Differentially expressed transcripts related to height in oil palm

Sharifah Shahrul Rabiah Syed Alwee, . and Parameswari Namasivayam, . and Mohamad Arif Abd Manaf, . and Intan Nur Ainni Mohamed Azni, . and Ho C. L., . Differentially expressed transcripts related to height in oil palm. pp. 308-316. ISSN 1511-2780

A subtractive cDNA library was constructed using MPOB Planting Series 1 (PS1) population to isolate differentially expressed transcripts associated with height increment in oil palm. After differential screening 98 clones were identified to be potentially positive with cDNA inserts ranging from 250 to 1000 bp. A total of 123 sequences generated and low quality sequences 20 were eliminated using Phred program to assess the sequence quality and determine the accurate consensus sequence. Contig assembly by CAP3 program generated 51 contigs and four singletons (55 unigenes). Blast search showed 49 unique sequences had significant match to various plant species in the GeneBank database with E-value 1e- 5 and four sequences showed no significant similarity. Gene ontology analysis output from Blast2GO program revealed that the sequences encoding for auxin responsive protein circadian clock-associated protein1 zinc-finger protein and basic leucine zipper protein were potentially associated to dwarfism. The genes were identified based on their putative functions in regulating height in plants particularly in growth hormone biosynthesis such as auxin (Aux/IAA) gibberellins (GA) and brassinosteroids (BR).

Full text available from: Official URL: http://jopr.mpob.gov.my/wp-content/uploads/2014/12...

Abstract

A subtractive cDNA library was constructed using MPOB Planting Series 1 (PS1) population to isolate differentially expressed transcripts associated with height increment in oil palm. After differential screening 98 clones were identified to be potentially positive with cDNA inserts ranging from 250 to 1000 bp. A total of 123 sequences generated and low quality sequences 20 were eliminated using Phred program to assess the sequence quality and determine the accurate consensus sequence. Contig assembly by CAP3 program generated 51 contigs and four singletons (55 unigenes). Blast search showed 49 unique sequences had significant match to various plant species in the GeneBank database with E-value 1e- 5 and four sequences showed no significant similarity. Gene ontology analysis output from Blast2GO program revealed that the sequences encoding for auxin responsive protein circadian clock-associated protein1 zinc-finger protein and basic leucine zipper protein were potentially associated to dwarfism. The genes were identified based on their putative functions in regulating height in plants particularly in growth hormone biosynthesis such as auxin (Aux/IAA) gibberellins (GA) and brassinosteroids (BR).

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Item Type:	Article
AGROVOC Term:	Oil palm
AGROVOC Term:	Planting
AGROVOC Term:	Transcription
AGROVOC Term:	Differential diagnosis
AGROVOC Term:	DNA sequence
AGROVOC Term:	Clones
AGROVOC Term:	Quality
AGROVOC Term:	Gene banks
AGROVOC Term:	ontology
AGROVOC Term:	Auxins
Depositing User:	Ms. Suzila Mohamad Kasim
Last Modified:	24 Apr 2025 06:29
URI:	http://webagris.upm.edu.my/id/eprint/24573

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