Gene expression of a gene family in maize based on noncollinear haplotypes - PubMed (original) (raw)

Comparative Study

. 2003 Jul 22;100(15):9055-60.

doi: 10.1073/pnas.1032999100. Epub 2003 Jul 9.

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Comparative Study

Gene expression of a gene family in maize based on noncollinear haplotypes

Rentao Song et al. Proc Natl Acad Sci U S A. 2003.

Abstract

Genomic regions of nearly every species diverged into different haplotypes, mostly based on point mutations, small deletions, and insertions that do not affect the collinearity of genes within a species. However, the same genomic interval containing the z1C gene cluster of two inbred lines of Zea mays significantly lost their gene collinearity and also differed in the regulation of each remaining gene set. Furthermore, when inbreds were reciprocally crossed, hybrids exhibited an unexpected shift of expression patterns so that "overdominance" instead of "dominance complementation" of allelic and nonallelic gene expression occurred. The same interval also differed in length (360 vs. 263 kb). Segmental rearrangements led to sequence changes, which were further enhanced by the insertion of different transposable elements. Changes in gene order affected not only z1C genes but also three unrelated genes. However, the orthologous interval between two subspecies of rice (not rice cultivars) was conserved in length and gene order, whereas changes between two maize inbreds were as drastic as changes between maize and sorghum. Given that chromosomes could conceivably consist of intervals of haplotypes that are highly diverged, one could envision endless breeding opportunities because of their linear arrangement along a chromosome and their expression potential in hybrid combinations ("binary" systems). The implication of such a hypothesis for heterosis is discussed.

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Figures

Fig. 1.

Fig. 1.

Sequence alignment of the two major haplotypes. The contiguous sequence of the B73 z1C-1 locus determined in this study was aligned with the previously sequenced orthologous region from BSSS53 by using orthologous markers. Conserved sequences are connected by vertical areas. Red arrows indicate polarity and position of zein gene copies. Zein gene copies that have been amplified, two duplications before and one triplication after formation of the haplotypes, are boxed in. Retrotransposons and transposons have been highlighted to illustrate noncollinear sequences and categorized (boxed-in names). Size markers for both contiguous sequences have been integrated to provide relative positions of sequence features.

Fig. 2.

Fig. 2.

Known and hypothetical transacting interactions of the major haplotypes of the z1C-1 locus in maize. Major haplotypes of z1C-1 interval are represented by bars with different color-coded segments that are recognized by specific probes (Inset). The numbers above ORF3 segments indicate different subhaplotypes of this segment. The number of occurrences of a particular haplotype within the core collection (Table 4) and representative inbreds is marked below each bar. Colored bars to the right indicate genes that control the expression of all or subsets of zein genes within each haplotype. Arrows with dotted lines indicate hypothetical interactions to unknown transacting factors.

Fig. 3.

Fig. 3.

Relative z1C gene expression in inbreds and hybrids. Different sets of samples from immature, 18 DAP, endosperm tissue were processed for the measurement of steady-state mRNA levels as described in Materials and Methods. Relative expression levels were determined for each set as shown in Table 2. Bars, color-coded for inbreds and their reciprocal hybrids as shown in the key, represent the average expression levels in percentage of the total 22-kDa zein mRNA mixture with confidence intervals for each gene (Table 2).

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