The brown fiber phenotype in cotton line SA-40 is linked to a missing Ty3-like retrotransposon upstream of the GhTT2_A07

Authors: PINNIKA, GANESH - Oak Ridge National Laboratory; Thyssen, Gregory; Madison, Crista; Li, Ping; Fang, David; Naoumkina, Marina; Hinchliffe, Doug

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/19/2025
Publication Date: 9/3/2025
Citation: Pinnika, G., Thyssen, G.N., Madison, C.A., Li, P., Fang, D.D., Naoumkina, M.A., Hinchliffe, D.J. 2025. The brown fiber phenotype in cotton line SA-40 is linked to a missing Ty3-like retrotransposon upstream of the GhTT2_A07. Frontiers in Plant Science. 16. Article 1668965. https://doi.org/10.3389/fpls.2025.1668965.
DOI: https://doi.org/10.3389/fpls.2025.1668965

Interpretive Summary: The naturally brown cotton fibers exist in varying shades. The current study aims to understand the genetic regulation of brown shades. We used a previously uncharacterized SA-40 germplasm that produces a rust-brown color of fibers. Genetic mapping linked the rust-brown phenotype of SA-40 to the transcription factor located on chromosome A07 (GhTT2_A07), which is responsible for the activation of the proanthocyanidin pathway (production of brown pigments in fiber). Comparison of the upstream sequence of GhTT2_A07 between the white fiber line and SA-40 revealed the absence of retrotransposon in the SA-40 line. No remnants of the retrotransposon in the SA-40 indicated that the retrotransposon insertion did not happen in that line. However, every white cotton line tested in the study contain the retrotransposon insertion upstream of GhTT2_A07. Transcript analysis showed that the absence of retrotransposon upstream of GhTT2_A07 was associated with higher expression of this gene but at lower levels than previously reported for the upstream inversion mutation, where the retrotransposon has been removed. Results of this study suggest that the shades of brown fibers are directly controlled by the expression level of GhTT2_A07, with higher expression levels resulting in darker fibers.

Technical Abstract: The naturally brown colored fibers of some cottons exist in varying shades of brown. Linkage analyses have revealed up to six individual loci (Lc1–Lc6) for brown color and suggested a separate genetic basis for each color value of fibers. It was previously reported that the brown color and flame-retardant (FR) properties of Lc1 fibers resulted from an upstream inversion mutation that highly upregulates the GhTT2_A07 gene and, consequently, the entire phenylpropanoid pathway. However, the genes responsible for the coloration and FR of other brown cotton fibers remained undetermined. In the current study, we used a previously uncharacterized SA-40 germplasm that produces rust-brown cotton. An F2 mapping population derived from the cross of SA-40 and TM-1 was used in an association mapping study to elucidate the genetics of SA-40 rust-brown fiber color and FR. The rust-brown locus was mapped to GhTT2 on chromosome A07 (GhTT2_A07). Comparison of the upstream sequence of GhTT2_A07 between TM-1 and SA-40 revealed the absence of gypsy-like LTR retrotransposon in the SA-40 line. No remnants of the LTR retrotransposon in the SA-40 indicated that the retrotransposon insertion did not happen in that line. However, all investigated white cotton lines in this study displayed the presence of the LTR retrotransposon upstream of GhTT2_A07. Transcript analysis showed that the absence of retrotransposon upstream of GhTT2_A07 was associated with higher expression of this gene, but at lower levels than previously reported for the upstream inversion mutation in the MC-BL line, where the retrotransposon has been removed by structural rearrangement. Our finding suggests that the value of brown coloration in Lc1 fibers is directly controlled by the expression level of GhTT2_A07, with higher expression levels resulting in darker fibers.