Co-expression network and comparative transcriptome analysis for fiber initiation and elongation reveal genetic differences in two lines from upland cotton CCRI70 RIL population
Xiao Jiang,
Liqiang Fan,
Pengtao Li,
Xianyan Zou,
Zhen Zhang,
Senmiao Fan,
Juwu Gong,
Youlu Yuan,
Haihong Shang
Affiliations
Xiao Jiang
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
Liqiang Fan
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
Pengtao Li
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, China
Xianyan Zou
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
Zhen Zhang
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
Senmiao Fan
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
Juwu Gong
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
Youlu Yuan
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
Haihong Shang
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
Upland cotton is the most widely planted for natural fiber around the world, and either lint percentage (LP) or fiber length (FL) is the crucial component tremendously affecting cotton yield and fiber quality, respectively. In this study, two lines MBZ70-053 and MBZ70-236 derived from G. hirsutum CCRI70 recombinant inbred line (RIL) population presenting different phenotypes in LP and FL traits were chosen to conduct RNA sequencing on ovule and fiber samples, aiming at exploring the differences of molecular and genetic mechanisms during cotton fiber initiation and elongation stages. As a result, 249/128, 369/206, 4296/1198 and 3547/2129 up-/down- regulated differentially expressed genes (DGEs) in L2 were obtained at −3, 0, 5 and 10 days post-anthesis (DPA), respectively. Seven gene expression profiles were discriminated using Short Time-series Expression Miner (STEM) analysis; seven modules and hub genes were identified using weighted gene co-expression network analysis. The DEGs were mainly enriched into energetic metabolism and accumulating as well as auxin signaling pathway in initiation and elongation stages, respectively. Meanwhile, 29 hub genes were identified as 14-3-3ω, TBL35, GhACS, PME3, GAMMA-TIP, PUM-7, etc., where the DEGs and hub genes revealed the genetic and molecular mechanisms and differences during cotton fiber development.