Download A detailed gene map of pig chromosome 4, where the first

Iowa State University Animal Industry Report 2004
Swine
A detailed gene map of pig chromosome 4, where the first
quantitative trait locus in livestock was mapped
A.S. Leaflet R1951
Christopher K. Tuggle, Professor of Animal Science
Yuandan Zhang, Postdoctoral Research Associate,
Max F. Rothschild, Distinguished Professor of
Animal Science
Maria Moller, Frida Berg, Leif Andersson
Swedish University of Agricultural Sciences
Uppsala, Sweden, Juliette Riquet, Denis Milan
Laboratoire de Genetique Cellulaire
INRA-Toulouse, France, Daniel Pomp
Department of Animal Science
University of Nebraska-Lincoln
Alan Archibald, Susan Anderson
Roslin Institute
Edinburgh, Scotland
Summary and Implications
The first quantitative trait locus (QTL) in pigs, FAT1,
was found on chromosome 4 using a wild-boar intercross.
Further mapping has refined the FAT1 QTL to a region
conserved on both human chromosome 1 and 8. We have
now improved the comparative map of the entire SSC4 by
mapping 105 loci to pig chromosome 4 (SSC4) and
defined the specific human chromosome region with
conservation to FAT1, using a combination of physical
and linkage mapping. These types of analysis have
resulted in maps with very good agreement. Comparative
analysis revealed that the gene order is very well
conserved across SSC4 compared to both human
chromosome 1 (HSA1) and to HSA8. This refined SSC4
map and the comparative analysis will be a great aid in
the search for the candidate genes for the FAT1 locus.
Introduction
Comparative genome analysis is a very powerful tool
in the days of the post-genomic era where a wealth of
information has been generated for many eukaryotic
genomes. Although significant effort and resources have
been dedicated to farm animals their genome maps are far
from reaching the high resolution available for the human
and mouse genome maps. Analysis of the genomes of
farm animals such as the search for genes underlying
complex traits; quantitative trait loci (QTLs) or
economical trait loci (ETLs) can therefore greatly benefit
from the possibility of extracting information from
homologous regions of other genomes. The molecular
identification of genes underlying QTLs is a challenging
task and there have not been many success stories
presented yet. A recent compilation of genes identified
from QTL studies summarized 29 genes so far; 28 those
were identified in human/mouse/rat and only one in a
livestock animal.
Porcine chromosome 4 (SSC4) harbor QTLs
affecting growth, carcass traits and fat deposition. The
first QTL on SSC4, denoted FAT1, was identified in a
European wild boar – Large White intercross. SSC4 has
previously been shown to share homology with human
chromosomes 1 (HSA1) and 8 (HSA8). SSC4 is divided
into two chromosomal blocks where the entire p arm and
the q arm proximal to 4q15-16 are homologous to HSA8
and the remaining major part of 4q shares homology with
HSA1. We wanted firstly to establish a dense comparative
map covering the entire SSC4 but also to define the
HSA1-HSA8 breakpoint accurately. This has been
achieved with a combined approach of EST mapping on a
radiation hybrid (RH) panel covering the entire
chromosome, and by linkage and RH mapping of new
markers developed around the breakpoint and across the
FAT1 QTL region.
Materials and Methods
Primers for physical mapping were designed from pig
gene sequence (EST) obtained from the Midwest
Consortium for Pig Reproduction Genomics project
headed by C. Tuggle. These primers amplify specific
gene loci so that the presence of the gene of interest can
be mapped relative to other gene locations using available
data (see URL). Genetic linkage mapping was performed
in Sweden using the wild-boar-Yorkshire cross available
there. All data was analyzed and a comprehensive
physical and linkage map was created.
Results and Discussion
Genetic Map development
The markers developed were screened for
polymorphisms among our 10 founder animals (2 wild
boars and 8 Large White) and polymorphism was
detected. Altogether, 11 genes were added to our
previously published linkage map of SSC4. The linkage
map comprising altogether 34 markers spans 135.9 cM
(Figure 1).
Iowa State University Animal Industry Report 2004
Physical mapping
As part of an EST-based comparative mapping
project with the aim to add 700 genes to the RH map
(http://pigest.genome.iastate.edu/), we selected HSA1 and
HSA8 genes to improve gene marker density across the
entire SSC4. For HSA1, emphasis was placed on
HSA1q21-24, as we previously showed this was the
region on HSA1 closest to the FAT1 QTL. Genes were
selected for RH mapping based on strength of BLAST
score; agreement of human cytogenetic mapping
localizations; and equal distribution across human
chromosomes. A total of 103 new genes were
successfully mapped onto SSC4.
Comparative mapping
Comparative mapping of SSC4 confirms clearly that
SSC4 corresponds to two large blocks on human
chromosomes 1 and 8 (Figure 2). Information of the
corresponding human gene homology is presented for 101
genes/markers from the RH and linkage maps, 34 that
maps to HSA8 and 67 to HSA1. The markers cover the
entire length of SSC4 but an emphasis has been made to
put markers within the region harbouring the FAT1 QTL,
23 markers has been added to this region (Figure 2).
