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Published online 1 November 2006
Published in Crop Sci 46:S-41-S-48 (2006)
© 2006 Crop Science Society of America
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REVIEW & INTERPRETATION

Ancestral Rice Blocks Define Multiple Related Regions in the Maize Genome

Wade Odland*, Andrew Baumgarten and Ronald Phillips

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

* Corresponding author (odla0014{at}umn.edu).


   ABSTRACT
TOP
 NOTES
 ABSTRACT
INTRODUCTION
 Materials and Methods
 Results
 Discussion
 REFERENCES
 
A simulated ancestral reference genome identifies the remnants of the complex evolution of the maize (Zea mays L.) genome. Syntenic regions were defined in Oxford grid comparisons by the analysis of diagonals from colinear arrangements of homologous sequences between chromosomes. A program called Crush and Compare was developed to manage the identification of syntenic regions, create ancestral gene arrangements, and create Oxford grids for graphical displays. Seventeen ancestral gene arrangements were created by computationally condensing the synteny within rice (Oryza sativa L.) into ancestral rice blocks (ARBs), simulating the nonduplicated state of all grass genomes. Permutation analyses found 14 of the rice syntenic regions to be significant with P < 0.05 and were used to identify the genomic duplications present in grass genomes. Synteny analysis of the ancestral gene arrangements within the ARBs revealed a new ancient duplication in the rice genome. An analysis with the maize genetic map identified 54% of its genome syntenic with the ARBs. Multiple evolutionarily related copies of the ARBs were identified in maize with an average of 3.0 related copies with a range of 1 to 6. Use of the ARBs as a reference for maize supports the theory of the maize genome once being an ancient tetraploid composed of genomes that also contained genomic duplications. Defining the genomic relationships within maize and between rice and maize can improve candidate gene discoveries.


   INTRODUCTION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
Materials and Methods
 Results
 Discussion
 REFERENCES
 
POACEAE (GRASSES) is a large angiosperm group that diverged from a common ancestor approximately 70 million years ago (Paterson et al., 2004; Kellogg 1998). Comparisons between these grass genomes have identified large structural similarities in their genomic organization (Gaut, 2001; Moore et al., 1995; Bennetzen and Freeling, 1993; Devos 2005; Appels 2002; Ahn et al., 1993; Helentjaris et al., 1988). Grass genomes contain large regions of conserved homologous sequences. Regions having colinear arrangements of homologous genes, also known as syntenic regions, are presumed to have evolved from a common ancestor. Therefore, synteny between different genomes defines their evolutionarily related regions, while synteny within a given genome defines a genomic duplication. The mechanisms by which these syntenic regions arose are speciation and large-scale genomic duplication events. Thus, detection of syntenic regions is important for understanding the evolutionary history of the grass genomes and taking advantage of their commonalities in comparative genomics and candidate gene discoveries. However, our ability to detect syntenic regions has decreased across evolutionary time because of genomic disturbances, such as differential loss of homologous sequences and local chromosomal inversion events, which degrade syntenic identification (Ma et al., 2005; Vision, 2005).

Comparisons that use a common reference genome can be used as a method for improving this identification of evolutionary relationships between diverged genomic regions. If the homologous sequences between related regions have become too diffuse, then identifying syntenic regions by direct sequence and gene order comparisons becomes nearly impossible. In the grasses, the rice genome has been used as the reference for comparisons (Moore et al., 1995; Devos, 2005; Devos and Gale, 2000). The rice genome has been fully sequenced (Matsumoto et al., 2005), leading to a high marker density that improves the detection of syntenic regions. Using the high marker density rice genome as a common reference defines evolutionary relationships between genomes that can be difficult to identify in direct comparisons. For example, an evolutionary relationship is defined between two genomes if they are both syntenic to the same portion of the common reference genome (Fig. 1 ). This use of a reference genome in genomic comparisons can improve the elucidation of evolutionary relationships between two genomic regions that would give negative results in a direct comparison because of diffuse amounts of homologous sequences.


Figure 1
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  		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.

