Isolation of Expressed Sequence Tags (Ests) from an Oil Palm (Elaeis Guineensis Jacq.) Male and Female Floral cDNA Library

The bottleneck of the current knowledge in understanding the oil palm flower development in term of abnormalities and sex ratio is the low number of known flower genes available. The shortage of these genes is a serious constraint in studying the mechanisms regulating gene expression in flowers....

Full description

Saved in:

Bibliographic Details
Main Author:	Choi, Mei Chooi
Format:	Thesis
Language:	English English
Published:	2003
Subjects:	Molecular cloning. Oil palm - Flowering.
Online Access:	http://psasir.upm.edu.my/id/eprint/8506/1/FSMB_2003_11_A%20D.pdf
Tags:	Add Tag No Tags, Be the first to tag this record!

id	my-upm-ir.8506
record_format	uketd_dc
spelling	my-upm-ir.85062022-01-26T00:25:25Z Isolation of Expressed Sequence Tags (Ests) from an Oil Palm (Elaeis Guineensis Jacq.) Male and Female Floral cDNA Library 2003 Choi, Mei Chooi The bottleneck of the current knowledge in understanding the oil palm flower development in term of abnormalities and sex ratio is the low number of known flower genes available. The shortage of these genes is a serious constraint in studying the mechanisms regulating gene expression in flowers. Therefore, it is vital to obtain as much information as possible on the complexity and type of genes expressed in the oil palm floral organ. To dissect the molecular mechanisms underlying these development processes, a vast amount of genetic resources are required as markers that would enable a complete picture of the complex floral development processes in oil palm to be determined. In this study, expressed sequence tags (ESTs) were used as a genetic resource to facilitate the identification of new gene markers on a large-scale basis and also to provide information on gene expression patterns. To date, about 1,600 EST clones were isolated and sequenced using cold plaque screening method. Among the 1,600 ESTs generated from eDNA libraries of oil palm flowers, 266 independent clones with insert size of more than 500bp were subjected to reverse Northern analysis and this has resulted in classification into 5 major subpopulations (opff and opmf) based on the level and specificity of expression. Subpopulation A consisted of clones that were highly expressed in all the tissues (41%) whereas sUbpopulation B contained clones that were female predominant and expressed at medium levels (23.3%). Subpopulation C and D consisted of clones that were expressed at low levels predominantly in the flower (17.7%) and young leaf (6%), respectively. The last group, subpopulation E contained all the clones that showed no hybridization signals to all the tissues (12%). Further characterization of selected opff and opmJ clones by sequence analysis has revealed 3 maj or classes of ESTs. Class A consisted of sequences with similarity to known proteins in the database (56%) while class B showed sequences similar to proteins with unknown function (30%) and class C showed no sequence similarity to proteins in the database (14%). Two clones were selected among the cDNA clones identified that have sequence homology to known sequences in database to be further characterized. They were putatively known as Squamosa Promoter Binding Protein (OPSBP) and GAstimulated transcript 1 (OPGAST), respectively. OPSBP was found to be constitutively expressed throughout flower developement and was localized to bracts, rachis and carpels. On the other hand, OPGAST was found ubiquitously expressed in all flower tissues but the transcript levels were higher in the shoot apex. This study suggested that OPSBP appears to be up-regulated during early flower development.Further characterization of these "clones by Southern genomic hybridization showed that OPSBP and OPGAST exist as a single copy gene and mUlti-copy genes, respectively, in the oil palm genome. In summary, the results indicate that the EST approach was efficient in identifying and isolating oil palm floral genes that range from those that are expressed at certain developmental stages to those that have undetectable expression throughout flower development. This achievement also demonstrated that genes isolated by cold plaque screening are not restricted to genes that are tissue specific or developmental stage specific but the technique also enables the isolation of genes that are generally expressed at low levels. Molecular cloning. Oil palm - Flowering. Plants, Sex in. 2003 Thesis http://psasir.upm.edu.my/id/eprint/8506/ http://psasir.upm.edu.my/id/eprint/8506/1/FSMB_2003_11_A%20D.pdf text en public masters Universiti Putra Malaysia Molecular cloning. Oil palm - Flowering. Plants, Sex in. Food Science and Technology Harikrishna, K. English
institution	Universiti Putra Malaysia
collection	PSAS Institutional Repository
language	English English
advisor	Harikrishna, K.
topic	Molecular cloning. Oil palm - Flowering. Molecular cloning.
