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Open Access Research article

Homoeolog-specific transcriptional bias in allopolyploid wheat

Alina R Akhunova1, Rustam T Matniyazov2, Hanquan Liang1 and Eduard D Akhunov2*

Author Affiliations

1 Integrated Genomics Facility, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS 66506, USA

2 Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS 66506, USA

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BMC Genomics 2010, 11:505  doi:10.1186/1471-2164-11-505

Published: 17 September 2010

Additional files

Additional file 1:

List of 40,281 parent-specific oligonucleotide features. File contains the list of 40,281 Affymetrix oligonucleotide features differentially hybridizing with AT and TC parental transcripts. The linear model described in Methods was fit to PM probe intensity data. Residuals containing the probe by genotype effect were tested for difference between genotypes by calculating the d-statistics [45] using the Significance Analysis of Microarrays (SAM) procedure implemented in the R package siggenes. The threshold Δ = 0.2 was selected to identify significantly different features at 0.1 false discovery rate.

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Additional file 2:

Validation of parent-specific features by comparing with 454 sequence data. Validation of parent-specific features by comparing with 454 sequence data. The table provides the list of PSFs showing significant blast hits with sequence reads obtained for cDNA libraries of Ae. tauschii, T. aestivum cv. Chinese Spring and T. aestivum cv. Jagger; PM - Affymetrix probe perfectly matches the 454 sequence read; MM - Affymetrix probe have a mismatch with the 454 sequence read; d-value is used in SAM for identification of PSFs.

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Additional file 3:

Distribution of PSFs across the wheat genome. List of Affymetrix probesets with parent-specific features (PSF), their locations on the deletion bin map and a list of deletion bin mapped ESTs showing similarity to transcripts interrogated by Affymetrix probesets. The map locations were calculated by averaging the deletion bin midpoints of homoeologous chromosomes and assigning them to one of the five intervals (0-0.2, 0.2-0.4, 0.4-0.6, 0.6-0.8, 0.8-1.0).

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Additional file 4:

Parent-specific gene expression in allopolyploid wheat. The method of contrasts was used to compare Ept intensity ratios between allopolyploid wheat and its parents. Two possible ratios of parental gene expression in the synthetic polyploid were tested assuming 1:1 (AT + TC)/2) and 1:2 (1AT+2TC)/3) in silico ratio of AT:TC gene expression in the SN transcriptome. The FDR was maintained at 0.05.

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Additional file 5:

Validation of Affymetrix microarray hybridization results by quantitative RT-PCR. Expression levels were converted to theoretical value R0 using the formula R0 = R(Ct) (1 + E)(-Ct), where R0 is the starting fluorescence, R(Ct) is the fluorescence at the threshold cycle Ct and E is the amplification efficiency. The R0 values were normalized to R0 of actin gene followed by log-transformation. The expression levels in SN and 1:1 mixture of AT and TC RNA were compared using the t-test.

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