Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of maize to evaluate target preparation methods for single-feature polymorphism detection in large complex plant genomes

ABSTRACT: We tested four gene enrichment and complexity reduction target preparation methods for scoring SFPs on the Affymetrix GeneChip 18k Maize Genome Array (âMaize GeneChipâ). Methylation filtration (MF), Cot filtration (CF), mRNA-derived cRNA, and amplified fragment length polymorphism (AFLP) methods were applied to three diverse maize inbred lines (B73, Mo17, and CML69) with three replications per line (36 Maize GeneChips). Due to large amounts of repetitive, mobile DNA, the maize genome requires a target preparation method that offers both a high level of gene enrichment and accurate scoring of SFPs. The objectives of this research are (i) to determine which target preparation method (CF, MF, mRNA, or AFLP) optimally enriches for gene sequences complementary to probe sequences on the Affymetrix GeneChip Maize Genome Array and (ii) to estimate SFP detection power for each target method. The AFLP technology is covered by patents, and patent applications owned by Keygene N.V. AFLP is a registered trademark of Keygene N.V. GeneChip. This work was supported in part by U.S. National Science Foundation grant DBI-0321467 and USDA-ARS. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Michael Gore. The equivalent experiment is ZM10 at PLEXdb.] Experiment Overall Design: protocol: mRNA - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: mRNA - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: mRNA - genotype: CML69 maize inbred(3-replications) Experiment Overall Design: protocol: Cot filtration (CF) - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: Cot filtration (CF) - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: Cot filtration (CF) - genotype: CML69 maize inbred(3-replications) Experiment Overall Design: protocol: Methylation filtration (MF) - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: Methylation filtration (MF) - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: Methylation filtration (MF) - genotype: CML69 maize inbred(3-replications) Experiment Overall Design: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred(3-replications)

ORGANISM(S): Zea mays

SUBMITTER: PLEXdb Curator Sudhansu Dash

PROVIDER: E-GEOD-12770 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Heterosis (hybrid vigor) refers to the superior performance of hybrid progeny relative to their parents. Although widely exploited in agriculture, the mechanisms responsible for heterosis are not well understood. As a monoecious organism, a given maize plant can be used as both male and female parents of crosses. Regardless of the cross direction, the maize inbred lines B73 and Mo17 produce hybrids that substantially out-perform their parents. These reciprocal hybrids differ phenotypically from each other despite having identical nuclear genomes. Consistent with these phenotypic observations, 30-50% of genes were differentially expressed between these reciprocal hybrids. An eQTL experiment conducted to better understand the regulation of gene expression in inbred and hybrid lines detected ~4,000 eQTL associations. The majority of these eQTL act in trans to regulate expression of genes on other chromosomes. Surprisingly, many of the trans-eQTL, when heterozygous, differentially regulated transcript accumulation in a manner consistent with gene expression in the hybrid being regulated exclusively by the paternally transmitted allele. The design of the eQTL experiment controlled for cytoplasmic and maternal effects, suggesting that widespread paternal genomic imprinting contributes to the regulation of gene expression in maize hybrids. Keywords: eQTL, parent-of-origin GPL4521 - SAM1.2 (Reciprocal Hybrid Comparison): Six replications of B73xMo17 and Mo17xB73 were grown in growth chambers to tightly control environmental variation. Seeds from each genotype were taken from a single source (ear) for all six replications. Within each replication, genotypes were randomly assigned growth locations. Six healthy seedlings for each genotype and replication were harvested at two weeks of age. For each replication, B73xMo17 and Mo17xB73 were hybridized to the SAM1.2 microarray (GPL4521) using a randomized, alternate dye assignment. GPL3333 - SAM1.1 and GPL3538 - SAM3.0 (eQTL Experiment): Four biological replications of the RIL, B73xRIL, and Mo17xRIL cross-types were planted in growth chambers using seed from a single source for each genotype. Each RIL and its crosses onto B73 and Mo17 were planted using a split-plot design with RIL group (RIL and its cross onto B73 and Mo17) as the whole-plot treatment factor and cross-type (RIL, B73xRIL, and Mo17xRIL) as the split-plot treatment factor. The whole-plot portion of the experiment was designed as a randomized complete block design with four replications carried out on four separate occasions in the same environment. For the split-plot portion of the design, twelve seedlings of each RIL and its crosses were randomized within two adjacent flats in a growth chamber (six healthy seedlings per genotype were randomly chosen and pooled at harvest). For each replication, RIL, B73xRIL, and Mo17xRIL cross-types were hybridized to custom cDNA microarrays using a loop design such that each loop included all pairwise comparisons between the RIL and its crosses with B73 and Mo17. Four biological replications were hybridized to the SAM1.1 (GPL3333) array and two of the four biological replications were hybridized to SAM3.0 (GPL3538). RNA samples were alternately labeled to provide dye balance within each loop and replication. GPL8734 - Gene Expression between two maize reciprocal hybrids Heterosis refers to the enhanced agronomic performance of a hybrid relative to its (usually) inbred parents. We have previously documented widespread differences in gene expression in the B73xMo17 hybrid relative to its inbred parents B73 and Mo17 (Swanson, et al., 2006, PNAS). The reciprocal B73xMo17 and Mo17xB73 hybrids are both highly heterotic, but despite having identical nuclear genomes exhibit statistically significant differences in multiple traits. RNA-seq experiment was conducted to compare the gene expression globally between the two reciprocal hybrids. 1 samples from B73XMo17 and Mo17XB73 RNAs were extracted from a single replication of 14-day-old B73xMo17 and Mo17xB73 seedlings. RNAs were purified using DNaseI treatment followed by cleanup with the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) as per manufacturer instructions. Sequencing library construction was completed using the Illumina mRNA-Seq sample preparation kit. Processed data file 'ZmB73_4a.53_filtered_genes.fasta' and its README file are linked below as supplementary files. The fasta file contains the gene model ID and corresponding sequence generated from maize genome project. This fasta file was used for the following samples: GSM418173, GSM418174, GSM420173, GSM420174, GSM422828, GSM422829.

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Transcription profiling of maize to evaluate target preparation methods for single-feature polymorphism detection in large complex plant genomes

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