Gold maize was made by the ancient people of Peru, like the Moche Culture, because they ate corn. Corn, or maize (Zea mays L.) among scientists, is now one of our planet's top crops. It is both food for billions of people and livestock and feedstock for biofuels and other products. Scientists, having sequenced already other plants such as rice, sorghum, poplar, grape, and Arabidopsis thaliana, have recently developed the Maize (Corn) Genome for future applications.
"Sequencing the corn genome will help researchers in the United States and around the world develop corn varieties to confront critical global challenges like climate change, hunger, and renewable energy," said Edward Knipling, administrator of USDA's Agricultural Research Service. "This effort will provide scientists a preliminary blueprint for identifying genetic pathways that will lead to a better understanding of corn and enable scientists to improve corn in a number of ways."
The Maize Genome: several aspects of the genome, including gene content, repeat content, genetic recombination, methyl-filtration, cross-species orthology, and centromere localization. [Historic Image]
The scientists sequenced a variety of corn known as B73 that was developed at Iowa State University for high grain yields and is used in both commercial corn breeding and research laboratories. The genetic code of corn consists of 2.3 billion DNA base-pairs; thus it is similar (79%) in size to the human genome, which contains 2.9 billion letters. Nevertheless, it is noteworthy that about 85 percent of the DNA segments are repeated in the B73 genome. Sequencing was also complicated by jumping genes, or transposons, that move from place to place make up a large portion of this genome.
A working draft of the maize genome had identified in 2008 the plant had more than 50,000 genes. After locating the many thousands of DNA segments onto chromosomes in the correct order and closing the remaining gaps, the same scientists revised the number of genes down to some 32,500, or about one-third more than the human genome. The Maize Genome distributes its estimated 32,500 genes unevenly along 10 chromosomes.
Wei Zhang et al., for example, describe in their paper the physical and genetic framework of the Maize B73 Genome. "After removal of sequence overlap and ordering and orienting sequence contigs within the overlapping regions," they say the scientists "were able to generate a maize AGP [a golden path] composed of 2048 Mb of pseudomolecule sequences in 61,161 scaffolds from 125,325 sequence contigs, which covers ~97% of the 2120-Mb physical map."+ Given below is their Table 3 to summarize "the sizes, scaffolds, and contig number of each maize chromosome plus those that are unanchored." The AGP and maize B73 RefGen_v1 are both available at: http://www2.genome.arizona.edu/genomes/maize .
Table for B73: Sequence summary of the maize chromosomes in B73 RefGen_v1. [Historic Data]
In addition, a large survey of genetic diversity in maize has produced a new gene map. Known as a haplotype map, this map charts genetic diversity and recombination across the genome of 27 inbred lines of maize. If the goal of the Maize Genome Sequencing project was to generate a reference genome sequence that was integrated with both the physical and genetic maps, then the recent publications appear to have met that goal. Solving the Maze ** by Catherine Feuillet et al. summarizes not only what was accomplished during the four years but also its significance in plant breeding.
One question remains on the gold standard for the maize genome: is the gene space of B73 (gene sequences and adjacent regulatory regions) finished quality to the Bermuda standard(s)?
Notes:
Photo 1 Credit: Wikipedia.
*P. S. Schnable et al., Science 326, 1112 (2009).
+Wei F, Zhang J, Zhou S, He R, Schaeffer M, et al. 2009. PLoS Genet 5(11): e1000715. doi:10.1371/journal.pgen.1000715
**C. Feuillet, K. Eversole, Science 326, 1071 (2009).
Photo 2 Credit: Iowa State University.
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