 
Despite the fact that many studies use the rice genome as a reference, the rice genome is in fact not the ideal common reference for comparisons among the grass genomes because of its diverged genomic duplications. One or more duplication events in the evolutionary history of the rice genome have resulted in approximately 50% of its transcriptome to be in genomic duplications (Paterson et al., 2004; Guyot and Keller, 2004; Wang et al., 2005). Duplicate regions deviate from each other through gene loss, sequence divergence, and local rearrangements. These evolutionary changes result in the diploidization of duplicate regions, which return them to a diploid-like state (Gaut et al., 2000; Vision, 2005; Vision et al., 2000; Wang et al., 2005; Van de Peer et al., 2001). What genes are lost and where local rearrangements occur during diploidization differ between genomic lineages. The unique results of each genome's diploidization process complicate the use of an evolved genome as a model system (Tarchini et al., 2000). These evolutionary changes between the duplicate regions of rice diminish their ability to identify synteny to the same evolutionary related regions in genomic comparisons.

The identification of evolutionary relationships can be improved by using the genome of a common ancestor as a reference. Synteny directly defines evolutionary relationships but the synteny between evolutionary relationships may be masked by evolution differences. The direct comparison between two diverged genomic segments can only reveal synteny using the sequences retained in both genomic regions (Ma et al., 2005). This dependency on both evolutionary histories accentuates the genomic differences by applying the evolutionary time of both genomic lineages to the comparison. In contrast, comparisons to a reference genome that is a common ancestor have only the effects of one lineage in the analysis, emphasizing what has been conserved in each genome. Thus, use of a common ancestral genome as a reference increases the detection of evolutionary relationships by focusing on what has been conserved from the common ancestor instead of only evaluating what was retained in two genome lineages.

The detection of evolutionary relationships can be improved not only by focusing on what has been retained in a genome but also by allowing for disturbances in the colinearity of homologous sequences. Previous genomic comparisons have underestimated evolutionary relationships because of the inability to accommodate local rearrangements that can disrupt the colinearity of homologous sequences. Synteny definitions that use a strict requirement of homologous sequences being in a colinear arrangement are vulnerable to underestimating the size of syntenic regions (Gaut, 2001). The reduction in size, and consequently the number of data points, of a syntenic region directly impacts its statistical significance. A larger syntenic region results in more data points defining it, which reduces the probability that the observed colinearity could have occurred by random chance.

A robust method of defining synteny in genomes that have disruptions in their colinearity of homologous sequences is by the quality of a diagonal that forms in genomic comparisons using an Oxford grid. An Oxford grid is a comparative-mapping tool that displays homologous sequences between two chromosomes on a two-dimensional grid (Fig. 1). DiagHunter (DH; Cannon et al., 2003) is a program that identifies such diagonals and measures their quality for defining a syntenic region based on the number and distribution of homologous sequences defining them. A major advantage to DH's approach to synteny analysis is its ability to deal with minor gene rearrangements that occur within syntenic regions.

In this study, we use DH to define the synteny between the maize genome and an ancestral grass genome to better define the remnants of maize's multiple duplication events. Previous studies have underestimated maize's duplication complexity and copy number. The ARBs were created (Fig. 2 ) to simulate gene linkage groups of the common grass ancestor before its major duplication event {approx}70 million years ago (Paterson et al., 2003). The comparisons of maize chromosomes and ARBs reveal several previously undetected evolutionary relationships within the maize and rice genomes while also defining the multiple relationships between the duplications of the respective genomes.


Figure 2
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  		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.

 

   Materials and Methods
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and Methods
Results
 Discussion
 REFERENCES
 
Sequence Homology
From The Institute for Genome Research (www.TIGR.org, verified 11 July 2006), 61 250 gene models were obtained for the rice pseudomolecules version 3.0. The 7873 sequenced markers on the maize IBM2 2004 neighbors genetic map were retrieved from Genbank (www.ncbi.nlm.nih.gov/Genbank, verified 11 July 2006). Gene model and marker sequences were compared for similarity using BLASTn under the default criteria (Altschul et al., 1990). Sequence pairs having e-values < e–10 were defined as homologous. Sequences that were found to have five or more homologs within their own genome were assumed to be part of a gene family and removed from synteny analysis.

Identifying Synteny
Syntenic regions were defined using DH (Cannon et al., 2003) as regions having near-colinear arrangements of homologous sequences that collectively surpass a quality measurement. DiagHunter calculates a diagonal quality for a syntenic region from the intervals between homologs (data points) defining a syntenic region. A minimum number of data points were required before a diagonal was classified as a syntenic region. Tandem arrays of sequences, defined as e-values < e–70 and clustered within 0.2% of a chromosome's length, had only one locus contributing to the diagonal quality calculations.

