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Orthology between genomes of Brachypodium, wheat and rice

DOI: 10.1186/1756-0500-2-93

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Abstract:

Comparative sequence analysis of 3,818 Brachypodium 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 Brachypodium, wheat and rice.The present study confirmed that Brachypodium is a better model than rice for analysis of the genomes of temperate cereals like wheat and barley. The whole genome sequence of Brachypodium, which should become available in the near future, will further facilitate greatly the studies involving comparative genomics of cereals.Cereals constitute the most important group of cultivated plants, and are known to have diverged from a common paleopolyploid ancestor ~45–47 million years ago (Mya) [1]. Despite this, a remarkable overall structural and functional similarity exists among different cereal genomes [2,3], although the size of these genomes differs greatly, ranging from 430 Mb in rice (Oryza sativa) to 16,000 Mb in hexaploid wheat (Triticum aestivum). Due to its small size and availability of whole genome sequence, rice has been used as a model system for a variety of experimental studies including map-based cloning [4]. However, recent studies resolved further the dynamic changes in rice genome sequences, thus questioning the utility of rice as a model crop [5], and necessitating the need for search of a more efficient model system.Brachypodium distachyon, a small temperate grass (sub-family Pooideae) has recently emerged as a better model system for the

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