Microsatellite repeat variation within the y1 gene of maize and teosinte
--Phelps, TL and Buckner, B

In a previous study we demonstrated that allele?specific length polymorphisms exist in a (CCA)n microsatellite that is present 11-bp upstream of the transcriptional initiation site within the maize y1 allele cloned from the hybrid line Q60 (Phelps and Buckner, MNL 69:84?85, 1995). We have extended this study to include additional maize alleles and one or two accessions of six teosinte species, subspecies or varieties. Sequence analyses demonstrate that the (CCA)n microsatellite varies in repeat number from 3 to 11 (Figure 1 and Table 1). In addition, the (CCA)_n repeat is flanked by the imperfect pentanucleotide repeat (PyCATC; Py = C or T). Three different organizations of the pentanucleotide repeat were observed (designated types 1, 2 and 3 in Table 1). Type 1 contains both the (CCATC) and (TCATC) sequence duplicated as well as a trinucleotide CTG repeated 33 bp 5' of the (CCA)_n repeat. Types 2 and 3 contain three copies of the pentanucleotide repeat but differ by a single base in the first repeat. We have further subdivided these categories based on the number of (CCA)_n repeats found. The only sequence variability found within the (CCA)_n repeat was a C to T transition in the second and fifth (CCA)_n repeats of type 3a and 3c, respectively. In total, 12 different sequence polymorphisms were observed in this study (Figure 1 and Table 1). Therefore, the (CCA)_n microsatellite, as well as the sequence directly adjacent to it, exhibit a high degree of variability.

Table 1. Sequence organization of the microsatellite-containing region of the y1 gene of maize and teosinte.

Figure 1. Sequence of the microsatellite?containing region of the y1 gene of maize and teosinte. Abbreviations are as follows: Q60, an allele present in the maize stock designated Q60, which is a hybrid of inbred lines Q66 and Q67; H99, M14 and B73, alleles present in inbred lines H99, M14 and B73 respectively; y1?8549 and y1?wmut, alleles described by Robertson and Anderson (J. Hered 52:53?60, 1961); y1?stand, standard recessive allele of y1, y1?lem, y1?lemon yellow provided by GF Sprague; BMS, Black Mexican Sweet; Straw, Strawberry popcorn; KWF, Knobless Wilbur's Flint; Z.h (441934), Z. mays var. huehuetenangensis (PI 441934); Z.h (21880), Z. mays var. huehuetenangensis (Ames 21880); Z. par, Z. mays ssp. parviglumis; Z.m (384060), Z. mays ssp. mexicana (PI 384060); Z.m (566681), Z. mays ssp. mexicana (PI 566681); Z.p (21875), Z. perennis (Ames 21875); Z.p (21881), Z. perennis (Ames 21881); Z.d, Z. diploperennis; Z.l, Z. luxurians. An asterisk indicates the same base as that found in the Q60 allele. A hyphen indicates the base found in the Q60 allele was not present.

Each of the annual teosinte types analyzed in this study can be distinguished based on the sequence of the microsatellite-containing region of y1 (Figure 1 and Table 1). In addition, sequence polymorphisms that flank the microsatellite region of y1 allow the two accessions of Z. mays ssp. mexicana and Z. mays var. huehuetenangensis to be distinguished (Figure 1 and Table 1). The perennial teosintes Z. diploperennis and Z. perennis (Ames 21881) were found to exhibit the type 3d organization of the pentanucleotide repeat with 3 (CCA) repeats, which was the least number of repeats observed. However, another accession of Z. perennis (i.e., Ames 21875) exhibited type 3c organization of the pentanucleotide repeat containing 6 (CCA) repeats. Therefore, the (CCA)_n repeat number is variable within this Zea species. Interestingly, the sequence flanking this region in Z. perennis Ames 21875 could be distinguished from that of the Z. may ssp. mays type 3c sequences by polymorphisms that flank the microsatellite (Figure 1 and Table 1). Further analysis of teosinte will be necessary to determine if the degree of variability in this region of the y1 gene is sufficient to make it a good marker for studying genetic variability within and among populations of teosinte. 

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