The Structure of the Maize Genome

Agriculture is reaching a new era. While in the past, breeding was based on phenotypes, future breeding will be based on knowledge of the genotype. Therefore, the future of agriculture is written into the genome. What conventional breeding cannot achieve is to separate and combine one or a select few genes with the rest of the genes, because during crossing all genes of one parent are transmitted, even those that could neutralize the benefit of another one. But how would one identify single genes of interest and their regulatory components within the total gene pool? Recent estimates are that the maize genome contains between 42,000 and 56,000 genes (Haberer et al. 2005). To identify a gene of interest could be like finding a needle in a haystack. While it has been possible to clone genes based on their gene products or their function, they only represent a tiny portion of the entire gene set. To obtain knowledge about all genes in the genome requires first that we know their structures and position in the genome.

The first genome of a flowering plant that was sequenced was Arabidopsis thaliana, mainly because it has one of the smallest genomes (Arabidopsis Genome Initiative, 2000). Furthermore, it was assumed that the C-value paradox teaches that the complexity of a multicellular organism was not proportional to the size of its genome (Thomas 1971). In other words, the smaller genome could serve as a reference gene set for the larger ones. However, many of the most important crop plants on earth belong to the monocotyledons, and Arabidopsis belongs to the dicotyledons. Indeed, it became clear that the sequence of the Arabidopsis genome is too distant to serve as a reference to monocot crop species. On the other hand, unique genes of the Poaceae, a monocot family, also known as the grasses, are conserved across these species to a degree that they could be used as heterologous probes to detect homologous gene sequences. Therefore, cross-hybridization of genetically mapped gene sequences made it possible to examine syntenic relationships among Poaceae (Hulbert et al. 1990; Whitkus et al. 1992; Ahn and Tanksley 1993). Because this family includes the cereals, it became possible to align entire chromosomal segments of the most important crops regardless of the sizes of their genomes (Moore et al. 1995; Gale and Devos 1998).