title: A first generation whole genome RH map of the river buffalo with comparison to domestic cattle.
abstract: BACKGROUND
  The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species.
  
  
  RESULTS
  A total of 3990 markers were typed on the BBURH5000 panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD >or= 8. The estimated total length of the WG-RH map is 36,933 cR5000. Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score >or= 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0).
  
  
  CONCLUSIONS
  We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.
authors.affiliation: Department of Biologia, UNESP - São Paulo State University, IBILCE, SP, Brazil. eamaral@cvm.tamu.edu
authors.forename: M Elisabete J
authors.initials: ME
authors.lastname: Amaral
authors.forename: Jason R
authors.initials: JR
authors.lastname: Grant
authors.forename: Penny K
authors.initials: PK
authors.lastname: Riggs
authors.forename: Nedenia B
authors.initials: NB
authors.lastname: Stafuzza
authors.forename: Edson A Rodrigues
authors.initials: EA
authors.lastname: Filho
authors.forename: Tom
authors.initials: T
authors.lastname: Goldammer
authors.forename: Rosemarie
authors.initials: R
authors.lastname: Weikard
authors.forename: Ronald M
authors.initials: RM
authors.lastname: Brunner
authors.forename: Kelli J
authors.initials: KJ
authors.lastname: Kochan
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Greco
authors.forename: Jooha
authors.initials: J
authors.lastname: Jeong
authors.forename: Zhipeng
authors.initials: Z
authors.lastname: Cai
authors.forename: Guohui
authors.initials: G
authors.lastname: Lin
authors.forename: Aparna
authors.initials: A
authors.lastname: Prasad
authors.forename: Satish
authors.initials: S
authors.lastname: Kumar
authors.forename: G Pardha
authors.initials: GP
authors.lastname: Saradhi
authors.forename: Boby
authors.initials: B
authors.lastname: Mathew
authors.forename: M Aravind
authors.initials: MA
authors.lastname: Kumar
authors.forename: Melissa N
authors.initials: MN
authors.lastname: Miziara
authors.forename: Paola
authors.initials: P
authors.lastname: Mariani
authors.forename: Alexandre R
authors.initials: AR
authors.lastname: Caetano
authors.forename: Stephan R
authors.initials: SR
authors.lastname: Galvão
authors.forename: Madhu S
authors.initials: MS
authors.lastname: Tantia
authors.forename: Ramesh K
authors.initials: RK
authors.lastname: Vijh
authors.forename: Bina
authors.initials: B
authors.lastname: Mishra
authors.forename: S T Bharani
authors.initials: ST
authors.lastname: Kumar
authors.forename: Vanderlei A
authors.initials: VA
authors.lastname: Pelai
authors.forename: Andre M
authors.initials: AM
authors.lastname: Santana
authors.forename: Larissa C
authors.initials: LC
authors.lastname: Fornitano
authors.forename: Brittany C
authors.initials: BC
authors.lastname: Jones
authors.forename: Humberto
authors.initials: H
authors.lastname: Tonhati
authors.forename: Stephen
authors.initials: S
authors.lastname: Moore
authors.forename: Paul
authors.initials: P
authors.lastname: Stothard
authors.forename: James E
authors.initials: JE
authors.lastname: Womack
mesh_terms: D000818:Animals; D002020:Buffaloes / Q000235:genetics*; D002417:Cattle / Q000235:genetics*; D033481:Chromosomes, Mammalian / Q000235:genetics; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D016678:Genome; D023281:Genomics; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D021101:Radiation Hybrid Mapping; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D005819:Genetic Markers