A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs.
BACKGROUND
The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited.


RESULTS
We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR(3500) and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish.


CONCLUSIONS
The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes.
Institut Génétique et Développement (UMR 6061) CNRS/Université de Rennes 1, Rennes, France.
Richard
R
Guyon
Michaelle
M
Rakotomanga
Naoual
N
Azzouzi
Jean Pierre
JP
Coutanceau
Celine
C
Bonillo
Helena
H
D'Cotta
Elodie
E
Pepey
Lucile
L
Soler
Marguerite
M
Rodier-Goud
Angelique
A
D'Hont
Matthew A
MA
Conte
Nikkie E M
NE
van Bers
David J
DJ
Penman
Christophe
C
Hitte
Richard P M A
RP
Crooijmans
Thomas D
TD
Kocher
Catherine
C
Ozouf-Costaz
Jean Francois
JF
Baroiller
Francis
F
Galibert
D000818:Animals; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics / Q000378:metabolism; D023681:Cichlids / Q000235:genetics*; D055028:Comparative Genomic Hybridization; D020224:Expressed Sequence Tags; D008040:Genetic Linkage; D016678:Genome; D005838:Genotype; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D021101:Radiation Hybrid Mapping