title: A genetic map of Xenopus tropicalis.
abstract: We present a genetic map for Xenopus tropicalis, consisting of 2886 Simple Sequence Length Polymorphism (SSLP) markers. Using a bioinformatics-based strategy, we identified unique SSLPs within the X. tropicalis genome. Scaffolds from X. tropicalis genome assembly 2.0 (JGI) were scanned for Simple Sequence Repeats (SSRs); unique SSRs were then tested for amplification and polymorphisms using DNA from inbred Nigerian and Ivory Coast individuals. Thus identified, the SSLPs were genotyped against a mapping cross panel of DNA samples from 190 F2 individuals. Nearly 4000 SSLPs were genotyped, yielding a 2886-marker genetic map consisting of 10 major linkage groups between 73 and 132cM in length, and 4 smaller linkage groups between 7 and 40cM. The total effective size of the map is 1658cM, and the average intermarker distance for each linkage group ranged from 0.27 to 0.75cM. Fluorescence In Situ Hybridization (FISH) was carried out using probes for genes located on mapped scaffolds to assign linkage groups to chromosomes. Comparisons of this map with the X. tropicalis genome Assembly 4.1 (JGI) indicate that the map provides representation of a minimum of 66% of the X. tropicalis genome, incorporating 758 of the approximately 1300 scaffolds over 100,000bp. The genetic map and SSLP marker database constitute an essential resource for genetic and genomic analyses in X. tropicalis.
authors: Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd., Houston TX 77204-5001, USA.
authors: Dan E
authors: DE
authors: Wells
authors: Laura
authors: L
authors: Gutierrez
authors: Zhenkang
authors: Z
authors: Xu
authors: Vladimir
authors: V
authors: Krylov
authors: Jaroslav
authors: J
authors: Macha
authors: Kerstin P
authors: KP
authors: Blankenburg
authors: Matthew
authors: M
authors: Hitchens
authors: Larry J
authors: LJ
authors: Bellot
authors: Mary
authors: M
authors: Spivey
authors: Derek L
authors: DL
authors: Stemple
authors: Andria
authors: A
authors: Kowis
authors: Yuan
authors: Y
authors: Ye
authors: Shiran
authors: S
authors: Pasternak
authors: Jenetta
authors: J
authors: Owen
authors: Thu
authors: T
authors: Tran
authors: Renata
authors: R
authors: Slavikova
authors: Lucie
authors: L
authors: Tumova
authors: Tereza
authors: T
authors: Tlapakova
authors: Eva
authors: E
authors: Seifertova
authors: Steven E
authors: SE
authors: Scherer
authors: Amy K
authors: AK
authors: Sater
mesh_terms: D000818:Animals; D002871:Chromosome Banding; D002874:Chromosome Mapping / Q000379:methods*; D005819:Genetic Markers / Q000235:genetics*; D016678:Genome / Q000235:genetics; D005838:Genotype; D020407:Internet; D018598:Minisatellite Repeats / Q000235:genetics; D011110:Polymorphism, Genetic; D032681:Spectral Karyotyping / Q000379:methods*; D014981:Xenopus / Q000235:genetics*; D029867:Xenopus Proteins / Q000235:genetics
chemical_list: D005819:Genetic Markers; D029867:Xenopus Proteins