title: Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA. barbara.jacobus@alumni.purdue.edu
authors.forename: Barbara L
authors.initials: BL
authors.lastname: Hass-Jacobus
authors.forename: Montona
authors.initials: M
authors.lastname: Futrell-Griggs
authors.forename: Brian
authors.initials: B
authors.lastname: Abernathy
authors.forename: Rick
authors.initials: R
authors.lastname: Westerman
authors.forename: Jose-Luis
authors.initials: JL
authors.lastname: Goicoechea
authors.forename: Joshua
authors.initials: J
authors.lastname: Stein
authors.forename: Patricia
authors.initials: P
authors.lastname: Klein
authors.forename: Bonnie
authors.initials: B
authors.lastname: Hurwitz
authors.forename: Bin
authors.initials: B
authors.lastname: Zhou
authors.forename: Fariborz
authors.initials: F
authors.lastname: Rakhshan
authors.forename: Abhijit
authors.initials: A
authors.lastname: Sanyal
authors.forename: Navdeep
authors.initials: N
authors.lastname: Gill
authors.forename: Jer-Young
authors.initials: JY
authors.lastname: Lin
authors.forename: Jason G
authors.initials: JG
authors.lastname: Walling
authors.forename: Mei Zhong
authors.initials: MZ
authors.lastname: Luo
authors.forename: Jetty Siva S
authors.initials: JS
authors.lastname: Ammiraju
authors.forename: Dave
authors.initials: D
authors.lastname: Kudrna
authors.forename: Hye Ran
authors.initials: HR
authors.lastname: Kim
authors.forename: Doreen
authors.initials: D
authors.lastname: Ware
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.forename: Phillip
authors.initials: P
authors.lastname: San Miguel
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics*; D016172:DNA Fingerprinting; D015342:DNA Probes; D019143:Evolution, Molecular; D015723:Gene Library; D005819:Genetic Markers; D018745:Genome, Plant; D009693:Nucleic Acid Hybridization; D012275:Oryza / Q000235:genetics*; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D045868:Sorghum / Q000235:genetics*; D013045:Species Specificity
chemical_list: D015342:DNA Probes; D005819:Genetic Markers