Analysis Of Transcriptomic Changes In Oil Palm (Elaeis Guineensis Jacq.) Root Upon Inoculation With Bacillus Sphaericus Upmb10 Using Cdna Microarray

Bacillus sphaericus UPMB10 is a plant growth promoting bacteria (PGPB) which enhances plant growth by acting as bioenhancer and biofertilizer. An oil palm cDNA microarray containing 2224 cDNA probes from root (partially derived from cDNA clones generated in this study), 828 from vegetative meristem...

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Main Author:	Lim, Kok Ang
Format:	Thesis
Language:	English English
Published:	2008
Subjects:	Oil palm - Bacillus spaericus - Analysis
Online Access:	http://psasir.upm.edu.my/id/eprint/4930/1/FBSB_2008_4.pdf
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spelling	my-upm-ir.49302013-05-27T07:19:12Z Analysis Of Transcriptomic Changes In Oil Palm (Elaeis Guineensis Jacq.) Root Upon Inoculation With Bacillus Sphaericus Upmb10 Using Cdna Microarray 2008 Lim, Kok Ang Bacillus sphaericus UPMB10 is a plant growth promoting bacteria (PGPB) which enhances plant growth by acting as bioenhancer and biofertilizer. An oil palm cDNA microarray containing 2224 cDNA probes from root (partially derived from cDNA clones generated in this study), 828 from vegetative meristem and 696 from zygotic embryo was generated to investigate the transcriptomic changes in two-month-old in vitro oil palm (Elaeis guineensis Jacq.) (Deli x Yangambi) roots after inoculation with B. sphaericus UPMB10 for 120 h. This study was initiated with the generation of 1824 expressed sequenced tags (ESTs) from the roots of oil palm. A total of 1173 tentative unique genes (TUGs) were assembled from 1566 ESTs with readable sequences. However, only 984 TUGs showed significant matches (E-value less than 10-5) to the non-redundant protein database in the GenBank and they were further divided into 13 groups based on their putative functions. Subsequent microarray result showed that 151 and 125 transcripts were significantly up- and down regulated, respectively in the roots of oil palm inoculated with B. sphaericus UPMB10. Although transcripts involved in protein synthesis were increased and the expression level of auxin responsive genes were altered in B. sphaericus UPMB10-inoculated oil palms, there was no conclusive result to support the presence of auxin secreted by B. sphaericus UPMB10 in the medium. Despite the capability of B. sphaericus UPMB10 to fix atmospheric nitrogen, 120 h might not be sufficient for it to establish efficient nitrogen fixation to relieve possible N deficiency in oil palms. The plant-microbe interaction might also have alerted the defense system that led to the up-regulation of transcripts related to synthesis of hydrogen peroxide in oil palm. Verification of microarray result by real time RT-PCR showed that nine out of 11 candidate genes (81.8%) were consistent in their expression patterns. In conclusion, this study has provided a brief understanding of the transcriptomic changes in the oil palm roots inoculated with B. sphaericus UPMB10. Oil palm - Bacillus spaericus - Analysis 2008 Thesis http://psasir.upm.edu.my/id/eprint/4930/ http://psasir.upm.edu.my/id/eprint/4930/1/FBSB_2008_4.pdf application/pdf en public masters Universiti Putra Malaysia Oil palm - Bacillus spaericus - Analysis Faculty of Biotechnology and Biomolecular sciences English
institution	Universiti Putra Malaysia
collection	PSAS Institutional Repository
language	English English
topic	Oil palm - Bacillus spaericus - Analysis
spellingShingle	Oil palm - Bacillus spaericus - Analysis Lim, Kok Ang Analysis Of Transcriptomic Changes In Oil Palm (Elaeis Guineensis Jacq.) Root Upon Inoculation With Bacillus Sphaericus Upmb10 Using Cdna Microarray
description	Bacillus sphaericus UPMB10 is a plant growth promoting bacteria (PGPB) which enhances plant growth by acting as bioenhancer and biofertilizer. An oil palm cDNA microarray containing 2224 cDNA probes from root (partially derived from cDNA clones generated in this study), 828 from vegetative meristem and 696 from zygotic embryo was generated to investigate the transcriptomic changes in two-month-old in vitro oil palm (Elaeis guineensis Jacq.) (Deli x Yangambi) roots after inoculation with B. sphaericus UPMB10 for 120 h. This study was initiated with the generation of 1824 expressed sequenced tags (ESTs) from the roots of oil palm. A total of 1173 tentative unique genes (TUGs) were assembled from 1566 ESTs with readable sequences. However, only 984 TUGs showed significant matches (E-value less than 10-5) to the non-redundant protein database in the GenBank and they were further divided into 13 groups based on their putative functions. Subsequent microarray result showed that 151 and 125 transcripts were significantly up- and down regulated, respectively in the roots of oil palm inoculated with B. sphaericus UPMB10. Although transcripts involved in protein synthesis were increased and the expression level of auxin responsive genes were altered in B. sphaericus UPMB10-inoculated oil palms, there was no conclusive result to support the presence of auxin secreted by B. sphaericus UPMB10 in the medium. Despite the capability of B. sphaericus UPMB10 to fix atmospheric nitrogen, 120 h might not be sufficient for it to establish efficient nitrogen fixation to relieve possible N deficiency in oil palms. The plant-microbe interaction might also have alerted the defense system that led to the up-regulation of transcripts related to synthesis of hydrogen peroxide in oil palm. Verification of microarray result by real time RT-PCR showed that nine out of 11 candidate genes (81.8%) were consistent in their expression patterns. In conclusion, this study has provided a brief understanding of the transcriptomic changes in the oil palm roots inoculated with B. sphaericus UPMB10.
format	Thesis
qualification_level	Master's degree
author	Lim, Kok Ang
author_facet	Lim, Kok Ang
author_sort	Lim, Kok Ang
title	Analysis Of Transcriptomic Changes In Oil Palm (Elaeis Guineensis Jacq.) Root Upon Inoculation With Bacillus Sphaericus Upmb10 Using Cdna Microarray
title_short	Analysis Of Transcriptomic Changes In Oil Palm (Elaeis Guineensis Jacq.) Root Upon Inoculation With Bacillus Sphaericus Upmb10 Using Cdna Microarray
title_full	Analysis Of Transcriptomic Changes In Oil Palm (Elaeis Guineensis Jacq.) Root Upon Inoculation With Bacillus Sphaericus Upmb10 Using Cdna Microarray
title_fullStr	Analysis Of Transcriptomic Changes In Oil Palm (Elaeis Guineensis Jacq.) Root Upon Inoculation With Bacillus Sphaericus Upmb10 Using Cdna Microarray
title_full_unstemmed	Analysis Of Transcriptomic Changes In Oil Palm (Elaeis Guineensis Jacq.) Root Upon Inoculation With Bacillus Sphaericus Upmb10 Using Cdna Microarray
title_sort	analysis of transcriptomic changes in oil palm (elaeis guineensis jacq.) root upon inoculation with bacillus sphaericus upmb10 using cdna microarray
granting_institution	Universiti Putra Malaysia
granting_department	Faculty of Biotechnology and Biomolecular sciences
publishDate	2008
url	http://psasir.upm.edu.my/id/eprint/4930/1/FBSB_2008_4.pdf
_version_	1747810312605663232

Analysis Of Transcriptomic Changes In Oil Palm (Elaeis Guineensis Jacq.) Root Upon Inoculation With Bacillus Sphaericus Upmb10 Using Cdna Microarray

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