Rapid Identification of a Candidate Gene Related to Fiber Strength Using a Superior Chromosome Segment Substitution Line from Gossypium hirsutum × Gossypium barbadense via Bulked Segregant RNA-Sequencing
  • Qi Zhang1,#, Pengtao Li2,#, Aiying Liu1, Shaoqi Li1, Quanwei Lu2, Qun Ge1, Junwen Li1, Wankui Gong1, Xiaoying Deng1, Haihong Shang1,3, Yuzhen Shi1,*, Youlu Yuan1,3,*
1 State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
2 School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China
3 Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
* Corresponding Authors: Yuzhen Shi. Email: shiyuzhen@caas.cn; Youlu Yuan. Email: yuanyoulu@caas.cn
# These authors made equal contributions
Received 26 September 2020; Accepted 09 December 2020 ;
Cotton is the most widely cultivated commercial crop producing natural fiber around the world. As a critical trait for fiber quality, fiber strength principally determined during the secondary wall thickening period. Based on the developed BC5F3:5 CSSLs (chromosome segment substitution lines) from Gossypium hirsutum CCRI36 × G. barbadense Hai 1, the superior MBI9915 was chosen to construct the secondary segregated population BC7F2 with its recurrent parent CCRI36, which was subsequently subjected to Bulk segregant RNA-sequencing (BSR-seq) for rapid identification of candidate genes related to fiber strength. A total of 4 fiber-transcriptome libraries were separately constructed and sequenced, including two parents (CCRI36 and MBI9915) and two extreme pools at 20 DPA (days post anathesis). Through multiple comparisons, 536 DEGs (differentially expressed genes) were overlapped at 20 DPA. Allelic-polymorphism comparison in mRNA sequences revealed 831 highly probable SNPs between two extreme pools related to fiber strength. Linkage analysis was performed between two extreme pools with SNP-index method. Eighteen correlated regions with 1981 annotation genes were obtained between two pools at 20 DPA, of which 12 common DEGs were similarly identified both between two parents and two pools. One gene (Gh_A07G0837) in the candidate region related to fiber strength was differentially expressed in both parents and extreme pools and involved in fiber strength development through reactive oxygen species (ROS) activity. Co-expression analysis of Gh_A07G0837 showed that Gh_A07G0837 may cooperate with other genes to regulate fiber strength. The reliability of BSR-seq results was validated by the quantitative real-time PCR (qRT-PCR) experiments on 5 common DGEs 20 DPA. Co-expressed analysis results indicated that there were some genes expressed especially low in MBI9915, resulting in good fiber strength. Focusing on bulked segregant analysis on the extreme pools derived from superior CSSL population, this study indicates that BSR-seq can be efficiently applied on rapid identification of candidate genes related to fiber strength, which make contributions to our understanding of fiber quality formation in cotton.
Cotton; Fiber strength; CSSLs; BSR-seq; gene clone; co-expressed analysis