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Abstract
Previous comparative maps between the genomes of rice (Oryza sativa) and wheat (Triticum aestivum) were linkage maps based on cDNA-RFLP markers, which are limited by a low frequency of polymorphism. The development of dense genetic maps in wheat and the number of available anchor points in the comparative maps has been limited by the number of polymorphic markers. Higher density comparative maps are necessary to better estimate the levels of colinearity of genes at both the gross (macro level) and fine scale (micro level).
Two approaches were developed to enhance comparative maps. First, to increase the number of anchor points between the two genetic maps, the use of microsatellite markers derived from non-redundant Expressed Sequence Tags (EST-SSRs) was proposed as an economic and fast alternative to RFLP. Homology between mRNA transcripts from the two species is inferred by sequence similarity, and location is determined when mapping the matched EST-SSR on both species, thus creating a link (anchor point) between the two genetic maps. A list of more than 13,000 primer pairs for potential markers in wheat, barley and rice was developed for validation by the cereal research community. Among the principal findings was a correlation between the density of genomic microsatellites and the density of transcribed regions in the sequence of rice chromosome 1.
A second approach to generate higher resolution maps, made use of sequence matching between the rice genome sequence and 5780 Triticeae EST sequences that have a corresponding location in the deletion bin-based physical map of wheat. A rice genome view of the homologous wheat genome locations shows general similarity to the previously published comparative maps based on RFLP. For most rice chromosomes there is a preponderance of wheat genes from one or two wheat chromosomes. This and the inverse view showing the relationship between the wheat deletion map and rice genomic sequence revealed a breakdown of gene content and order. An average of 35% of putative single copy genes matched rice chromosomes other than the one that was most similar to the wheat bin they mapped to, suggesting an abundance of rearrangements eroding the ancestral wheat-rice genome relationships.
