A Domestic cat X Chromosome Linkage Map and the Sex-LinkedorangeLocus: Mapping oforange, Multiple Origins and Epistasis Overnonagouti

Schmidt‐Küntzel, Anne; Nelson, George W.; David, Victor A.; Schäffer, Alejandro A.; Eizirik, Eduardo; Roelke, Melody E.; Kehler, J. S.; Hannah, Steven S.; O’Brien, Stephen J.; Menotti‐Raymond, Marilyn

doi:10.1534/genetics.108.095240

Cited by 35 publications

(32 citation statements)

References 57 publications

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“…These blocks correspond to one ∼45-Mb recombination cold spot and at least two smaller 5-to 10-Mb cold spots on the domestic cat X Chromosome (Schmidt-Kuntzel et al 2009), a genomic feature virtually absent on autosomes (Fig. 4B).…”

Section: Big Cat Hybridization and Remarkable Patterns Of X Chromosommentioning

confidence: 99%

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

et al. 2015

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Inter-species hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that considers all modes of inheritance and overcomes systematic problems due to rapid lineage diversification by sampling large genomic character sets. Here, we assessed genome-wide phylogenetic variation across a diverse mammalian family, Felidae (cats). We combined genotypes from a genome-wide SNP array with additional autosomal, X-and Y-linked variants to sample ∼150 kb of nuclear sequence, in addition to complete mitochondrial genomes generated using light-coverage Illumina sequencing. We present the first robust felid time tree that accounts for unique maternal, paternal, and biparental evolutionary histories. Signatures of phylogenetic discordance were abundant in the genomes of modern cats, in many cases indicating hybridization as the most likely cause. Comparison of big cat whole-genome sequences revealed a substantial reduction of X-linked divergence times across several large recombination cold spots, which were highly enriched for signatures of selection-driven postdivergence hybridization between the ancestors of the snow leopard and lion lineages. These results highlight the mosaic origin of modern felid genomes and the influence of sex chromosomes and sex-biased dispersal in post-speciation gene flow. A complete resolution of the tree of life will require comprehensive genomic sampling of biparental and sex-limited genetic variation to identify and control for phylogenetic conflict caused by ancient admixture and sex-biased differences in genomic transmission.

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Section: Big Cat Hybridization and Remarkable Patterns Of X Chromosommentioning

confidence: 99%

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

et al. 2015

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“…We thus established three independent pedigrees, each of which segregated for a single ''Tabby'' variant, relative to a standard. Pedigree 1 was a multigenerational outbred (and nonbreed) domestic cat pedigree maintained by the Nestlé Purina PetCare Company for nutrition studies, which we have previously used to build a genetic linkage map of the domestic cat genome (MenottiRaymond et al 2009;Schmidt-Kü ntzel et al 2009) and also to identify genes involved in coat color and hair length (Eizirik et al 2003;Ishida et al 2006;Kehler et al 2007). It consisted of 287 individuals, 256 of which were genotyped.…”

Section: Pedigrees and Phenotypingmentioning

confidence: 99%

Defining and Mapping Mammalian Coat Pattern Genes: Multiple Genomic Regions Implicated in Domestic Cat Stripes and Spots

et al. 2010

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Mammalian coat patterns (e.g., spots, stripes) are hypothesized to play important roles in camouflage and other relevant processes, yet the genetic and developmental bases for these phenotypes are completely unknown. The domestic cat, with its diversity of coat patterns, is an excellent model organism to investigate these phenomena. We have established three independent pedigrees to map the four recognized pattern variants classically considered to be specified by a single locus, Tabby; in order of dominance, these are the unpatterned agouti form called ''Abyssinian'' or ''ticked'' (T . We demonstrate that at least three different loci control the coat markings of the domestic cat. One locus, responsible for the Abyssinian form (herein termed the Ticked locus), maps to an 3.8-Mb region on cat chromosome B1. A second locus controls the Tabby alleles T M and t b , and maps to an 5-Mb genomic region on cat chromosome A1. One or more additional loci act as modifiers and create a spotted coat by altering mackerel stripes. On the basis of our results and associated observations, we hypothesize that mammalian patterned coats are formed by two distinct processes: a spatially oriented developmental mechanism that lays down a species-specific pattern of skin cell differentiation and a pigmentation-oriented mechanism that uses information from the preestablished pattern to regulate the synthesis of melanin profiles.

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“…Schmidt-Kuentzel et al (2009) found significant linkage to the O locus for the markers FCA1466 and FCA1494. Although these 2 loci were included in our original set of 131 cat loci, they were not efficiently amplified and showed low polymorphism.…”

Section: Discussionmentioning

confidence: 90%

Selecting representative microsatellite loci for genetic monitoring and analyzing genetic structure of an outbred population of orange tabby cats in China

Huo

et al. 2015

Genet. Mol. Res.

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ABSTRACT. We optimized a panel of microsatellite markers from cat and tiger genetic data for efficient genetic monitoring and used it to analyze the genetic structure of an outbred cat stock in China. We selected a set of rich polymorphic microsatellite loci from 131 cat microsatellite loci and 3 Sumatran tiger microsatellite loci using agarose gel electrophoresis. Next, the set of optimized genetic markers was used to analyze the genetic variation in an outbred population of orange tabby cats in China by simple-tandem repeat scanning. Thirty-one loci rich in polymorphisms were selected and the highest allele number in a single locus was 8. Analysis of the orange tabby cat population illustrated that the average observed number of alleles, mean effective allele number, mean Shannon's information index, mean expected heterozygosity, and observed heterozygosity were 3.8387, 1789Genetic structure of cats detected by microsatellite marker ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (1): 1788-1797(2015 2.4027, 0.9787, 0.5565, and 0.5528, respectively. The 31 microsatellite markers used were polymorphic and suitable for analyzing the genetic structure of cats. The population of orange tabby cats was confirmed to be a well-outbred stock.

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A Domestic cat X Chromosome Linkage Map and the Sex-LinkedorangeLocus: Mapping oforange, Multiple Origins and Epistasis Overnonagouti

Cited by 35 publications

References 57 publications

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

Defining and Mapping Mammalian Coat Pattern Genes: Multiple Genomic Regions Implicated in Domestic Cat Stripes and Spots

Selecting representative microsatellite loci for genetic monitoring and analyzing genetic structure of an outbred population of orange tabby cats in China

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