spellingShingle	Molecular cloning. Oil palm - Flowering. Molecular cloning. Choi, Mei Chooi Isolation of Expressed Sequence Tags (Ests) from an Oil Palm (Elaeis Guineensis Jacq.) Male and Female Floral cDNA Library
description	The bottleneck of the current knowledge in understanding the oil palm flower development in term of abnormalities and sex ratio is the low number of known flower genes available. The shortage of these genes is a serious constraint in studying the mechanisms regulating gene expression in flowers. Therefore, it is vital to obtain as much information as possible on the complexity and type of genes expressed in the oil palm floral organ. To dissect the molecular mechanisms underlying these development processes, a vast amount of genetic resources are required as markers that would enable a complete picture of the complex floral development processes in oil palm to be determined. In this study, expressed sequence tags (ESTs) were used as a genetic resource to facilitate the identification of new gene markers on a large-scale basis and also to provide information on gene expression patterns. To date, about 1,600 EST clones were isolated and sequenced using cold plaque screening method. Among the 1,600 ESTs generated from eDNA libraries of oil palm flowers, 266 independent clones with insert size of more than 500bp were subjected to reverse Northern analysis and this has resulted in classification into 5 major subpopulations (opff and opmf) based on the level and specificity of expression. Subpopulation A consisted of clones that were highly expressed in all the tissues (41%) whereas sUbpopulation B contained clones that were female predominant and expressed at medium levels (23.3%). Subpopulation C and D consisted of clones that were expressed at low levels predominantly in the flower (17.7%) and young leaf (6%), respectively. The last group, subpopulation E contained all the clones that showed no hybridization signals to all the tissues (12%). Further characterization of selected opff and opmJ clones by sequence analysis has revealed 3 maj or classes of ESTs. Class A consisted of sequences with similarity to known proteins in the database (56%) while class B showed sequences similar to proteins with unknown function (30%) and class C showed no sequence similarity to proteins in the database (14%). Two clones were selected among the cDNA clones identified that have sequence homology to known sequences in database to be further characterized. They were putatively known as Squamosa Promoter Binding Protein (OPSBP) and GAstimulated transcript 1 (OPGAST), respectively. OPSBP was found to be constitutively expressed throughout flower developement and was localized to bracts, rachis and carpels. On the other hand, OPGAST was found ubiquitously expressed in all flower tissues but the transcript levels were higher in the shoot apex. This study suggested that OPSBP appears to be up-regulated during early flower development.Further characterization of these "clones by Southern genomic hybridization showed that OPSBP and OPGAST exist as a single copy gene and mUlti-copy genes, respectively, in the oil palm genome. In summary, the results indicate that the EST approach was efficient in identifying and isolating oil palm floral genes that range from those that are expressed at certain developmental stages to those that have undetectable expression throughout flower development. This achievement also demonstrated that genes isolated by cold plaque screening are not restricted to genes that are tissue specific or developmental stage specific but the technique also enables the isolation of genes that are generally expressed at low levels.
format	Thesis
qualification_level	Master's degree
author	Choi, Mei Chooi
author_facet	Choi, Mei Chooi
author_sort	Choi, Mei Chooi
title	Isolation of Expressed Sequence Tags (Ests) from an Oil Palm (Elaeis Guineensis Jacq.) Male and Female Floral cDNA Library
title_short	Isolation of Expressed Sequence Tags (Ests) from an Oil Palm (Elaeis Guineensis Jacq.) Male and Female Floral cDNA Library
title_full	Isolation of Expressed Sequence Tags (Ests) from an Oil Palm (Elaeis Guineensis Jacq.) Male and Female Floral cDNA Library
title_fullStr	Isolation of Expressed Sequence Tags (Ests) from an Oil Palm (Elaeis Guineensis Jacq.) Male and Female Floral cDNA Library
title_full_unstemmed	Isolation of Expressed Sequence Tags (Ests) from an Oil Palm (Elaeis Guineensis Jacq.) Male and Female Floral cDNA Library
title_sort	isolation of expressed sequence tags (ests) from an oil palm (elaeis guineensis jacq.) male and female floral cdna library
granting_institution	Universiti Putra Malaysia
granting_department	Food Science and Technology
publishDate	2003
url	http://psasir.upm.edu.my/id/eprint/8506/1/FSMB_2003_11_A%20D.pdf
_version_	1747810821012979712

Isolation of Expressed Sequence Tags (Ests) from an Oil Palm (Elaeis Guineensis Jacq.) Male and Female Floral cDNA Library

Similar Items