0.56 for morphological traits and 0.08 to 0.36 for physiological traits. In total, 4 and 20 gene models were detected using the single‐trait and multitrait association methods, respectively. Several of these associations were corroborated by additional lines of evidence, including co‐expression networks, metabolite analyses, and direct confirmation of gene function through RNAi. Multitrait association identified many more significant associations than single‐trait association, potentially revealing pleiotropic effects of individual genes. This approach can be particularly useful for challenging physiological traits such as water‐use efficiency or complex traits such as leaf morphology, for which we were able to identify credible candidate genes by combining multitrait association with gene co‐expression and co‐methylation data.

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“…This specific gene has not been characterized well, but studies characterizing families of genes with GATA zinc finger domains have connected them to circadian clock regulation and plant development in Arabidopsis and rice (Behringer & Schwechheimer, 2015 ; Reyes et al, 2004 ), and a variety of potential regulatory roles in Populus including circadian clock, phytohormone, plant development, and stress response (An et al, 2020 ). Multi‐trait GWA resulted in only one new association for multi‐trait group MT24 (herbivory, salicylic acid, disease, total phenolic glycosides), located in an expansin‐like A2 gene potentially involved in growth and defense (Abuqamar et al, 2013 ; Yang et al, 2014 ).…”

Section: Resultsmentioning

confidence: 99%

Genomic and transcriptomic analyses reveal polygenic architecture for ecologically important traits in aspen (Populus tremuloides Michx.)

Riehl,

Cole,

Morrow

et al. 2023

Ecology and Evolution

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Intraspecific genetic variation in foundation species such as aspen (Populus tremuloides Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single‐locus genome‐wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this “missing heritability” phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a highly polygenic architecture, with most variation explained by loci with small effects (likely below the detection levels of single‐locus GWA methods). Consistent with a polygenic architecture, our single‐locus GWA analyses found only 38 significant SNPs in 22 genes across 15 traits. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This complementary method to traditional GWA discovered 1243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (241 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our work reveals that ecologically important traits governing higher‐order community‐ and ecosystem‐level attributes of a foundation forest tree species have complex underlying genetic structures and will require methods beyond traditional GWA analyses to unravel.

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Identification of Genes Differentially Expressed in Shoot Apical Meristems and in Mature Xylem of Populus tomentosa

Cited by 8 publications

References 65 publications

Nitrogen-driven stem elongation in poplar is linked with wood modification and gene clusters for stress, photosynthesis and cell wall formation

Nitrogen-driven stem elongation in poplar is linked with wood modification and gene clusters for stress, photosynthesis and cell wall formation

Multitrait genome‐wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits

Genomic and transcriptomic analyses reveal polygenic architecture for ecologically important traits in aspen (Populus tremuloides Michx.)

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