Physical and genetic structure of the maize genome reflects its complex evolutionary history

Abstract

Maize (Zea mays L.) is one of the most important cereal crops and a model for the study of genetics, evolution, and domestication. To better understand maize genome organization and to build a framework for genome sequencing, we constructed a sequence-ready fingerprinted contig-based physical map that covers 93.5% of the genome, of which 86.1% is aligned to the genetic map. The fingerprinted contig map contains 25,908 genic markers that enabled us to align nearly 73% of the anchored maize genome to the rice genome. The distribution pattern of expressed sequence tags correlates to that of recombination. In collinear regions, 1 kb in rice corresponds to an average of 3.2 kb in maize, yet maize has a 6-fold genome size expansion. This can be explained by the fact that most rice regions correspond to two regions in maize as a result of its recent polyploid origin. Inversions account for the majority of chromosome structural variations during subsequent maize diploidization. We also find clear evidence of ancient genome duplication predating the divergence of the progenitors of maize and rice. Reconstructing the paleoethnobotany of the maize genome indicates that the progenitors of modern maize contained ten chromosomes.

Figure 1. Dotplot Analysis of the Integrated Maize Map against Rice Pseudomolecules

Synteny blocks were detected, and background noise was filtered with SyMAP [37]. The interactive dotplot can be viewed at http://www.agcol.arizona.edu/symap. When clicking the related synteny block, the detailed window with contig number will pop up. The viewer can select the preferred area and double click the selection, and then a graphic alignment is displayed.

Figure 2. Graphic Display of Two Rounds of Maize Genome Duplication

The picture was captured from the comparative block display of the integrated maize–rice synteny map generated by SyMAP [37]. Green alignment line showed result from overgo markers, and violet line showed alignment from low-copy BES. (A) Recent duplication resulted from ditetraploidization of maize chr4L and 5L with reference to rice 2L. (B) Ancient duplication before maize and rice divergence of maize chr2S and chr10L with reference to rice 2L is presented. (C and D) show that with reference to rice chr4L, recent and ancient duplications have occurred of maize chr2S and chr10L, and chr4L and chr5L, respectively.

Figure 3. Change of Chromosome Numbers during Speciation of Cereals

Based on the dotplot comparison of rice, maize, sorghum, and wheat chromosomes, synteny blocks have been used to assemble progenitor chromosomes of these species. Rice synteny blocks have been color coded. (A) Using the rice color-code sytenic block from Table 3 and Table S4, the chromosomes of the progenitors of maize have been reconstructed. The block names in the figure are the same in Table 3. No change in chromosome number occurred, but an increase of maize chromosome sizes did. (B) Comparison of the relationship of the maize progenitors with sorghum and wheat has been used to reconstruct the changes and conservation of chromosomes during speciation.