Horsemap3Penedo

Chromosome/Gene Workshops or Reports
Cytogenet Genome Res 111:5–15 (2005)
DOI: 10.1159/000085664
International equine gene mapping workshop
report: a comprehensive linkage map
constructed with data from new markers and by
merging four mapping resources
M.C.T. Penedo,
a
L.V. Millon,
a
D. Bernoco,
b
E. Bailey,
c
M. Binns,
d
G. Cholewinski,
e
N. Ellis,
f
J. Flynn,
g
B. Gralak,
h
A. Guthrie,
i
T. Hasegawa,
j
G. Lindgren,
k
L.A. Lyons,
l
K.H. Røed,
m
J.E. Swinburne,
n
T. Tozaki
o
a
Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA (USA);
b
Stormont Laboratories, Inc., Woodland, CA (USA);
c
MH Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY (USA);
d
The Royal Veterinary College, London (UK);
e
Horse Genetic Markers Laboratory, Agricultural University of Poznan (Poland);
f
University of Sydney, Faculty of Veterinary Science, Centre for Advanced Technologies in Animal Genetics and
Reproduction-ReproGen, Camden (Australia);
g
Weatherby’s Ireland Blood Typing Laboratory, Kildare (Ireland);
h
Institute of Genetics and Animal Breeding, PAS, Jastrzebiec, Wolka Kosowska (Poland);
i
University of Pretoria, Onderstepoort (Republic of South Africa);
j
Japan Racing Association, Utsunomiya (Japan);
k
Department of Evolutionary Biology and Department of Medical Biochemistry and Microbiology,
Uppsala University (Sweden);
l
Department of Population Health and Reproduction, School of Veterinary Medicine, University of California,
Davis, CA (USA);
m
Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, Oslo (Norway);
n
Animal Health Trust, Newmarket (UK);
o
Department of Molecular Genetics, Laboratory of Racing Chemistry, Utsunomiya (Japan)
Manuscript received 26 August 2004; accepted in revised form for publication by M. Schmid 26 August 2004.
This work was conducted under the auspices of and with support from The Dorothy
Russell Havemeyer Foundation, Inc. Workshop support was also provided by
funds available through the USDA-NRSP-8 horse technical committee. Individ-
ual laboratories received financial support from many other sources and we
gratefully acknowledge the contributions of the American Quarter Horse Foun-
dation, The Morris Animal Foundation, Laboratory of Racing Chemistry and
Japan Racing Association, Utsunomiya, Japan, Veterinary Genetics Laboratory
at the University of California, Davis, Polish State Committee for Scientific
Research (Grant no. 5 P06D 027 18), Horserace Betting Levy Board and the
Childwick Trust, United Kingdom, Norwegian Trotting Association, Norway
and The Knut and Alice Wallenberg Foundation, Sweden.
Request reprints from M.C.T. Penedo, Veterinary Genetics Laboratory
University of California, One Shields Avenue
Davis, CA 95616-8744 (USA); telephone: 530-752-7460
fax: 530-752-3556; e-mail: mctorrespenedo@ucdavis.edu
ABC
Fax +41 61 306 12 34
E-mail karger@karger.ch
www.karger.com
© 2005 S. Karger AG, Basel
1424–8581/05/1111–0005$22.00/0
Accessible online at:
www.karger.com/cgr
Abstract. A comprehensive male linkage map was gener-
ated by adding 359 new, informative microsatellites to the
International Equine Gene Map half-sibling reference families
and by combining genotype data from three independent map-
ping resources: a full sibling family created at the Animal
Health Trust in Newmarket, United Kingdom, eight half-sib-
ling families from Sweden and two half-sibling families from
the University of California, Davis. Because the combined data
were derived primarily from half-sibling families, only autoso-
mal markers were analyzed. The map was constructed from a
total of 766 markers distributed on the 31 equine chromo-
somes. It has a higher marker density than that of previously
reported maps, with 626 markers linearly ordered and 140 oth-
er markers assigned to a chromosomal region. Fifty-nine mark-
ers (7%) failed to meet the criteria for statistical evidence of
linkage and remain unassigned. The map spans 3,740 cM with
an average distance of 6.3 cM between markers. Fifty-five per-
cent of the intervals are ^5 cM and only 3% 620 cM. The
present map demonstrates the cohesiveness of the different
data sets and provides a single resource for genome scan analy-
ses and integration with the radiation hybrid map.
