Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Comparative Analysis Of Gene Conservation And Gene Movement In The Genomes Of Sorghum, Rice, And Maize

Patricia E Klein^1,2 , Bin Zhou¹ , Doreen Ware^3,4 , Joshua Stein³ , Bonnie Hurwitz³ , Robert R Klein⁵ , John E Mullet^1,6

¹  Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, 77843, USA

²  Department of Horticulture, Texas A&M University, College Station, TX, 77843, USA

³  Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA

⁴  USDA-ARS U.S. Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, NY, 14853, USA

⁵  USDA-ARS Southern Plains Agricultural Research Center, College Station, TX, 77845, USA

⁶  Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA

The recently completed rice genome sequence provides an unprecedented opportunity to accelerate genome research on all grass species through comparative genome analysis. High resolution genome alignment will not only enhance our understanding of cereal genome evolution and structure but will also accelerate progress on the annotation of biologically important genes. To this end, the TAMU-USDA sorghum genomics group has constructed a high-quality integrated genetic/physical/cytogenetic map of the sorghum genome and utilized sequence scans of mapped BACs to align the sorghum map to rice and maize. Approximately 1650 gene sequence tags from 850 sorghum BACs have provided high resolution sequence-based alignment to the rice pseudomolecule. Extensive conservation of gene content and order between sorghum and rice chromosomes was observed although numerous exceptions were detected. Maize sequence data obtained from TIGR (http://www.tigr.org/tdb/tgi/maize/) was used to align maize and rice chromosomes. Of the nearly 1400 gene alignments between maize and rice, ~56% appeared in colinear blocks. To examine the extent of gene loss and/or movement between these three grasses more closely, BAC tiling paths for regions of sorghum chromosome 3 and maize chromosome 8 homeologous to a ~5.5Mb region of rice chromosome 1 were constructed. Using a combination of BAC pooling and low-pass sequence skimming we were able to construct a high resolution comparative map across this region. The results of this analysis will be presented and can be viewed at http://ware.cshl.org/yia/view_yia.html. This work was supported by NSF grants #0333074 and #0321578 and the USDA-ARS.