State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agriculture Sciences, Anyang, 455000, China.
J Integr Plant Biol. 2013 Jul;55(7):631-42. doi: 10.1111/jipb.12073.
To get a broader view on the molecular mechanisms underlying somatic embryogenesis (SE) in cotton (Gossypium hirsutum L.), global analysis of cotton transcriptome dynamics during SE in different sister lines was performed using RNA-Seq. A total of 204 349 unigenes were detected by de novo assembly of the 214 977 462 Illumina reads. The quantitative reverse transcription-polymerase chain reaction (qRT-PCR) measurements were positively correlated with the RNA-Seq results for almost all the tested genes (R(2) = 0.841, correlation was significant at the 0.01 level). Different phytohormone (auxin and cytokinin) concentration ratios in medium and the endogenous content changes of these two phytohormones at two stages in different sister lines suggested the roles of auxin and cytokinin during cotton SE. On the basis of global gene regulation of phytohormone-related genes, numerous genes from all the differentially expressed transcripts were involved in auxin and cytokinin biosynthesis and signal transduction pathways. Analyses of differentially expressed genes that were involved in these pathways revealed the substantial changes in gene type and abundance between two sister lines. Isolation, cloning and silencing/overexpressing the genes that revealed remarkable up- or down-expression during cotton SE were important. Furthermore, auxin and cytokinin play a primary role in SE, but potential cross-talk with each other or other factors remains unclear.
为了更全面地了解棉花体细胞胚胎发生（SE）的分子机制，本研究利用 RNA-Seq 对不同姊妹系 SE 过程中的棉花转录组动态进行了全球分析。通过对 214,977,462 个 Illumina 读取的从头组装，共检测到 204,349 个 unigenes。几乎所有测试基因的定量逆转录聚合酶链反应（qRT-PCR）测量结果与 RNA-Seq 结果呈正相关（R²=0.841，相关性在 0.01 水平上显著）。不同培养基中植物激素（生长素和细胞分裂素）浓度比以及不同姊妹系两个阶段这两种植物激素的内源性含量变化表明，生长素和细胞分裂素在棉花 SE 过程中发挥作用。基于与植物激素相关基因的全局基因调控，所有差异表达转录本中的大量基因都参与了生长素和细胞分裂素的生物合成和信号转导途径。对这些途径中差异表达基因的分析表明，两个姊妹系之间基因类型和丰度发生了重大变化。分离、克隆和沉默/过表达在棉花 SE 过程中表现出显著上调或下调的基因非常重要。此外，生长素和细胞分裂素在 SE 中起主要作用，但它们之间或与其他因素的潜在相互作用尚不清楚。
