Wong Yick Ching, Kwong Qi Bin, Lee Heng Leng, Ong Chuang Kee, Mayes Sean, Chew Fook Tim, Appleton David R, Kulaveerasingam Harikrishna
Sime Darby Technology Centre, Universiti Putra Malaysia, 1st Floor, Block B, UPM-MTDC Technology Centre III, Lebuh Silikon, 43400 Serdang, Selangor, Malaysia.
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Microarrays (Basel). 2014 Nov 13;3(4):263-81. doi: 10.3390/microarrays3040263.
Gene expression changes that occur during mesocarp development are a major research focus in oil palm research due to the economic importance of this tissue and the relatively rapid increase in lipid content to very high levels at fruit ripeness. Here, we report the development of a transcriptome-based 105,000-probe oil palm mesocarp microarray. The expression of genes involved in fatty acid (FA) and triacylglycerol (TAG) assembly, along with the tricarboxylic acid cycle (TCA) and glycolysis pathway at 16 Weeks After Anthesis (WAA) exhibited significantly higher signals compared to those obtained from a cross-species hybridization to the Arabidopsis (p-value < 0.01), and rice (p-value < 0.01) arrays. The oil palm microarray data also showed comparable correlation of expression (r² = 0.569, p < 0.01) throughout mesocarp development to transcriptome (RNA sequencing) data, and improved correlation over quantitative real-time PCR (qPCR) (r² = 0.721, p < 0.01) of the same RNA samples. The results confirm the advantage of the custom microarray over commercially available arrays derived from model species. We demonstrate the utility of this custom microarray to gain a better understanding of gene expression patterns in the oil palm mesocarp that may lead to increasing future oil yield.
由于中果皮组织具有重要经济价值，且在果实成熟时脂质含量会相对快速地增加到很高水平，因此中果皮发育过程中发生的基因表达变化是油棕研究的一个主要焦点。在此，我们报告了一种基于转录组的、包含105,000个探针的油棕中果皮微阵列的开发情况。与通过与拟南芥（p值<0.01）和水稻（p值<0.01）阵列进行跨物种杂交获得的信号相比，在花后16周（WAA）时，参与脂肪酸（FA）和三酰甘油（TAG）组装以及三羧酸循环（TCA）和糖酵解途径的基因表达显示出显著更高的信号。油棕微阵列数据还表明，在整个中果皮发育过程中，其表达与转录组（RNA测序）数据具有相当的相关性（r² = 0.569，p < 0.01），并且相对于相同RNA样本的定量实时PCR（qPCR）（r² = 0.721，p < 0.01），相关性有所提高。结果证实了定制微阵列相对于源自模式物种商业可用阵列的优势。我们展示了这种定制微阵列在更好地理解油棕中果皮基因表达模式方面的实用性，这可能有助于提高未来的油产量。
