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Comparative transcriptome analysis reveals novel insights into transcriptional responses to phosphorus starvation in oil palm (Elaeis guineensis) root
BMC Genetics ( IF 2.9 ) Pub Date : 2021-02-05 , DOI: 10.1186/s12863-021-00962-7
Sze-Ling Kong 1 , Siti Nor Akmar Abdullah 1, 2 , Chai-Ling Ho 1, 3 , Mohamed Hanafi Bin Musa 4 , Wan-Chin Yeap 5
Affiliation  

Phosphorus (P), in its orthophosphate form (Pi) is an essential macronutrient for oil palm early growth development in which Pi deficiency could later on be reflected in lower biomass production. Application of phosphate rock, a non-renewable resource has been the common practice to increase Pi accessibility and maintain crop productivity in Malaysia. However, high fixation rate of Pi in the native acidic tropical soils has led to excessive utilization of P fertilizers. This has caused serious environmental pollutions and cost increment. Even so, the Pi deficiency response mechanism in oil palm as one of the basic prerequisites for crop improvement remains largely unknown. Using total RNA extracted from young roots as template, we performed a comparative transcriptome analysis on oil palm responding to 14d and 28d of Pi deprivation treatment and under adequate Pi supply. By using Illumina HiSeq4000 platform, RNA-Seq analysis was successfully conducted on 12 paired-end RNA-Seq libraries and generated more than 1.2 billion of clean reads in total. Transcript abundance estimated by fragments per kilobase per million fragments (FPKM) and differential expression analysis revealed 36 and 252 genes that are differentially regulated in Pi-starved roots at 14d and 28d, respectively. Genes possibly involved in regulating Pi homeostasis, nutrient uptake and transport, hormonal signaling and gene transcription were found among the differentially expressed genes. Our results showed that the molecular response mechanism underlying Pi starvation in oil palm is complexed and involved multilevel regulation of various sensing and signaling components. This contribution would generate valuable genomic resources in the effort to develop oil palm planting materials that possess Pi-use efficient trait through molecular manipulation and breeding programs.

中文翻译:

比较转录组分析揭示了对油棕(Elaeis guineensis)根中磷饥饿的转录反应的新见解

磷 (P) 的正磷酸盐形式 (Pi) 是油棕早期生长发育的必需常量营养素,其中磷的缺乏日后可能会反映在较低的生物量产量上。在马来西亚,磷酸盐岩是一种不可再生资源,已成为增加磷的可及性和维持作物生产力的常见做法。然而,天然酸性热带土壤中磷的高固定率导致磷肥的过度利用。这造成了严重的环境污染和成本增加。即便如此,作为作物改良的基本先决条件之一的油棕缺磷反应机制仍然很大程度上未知。以幼根提取的总RNA为模板,我们对油棕在 14 天和 28 天的磷剥夺处理和充足的磷供应下进行了比较转录组分析。通过使用 Illumina HiSeq4000 平台,成功地对 12 个双末端 RNA-Seq 文库进行了 RNA-Seq 分析,总共产生了超过 12 亿条干净的 read。通过每千碱基每百万片段的片段 (FPKM) 估计的转录本丰度和差异表达分析揭示了分别在 14 天和 28 天在 Pi 饥饿根中差异调节的 36 和 252 个基因。在差异表达的基因中发现了可能参与调节Pi稳态、营养吸收和转运、激素信号和基因转录的基因。我们的研究结果表明,油棕中磷缺乏的分子反应机制是复杂的,涉及对各种传感和信号成分的多层次调控。这一贡献将产生宝贵的基因组资源,以通过分子操作和育种计划开发具有高效利用 Pi 特性的油棕种植材料。
更新日期:2021-02-05
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