Molecular Genetics and Genomics

, Volume 294, Issue 1, pp 23–34 | Cite as

Comparative transcriptome analysis of TUCPs in Gossypium hirsutum Ligon-lintless-1 mutant and their proposed functions in cotton fiber development

  • Haron Salih
  • Wenfang Gong
  • Shoupu He
  • Nada S. Mustafa
  • Xiongming DuEmail author
Original Article


Transcripts of uncertain coding potential (TUCP) are part of the LncRNAs, which encode some polypeptides. However, the abundance of TUCP transcripts and their roles in Ligon-linless-1 (Li-1) cotton mutant during the early termination of fiber development are still not documented. Li-1 mutant is one of the excellent modules for investigating fiber elongation processes due to its unique fiber developmental stages. To examine the function of TUCP in cotton fiber development, it is important to identify TUCPs and their involvement in fiber development. In this study, we found that 11104 TUCP transcripts were removed by coding potential criteria of Pfam domain scan. Additionally, differential expression levels of TUCP transcripts were detected between Li-1 mutant and the wild-type (WT), which imply their possible functions in cotton fiber development. These results further revealed that a great number of differentially expressed TUCP transcripts in cotton were identified at 8 DPA, followed by 0 DPA and stem. However, these might explain an undesirable function in cotton fiber development. The gene ontology and pathway analysis, based on differential expression patterns of TUCP transcripts on targeted genes, identified the transport process, cytoskeleton structure, membrane permeability and fatty acids. These give new insight into significant involvement in early cessation of cotton fiber development and abnormal stem. The RNA-seq and qRT-PCR expression analyses of TUCP transcripts evidently singled out three possible genes, TUCP_010675, TUCP_001475, TUCP_009444 and other targeted mRNAs. The expression pattern of TUCP transcripts and their mRNA targets provided valuable evidence for further investigations on the biological functions of TUCP in cotton fiber development. The study findings may serve as a useful tool for comparative analysis of TUCP transcripts in cotton species and assist in selection of the applicable candidate genes for further functional analyses, genetic improvement and genetic engineering of cotton fiber development.


Comparative analysis Expression pattern TUCPs Ligon-lintless-1 mutant Wild-type Fiber development 



The authors appreciate the support of the National Natural Science Fundation of China (No. 31601353) and the National Key Project of Research and Development Plan (No. 2016YFD0100203).


This study was supported by the National Science and Technology of China and China Scholarship Council (CSC) all contributed with funding towards the research.

Compliance with ethical standards

Conflict of interest

The author(s) declare(s) that they have no competing interests.

Availability of materials and data

All related data are available within the manuscript and its additional files.

Supplementary material

438_2018_1482_MOESM1_ESM.pdf (10 kb)
Supplementary figure 1. Pearson Correlation Coefficient of the genes identified different cotton samples. (PDF 10 KB)
438_2018_1482_MOESM2_ESM.pdf (372 kb)
Supplementary figure 2. Gene ontology (GO) enrichment analysis of TUCP transcripts-target genes. (A) Up-regulated and down-regulated genes at 8 DPA; (B) Up-regulated and down-regulated genes at cotton stem. (PDF 372 KB)
438_2018_1482_MOESM3_ESM.xls (2 mb)
Supplementary table 1. List of TUCP transcripts identified by RNA-seq, including the position and expression pattern in each sample with three biological replicates. (XLS 2023 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Haron Salih
    • 1
    • 2
    • 3
  • Wenfang Gong
    • 1
  • Shoupu He
    • 1
  • Nada S. Mustafa
    • 1
  • Xiongming Du
    • 1
    Email author
  1. 1.State Key Laboratory of Cotton Biology/Institute of Cotton ResearchChinese Academy of Agricultural ScienceAnyangChina
  2. 2.College of life sciencesHuazhong Agricultural UniversityWuhanChina
  3. 3.Zalingei UniversityCentral DarfurSudan

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