dc.contributor.author	Zhou, Lecong	en
dc.contributor.author	Mideros, Santiago X.	en
dc.contributor.author	Bao, Lei	en
dc.contributor.author	Hanlon, Regina	en
dc.contributor.author	Arredondo, Felipe D.	en
dc.contributor.author	Tripathy, Sucheta	en
dc.contributor.author	Krampis, Konstantinos	en
dc.contributor.author	Jerauld, Adam	en
dc.contributor.author	Evans, Clive	en
dc.contributor.author	St Martin, Steven K.	en
dc.contributor.author	Saghai-Maroof, Mohammad A.	en
dc.contributor.author	Hoeschele, Ina	en
dc.contributor.author	Dorrance, Anne E.	en
dc.contributor.author	Tyler, Brett M.	en
dc.contributor.department	Fralin Life Sciences Institute	en
dc.contributor.department	School of Plant and Environmental Sciences	en
dc.date.accessioned	2012-08-24T11:50:54Z	en
dc.date.available	2012-08-24T11:50:54Z	en
dc.date.issued	2009-01-26	en
dc.date.updated	2012-08-24T11:50:54Z	en
dc.description.abstract	Background High throughput methods, such as high density oligonucleotide microarray measurements of mRNA levels, are popular and critical to genome scale analysis and systems biology. However understanding the results of these analyses and in particular understanding the very wide range of levels of transcriptional changes observed is still a significant challenge. Many researchers still use an arbitrary cut off such as two-fold in order to identify changes that may be biologically significant. We have used a very large-scale microarray experiment involving 72 biological replicates to analyze the response of soybean plants to infection by the pathogen Phytophthora sojae and to analyze transcriptional modulation as a result of genotypic variation. Results With the unprecedented level of statistical sensitivity provided by the high degree of replication, we show unambiguously that almost the entire plant genome (97 to 99% of all detectable genes) undergoes transcriptional modulation in response to infection and genetic variation. The majority of the transcriptional differences are less than two-fold in magnitude. We show that low amplitude modulation of gene expression (less than two-fold changes) is highly statistically significant and consistent across biological replicates, even for modulations of less than 20%. Our results are consistent through two different normalization methods and two different statistical analysis procedures. Conclusion Our findings demonstrate that the entire plant genome undergoes transcriptional modulation in response to infection and genetic variation. The pervasive low-magnitude remodeling of the transcriptome may be an integral component of physiological adaptation in soybean, and in all eukaryotes.	en
dc.description.version	Published version	en
dc.format.mimetype	application/pdf	en
dc.identifier.citation	BMC Genomics. 2009 Jan 26;10(1):49	en
dc.identifier.doi	https://doi.org/10.1186/1471-2164-10-49	en
dc.identifier.uri	http://hdl.handle.net/10919/18878	en
dc.language.iso	en	en
dc.rights	Creative Commons Attribution 4.0 International	en
dc.rights.holder	Lecong Zhou et al.; licensee BioMed Central Ltd.	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	en
dc.title	Infection and genotype remodel the entire soybean transcriptome	en
dc.title.serial	BMC Genomics	en
dc.type	Article - Refereed	en
dc.type.dcmitype	Text	en

Infection and genotype remodel the entire soybean transcriptome

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