The differences of scale between centimorgan (cM) and base pair (bp) maps were normalized by the use of a common scale. The scales of the maize genetic and rice sequence maps were each normalized to equal 10 billion map units. This conversion retained the original marker distributions along the chromosomes while proportionally adjusting each chromosome's size. The inherent differences between genetic and sequence maps, based on recombination rates and physical locations, respectively, are still present after the conversion of the map scales. The rice chromosome physical sizes were obtained from the length of the respective pseudomolecules (www.TIGR.org, verified 11 July 2006). The maize chromosome proportions were inferred from the length of each chromosome's genetic map. The ARBs as a set were also normalized with each block size adjusted by its proportion of gene models.

The probability for a syntenic region and the false positive rates were calculated from 10 000 permutations of each dataset. A syntenic region's probability was scored as the proportion of permutation runs that identified syntenic regions with the same number of data points. The false positive rate for the DH settings was calculated as the average number of identified diagonals per chromosome comparison in the permutations with the average number of data points in each diagonal indicating the minimum size requirement.

The ARBs, used as an ancestral reference genome, defined the complex duplicate structure of the maize genome.

Condensing Genomic Duplications
A Perl script, called Crush and Compare, was developed to condense syntenic regions into blocks emulating the ancestral gene order (http://corn.ccgb.umn.edu, verified 22 Aug. 2006). Crush and Compare used the data points that defined the syntenic relationships as anchors to align related regions. Homologous sequence pairs defining syntenic regions were arrayed in tandem. All nonduplicated sequences lying between homologous anchor points were arrayed according to their proportionate location between the homologous anchors. After all syntenic regions were condensed a final composite block was created of the remaining nonduplicated regions not included in any other ARB. All Oxford grids were created using the Crush and Compare program which places a red and blue "CC" logo in the upper left corner of the grids.


   Results
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and Methods
 Results
Discussion
 REFERENCES
 
Rice–Rice Synteny Criteria
DiagHunter identified synteny within the rice genome as those regions that possessed at least seven homologous sequences (data points) and had a diagonal quality score of 10 or less. Rice gene models (coding sequences) deciphered from The Institute for Genome Research rice pseudomolecules version 3.0 (www.TIGR.org, verified 11 July 2006) represented the rice genome. The 61 278 rice gene models were analyzed for homologous sequences and syntenic regions. The majority of rice genome duplications encompassed at least a third of a chromosome (Fig. 3 ). Fourteen of the 16 syntenic regions identified by DH were found to be significant with P values < 0.05 (Table 1) and included 51.7% of the rice gene models.


Figure 3
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  		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.

 

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  		Table 1. Rice–rice synteny.

 
The syntenic regions identified in 10 000 permutations of the rice–rice dataset were used to estimate the false discovery rate of the DH settings. The false discovery rate for the rice–rice synteny criteria setting was 1.15 ± 0.006 diagonals per chromosome comparison with an average of 16.9 ± 0.03 data points defining them. The syntenic regions found in the true dataset were much larger having an average of 48.9 ± 18.3 data points.

Simulating Ancestral Rice Blocks
All identified syntenic regions within the rice genome were condensed into ARBs (Supplemental Table 1). Fourteen syntenic regions were identified as significant (Table 1) and condensed into ARBs to represent the ancestral gene arrangements for the duplications found in all grass genomes. The syntenic regions used to create ARBs 15 and 16 were not significant in the permutations probably because of the low number of data points defining them. A final block, ARB 17, was created composed of the remaining nonduplicated portions of the rice genome. ARBs 15 through 17 were retained in the analysis to create a complete set of ARBs that represent all the rice genes in an ancestral arrangement devoid of macroduplications.

Synteny analysis was also done on the ARBs to look for the presence of duplications between the ancestral gene arrangements. An undiscovered duplication was identified in the rice genome between chromosomes 2, 6, 8, and 9 by synteny between ARBs 3 and 6 (Supplemental Fig. 1). This synteny between the blocks is composed of 1.6% of the rice gene models and has a P value of 0.0001.

