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Ancestral Rice Blocks Define Multiple Related Regions in the Maize Genome

W. Odland and R. Phillips, Univ. of Minnesota, Agronomy and Plant Genetics Dep., 411 Borlaug Hall, 1991 Upper Buford Cir., St. Paul, MN 55108; Andrew Baumgarten, Pioneer Hi-Bred International, Inc., 19456 State Hwy. 22, Mankato, MN 56001. Funding for this project came from the National Science Foundation under Grant No. 0110134 and the McKnight Presidential Chair in Genomics

View larger version (27K): [in this window] [in a new window]   Fig. 1. Increasing synteny detection. Dots on these Oxford grids denote homologous sequences plotted by their genomic locations on duplications (Dup.) 1 and 2. Diagonals are observed between regions having a colinear arrangement of homologous sequences and define synteny. (A) Direct comparison between the diverged duplications reveal a weak diagonal composed of only four data points. (B) Comparisons between Dup. 1 and 2 with a reference that simulates a common ancestor, revealing stronger diagonals with eight and 10 data points, respectively. Dup. 1 and 2 are defined as related by both regions being syntenic to the same portion of the reference.

View larger version (31K): [in this window] [in a new window]   Fig. 2. Evolutionary divergence and ancestral simulation. Represented here is a genomic duplication, its diploidization, and an illustration of how the ancestral gene arrangement is simulated from the diverged duplicated regions. Vertical bars with horizontal lines represent chromosomal segments and genes. Dashed lines connecting matching colored lines identify homologous genes. (A) Two identical genomic segments, 1 and 2, are created from a duplication event. (B) The effects of the diploidization process have reduced the similarities between the duplicate regions to only four colinear homologous sequences. (C) An ancestral gene arrangement is simulated by condensing the two related regions into one. The genes in the simulated, ancestral region are arrayed by their relative spacing between homologous anchor points. (A and C) A comparison of the simulated ancestral region with the original shows how the computational condensing of two diverged, related regions can model their original progenitor.

View larger version (64K): [in this window] [in a new window]   Fig. 3. Rice–rice synteny. This Oxford grid displays the homologous sequences within the rice genome plotted by the physical locations. In the upper-right half of the grid all homologous sequences within the rice gene models are plotted by their locations. Enlarged dots identify the syntenic regions. The lower-left portion of the grid displays the 16 identified syntenic regions which are labeled by the ancestral rice block (ARB) that represents them. Syntenic regions that have significance (P < 0.05) are colored red, while syntenic regions that had P values greater than 0.05 are green. ARB 17 is not displayed because it is a composite of the remaining nonduplicated regions not incorporated into ARBs 1–16.

View larger version (48K): [in this window] [in a new window]   Fig. 4. Direct comparison of rice–maize synteny. (A) Homologous sequences between the rice and maize chromosomes are displayed in an Oxford grid. Enlarged dots represent syntenic regions. The different colors for the syntenic regions are associated with each of the rice chromosomes. (B) Compacting the Oxford grid into linear maize chromosomes emphasizes the complexity of defining relationships with the duplicated rice genome. The synteny to each rice chromosome in the Oxford grid is compressed into a color highlight on the linear maize chromosomes. Multiple rows represent overlapping rice syntenic regions.

View larger version (37K): [in this window] [in a new window]   Fig. 5. Multiple related copies in maize. Synteny to the ancestral rice blocks (ARBs) defines multiple related copies within the maize genome. (A) Homologous sequences are plotted by their location on maize chromosomes and placement in ARBs. Enlarged colored dots denote syntenic regions. (B) A condensed view of the synteny between the maize chromosomes and the ARBs is presented along the bottom. A linear display of the maize chromosomes with the synteny to the ARBs highlighted by their respective colors reveals multiple related copies within the maize genome. The ARBs, being devoid of major duplications, identify the remnants of the duplication events in the maize evolutionary lineage.