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
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.
KeywordsG. 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).
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Conflict of interest
The authors declare that they have no conflict of interest.
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