A Ty1 LTR-Retrotransposon Insertion in GbHD1 Gene Is the Prevailing Cause of Trichomeless Phenotypes in Sea Island Cotton (G. barbadense)

Stem/leaf trichomes and seed fibers of cotton are both developed from the epidermal cells and likely rely on shared biochemical pathways and genetic basis. Understanding the genetic mechanisms regulating trichome growth helps to reveal genetic foundation of fiber development. In this study, a homeodomain leucine zipper gene (HD1) is found to be co-segregating with cotton stem trichome phenotype and mapped to Chr.06 (A). Characterizations of the HD1 gene sequences in both glabrous and pubescent cotton accessions revealed that the absence of stem trichome in Sea Island cotton (G. barbadense) is linked to a large retrotransposon insertion in the HD1 gene of Chr.06(A). Gene expression experiments confirmed the inactivation of the gene due to this insertion. In the ancient Sea Island cottons, except for the same retrotransposon insertion as that of the modern varieties in some accessions, the same retrotransposon insertion was also detected in a different site of the GbHD1 gene on Chr.06(A) in some other accessions, indicating that this insertion may have happened in the early days of cotton evolution and the modern varieties carrying the  retrotransposon insertion are the results of the selection during the domestication. Interestingly, we have also observed that in the self-pollinated offspring of some accessions segregation of glabrous vs pubescent stem phenotypes that still correlate perfectly with the same transposon insertion in the HD1 gene, repeatedly confirming that HD1 gene on At sub-genome is critical for epidermal cell growth. In summary, we have found the evidence from gene mapping, gene expression analysis and association analysis that the HD1 gene is an important gene in controlling the outgrowth of epidermal cells into trichome in cotton species, and probably is the  T1 gene controlling the trichome growth on Chr.06(A) recognized by classic genetics. The inter-specific phenotypic difference in stem trichome can largely be attributed to a same type of retrotransposon insertion in the HD1 gene.