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

The rust-brown locus was mapped to <i>GhTT2</i> on chromosome A07 (<i>GhTT2_A07</i>). Comparison of the upstream sequence of <i>GhTT2_A07</i> 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 <i>GhTT2_A07</i>. Transcript analysis showed that the absence of retrotransposon upstream of <i>GhTT2_A07</i> 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 <i>Lc1</i> fibers is directly controlled by the expression level of <i>GhTT2_A07</i>, with higher expression levels resulting in darker fibers.