Copyright © 2005 S. Karger AG, Basel
6 Cytogenet Genome Res 111:5–15 (2005)
Horse gene mapping research, organized as the Internation-
al Equine Gene Mapping Workshop, has taken place under the
auspices of The Dorothy Russell Havemeyer Foundation and
the collaboration among scientists worldwide. The goal of the
workshop has been to develop and make available to scientists
basic resources such as genetic maps that are critical to genomic
research. Horse genomic information thus developed has been
used for applications to map phenotypic traits as well as to
study the natural history of horses (Vila´ et al., 2001; Chowdha-
ry and Bailey, 2003). One of the primary resources of the work-
shop is the horse linkage map.
Four linear maps for the horse genome have been published,
including three linkage maps with 140 (Lindgren et al., 1998),
353 (Swinburne et al., 2000a) and 344 (Guérin et al., 1999,
2003) markers and a radiation hybrid (RH) map with 730
markers (Chowdhary et al., 2003). Cytogenetic and compara-
tive mapping research has further contributed to the integrity
of the linear genetic maps and extended the genomic informa-
tion for the horse (reviewed in Chowdhary and Bailey, 2003).
Comparison of the maps and use of the information has been
facilitated by overlap of markers contained in each of the maps.
In this report we describe the expansion of the workshop link-
age map to 766 loci based on 839 markers derived from new
and previously published linkage data to create a comprehen-
sive map. The map constructed by this approach provides
expanded coverage of horse chromosomes that will significant-
ly improve the genomic information for the horse. The integra-
tion of all available linkage data into one map benefits scien-
tists by facilitating the identification and selection of markers
that are critical for discovery of genes associated with pheno-
typic traits, health and performance in the horse.
Materials and methods
Reference family panels
Twenty-four families with a total of 921 offspring were used to construct
the linkage map. They consisted of the 13 paternal half-sib families with 500
offspring from the International Horse Reference Family Panel (IHRFP)
(Guérin et al., 1999, 2003), the eight paternal half-sib reference families with
262 offspring from Uppsala, Sweden (SRF) (Lindgren et al., 1998), the two
three-generation, full-sib reference families with 67 offspring created at the
Animal Health Trust, Newmarket, UK (NRF) (Swinburne et al., 2000a) and
two paternal half-sib Quarter Horse families with 92 offspring from the
Veterinary Genetics Laboratory, University of California, Davis (VGL)
(Locke et al., 2002).
Markers and analysis
The genotypic data assembled contained 839 informative markers repre-
senting 825 autosomal and 14 X-linked loci. The set of markers was obtained
by combining genotype files for 344 loci from the two workshop reports
(Guérin et al., 1999, 2003), 144 markers from the SRF, 353 markers from the
NRF, 100 markers from VGL and by genotyping 359 new microsatellites on
the IHRFP resource of which 278 (77%) were typed by one laboratory (code
DAV). A complete list of markers and source of data for this report is shown
in supplement Table S1 available at http://www.uky.edu/Horsemap/Consen-
susMap. For the purpose of merging and analyzing data, the genotype file
was edited to assign a common name to markers representing the same locus
but having different names in separate mapping resources. For example,
HMB2, HMB3, HMB4, HMB5, HMB6 and Ext in SRF data correspond to
AHT002, AHT003, AHT004, AHT005, AHT006 and MC1R in other map-
ping resources, including cytogenetic and RH maps. For these cases, the lat-
ter names were used as locus identifiers in the SRF set. A similar approach
was used for other loci and for all instances the locus name of choice followed
the nomenclature in the Horsemap database (http://locus.jouy.inra.fr/cgi-
bin/lgbc/mapping/common/main.pl?BASE=horse).
In the course of testing, three pairs of DNA samples from the IHRFP,
each from a different family, were found to have almost identical results
(10029 and 10031, 13039 and 13045, 20008 and 20011). The most likely
explanation is that three horses were accidentally sampled in duplicate.
Therefore, individuals 10031, 13045 and 20008 were removed from the data
set. Individual 10031 was excluded because X-linked markers showed it to be
female (same sex as 10029) and not male as specified in the pedigree file.
Individuals 13045 and 20008 were excluded because they had fewer reported
genotypes and contributed fewer meioses than their duplicates, perhaps
because of lower quality or quantity of the extracted DNA. A list of the new
markers typed on the IHRFP is given in Table S2 as supplementary informa-
tion available at http://www.uky.edu/Horsemap/ConsensusMap.
Relative to the total number of autosomal markers in the data set, 294
markers (36%) were typed in two or more mapping resources, 430 markers
(52%) were typed only in the IHRFP, 80 markers (10%) were typed only in
the NRF and 20 markers (2.4%) were typed only in the SRF. Dams were
available for two IHRFP families, the NRF family and two VGL fa