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United States Department of Agriculture

Agricultural Research Service

Title: Sequence-Based Alignment of Sorghum Chromosome 3 and Rice Chromosome 1 Reveals Extensive Conservation of Gene Order and One Major Chromosomal Rearrangement

item Klein, Patricia - TEXAS A&M UNIVERSITY
item Klein, Robert
item Verbalov, Julia - BOYCE THOMPSON INSTIT
item Mullet, John - TEXAS A&M UNIVERSITY

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 1, 2002
Publication Date: N/A

Interpretive Summary: Major advancements in science hinge on the development of new tools including maps of genes. Genes are tiny packets of genetic blueprint material that are found inside the cells of all plants and animals and control all of the physical characteristics of these organisms. Our work focuses on improving major grain crops and, with a gene map, the genetic blueprint will be visible and this information can make improving the plants more efficient. This study details the alignment of the gene maps of rice and sorghum, two closely related cereal crop species. The direct comparison of the gene map of rice and sorghum will permit more efficient identification and understanding of the function of each 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: In this study, methods were developed for sequence-based alignment of sorghum and rice chromosomes and for refining the sorghum genome map based on the rice genome sequence. A framework of 135 contigs of large insert clones spanning 33 million base pairs was anchored to sorghum chromosome 3. A limited number of sequences were collected from 118 of the clones and subjected to BLASTX analysis to identify genes, and BLASTN analysis to identify sequence matches to the rice genome. Extensive conservation of gene content and order between sorghum chromosome 3 and the homeologous rice chromosome 1 was observed. One large-scale rearrangement was detected involving the inversion of a ~59 CentiMorgan block of the short arm of sorghum chromosome 3. Several small-scale changes in gene arrangement were detected indicating that single genes and/or small clusters of genes have moved since the divergence of sorghum and rice. Additionally, the alignment of the sorghum physical map to the rice genome sequence allowed sequence-assisted assembly of a contiguous array of 1.6 million base pairs of sorghum Chromosome 3.

Last Modified: 4/18/2015
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