Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Construction And Use Of An Integrated Genetic, Cytological And Physical Map Of Sorghum That Is Aligned To The Maize And Rice Genomes

Patricia E. Klein¹ , Robert R. Klein² , John E. Mullet ¹

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

²  USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, 77845, USA

The development of a high-quality integrated genetic/physical/cytogenetic sorghum map as a tool for map-based cloning genes of agronomic importance has been a long term goal of the TAMU-ARS sorghum genomics group. We have recently cross referenced four QTL for the sorghum ‘stay-green’ trait identified in a cross between B35 (‘stay-green’) X Tx7000 (non ‘stay-green’) onto the TAMU-ARS genetic map as a first step in identifying the ‘stay-green’ genes. High-resolution alignment of the sorghum genome map to maps from other grass species will also prove valuable for comparative analysis of the ‘stay-green’ QTL across species and eventual candidate gene(s) identification. Here we report on high-resolution sequence-based alignment of sorghum, maize and rice chromosomes. Alignment of sorghum to rice chromosomes was accomplished by sequence scanning (16-32 sequences/BAC) ~930 sorghum BACs previously anchored to our high-density genetic map and analysis by BLASTX to identify putative genes and BLASTN to identify sequence matches to the rice genome. Extensive conservation of gene content and order between sorghum and rice chromosomes was observed. The level of colinearity between homeologous sorghum and rice chromosomes ranged from ~47 to 88% with an average of ~74%. To align maize and rice chromosomes, maize sequence data obtained from TIGR (http://www.tigr.org/tdb/tgi/maize/) was analyzed by BLASTX and BLASTN to identify sequence matches to the rice genome. Of the nearly 1400 sequence-based gene alignments between maize and rice, ~56% appeared in colinear blocks between these two grasses. Analysis of these comparative maps within the Stg QTL may provide insights to the genes conditioning sorghum’s exceptional tolerance to water-limited environments.