Dataset Information

Evaluation of reference genes for quantitative real-time PCR in oil palm elite planting materials propagated by tissue culture.

ABSTRACT:

Background

The somatic embryogenesis tissue culture process has been utilized to propagate high yielding oil palm. Due to the low callogenesis and embryogenesis rates, molecular studies were initiated to identify genes regulating the process, and their expression levels are usually quantified using reverse transcription quantitative real-time PCR (RT-qPCR). With the recent release of oil palm genome sequences, it is crucial to establish a proper strategy for gene analysis using RT-qPCR. Selection of the most suitable reference genes should be performed for accurate quantification of gene expression levels.

Results

In this study, eight candidate reference genes selected from cDNA microarray study and literature review were evaluated comprehensively across 26 tissue culture samples using RT-qPCR. These samples were collected from two tissue culture lines and media treatments, which consisted of leaf explants cultures, callus and embryoids from consecutive developmental stages. Three statistical algorithms (geNorm, NormFinder and BestKeeper) confirmed that the expression stability of novel reference genes (pOP-EA01332, PD00380 and PD00569) outperformed classical housekeeping genes (GAPDH, NAD5, TUBULIN, UBIQUITIN and ACTIN). PD00380 and PD00569 were identified as the most stably expressed genes in total samples, MA2 and MA8 tissue culture lines. Their applicability to validate the expression profiles of a putative ethylene-responsive transcription factor 3-like gene demonstrated the importance of using the geometric mean of two genes for normalization.

Conclusions

Systematic selection of the most stably expressed reference genes for RT-qPCR was established in oil palm tissue culture samples. PD00380 and PD00569 were selected for accurate and reliable normalization of gene expression data from RT-qPCR. These data will be valuable to the research associated with the tissue culture process. Also, the method described here will facilitate the selection of appropriate reference genes in other oil palm tissues and in the expression profiling of genes relating to yield, biotic and abiotic stresses.

SUBMITTER: Chan PL

PROVIDER: S-EPMC4057393 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Publications

Evaluation of reference genes for quantitative real-time PCR in oil palm elite planting materials propagated by tissue culture.

Chan Pek-Lan PL Rose Ray J RJ Abdul Murad Abdul Munir AM Zainal Zamri Z Low Eng-Ti Leslie ET Ooi Leslie Cheng-Li LC Ooi Siew-Eng SE Yahya Suzaini S Singh Rajinder R

PloS one 20140613 6

<h4>Background</h4>The somatic embryogenesis tissue culture process has been utilized to propagate high yielding oil palm. Due to the low callogenesis and embryogenesis rates, molecular studies were initiated to identify genes regulating the process, and their expression levels are usually quantified using reverse transcription quantitative real-time PCR (RT-qPCR). With the recent release of oil palm genome sequences, it is crucial to establish a proper strategy for gene analysis using RT-qPCR. ...[more]

PMID: 24927412

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Project description:A semi-mechanistic oil palm growth and yield model called Sawit.jl was developed to account for a wide range of planting densities and soil textures under Malaysia's climate conditions. The model comprises components related to meteorology, photosynthesis, energy balance, soil water content, and crop growth. The model simulates instantaneous meteorological properties using daily weather data, calculates simultaneous evaporation from crop and soil with the Shuttleworth-Wallace model, determines soil water content through Darcy's law, and adapts a biochemical C3 model for photosynthesis. The model is also parameterized using updated measurements from the newer tenera oil palm, including temperature-dependent Rubisco kinetics, specific leaf area, and the partitioning of nutrients and dry matter between various tree parts. Sawit.jl was validated using historical field measurement data from seven Malaysian oil palm sites, encompassing palm ages spanning 1-23 years. These seven sites differed in soil type (Inceptisols and Ultisols), planting density (82-299 palms ha-1), soil texture (27-59 % clay and 7-67 % sand), and rainfall (1800-2800 mm yr-1). The model showed overall good accuracy in simulating oil palm parameters (except for trunk weight) across diverse conditions, with model agreement metrics ranging from 6 to 27 % for model absolute errors, -22 to +17 % for model bias, and 0.38 to 0.98 for the Kling-Gupta Efficiency index. The model also predicted the response of oil palm yield to abrupt rainfall changes, such as those during El Niño and La Niña events, while accounting for how soil texture, rainfall, and other meteorological factors influence water deficits and crop photosynthesis. However, model accuracy varied by site, planting density, and oil palm parameter. Model accuracy can be increased by more accurately representing the oil palm microclimate, incorporating fruiting activity, and refining the dry matter partitioning mechanism for the trunk.

Dataset Information

Evaluation of reference genes for quantitative real-time PCR in oil palm elite planting materials propagated by tissue culture.

Background

Results

Conclusions

Publications

Evaluation of reference genes for quantitative real-time PCR in oil palm elite planting materials propagated by tissue culture.

Similar Datasets

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