Khokha MK , Krylov V , Reilly MJ , Gall JG , Bhattacharya D , Cheung CY , Kaufman S , Lam DK , Macha J , Ngo C , Prakash N , Schmidt P , Tlapakova T , Trivedi T , Tumova L , Abu-Daya A , Geach T , Vendrell E , Ironfield H , Sinzelle L , Sater AK , Wells DE , Harland RM , Zimmerman LB .

1R01DE018824 NIDCR NIH HHS, 7R01HD042276 NICHD NIH HHS , GM42341 NIGMS NIH HHS , Medical Research Council , R01 DE018824-04 NIDCR NIH HHS, R01 GM042341-24 NIGMS NIH HHS , R01 HD042276-04 NICHD NIH HHS , R01 DE018824 NIDCR NIH HHS, MC_U117560482 Medical Research Council , R01 GM042341 NIGMS NIH HHS , R01 HD042276 NICHD NIH HHS , T32 GM007205 NIGMS NIH HHS , MRC_MC_U117560482 Medical Research Council

	Figure 1. Gynogenesis and centromere mapping. A:X. tropicalis N and IC strains differ at many sequence polymorphisms, schematized in red and blue. Hybrids contain both N and IC parental chromosomes, which recombine during meiosis I. Shortly after fertilization, one set of sister chromatids is extruded as a polar body, resulting in a haploid embryo if eggs are fertilized with ultraviolet-irradiated sperm. Cold shock suppresses polar body formation, resulting in a gynogenote containing the sister chromatids of meiosis II. Loci very close to centromeres are homozygous in gynogenotes, but meiotic recombination can produce heterozygous noncentromeric loci. B: Centromeres were mapped by assaying frequency of homozygosity at polymorphic loci in gynogenotes. Three markers on Chr 1/LG1 were tested on the same set of gynogenotes. Proximity to centromere is reflected by relative frequency of heterozygosity, with marker 013H11 (2/19) closer than 013D04 (9/19) and 003D01 (17/20).Download figure to PowerPoint
	Figure 2. Cytological localization of centromeric markers. Fluorescence in situ hybridization (FISH) probes were generated from cDNAs of genes on centromere-linked scaffolds identified by gynogenesis. Probe name, location: Chr1/LG1: mast3, q0.13; Chr2/LG6: epb41, q0.22; Chr3/LG8: gemin5, p0.00; Chr4/LG7: znf423, p0.00; Chr5/LG9: olig3, p0.00; Chr6/LG2: fbxl7, q0.13; Chr7/LG4: mat1a, p0.12; Chr8/LG5: naif1, p0.00; Chr9/LG3: stat4, q0.09; Chr10/LG10: ezh1, q0.03.Download figure to PowerPoint
	Figure 3. Mapping mutations with centromere markers and gynogenesis. Bulk segregant analysis of pools of 20 mrs lot mutant (mlo) and sibling wild-type (WT) gynogenotes scored with centromeric markers (LG1 013H11, LG2 025H10, LG3 025G03, LG4 010E04, LG5 049C11, LG6 016H09, LG7 047F06, LG8 051H02, LG9 026H07, LG10 028C03) from the 10 X. tropicalis linkage groups. mrs lot shows clear linkage to LG3.Download figure to PowerPoint
	Figure 4. Interference in X. tropicalis. A: Individual gynogenotes (48 lanes total) scored with four markers from the q arm of Chr2/LG6 with centromere-proximal marker (top) to distal (bottom) (016H09, LG6 map position 0.00 cM, 043H07/2.72 cM, 020E05/27.46 cM, and 025E03/44.7cM). Crossovers can be detected by changes between homo- and heterozygosity within a lane; embryos 3, 8, 11, 15, 16, 19, and 27 show more than one crossover between the centromere and the most distal marker. Heterozygosity in the most proximal marker in lanes 8 and 19 reflects a crossover between the centromere and that marker. Lanes 5 and 23 do not display crossovers. B: Some species of double crossover uncouple linkage of distal loci to centromere markers. In the “two-strand double crossover” (left), a distal recessive mutant locus (asterisks) remains linked to the white parental centromere allele after two intervening crossovers (parental ditype, PD). In the “four-strand double crossover” (right), mutant gynogenote shows dark nonparental ditype (NPD) centromeric alleles. C: Multiple chiasmata (white arrowheads) in a 4′,6-diamidine-2-phenylidole-dihydrochloride (DAPI) -stained lampbrush preparation of Chromosome 1.Download figure to PowerPoint
	Figure 5. A: Sex-specific recombination rates crossover frequencies in male and female germlines were compared using a set of homozygous mutant cyd embryos and a “three-allele” polymorphism (simple sequence length polymorphism [SSLP] 011A08) ∼10 cM away. Parental female and male chromosomes (left) bearing the mutant cyd allele share one 011A08 allele (thin black bar) but have distinct 011A08 alleles in repulsion to cyd (maternal allele, solid gray box; paternal allele, hollow gray box). cyd mutant embryos homozygous for the coupled 011A08 allele indicate no recombination (top right, 170/217 cyd embryos assayed); 47 embryos were heterozygous at 011A08, indicating an intervening crossover. Recombination in maternal germline denoted by the intermediate MW solid gray maternal 011A08 allele (middle right) was detected in 39/47 (83%) recombinants, and in the paternal germline (high MW allele) in 8/47 (17%) (bottom right). No embryos showed recombination in both parents. B: Representative genotyping results at marker 011A08: left lanes, female and male parents showing distinct intermediate and high MW alleles; progeny lanes: homozygous low MW band = no recombination; black asterisks, intermediate MW allele = maternal recombination; white asterisk, high MW allele = paternal recombination.Download figure to PowerPoint