Comparative Genomics
The maize genome, represented by 7873 sequenced markers on the IBM2 neighbors map set (www.maizegdb.org, verified 11 July 2006), was compared with the rice gene models for identification of homologous sequences and syntenic regions. The rice–maize synteny analysis identified 42 syntenic regions between rice and maize chromosomes. Eighty-eight percent of the identified syntenic regions were significant (P < 0.05; Supplemental Table 2). The syntenic regions covered 68.1% of the maize genetic map and 47.8% of the rice gene models. The synteny criteria settings for the rice–maize dataset had a false positive rate of 0.16 ± 0.001 diagonals per chromosome comparison.

The ARBs, used as an ancestral reference genome, defined the complex duplicate structure of the maize genome. Sixty-three maize genomic regions were found syntenic to the ARBs (Supplemental Table 3, available at http://crop.scijournals.org/) by DH. The significant ARBs, 1 through 14, represented the grass genome duplications and identified 41.5% of the maize genetic map as syntenic. Fifty-two percent of these syntenic regions were found significant with P < 0.05 in the permutations. The ARBs having synteny with the maize genome had an average of 3.0 ± 0.74 evolutionarily related copies within the maize genome with a range of one to six copies.

The three remaining ARBs that do not represent the grass genome duplications were also compared with the maize genome to complete an ancestral genome comparison within maize. As a whole, the ARB 17 does not represent an ancestral gene arrangement because of its composite nature, but the nonduplicated rice segments that compose it do. These nonduplicated rice segments identified 29 syntenic regions within the maize genome. Twenty-six percent of these syntenic regions were syntenic to overlapping portions of ARB 17 to identify two to four evolutionary related copies within the maize genome. Overall, the synteny analysis with DH using the complete ARB set as a reference identified 53.9% of the maize genetic map as being syntenic.


   Discussion
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and Methods
 Results
 Discussion
REFERENCES
 
Ancestral Rice Blocks as a Reference and Synteny Detection
This study takes advantage of the high marker density from the sequenced rice genome to improve the analysis of the duplications within the maize genome. Genomic duplication analysis based solely on the comparison within a genetic map is limited to the markers with more than one mapped loci. Comparisons between two different genetic maps are prone to missing syntenic regions by not having the homologous sequences mapped in both maps (Gaut, 2002; Devos and Gale, 2000), while the use of a reference with a high marker density improves the potential of identifying homologous sequences (Fig. 1). The most complete list of coding sequences, and thus the highest marker density, for a grass genome is the gene models representing the coding sequences deciphered from the rice pseudomolecules. Using this complete set of coding sequences as a common reference reduces the effects of the maize genetic map marker bias in synteny detection.

The ultimate common reference for genomic comparisons is not only a complete set of coding sequences but also an ancestral gene arrangement. A comparison between a genome and its ancestral genome differ only by the evolutionary changes that have occurred in the evolved genome's lineage. Direct comparisons have the impact of both genomes' evolutionary time. For example, a comparison of rice and maize chromosomes have {approx}90 million years of evolutionary effects present as a result of the two genomes being diverged {approx}45 million years ago from a common ancestor. The ARBs simulate gene arrangements of the rice genome {approx}70 million years ago before the major duplication of all grass genomes (Paterson et al., 2004). Thus, genomic comparisons using the ARBs as a reference have less divergence in the comparisons than direct comparisons of extant genomes and increase the detection of evolutionarily related regions.

The design of the ARBs was to maximize their homology to evolutionarily related regions. The incorporation of all sequences within defined syntenic regions into an ARB improves the potential of finding a homologous match. The homologous sequences between two syntenic regions were used as anchors to align syntenic regions. Both homologous sequences were consecutively incorporated into the ARBs to imitate tandem duplications and retain the evolved sequence diversity. Because DH is designed to handle tandem duplications, the incorporation of both homologs does not inflate the detection of syntenic regions.

The analysis of synteny by DH is robust and allows flexibility for evolutionary changes. A local shuffling of genic sequences is common between evolutionarily related regions (Song et al., 1995; Pontes et al., 2004; Vision, 2005). The robustness in synteny analysis by DH comes from evaluating only homologous sequences that form a diagonal and excluding the erroneous number of transposed sequences. An overall robustness of the analysis by DH is evident by nearly symmetrical results from reciprocal comparisons.

