Identification of differentially expressed genes related to height increment in oil palm (Elaeis guineensis Jacq.)

The effort towards developing dwarf palm population with novel traits has great importance to the oil palm industry, mainly due to the high cost of harvesting fruits from tall palms and crop improvements. Reducing palm height not only brings positive effect on harvesting cost, it will significantly...

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Main Author:	Mohamed Azni, Intan Nur Aini
Format:	Thesis
Language:	English
Published:	2014
Subjects:	Oil palm Oil palm - Genetic engineering
Online Access:	http://psasir.upm.edu.my/id/eprint/51998/1/FBSB%202014%2018RR.pdf
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spelling	my-upm-ir.519982017-05-16T08:53:59Z Identification of differentially expressed genes related to height increment in oil palm (Elaeis guineensis Jacq.) 2014-06 Mohamed Azni, Intan Nur Aini The effort towards developing dwarf palm population with novel traits has great importance to the oil palm industry, mainly due to the high cost of harvesting fruits from tall palms and crop improvements. Reducing palm height not only brings positive effect on harvesting cost, it will significantly extent the economic cropping cycle. Through the advancement in molecular technologies, identification of potential candidate genes that regulate in dwarfism can be achieved. In this study, six subtracted cDNA libraries were constructed by the Suppression Subtractive Hybridization (SSH) method using spear leaf tissue samples from MPOB Planting Series 1 (PS1) and FELDA P.P.P. Tun Razak (BACKCROSS, AG1) breeding lines. A total of 973 sequences (forward and reverse) were generated from six subtracted libraries. The similarity searches using BLASTX revealed that six clones were identified to be involved in dwarfism based on its putative functions. The gene transcripts encoding for: brassinosteroid biosynthesis-like protein (DWF1),BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor,putative (BRI1), late elongated hypocotyl protein (LHY), gibberellin receptor GID1,putative (GID1), sterol 24-methyltransferase 1 (SMT1) and E3 ubiquitin-proteinigase MARCH6 (E3Ub). These candidate dwarfing genes were reported to be involved in various stages of brassinosteroids (BRs) and gibberellins (GAs) biosynthesis and signaling pathways for plants growth and development. BRs areplant steroids that present in vegetative tissues such as shoot, leaves and stems; pollen grains, anthers and seeds. BRs control diverse physiological processes including cell division and elongation, embryogenesis, fertility, delayed senescence and vascular differentiation. GAs stimulate critical stages in plant growth and development such as plant height, cell wall modification, seed germination,flowering and leaf expansion. Gene validation analysis via qRT-PCR has revealedthe expression levels of each potential candidate dwarfing genes in all tested samples, normalized by two most stable reference genes, manganese superoxide dismutase-like protein (PD569) and hypothetical protein (EA1332). Based on the analysis, higher expression level of BRI1, LHY and SMT1 genes were observed in dwarf palms compared to standard palms with normalized fold-difference of 2.3285,1.5620 and 4.9044, respectively. However, lower expression of DWF1, GID1 and E3Ub were observed in dwarf palms compared to standard palms with normalized fold-difference of 0.8378, 0.7003 and 0.9631, respectively. Statistical analysis using Paired Samples T-Test showed that the expression levels of DWF1, BRI1, LHY,GID1 and E3Ub were not significantly expressed in dwarf palms. However, the SMT1 expression level was highly significant in dwarf palm, AG1-22. The expression profile of SMT1 in all tested samples was carried out using AG1-22 as the control baseline (1.0000 expression levels), where the GOI expression level below 1.0000 indicates as down-regulated; and above 1.0000 is up-regulated. The result showed that the dwarf palm, AG1-12 was up-regulated with 1.3161 expression value. Therefore, SMT1 gene may be potentially useful molecular marker for the screening of dwarf palm planting materials. Oil palm Oil palm - Genetic engineering 2014-06 Thesis http://psasir.upm.edu.my/id/eprint/51998/ http://psasir.upm.edu.my/id/eprint/51998/1/FBSB%202014%2018RR.pdf application/pdf en public masters Universiti Putra Malaysia Oil palm Oil palm - Genetic engineering
institution	Universiti Putra Malaysia
collection	PSAS Institutional Repository
language	English
topic	Oil palm Oil palm - Genetic engineering
