Custom oligonucleotide microarray design and analysis for oil palm gene expression quantification

Clough James, . (2009) Custom oligonucleotide microarray design and analysis for oil palm gene expression quantification. [Proceedings Paper]

MPOB has formalised collaboration to develop its own proprietary design olignucleotide microarray to conduct a comprehensive deep analysis and cohort study of Oil Palm gene functionality. A key application is to identify and validate specifiC gene functionality associated with traits of commercial value such as oil yield and disease resistance. A secondary aim is to develop an MPOB screening mini-array to enable fast accurate and highly sensitive screening of seedlings exhibiting strong commercial potential based on specific markers. MPOB provided a total of up to 500 000 gene thresher sequences and 50 000 ESTs as the input sequence data. This was optimised and informatically collapsed into a design comprising 348 800 probes on a 2x 400k oligonucleotide array slide format. Oligonucleotide microarrays probes consist ofshort sequences designed to match parts ofthe sequence of known or predicted open reading frames. Such design formats are ideal for representing single gene or family ofgene splice variants by synthesising sequences directly onto an array surface as opposed to depositing intact sequences. The initial design component of the project was further made more complicated due to the highly repetitive nature of Oil Palm 60 high repeats. The end product oligonucleotide array has been applied to a large cohort study for discovery of gene regulation pathways that may be involved in various traits.

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Abstract

MPOB has formalised collaboration to develop its own proprietary design olignucleotide microarray to conduct a comprehensive deep analysis and cohort study of Oil Palm gene functionality. A key application is to identify and validate specifiC gene functionality associated with traits of commercial value such as oil yield and disease resistance. A secondary aim is to develop an MPOB screening mini-array to enable fast accurate and highly sensitive screening of seedlings exhibiting strong commercial potential based on specific markers. MPOB provided a total of up to 500 000 gene thresher sequences and 50 000 ESTs as the input sequence data. This was optimised and informatically collapsed into a design comprising 348 800 probes on a 2x 400k oligonucleotide array slide format. Oligonucleotide microarrays probes consist ofshort sequences designed to match parts ofthe sequence of known or predicted open reading frames. Such design formats are ideal for representing single gene or family ofgene splice variants by synthesising sequences directly onto an array surface as opposed to depositing intact sequences. The initial design component of the project was further made more complicated due to the highly repetitive nature of Oil Palm 60 high repeats. The end product oligonucleotide array has been applied to a large cohort study for discovery of gene regulation pathways that may be involved in various traits.

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Item Type:	Proceedings Paper
Additional Information:	Available at Perpustakaan Sultan Abdul Samad Universiti Putra Malaysia 43400 UPM Serdang Selangor Darul Ehsan Malaysia. mal TP684 P3I61 2009 vol. 1 Call Number
AGROVOC Term:	Oil palm
AGROVOC Term:	Gene expression
AGROVOC Term:	Seedlings
AGROVOC Term:	analysis
AGROVOC Term:	Design
AGROVOC Term:	Genetic markers
AGROVOC Term:	Disease resistance
AGROVOC Term:	Yield factors
Geographical Term:	MALAYSIA
Depositing User:	Ms. Suzila Mohamad Kasim
Last Modified:	24 Apr 2025 05:15
URI:	http://webagris.upm.edu.my/id/eprint/12364

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