Infection and genotype remodel the entire soybean transcriptome

Simple item page
dc.contributor.authorZhou, Lecongen
dc.contributor.authorMideros, Santiago X.en
dc.contributor.authorBao, Leien
dc.contributor.authorHanlon, Reginaen
dc.contributor.authorArredondo, Felipe D.en
dc.contributor.authorTripathy, Suchetaen
dc.contributor.authorKrampis, Konstantinosen
dc.contributor.authorJerauld, Adamen
dc.contributor.authorEvans, Cliveen
dc.contributor.authorSt Martin, Steven K.en
dc.contributor.authorSaghai-Maroof, Mohammad A.en
dc.contributor.authorHoeschele, Inaen
dc.contributor.authorDorrance, Anne E.en
dc.contributor.authorTyler, Brett M.en
dc.contributor.departmentFralin Life Sciences Instituteen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2012-08-24T11:50:54Zen
dc.date.available2012-08-24T11:50:54Zen
dc.date.issued2009-01-26en
dc.date.updated2012-08-24T11:50:54Zen
dc.description.abstractBackground 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.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBMC Genomics. 2009 Jan 26;10(1):49en
dc.identifier.doihttps://doi.org/10.1186/1471-2164-10-49en
dc.identifier.urihttp://hdl.handle.net/10919/18878en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderLecong Zhou et al.; licensee BioMed Central Ltd.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleInfection and genotype remodel the entire soybean transcriptomeen
dc.title.serialBMC Genomicsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

Files

Original bundle
Now showing 1 - 5 of 10
Thumbnail Image
Name:
1471-2164-10-49.pdf
Size:
661.29 KB
Format:
Adobe Portable Document Format
Download
Thumbnail Image
Name:
1471-2164-10-49-S1.PDF
Size:
207.4 KB
Format:
Adobe Portable Document Format
Download
Thumbnail Image
Name:
1471-2164-10-49-S2.PDF
Size:
63.58 KB
Format:
Adobe Portable Document Format
Download
Thumbnail Image
Name:
1471-2164-10-49-S3.PDF
Size:
57.87 KB
Format:
Adobe Portable Document Format
Download
Thumbnail Image
Name:
1471-2164-10-49-S4.PDF
Size:
87.74 KB
Format:
Adobe Portable Document Format
Download
License bundle
Now showing 1 - 1 of 1
Name:
license.txt
Size:
1.5 KB
Format:
Item-specific license agreed upon to submission
Description:
Download

Collections

Journal Articles, BioMed Central and SpringerOpen
Scholarly Works, Fralin Life Sciences Institute
Scholarly Works, School of Plant and Environmental Sciences