Preferential insertion of a Ty1 LTR-retrotransposon into the A sub-genome’s HD1 gene significantly correlated with the reduction in stem trichomes of tetraploid cotton

  • Mengling Tang
  • Xingcheng Wu
  • Yuefen Cao
  • Yuan Qin
  • Mingquan Ding
  • Yurong Jiang
  • Chengdong Sun
  • Hua Zhang
  • Andrew H. Paterson
  • Junkang RongEmail author
Original Article


Stem trichomes and seed fibers originate from epidermal cells and partially share a regulatory pathway at the molecular level. In Gossypium barbadense, two insertions of a Ty1 long-terminal repeat-retrotransposon [transposable element TE1 and TE2] in a homeodomain-leucine zipper gene (HD1) result in glabrous stems. The primers used to identify the TE insertions in G. barbadense were applied to screen for the same events in 81 modern G. hirsutum varieties and 31 wild races. Three wild races were found carrying the same TEs as G. barbadense. However, the TE insertions in two of these wild races occurred at different sites (4th exon), therefore, named TE3, while the TE in the other wild race occurred at the same site as TE2. An RNA sequencing and qRT-PCR analysis indicated that the loss of HD1 function was caused by the TE insertion. Genetic mapping revealed a strong association between glabrous stems and TE3 insertions, confirming that HD1 is a critical gene for stem trichome initiation in G. hirsutum, as in G. barbadense. Using the long-terminal repeat sequence as a query to search against the Texas Marker-1 reference genome sequence, we found that the TE occurred after tetraploid cotton formation and evolved at different rates in G. hirsutum and G. barbadense. Interestingly, at least three independent insertion events of the same retrotransposon occurred preferentially in the A sub-genome’s HD1 gene, but not in the D sub-genome of G. hirsutum or G. barbadense, suggesting that an unknown TE insertion mechanism and resultant gene function changes may have hastened cotton speciation.


G. hirsutum LTR-retrotransposons Stem trichome Homeodomain-leucine zipper Genetic mapping 



We thank Prof. Fang Liu at the Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS) for providing us with wild G. hirsutum races. This work was supported by the National Key R & D Program for Crop Breeding (Grant no. 2016YFD0101417) to MD and the National Natural Science Foundation of China to YC (Grant no. 31501349) and YJ (Grant no. 31301372).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Supplementary material 1 (XLSX 230 kb)
438_2019_1602_MOESM2_ESM.docx (283 kb)
Supplementary material 2 (DOCX 282 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Mengling Tang
    • 1
  • Xingcheng Wu
    • 1
  • Yuefen Cao
    • 1
  • Yuan Qin
    • 2
  • Mingquan Ding
    • 1
  • Yurong Jiang
    • 1
  • Chengdong Sun
    • 1
  • Hua Zhang
    • 1
  • Andrew H. Paterson
    • 3
  • Junkang Rong
    • 1
    Email author
  1. 1.The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, School of Agriculture and Food ScienceZhejiang A&F UniversityHangzhouChina
  2. 2.State Key Laboratory of Cotton BiologyInstitute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)AnyangChina
  3. 3.Plant Genome Mapping LaboratoryUniversity of GeorgiaAthensUSA

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