Simplifying the Duplication Complexities
Although the rice and maize chromosome comparison defines many syntenic regions, the relationship between the duplications in each genome is masked by evolutionary changes. For example, rice chromosome 1 has synteny to maize chromosomes 3, 6, and 8 (Fig. 4 ). Rice chromosome 5 is syntenic to portions of maize chromosomes 3, 4, and 6. The chromosomes 1 and 5 of rice are largely syntenic with their duplications represented by ARBs 1 and 11. Synteny analysis using ARBs 1 and 11 as common references identified how maize chromosomes 3, 6, and 8 are related to each other while also defining their evolutionarily relationship to rice chromosomes 1 and 5 (Fig. 5 ). The relationship between maize chromosomes 3 and 8 and chromosomes 6 and 8 have been identified before using maize genetic maps and comparisons to the rice genome (Gaut, 2001; Salse et al., 2004; Gale and Devos, 1998; Ahn et al., 1993; Helentjaris et al., 1988; Wilson et al., 1999). A similar analysis by Salse et al. (2004) revealed the complexity in synteny analysis between duplications present in the maize and rice genomes. The ancestral gene arrangements used as a reference simplify this complexity to define the evolutionary relationship of the rice duplications to the multiple related copies in the maize genome.


Figure 4
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  		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.

 

Figure 5
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  		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.

 
This enhanced analysis of the maize genome duplicate structure has revealed the remnants of its ancient tetraploid state that was created from two genomes that would have already contained duplications. Comparisons among the grass genomes using the rice genome as a reference reveal that the genes have been retained in block-like structures (Moore et al., 1995). The evolution theories of the maize genome indicate that some of the duplications within the maize genome are the remnants of a tetraploidization event {approx}11 million years ago (Gaut and Doebley, 1997; Wilson et al., 1999; Swigonova et al., 2004), while the grass family had a duplication event {approx}70 million years ago. Putting all of these observations together predicts that maize would have more than two evolutionarily related copies of the duplications common to all grass genomes. Our result of 3.0 average evolutionarily related copies of the grass genome duplications in maize supports this prediction and increases the knowledge of what evolutionary events occurred in the maize genome. The range of one to six evolutionarily related copies within the maize genome points to a further restructuring of the genome, besides a straightforward doubling of the genome, which needs to be studied.

This improved understanding of the multiple genomic relationships between rice and maize genomes through an ancestral reference genome also improves candidate gene searches. Analysis of the regions in the rice genome that are related to a maize quantitative trait locus (QTL) can produce a list of candidate genes that confer the phenotype of interest (Chardon et al., 2004; Ma et al., 2005; Tarchini et al., 2000). Given that approximately 50% of the genes in duplicated regions randomly lose one copy through evolution (Ilic et al., 2003; Wang et al., 2005), it is important to evaluate all related regions to improve the chances of identifying sequences of interest. This effect of genome specific diploidization has been observed between sorghum and rice genomes with a significant amount of homologs between the genomes being identified in the duplicate regions instead of where they were expected (Paterson et al., 2004). Synteny to the ARBs can directly define a more complete list of all sequences associated with an ancestral region than a direct orthologous region.

The ARBs simulate groups of genes associated with ancestral regions but do not represent the actual ancestral chromosomes. Because the duplication event {approx}70 million year ago that created most of the duplications in the rice genome was not, or did not remain, a complete doubling of the ancient grass genome, the chromosomes cannot be simulated from rice alone. Many theories have proposed a base chromosome number for the grasses that varies from five to more than eight (Anderson 1945; Wilson et al., 1999; Swigonova et al., 2004). These variations in the base number estimations display the uncertainty in the theories for reconstructing whole ancestral chromosomes, but do not dismiss the fact that members of the grass family retain genes in blocks. When more grass genomes are sequenced and higher resolution comparisons are done, we will be able to better evaluate and understand the effects of evolution and further improve candidate gene mapping.


   ACKNOWLEDGMENTS
 
Special thanks go to Steven Cannon for his assistance in the development of the Perl scripts. During the time of this project all authors were at the University of Minnesota. This research was supported by the National Science Foundation under Grant No. 0110134 and the McKnight Presidential Chair in Genomics.


   NOTES
TOP
 NOTES
ABSTRACT
 INTRODUCTION
 Materials and Methods
 Results
 Discussion
 REFERENCES
 
Abbreviations: ARB, ancestral rice block; DH, DiagHunter.

Received for publication May 18, 2006.


   REFERENCES
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and Methods
 Results
 Discussion
 REFERENCES
 





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