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Collinearity of Maize and Sorghum at the DNA Sequence Level

It has been proposed that maize has evolved as an allotetraploid from two progenitors, one of them in common with sorghum. In the time since maize and sorghum separated, the size of the maize genome has increased due to the amplification of retroelements, further reducing the gene density relative to sorghum. We have selected a small number of orthologous regions from both subgenomes of maize and comparing them with sorghum. Since all rice chromosomes have now been sequenced, it becomes possible to extend this comparison to rice as well

This project is now in its last phase. Originally, we had proposed to study ten selected orthologous regions between maize and sorghum. Because several regions from maize were obtained from duplicate factors, reflecting the two orthologous subgenomes of maize (an ancient allotetraploid), and because the larger size of the maize genome requires overlapping clones for several regions, we had planned to sequence 10 BAC clones from sorghum and 20 BAC clones from maize. Depending on the size of these BAC clones we expected to sequence up to 5 Mb of the two cereal genomes. We now can say that we will exceed these goals significantly based on savings in reagent costs and the accelerated rate of chromosome walking. This is in part due to the benefits of the total DNA fingerprinting of the BAC libraries that have been constructed in a joint effort between PGIR and the Maize Mapping Project (MMP) under the auspices of the University of Missouri at Columbia. This project is a collaboration with the Bennetzen laboratory at Purdue University and is supported by the NSF plant genome program (#9975618).

Recent Publications:

Clark RM, Linton E, Messing J and Doebley DF (2004). Pattern of diversity in the genomic region near the maize domestication gene, tb1. Proc Natl Acad Sci USA 101, 700-707.
Stam M, Belele C, Ramakrishna W, Dorweiler JE, Bennetzen JL, and Chandler VL (2002). The regulatory regions required for B' paramutation and expression are located far upstream of the maize b1 transcribed sequences. Genetics 162, 917-930.
Ramakrishna W, Emberton J, Ogden M, SanMiguel P, and Bennetzen JL(2002). Structural analysis of the maize rp1 complex reveals numerous sites and unexpected mechanisms of local rearrangement. Plant Cell 14, 3213-23.
Yuan Y, SanMiguel PJ, and Bennetzen JL(2002). Methylation-spanning linker libraries link gene-rich regions and identify epigenetic boundaries in Zea mays. GenomeRes 12, 1345-1349.
Ramakrishna W Ma J SanMiguel P Emberton J Dubcovsky J Shiloff BA Jiang Z Rostocks N Busso CS Ogden M Linton E Kleinhofs A Devos K Messing J Bennetzen J (2002). Frequent genic rearrangements in two regions of grass genomes identified by comparative sequence analysis. CompFunct Genom 3, 165-166.
Song R, Llaca V, and Messing J (2002). Mosaic organization of orthologous sequences in grass genomes. Genome Research 12, 1549-1555.
Ramakrishna W Emberton J SanMiguel P Ogden M Llaca V Messing J and Bennetzen J (2002). Comparative sequence analysis of the sorghum Rph region and the maize Rp1resistance gene complex. Plant Physiol. 130, 1728-1738.
Yim Y-S, Davis G, Duru N, Musket T, Linton E, Messing J, McMullen M, Soderlund C, Polacco M, Gardiner J, and Coe Jr E (2002). Characterization of three maize BAC libraries toward anchoring of the physical map to the genetic map using high density BAC filter hybridization. Plant Physiol. 130, 1686-1696.

Collinearity Table

Gene-Specific BACs: Probe Information

Clark RM, Linton E, Messing J and Doebley DF (2004). Pattern of diversity in the genomic region near the maize domestication gene, tb1. Proc Natl Acad Sci USA 101, 700-707.
Stam M, Belele C, Ramakrishna W, Dorweiler JE, Bennetzen JL, and Chandler VL (2002). The regulatory regions required for B' paramutation and expression are located far upstream of the maize b1 transcribed sequences. Genetics 162, 917-930.
Ramakrishna W, Emberton J, Ogden M, SanMiguel P, and Bennetzen JL(2002). Structural analysis of the maize rp1 complex reveals numerous sites and unexpected mechanisms of local rearrangement. Plant Cell 14, 3213-23.
Yuan Y, SanMiguel PJ, and Bennetzen JL(2002). Methylation-spanning linker libraries link gene-rich regions and identify epigenetic boundaries in Zea mays. GenomeRes 12, 1345-1349.
Ramakrishna W Ma J SanMiguel P Emberton J Dubcovsky J Shiloff BA Jiang Z Rostocks N Busso CS Ogden M Linton E Kleinhofs A Devos K Messing J Bennetzen J (2002). Frequent genic rearrangements in two regions of grass genomes identified by comparative sequence analysis. CompFunct Genom 3, 165-166.
Song R, Llaca V, and Messing J (2002). Mosaic organization of orthologous sequences in grass genomes. Genome Research 12, 1549-1555.
Ramakrishna W Emberton J SanMiguel P Ogden M Llaca V Messing J and Bennetzen J (2002). Comparative sequence analysis of the sorghum Rph region and the maize Rp1resistance gene complex. Plant Physiol. 130, 1728-1738.
Yim Y-S, Davis G, Duru N, Musket T, Linton E, Messing J, McMullen M, Soderlund C, Polacco M, Gardiner J, and Coe Jr E (2002). Characterization of three maize BAC libraries toward anchoring of the physical map to the genetic map using high density BAC filter hybridization. Plant Physiol. 130, 1686-1696.

Collinearity Table

Gene-Specific BACs: Probe Information