Co-Expression Network Analysis and Introgressive Gene Identification for Fiber Length and Strength Reveal Transcriptional Differences in 15 Cotton Chromosome Substitution Segment Lines and Their Upland and Sea Island Parents
Pengtao Li,
Yu Chen,
Rui Yang,
Zhihao Sun,
Qun Ge,
Xianghui Xiao,
Shuhan Yang,
Yanfang Li,
Qiankun Liu,
Aiming Zhang,
Baoguang Xing,
Bei Wu,
Xue Du,
Xiaoyan Liu,
Baomeng Tang,
Juwu Gong,
Quanwei Lu,
Yuzhen Shi,
Youlu Yuan,
Renhai Peng,
Haihong Shang
Affiliations
Pengtao Li
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
Yu Chen
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
Rui Yang
National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
Zhihao Sun
National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
Qun Ge
National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
Xianghui Xiao
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
Shuhan Yang
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
Yanfang Li
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
Qiankun Liu
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
Aiming Zhang
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
Baoguang Xing
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
Bei Wu
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
Xue Du
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
Xiaoyan Liu
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
Baomeng Tang
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
Juwu Gong
National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
Quanwei Lu
National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
Yuzhen Shi
National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
Youlu Yuan
National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
Renhai Peng
School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
Haihong Shang
National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
Fiber length (FL) and strength (FS) are the core indicators for evaluating cotton fiber quality. The corresponding stages of fiber elongation and secondary wall thickening are of great significance in determining FL and FS formation, respectively. QTL mapping and high-throughput sequencing technology have been applied to dissect the molecular mechanism of fiber development. In this study, 15 cotton chromosome segment substitution lines (CSSLs) with significant differences in FL and FS, together with their recurrent parental Gossypium hirsutum line CCRI45 and donor parent G. barbadense line Hai1, were chosen to conduct RNA-seq on developing fiber samples at 10 days post anthesis (DPA) and 20 DPA. Differentially expressed genes (DEGs) were obtained via pairwise comparisons among all 24 samples (each one with three biological repeats). A total of 969 DEGs related to FL-high, 1285 DEGs to FS-high, and 997 DEGs to FQ-high were identified. The functional enrichment analyses of them indicated that the GO terms of cell wall structure and ROS, carbohydrate, and phenylpropanoid metabolism were significantly enriched, while the GO terms of glucose and polysaccharide biosynthesis, and brassinosteroid and glycosylphosphatidylinositol metabolism could make great contributions to FL and FS formation, respectively. Weighted gene co-expressed network analyses (WGCNA) were separately conducted for analyzing FL and FS traits, and their corresponding hub DEGs were screened in significantly correlated expression modules, such as EXPA8, XTH, and HMA in the fiber elongation and WRKY, TDT, and RAC-like 2 during secondary wall thickening. An integrated analysis of these hub DEGs with previous QTL identification results successfully identified a total of 33 candidate introgressive DEGs with non-synonymous mutations between the Gh and Gb species. A common DEG encoding receptor-like protein kinase 1 was reported to likely participate in fiber secondary cell thickening regulation by brassionsteroid signaling. Such valuable information was conducive to enlightening the developing mechanism of cotton fiber and also provided an abundant gene pool for further molecular breeding.
