Horsemap3Penedo

ted its loca-
tion on ECA6 and not ECA10 as suggested by FISH results (Ka-
koi et al., 2000). Our assignment of HMS076 to ECA14, sup-
ported by significant linkage to COR103 (theta = 0, lod = 3.61)
and COR104 (theta = 0, lod = 7.83), indicated another poten-
tial discrepancy since this marker was located on ECA5 by
FISH (Mariat et al., 2001). However, we view our linkage
assignment as tentative because of the low number of informa-
tive meioses (46) for HMS076 contributed by a single family.
Improvement of genotype data by testing this marker on anoth-
er resource family may help pinpoint its correct linkage assign-
ment.
Cytogenet Genome Res 111:5–15 (2005) 9
10 Cytogenet Genome Res 111:5–15 (2005)
Cytogenet Genome Res 111:5–15 (2005) 11
12 Cytogenet Genome Res 111:5–15 (2005)
Cytogenet Genome Res 111:5–15 (2005) 13
14 Cytogenet Genome Res 111:5–15 (2005)
The total length of 3,740 cM for the map exceeded projec-
tions of about 2,700 cM suggested by Lindgren et al. (1998) and
stands as one of the longest male-based maps among livestock
species. A longer male map with 1,015 markers and spanning
3,876 cM has been reported in sheep (Maddox et al., 2001).
However, comparisons among maps are difficult since recom-
bination rates may vary among (Pardo-Manuel de Villena and
Sapienza, 2001) and within (Lien et al., 2000; Weiman et al.,
2003) species. Furthermore, different strategies have been used
to build mapping resources and the number of individuals con-
tributing to map development also varied. The 24 families used
to construct the present map represent several different breeds
of horses. Genotyping errors that inflate recombination frac-
tions between markers are a factor for map length expansion. In
Cytogenet Genome Res 111:5–15 (2005) 15
humans, it has been estimated that F0.08% of genotype errors,
primarily caused by mistyping but also by mutation or gene
conversion, could increase map length by F25% (Broman et
al., 1998). Comparison of genotype data for duplicate samples
in the IHRFP suggested an error rate of about 0.6% affecting
male recombination. Although we identified and corrected
some errors that resulted in unlikely recombination events, we
recognize that genotyping errors still present in the data set
might have artificially expanded the map length. Nevertheless,
the order of markers obtained for each chromosome is consis-
tent with data from cytogenetic and RH maps.
Progress in the development of linkage maps for other live-
stock species, such as pig, cattle and sheep, has been achieved
through merger of data from independent mapping resources
(e.g. Kapke et al., 1996; Campbell et al., 2001; Casas et al.,
2001; Kurar et al., 2002 to name only a few examples) or by
combining genotype data for one mapping resource collected
by different laboratories (e.g. Maddox et al., 2001). These map-
ping efforts share the objective of integrating genetic informa-
tion and developing, as a community resource, high-resolution
linkage maps that allow more efficient mapping of single gene
and polygenic traits. The goals and efforts of the present horse
gene mapping workshop to combine independent mapping
data and to increase resolution of the linkage map parallel those
of other species.
The linkage map described herein, albeit still at low density,
represents a significant improvement over previous maps and
provides a more useful resource from which to select markers
for genomic analyses to map traits in the horse. Most of the new
markers added to the IHRFP have also been recently typed on
the RH panel and, as a new generation of the RH map becomes
available, integration of the two maps will be possible to obtain
a comprehensive map with physically ordered markers. The
increase in map density will allow for better resolution of mark-
er order and distance, particularly in regions where distances
between adjacent markers are greater than 18 cM. Future work-
shop activities should address these issues.
Acknowledgements
We most gratefully acknowledge Irmina Bienkowska, Leah Brault, Ste-
phanie Bricker, Ewa Iwanczyk, Janelle Katz, Liv Midthjell, Rosane Oliveira,
Dianna Pettigrew, Elaine Philbrick, Angel del Valle, Thea Ward and Amy
Young for their assistance with marker development and genotyping. We
also thank Aaron Wong for his help with illustrations.
References
Bowling AT, Breen M, Chowdhary BP, Hirota K, Lear
T, Millon LV, Ponce de Leon FA, Raudsepp T,
Stranzinger G: International system for cytogene-
tics nomenclature of the domestic horse. Report of
the Third International Committee for the Stan-
dardization of the domestic horse karyotype, Da-
vis, CA, USA, 1996. Chromosome Res 5:433–443
(1997).
Broman KW, Murray JC, Sheffield VC, White RL,
Weber JL: Comprehensive human genetic maps:
individual and sex-specific variation in recombina-
tion. Am J Hum Genet 63:861–869 (1998).
Campbell EMG, Fahrenkrug SC, Vallet JL, Smith TPL,
Rohrer GA: An updated linkage and comparative
map of porcine chromosome 18. Anim Genet
32:375–379 (2001).
Casas E, Bennett GL, Bottema CDK, Crawford A,
Kalm E, Kappes SM, Kister A, Lewin HA, Lien S,
Morris CA, Olsaker I, Pitchford WS, Schmutz SM,
Thomsen H, Xu N: Comprehensive linkage map of
bovine chromosome 11. Anim Genet 32:92–94
(2001).
Chowdhary BP, Bailey E: Equine genomics: galloping
to new frontiers. Cytogenet Genome Res 102: 184–
188 (2003).
