Orthology between genomes of <it>Brachypodium</it>, wheat and rice

• Main Authors: Balyan Harindra S, Mohan Amita, Kumar Sachin, Gupta Pushpendra K
• Format: Article
• Language: English
• Published: BMC 2009-05-01
• Series: BMC Research Notes
• Online Access: http://www.biomedcentral.com/1756-0500/2/93

<p>Abstract</p> <p>Background</p> <p>In the past, rice genome served as a good model for studies involving comparative genomics of grass species. More recently, however, <it>Brachypodium distachyon </it>genome has emerged as a better model system for genomes of temperate cereals including wheat. During the present study, <it>Brachypodium </it>EST contigs were utilized to resolve orthologous relationships among the genomes of <it>Brachypodium</it>, wheat and rice.</p> <p>Findings</p> <p>Comparative sequence analysis of 3,818 <it>Brachypodium </it>EST (bEST) contigs and 3,792 physically mapped wheat EST (wEST) contigs revealed that as many as 449 bEST contigs were orthologous to 1,154 wEST loci that were bin-mapped on all the 21 wheat chromosomes. Similarly 743 bEST contigs were orthologous to specific rice genome sequences distributed on all the 12 rice chromosomes. As many as 183 bEST contigs were orthologous to both wheat and rice genome sequences, which harbored as many as 17 SSRs conserved across the three species. Primers developed for 12 of these 17 conserved SSRs were used for a wet-lab experiment, which resolved relatively high level of conservation among the genomes of <it>Brachypodium</it>, wheat and rice.</p> <p>Conclusion</p> <p>The present study confirmed that <it>Brachypodium </it>is a better model than rice for analysis of the genomes of temperate cereals like wheat and barley. The whole genome sequence of <it>Brachypodium</it>, which should become available in the near future, will further facilitate greatly the studies involving comparative genomics of cereals.</p>