Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum

Authors: HASS-JACOBUS, BARBARA - PURDUE UNIVERSITY; FUTRELL-GRIGGS, MONTONA - PURDUE UNIVERSITY; ABERNATHY, BRIAN - PURDUE UNIVERSITY; WESTERMAN, RICK - PURDUE UNIVERSITY; GOICOECHEA, JOSE-LUIS - UNIV. OF ARIZONA; STEIN, JOSHUA - COLD SPRING HARBOR LAB; Ware, Doreen

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2007
Publication Date: 3/5/2007
Citation: Hass-Jacobus, B., Futrell-Griggs, M., Abernathy, B., Westerman, R., Goicoechea, J., Stein, J., Ware, D. 2007. Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum. Biomed Central (BMC) Genomics. 7:199.

Interpretive Summary: This study tested the feasibility of using oligonucleotide probes as interspecific markers within the rice genus and across more distantly related cereal genomes. Probes were designed from the genome of domesticated rice (Oryza sativa) and used in conjunction with BAC physical mapping to build comparative maps with two wild Oryza species and with Sorghum. Successful hybridization of probes was sensitive to the level of nucleotide mismatch between the probe and target genome, such that the utility of probes as interspecific markers declined with increasing evolutionary distance. Nevertheless, this study showed that oligonucleotide probes can be used as markers in distantly-related grass species, especially if efforts are made to select conserved sequences.

Technical Abstract: Background 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. 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. Results Overgo 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. Conclusion The 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.