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United States Department of Agriculture

Agricultural Research Service

Title: Comprehensive Molecular Cytogenetic Analysis of Sorghum Genome Architecture; Distribution of Euchromatin, Heterochromatin, Genes and Recombination in Comparison to Rice

Authors
item Kim, J - TEXAS A&M UNIVERSITY
item Islam-Faridi, Nurul - TEXAS A&M UNIVERSITY
item Klein, Patricia - TEXAS A&M UNIVERSITY
item Stelly, David - TEXAS A&M UNIVERSITY
item Price, Howard - TEXAS A&M UNIVERSITY
item Klein, Robert
item Mullet, John - TEXAS A&M UNIVERSITY

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 21, 2005
Publication Date: December 15, 2005
Citation: Kim, J.S., Islam-Faridi, N., Klein, P.E., Stelly, D., Price, H.J., Klein, R.R., Mullet, J.E. 2005. Comprehensive molecular cytogenetic analysis of sorghum genome architecture: Distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice. Genetics. 171:1963-1976.

Interpretive Summary: Major advancements in science hinge on the development of new tools including a detailed understanding of the architecture of chromosomes. Chromosomes are the structures found in cells that harbor genes, the tiny packets of genetic blueprint material that are found in all plants and animals and control all of the physical characteristics of these organisms. Our work focuses on improving major grain crops and, with detailed knowledge of chromosomes, the genetic blueprint will be visible and this information can make improving the plants more efficient. This study details a microscopic overview of all 10 sorghum chromosomes, and allows us to establish the architecture of each unique chromosome. By detailing chromosome architecture, we have been able to approximate how many genes are found in sorghum which number greater than thirty thousand. Many of these genes reside in chromosome regions rich in genes, while other genes are found in a virtual gene desert where gene numbers are sparse. This information should therefore speed scientific progress towards cloning important genes, and will help determine whether the chromosome location of a gene will facilitate or preclude getting to that gene. Information will be primarily used by fellow scientists but the work should ultimately result in better adapted, higher producing crop varieties available to American farmers.

Technical Abstract: Cytogenetic maps of sorghum chromosomes were constructed based on the fluorescence in situ hybridization of Bacterial Artificial Chromosome probes mapped across each of these sorghum chromosomes. Distal regions of euchromatin and pericentromeric regions of heterochromatin were delimited for all ten sorghum chromosomes and their DNA content quantified. Euchromatic DNA spans 50 percent of the sorghum genome, ranging from 60 percent of chromosome 1 to 33 percent of chromosome 7. This portion of the sorghum genome is predicted to encode 34,000 genes (1 gene per 12 kilobase pairs) or 75 percent of the sorghum gene complement. Heterochromatin spans 411 megabase pairs of the sorghum genome, a region characterized by a 34 fold lower rate of recombination and a predicted 3 fold lower gene density compared to euchromatic DNA. The distal euchromatic regions of sorghum chromosomes are 1.8 fold larger overall and exhibit a 1.5 fold lower average rate of recombination than the colinear regions of the homeologous rice chromosomes. By contrast, the pericentromeric heterochromatic regions of these chromosomes are 3.6 fold larger in sorghum and recombination is suppressed 15 fold compared to the colinear regions of rice chromosomes. Therefore, the larger size of the sorghum genome relative to rice is due disproportionately to the increased size of pericentromeric heterochromatic regions of low recombination.

Last Modified: 10/25/2014
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