Chromosome-Specific Single-Locus FISH Probes Allow Anchorage of an 1800-Marker Integrated Radiation-Hybrid/Linkage Map of the Domestic Dog Genome to All Chromosomes
ABSTRACT We present here the first fully integrated, comprehensive map of the canine genome, incorporating detailed cytogenetic, radiation hybrid (RH), and meiotic information. We have mapped a collection of 266 chromosome-specific cosmid clones, each containing a microsatellite marker, to all 38 canine autosomes by fluorescence in situ hybridization (FISH). A 1500-marker RH map, comprising 1078 microsatellites, 320 dog gene markers, and 102 chromosome-specific markers, has been constructed using the RHDF5000-2 whole-genome radiation hybrid panel. Meiotic linkage analysis was performed, with at least one microsatellite marker from each dog autosome on a panel of reference families, allowing one meiotic linkage group to be anchored to all 38 dog autosomes. We present a karyotype in which each chromosome is identified by one meiotic linkage group and one or more RH groups. This updated integrated map, containing a total of 1800 markers, covers >90% of the dog genome. Positional selection of anchor clones enabled us, for the first time, to orientate nearly all of the integrated groups on each chromosome and to evaluate the extent of individual chromosome coverage in the integrated genome map. Finally, the inclusion of 320 dog genes into this integrated map enhances existing comparative mapping data between human and dog, and the 1000 mapped microsatellite markers constitute an invaluable tool with which to perform genome scanning studies on pedigrees of interest.
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ABSTRACT: Various monitoring methods have been developed for large carnivores, but not all are practical or sufficiently accurate for long-term monitoring over large spatial scales. From 2009 to 2010, we used a predictive habitat model to locate gray wolf rendezvous sites in 4 study areas in Idaho, USA and conducted noninvasive genetic sampling (NGS) of scat and hair found at the sites. We evaluated species and individual identification PCR success rates across the study areas, and estimated population size with a single-session population estimator using 2 different recapture-coding methods. We then compared NGS population estimates to estimates generated concurrently from telemetry data. We collected 1,937 scat and 166 hair samples and identified 193 unique individuals over 2 years. For fecal DNA samples, species identification success rates were consistently high (>92%) across areas. Individual identification success rates ranged from 78% to 80% in the drier study areas and dropped to 50% in the wettest study area. The degree of agreement between NGS- and telemetry-derived population estimates varied by recapture-coding method with considerable variability in 95% confidence intervals. Population estimates derived from NGS methods were most influenced by the average number of detections per individual. We demonstrate how changes in field effort and recapture-coding method can affect population estimates in a widely used single-session population estimation model. Our study highlights the need to further develop reliable population estimation tools for single-session NGS data, especially those with large differences in capture frequencies among individuals stemming from severe capture heterogeneity (i.e., overdispersion). © 2014 The Wildlife Society.Journal of Wildlife Management 08/2014; 78(6). DOI:10.1002/jwmg.736 · 1.61 Impact Factor