Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression in whole-roots of a Populus trichocarpa and Populus deltoides pseudo-backcross population

ABSTRACT: A microarray analysis of whole-genome gene expression in roots was carried out in a (Populus trichocarpa X Populus deltoides) X Populus deltoides pseudo-backcross pedigree. Genetic variation in gene expression was quantified for 55,793 predicted gene models based on a single probe per gene. Resultant data contributed to the analysis of the genetic architecture of gene expression in roots of Populus. Data include one biological replicate of 163 individuals segregating from a pseudo-backcross pedigree of (Populus trichocarpa X Populus deltoides) X Populus deltoides analyzed for gene expression (GE) in roots using one probe per gene for 55793 independent gene models (probes E_POPLARSxxxxxPxxxxx) and single feature sequence polymorphism (SFP) using one probe per gene for 12084 independent gene models (probes G_POPLARSxxxxxPxxxxx). GE and SFP probes were selected from 6-7 probes per gene previously tested in a pilot study of the two parent trees of the cross (Populus deltoides X Populus trichocarpa)

ORGANISM(S): Populus trichocarpa x Populus deltoides

SUBMITTER: Matias Kirst

PROVIDER: E-GEOD-20118 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus.

Drost Derek R DR Benedict Catherine I CI Berg Arthur A Novaes Evandro E Novaes Carolina R D B CR Yu Qibin Q Dervinis Christopher C Maia Jessica M JM Yap John J Miles Brianna B Kirst Matias M

Proceedings of the National Academy of Sciences of the United States of America 20100419 18

A fundamental goal of systems biology is to identify genetic elements that contribute to complex phenotypes and to understand how they interact in networks predictive of system response to genetic variation. Few studies in plants have developed such networks, and none have examined their conservation among functionally specialized organs. Here we used genetical genomics in an interspecific hybrid population of the model hardwood plant Populus to uncover transcriptional networks in xylem, leaves, ...[more]

PMID: 20404162

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Project description:Adventitious roots (AR) develop from tissues other than the primary root, in a developmental process physiologically regulated by phytohormones. Adventitious roots provide structural support and contribute to water and nutrient absorption, and are critical for commercial vegetative propagation of several crops. Here we quantified the number of AR, root architectural traits and root biomass in cuttings from a pseudo-backcross population of Populus deltoides and Populus trichocarpa. Quantitative trait loci (QTL) mapping and whole-transcriptome analysis of individuals carrying alternative QTL alleles for AR number wereas used to identify putative regulatorsregions in the genome that regulateof AR development in the genome., and putative candidate genesregulators. Gene expression in three individuals carrying alleles that originated from the P. trichocarpa grandparent (UF352, UF498 and UF926, referred hereafter as the PtQTL genotype category) was contrasted with those with alleles from the P. deltoides grandparent (UF717, UF209 and UF912, or the PdQTL genotype category). 25 cuttings of each of the six selected genotypes (3 PtQTL and 3 PdQTL) were grown in hydroponic solution, and basal (1 cm) cutting sections from four biological replicates of each genotype were collected at each of five time points (0, 24, 48, 96 and 192 hours after cuttings were harvested). Total RNA was extracted from the bottom 1 cm stem section collected from each sample. The sample included xylem, phloem and bark. RNA was purified using RNeasy Mini Kit columns (Qiagen), and DNase treated with RNase-Free DNase set (Qiagen). RNA quality was evaluated in 1% w/v agarose gels. RNA was amplified and cRNA synthesized and labeled using Two Dyes Agilent Low Input Quick Amp Labeling Kit (Agilent). The microarray platform used consisted of single 60-mer probes designed for each of 43,803 predicted gene models from the sequenced genome of P. trichocarpa version 2. These probes were previously selected for being suitable for analysis of gene expression in this mapping population. A total of 60 microarrays were used in the transcriptome analysis and each microarray was hybridized with 2 samples labeled with Cy3 or Cy5. Gene expression of each of six genotypes was analyzed in five time points (0, 24, 48, 96 and 192 hours), with four biological replicates per genotype and time point, following a âbird cageâ design . The design was selected to favor contrasting gene expression of samples from different QTL categories (PtQTL and PdQTL) at each time point, as well as samples from the same genotype, collected from different time points. Median values of signal intensities were quantile normalized and log2 transformed. Normalized signals were analyzed in SAS 9.2 (SAS Institute Inc. 9.2Â® 2004, Cary, NC, USA) using a mixed-model ANOVA with genotype and genotype Ã time interactions as fixed effects, and microarray as random effect. Differences in expression between the group of genotypes from the PtQTL and PdQTL categories were estimated at each time point, and the significance was determined based on a false discovery rate (FDR) of 5%

Dataset Information

Gene expression in whole-roots of a Populus trichocarpa and Populus deltoides pseudo-backcross population

Publications

Diversification in the genetic architecture of gene expression and transcriptional networks in organ differentiation of Populus.

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