Amaya, Frog genetics: Xenopus tropicalis jumps into the future. 1998, Pubmed, Xenbase

Amaya, Frog genetics: Xenopus tropicalis jumps into the future. 1998, Pubmed , Xenbase
Bassam, Fast and sensitive silver staining of DNA in polyacrylamide gels. 1991, Pubmed
Caspary, Uncovering the uncharacterized and unexpected: unbiased phenotype-driven screens in the mouse. 2006, Pubmed
Cherfas, [Diploid radiation-induced gynogenesis in carp. II. Segragation according to morphological traits in gynogenetic progenies]. 1977, Pubmed
Courtet, Major histocompatibility complex and immunoglobulin loci visualized by in situ hybridization on Xenopus chromosomes. 2001, Pubmed , Xenbase
Cresko, Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish. 2003, Pubmed
Dib, A comprehensive genetic map of the human genome based on 5,264 microsatellites. 1996, Pubmed
Du Pasquier, The expression of antibody diversity in natural and laboratory-made polyploid individuals of the clawed toad Xenopus. 1982, Pubmed , Xenbase
Fankhauser, Induction of Triploidy and Haploidy in the Newt, Triturus Viridescens, by Cold Treatment of Unsegmented Eggs. 1939, Pubmed
Force, Preservation of duplicate genes by complementary, degenerative mutations. 1999, Pubmed
Goda, Genetic screens for mutations affecting development of Xenopus tropicalis. 2006, Pubmed , Xenbase
Grammer, Identification of mutants in inbred Xenopus tropicalis. 2005, Pubmed , Xenbase
Hirsch, Xenopus, the next generation: X. tropicalis genetics and genomics. 2002, Pubmed , Xenbase
Johnson, Centromere-linkage analysis and consolidation of the zebrafish genetic map. 1996, Pubmed
Johnson, Half-tetrad analysis in zebrafish: mapping the ros mutation and the centromere of linkage group I. 1995, Pubmed
Kauffman, Microsatellite-centromere mapping in the zebrafish (Danio rerio). 1995, Pubmed
Khokha, Techniques and probes for the study of Xenopus tropicalis development. 2002, Pubmed , Xenbase
Kile, Functional genetic analysis of mouse chromosome 11. 2003, Pubmed
Klein, Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative. 2002, Pubmed , Xenbase
Krotoski, Developmental mutants isolated from wild-caught Xenopus laevis by gynogenesis and inbreeding. 1985, Pubmed , Xenbase
Krylov, Localization of the single copy gene Mdh2 on Xenopus tropicalis chromosomes by FISH-TSA. 2007, Pubmed , Xenbase
Krylov, Localization of human coagulation factor VIII (hFVIII) in transgenic rabbit by FISH-TSA: identification of transgene copy number and transmission to the next generation. 2008, Pubmed , Xenbase
Naruse, A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. 2004, Pubmed
Noramly, A gynogenetic screen to isolate naturally occurring recessive mutations in Xenopus tropicalis. 2005, Pubmed , Xenbase
PERKINS, Crossing-over and interference in a multiply marked chromosome arm of Neurospora. 1962, Pubmed
PERKINS, Tetrads and crossing over. 1955, Pubmed
Perkins, The Detection of Linkage in Tetrad Analysis. 1953, Pubmed
Postlethwait, The zebrafish genome in context: ohnologs gone missing. 2007, Pubmed
Postlethwait, Zebrafish comparative genomics and the origins of vertebrate chromosomes. 2000, Pubmed
Reinschmidt, Gene-centromere mapping in Xenopus laevis. 1985, Pubmed , Xenbase
Showell, Decoding development in Xenopus tropicalis. 2007, Pubmed , Xenbase
Singer, Sex-specific recombination rates in zebrafish (Danio rerio). 2002, Pubmed
Streisinger, Segregation analyses and gene-centromere distances in zebrafish. 1986, Pubmed
Thiébaud, Diploid gynogenesis in Xenopus laevis and the localization with respect to the centromere of the gene for periodic albinism ap. 1984, Pubmed , Xenbase
Thorgaard, Gene-Centromere Mapping in Rainbow Trout: High Interference over Long Map Distances. 1983, Pubmed
Tompkins, Experimentally induced homozygosity in Xenopus laevis. 1991, Pubmed , Xenbase
Tymowska, Karyotype analysis of Xenopus tropicalis Gray, Pipidae. 1973, Pubmed , Xenbase
Tymowska, A comparison of the karyotype, constitutive heterochromatin, and nucleolar organizer regions of the new tetraploid species Xenopus epitropicalis Fischberg and Picard with those of Xenopus tropicalis Gray (Anura, Pipidae). 1982, Pubmed , Xenbase