Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression and intragenic polymorphism in a Populus trichocarpa and Populus deltoides pseudo-backcross pedigree

ABSTRACT: A microarray analysis of whole-genome gene expression and single feature polymorphism 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. Concurrently, sequence-level polymorphism was analyzed based on dedicated probes identified in a pilot study comprised of the two parent genotypes (GPL7169). Resultant data contributed to a high density genetic map and to analysis of the genetic architecture of gene expression in Populus. Keywords: Genetic analysis of gene expression and polymorphism, eQTL Data include one biological replicate of 178 segregating pseudobackcross progeny analyzed for gene expression (GE) 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-12623 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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%

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Gene expression and intragenic polymorphism in a Populus trichocarpa and Populus deltoides pseudo-backcross pedigree

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