Differential Gene Expression and Epiregulation of Alpha Zein Gene Copies in Maize Haplotypes

Abstract

Multigenic traits are very common in plants and cause diversity. Nutritional quality is such a trait, and one of its factors is the composition and relative expression of storage protein genes. In maize, they represent a medium-size gene family distributed over several chromosomes and unlinked locations. Two inbreds, B73 and BSSS53, both from the Iowa Stiff Stock Synthetic collection, have been selected to analyze allelic and non-allelic variability in these regions that span between 80–500 kb of chromosomal DNA. Genes were copied to unlinked sites before and after allotetraploidization of maize, but before transposition enlarged intergenic regions in a haplotype-specific manner. Once genes are copied, expression of donor genes is reduced relative to new copies. Epigenetic regulation seems to contribute to silencing older copies, because some of them can be reactivated when endosperm is maintained as cultured cells, indicating that copy number variation might contribute to a reserve of gene copies. Bisulfite sequencing of the promoter region also shows different methylation patterns among gene clusters as well as differences between tissues, suggesting a possible position effect on regulatory mechanisms as a result of inserting copies at unlinked locations. The observations offer a potential paradigm for how different gene families evolve and the impact this has on their expression and regulation of their members.

Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads

“…We have previously sequenced these regions in two maize inbreds, B73 and BSSS53, using overlapping BAC clones (23)(24)(25). Although we already know that maize inbreds are quite diverse, we thought that it might be quite useful to compare chromosomal regions between two different heterotic groups.…”

“…In maize, there are six loci of alpha zeins, each representing a subfamily, distributed over three chromosomes (23) (Fig. 1).…”

“…Our results show that the different inbreds not only exhibit CNV but also genotype-specific expression patterns. In B73, there are seven z1B genes expressed, z1B-1, -2, -3, -4, -5, -6, and -9 (23,35). In W22, the number of expressed z1B genes is the same.…”

“…It was reported that older copies became damaged and new copies account for the majority of the expression of zein genes (23). The older copies at the W22 z1A1 locus (i.e., z1A1-1, -8, and -9) are not expressed because of a premature stop codon (z1A1-1), a missing A at the start codon (z1A1-8), or severely truncated 3′ end (z1A1-9 is only 340 bp long) in three inbred lines.…”

“…Tandem amplification of zein gene copies at each locus was followed by the insertion of transposable elements, resulting in the divergence of each locus (23). The percentage of retrotransposon at the BSSS53 z1A1 locus is 70%, whereas the percentage of transposon or retrotransposon space in B73 is similar to that of W22 (55%) ( Table 1).…”