title: De novo transcriptome analysis reveals insights into dynamic homeostasis regulation of somatic embryogenesis in upland cotton (G. hirsutum L.).
abstract: Plant regeneration via somatic embryogenesis (SE) is the key step for genetic improvement of cotton (Gossypium hirsutum L.) through genetic engineering mediated by Agrobacteria, but the molecular mechanisms underlying SE in cotton is still unclear. Here, RNA-Sequencing was used to analyze the genes expressed during SE and their expression dynamics using RNAs isolated from non-embryogenic callus (NEC), embryogenic callus (EC) and somatic embryos (SEs). A total of 101, 670 unigenes were de novo assembled. The genes differentially expressed (DEGs) amongst NEC, EC and SEs were identified, annotated and classified. More DEGs were found between SEs and EC than between EC and NEC. A significant number of DEGs were related to hormone homeostasis, stress and ROS responses, and metabolism of polyamines. To confirm the expression dynamics of selected DEGs involved in various pathways, experiments were set up to investigate the effects of hormones (Indole-3-butytric acid, IBA; Kinetin, KT), polyamines, H2O2 and stresses on SE. Our results showed that exogenous application of IBA and KT positively regulated the development of EC and SEs, and that polyamines and H2O2 promoted the conversion of EC into SEs. Furthermore, we found that low and moderate stress is beneficial for proliferation of EC and SEs formation. Together, our global analysis of transcriptomic dynamics reveals that hormone homeostasis, polyamines, and stress response synergistically regulating SE in cotton.
authors: The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China.
authors: Wen-Han
authors: WH
authors: Cheng
authors: The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China.
authors: Hua-Guo
authors: HG
authors: Zhu
authors: The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China.
authors: Wen-Gang
authors: WG
authors: Tian
authors: The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China.
authors: Shou-Hong
authors: SH
authors: Zhu
authors: The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China.
authors: Xian-Peng
authors: XP
authors: Xiong
authors: The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China.|Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China.
authors: Yu-Qiang
authors: YQ
authors: Sun
authors: CSIRO Agriculture Flagship, GPO Box 1600, Canberra, 2601, Australia.
authors: Qian-Hao
authors: QH
authors: Zhu
authors: The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi, 832000, Xinjiang, China. sunjie@shzu.edu.cn.
authors: Jie
authors: J
authors: Sun
mesh_terms: D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D003368:Gossypium / Q000196:embryology / Q000235:genetics*; D006706:Homeostasis / Q000235:genetics*; D007701:Kinetin / Q000235:genetics
chemical_list: D007701:Kinetin
keywords: Gossypium hirsutum L.; Indole-3-butytric acid; Kinetin; Polyamines; Somatic embryogenesis (SE); Stress-response; Transcriptome