The comparative genome analysis also clearly reveals
that there are no major rearrangements between the two
synteny blocks. The gene order seems to be overall very
well conserved as opposed to several other porcine
chromosomes that display several large intrachromosomal
rearrangements. However there is some evidence to
suggest a small inversion of the gene order compared to
HSA8 around the centromere on SSC4.
Improved Mapping of the FAT1 QTL
There appears to be several QTLs affecting, growth,
fat, and carcass traits on porcine chromosome 4. Our
intention of creating a dense comparative gene map
between SSC4 and HSA1/8 has clearly been fulfilled by
adding another 101 genes/markers to the map and an
additional 5 markers where comparative information has
not yet been obtained. The FAT1 QTL region which
boundaries are defined by the Sw1364 – S0214 markers
has had an increase of 23 genes/markers.
We used two different methods to develop SSC4
chromosome maps; radiation hybrid mapping and linkage
mapping. The maps are in very good agreement, however
on some parts of the linkage map, the gene order could
not be resolved due to no recombination events between
markers. To resolve the order of the markers on the most
Swine
dense area they could be mapped on the latest RH panel
developed for pig by colleagues in France.
Acknowledgements
This work was supported by USDA-NRICGP 9935205-8370. We thank Katie Barry and Darla Hartzler for
excellent technical assistance in gene selection.
FAT1
QTL
Region
Figure 1. Genetic Linkage map of Pig
Chromosome 4, emphasizing the FAT1
region.
This map contains 33 markers, of which 11 are
newly reported in this paper.
Iowa State University Animal Industry Report 2004
Swine
HSA8
GPT1
SIAHBP1
14
0
SSC4
GPT1
SIAHBP1
SLA
DDEF1
NSE2
MYC
C8FW
SQLE
ZHX1
SNTB
1
ZFPM2
OXR1
ATP6V1C1
PABPC
LOC157567
1
RNF1
PLEKHF2
9
UQCRB PGC
LAPTM4B KIAA1750
P
CBFA2T1
IMAGE:361836
LOC8369
5
TOG39053
0
MGC39325
TO 5
MGC2217
X
PLAG MO
1 ATP6V1H
S
MCM4 UBE2V
ATP1B1
SELE
2
ATP1B1
POU2F
KIAA1513
1
RXRG
SDHC NDUFS FCER1G
PPOX USF1
2
DUSP1 APOA2
NCSTN
2
ATP1A2
KCNJ PEA1 COP
9
5PEA1 AH32
CASQ1
5
6
APCS
MRPL2
4 BCA
FDPS MGC13102 EFNA
N
KIAA0446
1
KIAA0080
KIAA0907 RUSC1
HAX1
NICE-3 SLC39A1
ILF2
SNAPAP
SPRR1
SELENBP1
B
KIAA1441
TMSG1
APH-1A
SEMA6CSPEC
1LASS
MCL1 DKFZP434K1772
2
HIST2H2A
CGI-143 A
LOC126964
NGF
BTSHB
FLJ22457
SLC16A4
AD-020
AMY1A
LOC5099
RPL5
9
12
0
10
0
5
80
10
60
15
SLA
DDEF1
MY
NSE2
C
C8FW
SQLE
ZHX1
SNTB
TOG39053
1
5
OXR1
ZFPM2
ATP6V1C1
PABPC1
LOC157567
RNF1
LAPTM4B
9
KIAA1750
PGCP
UQCRB
PLEKHF2
CBFA2T1
DKFZp762O07
6
IMAGE:361836
5
LOC83690
TO
MGC39325
X
MGC2217
PLAG
MOS
1
ATP6V1H
MCM4
UBE2V
2
40
ADRB3
20
SSC15
SSC9
HSA1
25
16
0
30
14
0
12
0
35
10
0
SSC6
SERPINC
PIG
SELE
C
ATP1B1
POU2F1
KIAA1513
RXR
DUSP12
G
SDHC
NDUFS2FCER1GAPOA2
PPOX
USF1
COPANCST
PEA15H326
N
ATP1A2
CASQ
KCNJ9
1
APCS
MRPL2
KIAA0446BCAN
4
MGC13102
KIAA0907
KIAA0080
FDPSRUSC1
EFNA
NICE-3
1 HAX
SLC39A1
1 ILF2
SNAPAP
SPRR1
SELENBP1
B
KIAA1441
SEMA6C
SPEC
TMSG
1 LASS2
DKFZP434K1772
MCL1
1
LOC126964
APH-1A
HIST2H2A CGI-143
A
NGF
TSHB
B
FLJ22457
SLC16A4
AD-020
AMY1A
LOC5099
9 RPL
5
UOX
PRKACB
Figure 2. A comparative map of SSC4 and HSA1/HSA8 chromosomes. The porcine distances are given in
Rays (measure of physical distance) and the human in Millions of base pairs from human genome
sequence. Green signifies high level of confidence in the porcine position; while blue is most likely position
for that gene. The red box indicates a region of possible gene order difference between pig and human.