AUTHOR=Pinnika Ganesh , Thyssen Gregory N. , Madison Crista A. , Li Ping , Fang David D. , Naoumkina Marina , Hinchliffe Doug J. 

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

JOURNAL=Frontiers in Plant Science

VOLUME=Volume 16 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2025.1668965

DOI=10.3389/fpls.2025.1668965

ISSN=1664-462X

ABSTRACT=IntroductionThe 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.MethodsIn 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. Results and discussionThe 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 a Ty3-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.