Ten nucleotide differences exist between Pl and Pl-Bh within a 7 kb region
--Owen A. Hoekenga and Karen C. Cone

Pl and its allele Pl-Bh are regulatory genes in the anthocyanin biosynthetic pathway. Pl conditions uniform purple pigment in the vegetative parts of the plant. Pl-Bh conditions pigment in the vegetative parts of the plant, as well as in the aleurone of the kernel. This pigmentation is not uniform, but variegated. Thus, relative to Pl, Pl-Bh has both a gain of function Ð increased tissue specificity Ð and a loss of function Ð variegated expression. We assumed that this striking difference in phenotypes would be mirrored by an equally striking difference in DNA sequence. Initial studies did not confirm this hypothesis; Pl-Bh has a single nucleotide insertion, approximately 630 bp downstream of the stop codon, relative to Pl (Cocciolone and Cone, Genetics 135:575, 1993). To extend the sequence analysis, I sequenced an additional 2.5 kb region upstream of the gene. Within this region, there are nine nucleotide differences. Over the 7 kb sequenced to date, there are ten nucleotide differences between Pl and Pl-Bh, as summarized below.

Relative to Pl-Bh, Pl has the following sequence differences: single nucleotide deletions at sites 1, 4, and 7; single nucleotide insertions at sites 3 and 5; two single nucleotide insertions, two nucleotides apart, at site 6; two cytosine to thymine transitions and a single nucleotide insertion within a twenty-five nucleotide span at site 2. We do not yet know if these ten nucleotide differences are responsible for the difference in phenotype observed between Pl and Pl-Bh. We are investigating this possibility as well as alternative hypotheses to explain the observed differences between Pl and Pl-Bh (see also Muszynski and Cone, MNL this issue).

Figure 1.  Restriction map of P1 and P1-Bh showing location of differences. E, EcoRI;  B, BamHI.

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