Genetic And Molecular Organization Of Bronze Genomic Region Of Maize

Most agriculturally important plants have complex genotypes, consisting of islands of hypomethylated, single-to low copy DNA, where most genes are found, surrounded by repetitive, methylated DNA of unknown function. Little is known about the organization of the key genie regions in such plants. Maize is prototype of higher plant with a complex genome, for which there exists an excellent genetic and cytogenetic knowledge a base. Characterization of well-studied genie regions should help us to understand how the genome is organized at a supragenic level.The bz locus is ideally suited for studying genetic organization in plants. This locus conditions anthocyanin pigmentation in the aleurone layer of the seed and in many parts of the plant. Bz intragenic recombinants occurring at meiosis in bz heteroallelic plants can be selected easily as exceptional purple seeds among the bronze testcross progeny and subjected to a genetic and molecular analysis. A series of Ac elements that transposed from the bz locus to its vicinity have been mapped fairly precisely and have been used as genetic markers. To study the molecular organization of the bz genomic region, we constructed a gene-rich partial bacterial artificial chromosome (BAC) genomic library of maize. Two adjacent BAC clones, which made up a 240kb contig of maize genome centered around the bz locus, were isolated and sequenced. We have found the bz locus lies in an unusually gene-rich region of the maize genome. Ten genes are contained in a 32-kb stretch of DNA that is uninterrupted by retrotransposons. The average intertranscript distance between genes is just lkb, revealing a surprisingly compact packaging of adjacent genes in this part of the genome. The gene-rich region is flanked by the 94kb proximal retrotransposon cluster and the approximately 100kb distal retrotransposon clusters. Recombination is almost 2 orders of magnitude higher in the gene-rich region.The repetitive retrotransposon DNA contributes little if any to genetic length.We sequenced and compared over 100kb from the bz genomic region of two different maize lines and found dramatic differences between them not only in the intergenic retrotransposon cluster make up and location relative to the genes in the bz region, but also in the genes themselves. We also surveyed the organization of the bz region in other inbred lines. Our finding has bearing on the underlying genetic basis of hybrid vigor in maize, and possibly other organisms, and on the measurement of genetic distances in different backgrounds.