spellingShingle	Oil palm Oil palm - Genetic engineering Mohamed Azni, Intan Nur Aini Identification of differentially expressed genes related to height increment in oil palm (Elaeis guineensis Jacq.)
description	The effort towards developing dwarf palm population with novel traits has great importance to the oil palm industry, mainly due to the high cost of harvesting fruits from tall palms and crop improvements. Reducing palm height not only brings positive effect on harvesting cost, it will significantly extent the economic cropping cycle. Through the advancement in molecular technologies, identification of potential candidate genes that regulate in dwarfism can be achieved. In this study, six subtracted cDNA libraries were constructed by the Suppression Subtractive Hybridization (SSH) method using spear leaf tissue samples from MPOB Planting Series 1 (PS1) and FELDA P.P.P. Tun Razak (BACKCROSS, AG1) breeding lines. A total of 973 sequences (forward and reverse) were generated from six subtracted libraries. The similarity searches using BLASTX revealed that six clones were identified to be involved in dwarfism based on its putative functions. The gene transcripts encoding for: brassinosteroid biosynthesis-like protein (DWF1),BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor,putative (BRI1), late elongated hypocotyl protein (LHY), gibberellin receptor GID1,putative (GID1), sterol 24-methyltransferase 1 (SMT1) and E3 ubiquitin-proteinigase MARCH6 (E3Ub). These candidate dwarfing genes were reported to be involved in various stages of brassinosteroids (BRs) and gibberellins (GAs) biosynthesis and signaling pathways for plants growth and development. BRs areplant steroids that present in vegetative tissues such as shoot, leaves and stems; pollen grains, anthers and seeds. BRs control diverse physiological processes including cell division and elongation, embryogenesis, fertility, delayed senescence and vascular differentiation. GAs stimulate critical stages in plant growth and development such as plant height, cell wall modification, seed germination,flowering and leaf expansion. Gene validation analysis via qRT-PCR has revealedthe expression levels of each potential candidate dwarfing genes in all tested samples, normalized by two most stable reference genes, manganese superoxide dismutase-like protein (PD569) and hypothetical protein (EA1332). Based on the analysis, higher expression level of BRI1, LHY and SMT1 genes were observed in dwarf palms compared to standard palms with normalized fold-difference of 2.3285,1.5620 and 4.9044, respectively. However, lower expression of DWF1, GID1 and E3Ub were observed in dwarf palms compared to standard palms with normalized fold-difference of 0.8378, 0.7003 and 0.9631, respectively. Statistical analysis using Paired Samples T-Test showed that the expression levels of DWF1, BRI1, LHY,GID1 and E3Ub were not significantly expressed in dwarf palms. However, the SMT1 expression level was highly significant in dwarf palm, AG1-22. The expression profile of SMT1 in all tested samples was carried out using AG1-22 as the control baseline (1.0000 expression levels), where the GOI expression level below 1.0000 indicates as down-regulated; and above 1.0000 is up-regulated. The result showed that the dwarf palm, AG1-12 was up-regulated with 1.3161 expression value. Therefore, SMT1 gene may be potentially useful molecular marker for the screening of dwarf palm planting materials.
format	Thesis
qualification_level	Master's degree
author	Mohamed Azni, Intan Nur Aini
author_facet	Mohamed Azni, Intan Nur Aini
author_sort	Mohamed Azni, Intan Nur Aini
title	Identification of differentially expressed genes related to height increment in oil palm (Elaeis guineensis Jacq.)
title_short	Identification of differentially expressed genes related to height increment in oil palm (Elaeis guineensis Jacq.)
title_full	Identification of differentially expressed genes related to height increment in oil palm (Elaeis guineensis Jacq.)
title_fullStr	Identification of differentially expressed genes related to height increment in oil palm (Elaeis guineensis Jacq.)
title_full_unstemmed	Identification of differentially expressed genes related to height increment in oil palm (Elaeis guineensis Jacq.)
title_sort	identification of differentially expressed genes related to height increment in oil palm (elaeis guineensis jacq.)
granting_institution	Universiti Putra Malaysia
publishDate	2014
url	http://psasir.upm.edu.my/id/eprint/51998/1/FBSB%202014%2018RR.pdf
_version_	1747812079199322112

Identification of differentially expressed genes related to height increment in oil palm (Elaeis guineensis Jacq.)

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