The cloned yl locus of maize was sequenced and found to encode phytoene synthase. Different “wild-type” alleles of the locus were found to differ by the insertion of transposable elements in their promoter and polyA addition regions, and by the length of a CCA tandem repeat series, without any obvious effect on function of the gene. A dominant Yl (“wild-type”) allele was observed to be expressed at highest levels in the seedling but also in the embryo and endosperm. The Mu3 transposable element insertion responsible for a pastel allele of yl, which gives lowered levels of carotenoids in the endosperm of kernels and seedlings grown at high temperatures, was located in the 5′ end of the gene. Although the size of the transcript from this yl mutation suggests that the Mu3 element provides the promoter for this allele, leaf tissue in this mutant line contained approximately normal amounts of yl mRNA. A recessive allele of yl, which conditions normal levels of carotenoids in the embryo and seedling, but almost no carotenoids in the endosperm, was found to accumulate normal amounts of yl mRNA in the seedling and embryo, while yl transcripts were not detected in the endosperm.