Abstract
BackgroundEarlier comparative maps between the genomes of rice (Oryza sativa L.), barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) were linkage maps based on cDNA-RFLP markers. The low number of polymorphic RFLP markers has limited the development of dense genetic maps in wheat and the number of available anchor points in comparative maps. Higher density comparative maps using PCR-based anchor markers are necessary to better estimate the conservation of colinearity among cereal genomes. The purposes of this study were to characterize the proportion of transcribed DNA sequences containing simple sequence repeats (SSR or microsatellites) by length and motif for wheat, barley and rice and to determine in-silico rice genome locations for primer sets developed for wheat and barley Expressed Sequence Tags.ResultsThe proportions of SSR types (di-, tri-, tetra-, and penta-nucleotide repeats) and motifs varied with the length of the SSRs within and among the three species, with trinucleotide SSRs being the most frequent. Distributions of genomic microsatellites (gSSRs), EST-derived microsatellites (EST-SSRs), and transcribed regions in the contiguous sequence of rice chromosome 1 were highly correlated. More than 13,000 primer pairs were developed for use by the cereal research community as potential markers in wheat, barley and rice.ConclusionTrinucleotide SSRs were the most common type in each of the species; however, the relative proportions of SSR types and motifs differed among rice, wheat, and barley. Genomic microsatellites were found to be primarily located in gene-rich regions of the rice genome. Microsatellite markers derived from the use of non-redundant EST-SSRs are an economic and efficient alternative to RFLP for comparative mapping in cereals.
Highlights
Earlier comparative maps between the genomes of rice (Oryza sativa L.), barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) were linkage maps based on cDNA-RFLP markers
The lack of anchor markers for bridging across species is exacerbated as new maps are constructed using PCR-based markers such as AFLP, genomic microsatellites and single nucleotide polymorphisms (SNPs) rather than the transferable but laborious cDNAbased RFLP markers
All these basic nucleotide motifs can be represented in variant forms of the same basic set or by their reverse complements but to keep a consistency in the database for estimating frequencies, they were transformed into the canonical motifs
Summary
Earlier comparative maps between the genomes of rice (Oryza sativa L.), barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) were linkage maps based on cDNA-RFLP markers. BMC Genomics 2005, 6:23 http://www.biomedcentral.com/1471-2164/6/23 current maps from different grass species (and in many cases, within the same species) seldom share an adequate number of common (anchor) markers to allow researchers to bridge across maps with an adequate resolution. This is especially true when comparing the genome maps of the Triticeae tribe with the maps of rice or maize, which on average share 3 to 4 markers per wheat homoeologous chromosome group. The lack of anchor markers for bridging across species is exacerbated as new maps are constructed using PCR-based markers such as AFLP, genomic microsatellites and single nucleotide polymorphisms (SNPs) rather than the transferable but laborious cDNAbased RFLP markers
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