Chowdhary BP, Raudsepp T, Kata SR, Goh G, Millon
LV, Allan V, Piumi F, Guérin G, Swinburne J,
Binns M, Lear TL, Mickelson J, Murray J, Antczak
DF, Womack JE, Skow LC: The first-generation
whole-genome radiation hybrid map in the horse
identifies conserved segments in human and
mouse genomes. Genome Res 13:742–751 (2003).
Godard S, Vaiman D, Oustry A, Nocart M, Bertaud M,
Guzylack S, Mériaux JC, Cribiu EP, Guérin G:
Characterization, genetic and physical mapping
analysis of 36 horse plasmid and cosmid-derived
microsatellites. Mamm Genome 8:745–750
(1997).
Green P, Fall KA, Crooks S: Documentation for CRI-
MAP, Version 2.4. (Washington University School
of Medicine, St. Louis 1990).
Guérin G, Bailey E, Bernoco D, Anderson I, Antczak
DF, Bell K, et al: Report of the International
Equine Gene Mapping Workshop: Male Linkage
Map. Anim Genet 30:341–354 (1999).
Guérin G, Bailey E, Bernoco D, Anderson I, Antczak
DF, Bell K, et al: The second generation of the
International Equine Gene Mapping Workshop
half-sibling linkage map. Anim Genet 34:1–8
(2003).
Kakoi H, Tozaki T, Hirota K, Mashima S, Kurosawa
M, Miura N: Ten equine microsatellite loci:
TKY25, TKY26, TKY27, TKY28, TKY29,
TKY267, TKY268, TKY269, TKY270 and
TKY271. Anim Genet 31:68–69 (2000).
Kapke P, Wang L, Helm J, Rothschild MF: Integration
of the PiGMaP and USDA maps for chromosome
14. Anim Genet 27:187–190 (1996).
Kurar E, Barendse W, Bottema CDK, Davis S, Föster
M, Kalm E, Kappes SM, Kister A, Lewin HA,
Klungland H, Medjugorac I, Olsaker I, Pitchford
WS, Schmutz SM, Taylor J, Thomsen H, Kirkpa-
trick BW: Consensus and comprehensive linkage
maps of bovine chromosome 24. Anim Genet
33:460–463 (2002).
Lien S, Szyda J, Schechinger B, Rappold G, Arnheim
N: Evidence for heterogeneity in recombination in
the human pseudoautosomal region high resolu-
tion analysis by sperm typing and radiation-hybrid
mapping. Am J Hum Genet 66:557–566 (2000).
Lindgren G, Sandberg K, Persson H, Marklund S,
Breen M, Sandgren B, Carlstén J, Ellegren H: A pri-
mary male autosomal linkage map of the horse
genome. Genome Res 8:951–966 (1998).
Locke MM, Penedo MCT, Bricker SJ, Millon LV, Mur-
ray JD: Linkage of the grey coat colour locus to
microsatellites on horse chromosome 25. Anim
Genet 33:329–337 (2002).
Maddox JF, Davies KP, Crawford AM, Hume DJ, Vai-
man D, Cribiu EP, et al: An enhanced linkage map
of the sheep genome comprising more than 1000
loci. Genome Res 11:1275–1289 (2001).
Mariat D, Oustry-Vaiman A, Cribiu EP, Raudsepp T,
Chowdhary BP, Guérin G: Isolation, characteriza-
tion and FISH assignments of horse BAC clones
containing type I and II markers. Cytogenet Cell
Genet 92:44–48 (2001).
Mickelson JR, Wu JT, Morrison LY, Swinburne JE,
Binns MM, Reed KM, Alexander LJ: Eighty-three
previously unreported equine microsatellite loci.
Anim Genet 34:71–74 (2003).
Pardo-Manuel de Villena F, Sapienza C: Recombina-
tion is proportional to the number of chromosome
arms in mammals. Mamm Genome 12:318–322
(2001).
Swinburne J, Gerstenberg C, Breen M, Aldridge V,
Lockhart L, Marti E, et al: First comprehensive
low-density horse linkage map based on two 3-gen-
eration, full-sibling, cross-bred horse reference
families. Genomics 66:123–134 (2000a).
Swinburne JE, Lockhart L, Aldridge V, Marti E, Breen
M, Binns MM: Characterisation of 25 new physi-
cally mapped horse microsatellite loci: AHT24-48.
Anim Genet 31:237–238 (2000b).
Swinburne JE, Turner A, Alexander LJ, Mickelson JR,
Binns MM: Characterization and linkage map as-
signments for 61 new horse microsatellite loci
(AHT49-109). Anim Genet 34:65–68 (2003).
Vilà C, Leonard JA, Götherström A, Marklund S,
Sandberg K, Liden K, Wayne RK, Ellegren H:
Widespread origins of domestic horse lineages.
Science 291:474–477 (2001).
Wagner ML, Goh G, Wu JT, Raudsepp T, Morrison
LY, Alexander LJ, Skow LS, Chowdhary BP,
Mickelson JR: Radiation hybrid mapping of 75
previously unreported equine microsatellite loci.
Anim Genet 35:68–71 (2004).
Weiman C, Kraus M, Gualy M, Erhardt G: Differences
in recombination rates on chromosome 23 between
German Angus and German Simmental and breed
specific linkage mapping. Anim Genet 34:229–231
(2003).