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Numerous transparent testa (tt) or tannin deficient seed (tds) mutants have been isolated in the model plant Arabidopsis thaliana. These mutants are characterized by a reduction or lack of proanthocyanidins in the testa, resulting in pale brown or yellow seeds. Among the tt mutants, all the corresponding genes have been cloned except for tt9 and 13. As a first step towards determining the identity of the tt9 locus, fine scale genetic mapping was carried out using a mapping population resulting from a cross between tt9 plants in the Landsberg erecta (Ler) ecotype background with wild-type Columbia (Col) plants. Several simple sequence length polymorphism markers were developed, and a large population of plants was analyzed. Extensive analysis of this mapping population suggests the tt9 locus is found in a 140,000 base pair region on chromosome three. According to the TAIR 10 genome release for Arabidopsis, there are thirty-four genes in this region. Several approaches were utilized in an effort to identify which of these genes is the TT9 locus, including sequencing of candidate genes, comparison of steady-state mRNA levels of candidate genes in the parental line and the tt9 mutant, and analysis of T-DNA tagged lines. However, the TT9 locus has not yet been identified based on any of these analyses. This suggests that the mutation of interest may lie in a non-coding region of a candidate gene, in a micro-RNA, or other as-yet-unannotated gene in the mapping interval. The fine-scale mapping described here will facilitate future efforts to identify a definitive causative mutation in this elusive locus, for example, by whole genome sequencing.