A high-resolution comparative RH map of porcine
Chromosome (SSC) 2
Annemieke P. Rattink, Marilyne Faivre, Bart J. Jungerius, Martien A.M. Groenen, Barbara Harlizius
Department of Animal Sciences, Animal Breeding and Genetics Group, Wageningen Institute of Animal Sciences, Wageningen University, PO Box
338, 6700 AH, Wageningen, The Netherlands
Received: 10 November 2000 / Accepted: 23 January 2001
Abstract. A high-resolution comparative map was constructed for
porcine Chromosome (SSC) 2, where a QTL for back fat thickness
(BFT) is located. A radiation hybrid (RH) map containing 33 genes
and 25 microsatellite markers was constructed for this chromo-
some with a 3000-rad porcine RH panel. In total, 16 genes from
human Chromosome (HSA) 11p, HSA19p, and HSA5q were
newly assigned to SSC2. One linkage group was observed at LOD
3.0, and five linkage groups at LOD 4.0. Comparison of the por-
cine RH map with homologous human gene orders identified four
conserved segments between SSC2 and HSA11, HSA19, and
HSA5. Concerning HSA11, a rearrangement of gene order is ob-
served. The segment HSA11p15.4-q13 is inverted on SSC2 when
compared with the distal tip of SSC2p, which is homologous to
HSA11p15.5. The boundaries of the conserved segments between
human and pig were defined more precisely. This high-resolution
comparative map will be a valuable tool for further fine mapping
of the QTL area.
Total genome scans have been successfully applied to map loci
affecting economically relevant traits in livestock. Recently, an
imprinted QTL accounting for differences in back fat thickness
(BFT) in a cross between Meishan and White breeds was detected
on porcine Chromosome (SSC) 2 (Nezer et al. 1999; Jeon et al.
1999; de Koning et al. 1999; Rattink et al. 2000). However, live-
stock genome maps lack the resolution required for further fine
mapping of QTL regions to finally identify the underlying genes.
The implementation of data from the much more detailed human
and murine maps is useful to accelerate the improvement of live-
stock maps. Comparisons at the phenotypic level concerning obe-
sity-related traits indicated a number of QTLs to be located on
HSA11 (Chagnon et al. 2000). However, these QTLs are not
mapped precisely either. To facilitate the switch from candidate
regions to candidate genes within small chromosome segments, the
homologous regions need to be defined accurately (Schibler et al.
The general picture of the comparative map between pig and
human is based on bi-directional chromosome painting (Retten-
berger et al. 1995; Goureau et al. 1996), somatic cell hybrid map-
ping, and FISH (http:\\www.toulouse.inra.fr/lgc/pig/cyto/gene/
chromo/SSC2.htm). Bi-directional chromosome painting indicated
homology between SSC2pter and HAS 11p15-q13. The q-arm
shows homology to HSA19pter (SSC2q12-q21) and HSA5q14-
q35 (SSC2q22-q29). In addition, EST mapping (Fridolfsson et al.
1997; Lahbib-Mansais et al. 1999) and the introduction of CATS
primers (Lyons et al. 1997) improved the comparative map. The
cytogenetic map of SSC2 (Yerle et al. 1996) encompasses 34
expressed sequences; five genes have been placed on the basic
genetic map (Archibald et al. 1995; Rohrer et al. 1996), and three
genes on the radiation hybrid (RH) map of Hawken et al. (1999).
QTL studies on meat quality traits presented the genetic mapping
of MYOD1 and IGF2 on SSC2, confirming homology between
SSC2pter and HSA11p15-q13 (Jeon et al. 1999; Nezer et al. 1999).
Nevertheless, considerable rearrangements within conserved
blocks between mammalian species have been described (Carver
and Stubbs 1997; Pinton et al. 2000). Therefore, a high-resolution
comparative gene map is needed.
In this study, a detailed comparative RH map was constructed
for SSC2. In addition to genes known or expected to be located on
SSC2, microsatellite markers were mapped on the RH panel for a
better link with the porcine genetic map. A gene-dense map of
SSC2 is presented, identifying precisely the borders to the human
Materials and methods
Development of PCR primers.
Existing primers for the genes known to
map to SSC2 were selected from the literature (Table 1). If a clear product
could not be obtained with these primers, new primers were designed based
on available sequence data in the database. In addition, the GDB sequence
database (http://gdbwww.gdb.org/) was searched for homologous porcine
sequences for all genes located on HSA11pter-q13 and HSA19q13.
BLAST searches were performed with gene name and with the accession
number. If possible, primers were developed with the Primer3 software
(Rozen and Skaletsky 2000) in the 3Ј-untranslated region (UTR) of the
porcine cDNA sequence to reduce the chance of amplification from the
rodent background in the cell lines. If no 3Ј-UTR sequence was available,
information on intron/exon boundaries was taken into account to design
primers. Otherwise, primers were selected on the basis of the available
sequence data. All PCR products resulting from previously unpublished
primers were sequenced to insure that the right locus was amplified.
For microsatellite markers, primer sequences and conditions have been
described previously for SW1650, SWR1445, SW1450, SW1686, SW2167,
SW1857, SWR1342, SW1883, SW2192, SWR2157, SW1564, SWR1338, and
SW1695 (Alexander et al. 1996a); SW2443, SWR2516, SWC9, SW2442,
and SW2513 (Alexander et al. 1996b); SW1201, SW240, SW1026, SW747,
SWR783, and SW776 (Rohrer et al. 1994); S0141 (Jung et al. 1994); S0091
(Ellegren et al. 1993); S0378 (Robic et al. 1997); S0010 (Fredholm et al.
1993); S0036 (Brown et al. 1994).
Typing of the porcine RH panel and map construction.
panel was purchased from Research Genetics (Huntsville, Ala., USA). The
RH panel was created by exposing the porcine cell line to 3000 rad of
x-rays and fusion with nonirradiated thymidine-deficient hamster recipient
cells (A23). The panel consists of 101 clones, complemented by a pig and
hamster genomic DNA as a control. For mapping, 94 cell lines were
selected (Lopez Corrales, pers. comm.) to fit a 96-well format panel. The
cell lines removed from the panel are Q7, Q10, T2, W4, X2, X7, and Y7.
Primers for 87 loci were first tested on the seven cell lines that were not
included in the final RH mapping panel. If no clear PCR product could be
Correspondence to: A. Rattink; E-mail: Annemieke.Rattink@alg.vf.wau.nl
Mammalian Genome 12, 366–370 (2001).
© Springer-Verlag New York Inc. 2001