Comparative mapping of BTA15 and HSA11 including a region
containing a QTL for meat tenderness
Caird E. Rexroad III,* Gary L. Bennett, Roger T. Stone, John W. Keele, Scott C. Fahrenkrug, Brad A. Freking,
Steven M. Kappes,** Timothy P.L. Smith
USDA, ARS, U.S. Meat Animal Research Center, Spur 18D, PO Box 166, Clay Center, Nebraska 68933-0166, USA
Received: 12 December 2000 / Accepted: 13 March 2001
Abstract. The starting point of the present study was the reported
identification of a chromosomal region on bovine Chromosome
(Chr) 15 (BTA15) carrying loci affecting meat tenderness. A com-
parative linkage map of BTA15 and human Chr 11 (HSA11) was
constructed to identify potential positional candidate genes and to
provide a resource of genetic markers to support marker-assisted
selection (MAS). Relative rearrangements between the bovine and
human genomes for these chromosomes are the most complex
observed in comparative mapping between the two species, with
nine alternating blocks of conserved synteny between HSA11 and
bovine Chrs 15 and 29. The results of this study were the addition
of nine genes to the HSA11/BTA15 comparative linkage map, and
development of five microsatellite markers within the quantitative
trait locus (QTL) interval. One gene with known effects on muscle
development (MYOD1) was mapped to the interval. A second
gene (CALCA) involved in regulation of calcium levels, a key
factor in postmortem tenderization, also mapped within the inter-
val. Refinement of the comparative map and QTL position will
reduce the interval on the human transcription map to be scanned
in search of candidates, reducing the effort and resources required
to identify the allelic variation responsible for the genetic effect.
A major goal of livestock genomic research is to understand the
basis of the genetic contribution to variation in production traits.
However, identification of genes and DNA sequence differences
that contribute to relatively minor (but still of substantial economic
importance) variation in phenotype is a daunting task. The most
promising avenue is the application of comparative mapping, mak-
ing use of the wealth of knowledge and resources produced from
the human genome project and biomedical research community.
This approach requires construction of detailed comparative maps,
to identify blocks of conserved synteny between species, define the
boundaries of these regions, and reveal changes in gene order
within these blocks. Some areas of the bovine genome show high
degrees of conserved synteny with the human genome, as well as
conserved gene order within these areas, while other regions ap-
pear to bear a less straightforward relationship (Band et al. 2000).
It appears that the most complicated set of relative rearrangements
involves genes found on HSA11, which appears to have alternating
blocks of conserved synteny with BTA15 and BTA29.
Recent construction of microsatellite-based genetic linkage
maps for cattle has made it possible to identify chromosomal re-
gions carrying loci that affect meat quality, reproductive effi-
ciency, and growth (Stone et al. 1999; Casas et al. 1998; Keele et
al. 1999). These mapping studies typically make use of diverse
germplasm, such as interbreed crosses, which provide strong phe-
notypic contrasts and increase the level of marker informativeness.
Meat tenderness is one important carcass quality trait to the beef
industry (NCBA 1998) for which a chromosomal region affecting
phenotype has been previously described (Keele et al. 1999). In
summary, Warner-Bratzler shear force measurements were ob-
tained on days 2 and 14 post-mortem for 294 progeny from a
mating of a Brahman × Hereford bull to Bos taurus cows. A
genome scan identified a QTL on BTA15 with a peak at 28 cM
from the most centromeric marker (MGTG13B) on the U.S. Meat
Animal Research Center (MARC) linkage map (Kappes et al.
1997), with a 95% confidence interval spanning 23 cM (between
positions 17 and 40 cM on the map).
The goals of the present study were to generate additional
markers for use in marker-assisted selection and refinement of the
QTL interval, and to identify positional candidate genes by using
comparative mapping to the gene-rich human map. Human Chr 11
shows alternating blocks of conserved synteny with BTA15 and
BTA29 (Chowdhary et al. 1996; Band et al. 2000; Amarante et al.
2000), but the low resolution with which these blocks have been
defined complicates the selection of positional candidate genes. In
order to improve this resolution and provide potential candidate
genes, we added nine genes to the bovine linkage map, three of
which fell within the QTL interval.
Materials and methods
Primer sets for nine genes were designed from sequence data avail-
able in GenBank or obtained from the literature (Table 1). Primer sets for
microsatellite screening of the RH panel were obtained from the MARC
website (http://www.marc.usda.gov/). Standard polymerase chain reactions
(PCR) included 50 ng DNA, 100
each of the four nucleotides, 0.1%
Triton X-100, 50 m
Tris-HCl pH 9.0, 1.5 m
each of forward and reverse primers, and ddH
O to a total reaction volume
of 10 l. Reactions were conducted in a PTC-200 DNA Engine (MJ
Research, Incline Village, NV). Thermocycling parameters were 95°C for
10 min, 35 cycles of 95°C for 30 s, 55–63°C for 30 s, and 72°C for 30 s,
with a final extension cycle of 72°C for 5 min. PCR products were elec-
trophoresed on 2% agarose gels and visualized with ethidium bromide.
Reactions were performed as recommended (Applied Bio-
systems, Foster City, CA). Single nucleotide polymorphisms (SNPs) were
identified by visual inspection of the chromatograms or by alignment with
the programs phrap, polyphred, and consed. Sequences were compared
with the GenBank database via BLASTN search (Altschul et al. 1990) to
verify that amplicons were specific to the target genes. PCR products were
generated from within each gene for each of the four F1 bulls in the MARC
reference families (Bishop et al. 1994) and sequenced for SNP discovery.
* Present address: USDA, ARS, NCCCWA, PO Box 100, Kearneysville,
WV 25430, USA.
** Present address: USDA, ARS, NPS, 5601 Sunnyside Ave., Rm 4-2164,
George Washington Carver Bldg. Beltsville, MD 20705-4736, USA.
Correspondence to: T.P.L. Smith; E-mail: email@example.com
Mammalian Genome 12, 561–565 (2001).
© Springer-Verlag New York Inc. 2001