Abstract
BackgroundWith the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding, and evolutionary studies. The genus Oryza includes 23 species that shared a common ancestor 8–10 million years ago making this an ideal model for investigations into the processes underlying domestication, as many of the Oryza species are still undergoing domestication. This study integrates high-throughput, hybridization-based markers with BAC end sequence and fingerprint data to construct physical maps of rice chromosome 1 orthologues in two wild Oryza species. Similar studies were undertaken in Sorghum bicolor, a species which diverged from cultivated rice 40–50 million years ago.ResultsOvergo markers, in conjunction with fingerprint and BAC end sequence data, were used to build sequence-ready BAC contigs for two wild Oryza species. The markers drove contig merges to construct physical maps syntenic to rice chromosome 1 in the wild species and provided evidence for at least one rearrangement on chromosome 1 of the O. sativa versus Oryza officinalis comparative map. When rice overgos were aligned to available S. bicolor sequence, 29% of the overgos aligned with three or fewer mismatches; of these, 41% gave positive hybridization signals. Overgo hybridization patterns supported colinearity of loci in regions of sorghum chromosome 3 and rice chromosome 1 and suggested that a possible genomic inversion occurred in this syntenic region in one of the two genomes after the divergence of S. bicolor and O. sativa.ConclusionThe results of this study emphasize the importance of identifying conserved sequences in the reference sequence when designing overgo probes in order for those probes to hybridize successfully in distantly related species. As interspecific markers, overgos can be used successfully to construct physical maps in species which diverged less than 8 million years ago, and can be used in a more limited fashion to examine colinearity among species which diverged as much as 40 million years ago. Additionally, overgos are able to provide evidence of genomic rearrangements in comparative physical mapping studies.
Highlights
With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding, and evolutionary studies
Overgo design and hybridization success in Oryza species The goal of this project was to design overgo markers from the rice (O. sativa) genomic sequence [14], hybridize those overgos to bacterial artificial chromosome (BAC) libraries constructed from wild Oryza species, and use the data generated, in conjunction with BAC fingerprinting and BAC end sequencing data generated by the Oryza Map Alignment Project (OMAP) [15], to link the physical maps of the wild Oryza species to the O. sativa reference genome sequence
Even given the current overgo design constraints, this study shows that overgos can be used successfully as markers for the construction of physical maps, as evidenced by our data from O. nivara and O. officinalis
Summary
With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding, and evolutionary studies. Efforts to improve our understanding of rice genetics, thereby improving the breeding and cultivation of rice, have led to numerous international collaborations, culminating in the completion of a publicly available genome sequence of rice in 2002 [2,3]. This sequence provides a powerful tool for the identification of agronomically important genes in rice, as well as for the identification of orthologous regions in other crop species. Other methods must be employed to harness the knowledge hidden in these wild rice genomes
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