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

Hass-Jacobus BL, Futrell-Griggs M, Abernathy B, Westerman R, Goicoechea JL, Stein J, Klein P, Hurwitz B, Zhou B, Rakhshan F, Sanyal A, Gill N, Lin JY, Walling JG, Luo MZ, Ammiraju JS, Kudrna D, Kim HR, Ware D, Wing RA, San Miguel P, Jackson SA - BMC Genomics (2006)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA. barbara.jacobus@alumni.purdue.edu

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.

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Comparative map between Sorghum chromosome 3 and rice chromosome 1. Hybridization of overgo probes detected the indicated BAC clones, which were previously anchored to the Sorghum genetic map using a variety of molecular markers [16, 17]. The rice physical map is based on the TIGR Release 3 pseudochromosome assembly [39]. The data show a previously identified inversion event affecting the short arms of the chromosomes. Probe 5jp233835 identified a locus that has possibly moved in one lineage relative to the other.
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Figure 9: Comparative map between Sorghum chromosome 3 and rice chromosome 1. Hybridization of overgo probes detected the indicated BAC clones, which were previously anchored to the Sorghum genetic map using a variety of molecular markers [16, 17]. The rice physical map is based on the TIGR Release 3 pseudochromosome assembly [39]. The data show a previously identified inversion event affecting the short arms of the chromosomes. Probe 5jp233835 identified a locus that has possibly moved in one lineage relative to the other.

Mentions: Based on the probe-to-BAC hybridization data and the integrated genetic and physical maps of sorghum [16,17], we drew a comparative map of sorghum chromosome 3 and rice chromosome 1. Shown in Figure 9, the map displays long-range colinearity between the two chromosomes, with the exception of one locus showing evidence of having relocated in one lineage relative to the other. In addition, the map detects an inversion event that was previously shown to encompass most of the short arms of each chromosome [16]. These results are in agreement with previous findings of a syntenic relationship between these chromosomes, with small-scale changes resulting from movement of individual or small clusters of genes [16,18].


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

Hass-Jacobus BL, Futrell-Griggs M, Abernathy B, Westerman R, Goicoechea JL, Stein J, Klein P, Hurwitz B, Zhou B, Rakhshan F, Sanyal A, Gill N, Lin JY, Walling JG, Luo MZ, Ammiraju JS, Kudrna D, Kim HR, Ware D, Wing RA, San Miguel P, Jackson SA - BMC Genomics (2006)

Comparative map between Sorghum chromosome 3 and rice chromosome 1. Hybridization of overgo probes detected the indicated BAC clones, which were previously anchored to the Sorghum genetic map using a variety of molecular markers [16, 17]. The rice physical map is based on the TIGR Release 3 pseudochromosome assembly [39]. The data show a previously identified inversion event affecting the short arms of the chromosomes. Probe 5jp233835 identified a locus that has possibly moved in one lineage relative to the other.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1590032&req=5

Figure 9: Comparative map between Sorghum chromosome 3 and rice chromosome 1. Hybridization of overgo probes detected the indicated BAC clones, which were previously anchored to the Sorghum genetic map using a variety of molecular markers [16, 17]. The rice physical map is based on the TIGR Release 3 pseudochromosome assembly [39]. The data show a previously identified inversion event affecting the short arms of the chromosomes. Probe 5jp233835 identified a locus that has possibly moved in one lineage relative to the other.
Mentions: Based on the probe-to-BAC hybridization data and the integrated genetic and physical maps of sorghum [16,17], we drew a comparative map of sorghum chromosome 3 and rice chromosome 1. Shown in Figure 9, the map displays long-range colinearity between the two chromosomes, with the exception of one locus showing evidence of having relocated in one lineage relative to the other. In addition, the map detects an inversion event that was previously shown to encompass most of the short arms of each chromosome [16]. These results are in agreement with previous findings of a syntenic relationship between these chromosomes, with small-scale changes resulting from movement of individual or small clusters of genes [16,18].

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA. barbara.jacobus@alumni.purdue.edu

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.

Show MeSH
Related in: MedlinePlus