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Detection and Sequencing of the Transposable Element ILS-1 in the Illinois Long-Term Selection Maize Strains

Restriction fragment-length polymorphism analysis performed on 100 FJ families derived from a cross of the IHP x ILP maize (Zea mays L.) strains detected a QTL linked with the Sh2 gene (Bhave et al., 1990; Shaw and Hannah, 1992) with large additive effects on starch concentration (Goldman et al., 1993). Sh2 encodes the large subunit of ADP-Glc pyrophosphorylase, which is involved in the rate-limiting step of starch biosynthesis in plants (Stark et al., 1992). Since it is known that major mutations at the Sh2 locus of maize greatly reduce starch levels in the endosperm through its effect on the starch synthetic enzyme ADP-Glc pyrophos-phorylase, we decided to determine if different Sh2 alleles were present in the ILP and IHP parents of the mapping population that exhibited a QTL for starch concentration at Sh2. During intron Sequence analysis this insertion is a new transposable element, which have designated ILS-1 because it was isolated from the Illinois Long-Term Selection Experiment maize strains. The ILS-1 element is inserted 4991 bp downstream of the transcription start site of the ILP Sh2 allele. The ZLS-1 element is 1248 bp in length and has 13-bp nearly perfect (12 of 13 bp) TIRs. This element is rich in A (30.6%) and T (37.9%)