Source: CORNELL UNIVERSITY submitted to
AN IMPROVED MEIOTIC LINKAGE MAP OF THE SILVER FOX GENOME
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
ANIMAL HEALTH
Reporting Frequency
Annual
Accession No.
0209836
Grant No.
(N/A)
Project No.
NYCV-473371
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Jan 1, 2007
Project End Date
Sep 30, 2009
Grant Year
(N/A)
Project Director
Acland, G. M.
Recipient Organization
CORNELL UNIVERSITY
(N/A)
ITHACA,NY 14853
Performing Department
JAMES A. BAKER INSTITUTE FOR ANIMAL HEALTH
Non Technical Summary
A genetic linkage map is a users guide to a species, and the first step in modern molecular biology to an appreciation of how the species functions. Such an understanding can be important for both practical/applied and academic/scientific purposes. Our laboratory is developing such a map for the fox, to increase our understanding of a broad range of the traits that they exhibit. These traits include behavioral characteristics that influence how well the foxes respond to farm rearing, and commercially important characteristics such as reproductive performance, and coat colours. A genetic linkage map of the fox will allow breeding programs to adopt marker assisted selection, to select for traits of commercial, scientific and other importance in foxes, to permit accelerated selection for domesticated behavior, maintenance of desired alleles for important coat color phenotypes and other traits, maintenance of genetic diversity in populations, permit parentage testing, and molecular identification/fingerprinting of individual foxes. It will further provide a necessary first step for organizing future research into the fox genome.
Animal Health Component
100%
Research Effort Categories
Basic
75%
Applied
25%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3030840108025%
3033899108025%
3150840108025%
3153899108025%
Knowledge Area
303 - Genetic Improvement of Animals; 315 - Animal Welfare/Well-Being and Protection;

Subject Of Investigation
0840 - Fur-bearing animals; 3899 - Other animals, general;

Field Of Science
1080 - Genetics;
Goals / Objectives
The specific objective of this research is to develop a comprehensive and high resolution meiotic linkage map of the Silver Fox genome, by adding 70 new, carefully chosen, highly informative markers to the current map, to extend its length, resolution, and power. This will result in a well ordered and spaced set of markers that can then be used for mapping traits of commercial, scientific and other importance in foxes, for marker assisted selection in fox breeding, to permit accelerated selection for domesticated behavior, maintenance of desired alleles for important coat color phenotypes and other traits, maintenance of genetic diversity in populations, permit parentage testing, and molecular identification/fingerprinting of individual foxes. The map created in this project will have further implications for concurrent and future research funded independendently from the current proposal, to create radiation hybrid map of the fox genome, and eventually to a survey sequence of the fox genome. The meiotic linkage map of the fox genome to be undertaken in the current proposal will be a necessary first step to organizing such later understandings of the fox genome, and in particular for exploiting current high resolution information from the canine genome and sequence for exploring the genetics of hereditary traits in foxes.
Project Methods
Thirty-seven 3-generation silver fox pedigrees from the ICG experimental farm, have previously had DNA extracted, and been genotyped using 181 markers at Marshfield and 139 markers from a marker set developed at Cornell. We also now have blood samples from additional fox pedigrees that will have DNA extracted using either Qiagen Maxi Blood kits (Qiagen, CA) or phenol-chloroform extraction methods and these pedigrees will be used to increase our mapping power. For Linkage Analysis for Map Construction, input data for map construction will comprise data generated 1) previously (pre-existing pedigrees with pre-existing markers), 2) by genotyping pre-existing pedigrees with new markers, and 3) by genotyping new pedigrees with previously mapped and new markers. All procedures will be undertaken in our laboratory at Baker Institute, Cornell University, which is fully equipped to undertake them.

Progress 01/01/07 to 09/30/09

Outputs
OUTPUTS: A meiotic linkage map of the silver fox (a variant of the red fox, Vulpes vulpes, was developed taking advantage of the known cytogenetic homologies between the dog and fox, and by the availability of high resolution canine genome maps and sequence data.The high genomic sequence identity between dog and fox enabled adaptation of canine microsatellites for genotyping and meiotic mapping in foxes. Using 320 such markers, we constructed the first meiotic linkage map of the fox genome. The resulting sex-averaged map covers 16 fox autosomes and the X chromosome with an average inter-marker distance of 7.5 cM. The total map length corresponds to 1480.2 cM. From comparison of sex-averaged meiotic linkage maps of the fox and dog genomes, suppression of recombination in pericentromeric regions of the metacentric fox chromosomes was apparent, relative to the corresponding segments of acrocentric dog chromosomes. Alignment of the fox meiotic map against the 7.6x canine genome sequence revealed high conservation of marker order between homologous regions of the two species. The fox meiotic map provides a critical tool for genetic studies in foxes and identification of genetic loci and genes implicated in fox domestication. We further tested whether canine-derived gene-containing bacterial artificial chromosome (BAC) clones could be exploited to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. We also, for the first time, localized the proto-oncogene C-KIT to red fox (Vulpes vulpes) B-chromosomes. Analyses of fox B-chromosomal C-KIT gene from a flow-sorted fox B-chromosome-specific library revealed the presence of intron-exon boundaries and high identity between sequenced regions of canine and fox B-chromosomal C-KIT copies. Identification of C-KIT gene on fox B-chromosomes provides new insight into the origin and evolution of these supernumerary chromosomes and their potential role in the genome. PARTICIPANTS: Gregory M. Acland, Professor of Medical Genetics, NYS College of Veterinary Medicine, PD/PI. Anna V Kukekova, Research Associate, Baker Institute for Animal Health, Co-investigator Jennifer Johnson, Research Support Specialist 1 TARGET AUDIENCES: Target audience includes scientists studying canid evolution, domestication, behavior, genetics and genomics; and fox breeders interested in applying modern genetics to breedong pracices. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
These studies provided the first linkage map of the fox genome, an essential tool for understanding a wide range of fox genetic traits, and for analyzing issues of domestication and evolution of canid species.

Publications

  • Kukekova AV, Trut LN, Oskina IN, Johnson JL, Temnykh SV, Kharlamova AV, Shepeleva DV, Gulievich RG, Shikhevich SG, Graphodatsky AS, Aguirre GD, Acland GM. A meiotic linkage map of the silver fox, aligned and compared to the canine genome. Genome Res. 2007 17(3):387-99.
  • Yudkin DV, Trifonov VA, Kukekova AV, Vorobieva NV, Rubtsova NV, Yang F, Acland GM, Ferguson-Smith MA, Graphodatsky AS. Mapping of KIT adjacent sequences on canid autosomes and B chromosomes. Cytogenet Genome Res. 2007;116(1-2):100-3.
  • Kukekova AV, Trut LN, Chase K, Shepeleva DV, Vladimirova AV, Kharlamova AV, Oskina IN, Stepika A, Klebanov S, Erb HN, Acland GM. Measurement of segregating behaviors in experimental silver fox pedigrees. Behav Genet. 2008 Mar;38(2):185-94. Epub 2007 Nov 21.
  • Kukekova AV, Vorobieva NV, Beklemisheva VR, Johnson JL, Temnykh SV, Yudkin DV, Trut LN, Andre C, Galibert F, Aguirre GD, Acland GM, Graphodatsky AS. Chromosomal mapping of canine-derived BAC clones to the red fox and American mink genomes. J Hered. 2009 Jul-Aug;100 Suppl 1:S42-53. Epub 2009 Jun 21.
  • Kharlamova AV, Trut LN, Chase K, Kukekova AV, Lark KG. Directional asymmetry in the limbs, skull and pelvis of the silver fox (V. vulpes). J Morphol. 2010 Dec;271(12):1501-8.
  • Graphodatsky AS, Kukekova AV, Yudkin DV, Trifonov VA, Vorobieva NV, Beklemisheva VR, Perelman PL, Graphodatskaya DA, Trut LN, Yang F, Ferguson-Smith MA, Acland GM, Aguirre GD. The proto-oncogene C-KIT maps to canid B-chromosomes. Chromosome Res. 2005;13(2):113-22.