Download Comparative mapping in cattle of genes located on human

Mammalian Genome 8, 530–532 (1997).
© Springer-Verlag New York Inc. 1997
Comparative mapping in cattle of genes located on human
Chromosome 18
Morris K. Agaba,1 Stephen J. Kemp,2 William Barendse,3 Alan Teale1
1
International Livestock Research Institute, P.O. Box 30709, Nairobi, Kenya
School of Biological Sciences, Donnan Labs, University of Liverpool, Liverpool L69 3BX, UK
3
CSIRO, Division of Tropical Animal Production, Molecular Animal Genetics Centre, Gehrmann Laboratories, Research Rd., University of
Queensland, St. Lucia 4072, Australia
2
Received: 7 December 1996 / Accepted: 25 February 1997
Human Chromosome (Chr) 18 (HSA18) contains approximately
85 million base pairs of DNA (Morton 1991). Thirty genes and
pseudogenes have been mapped to HSA18 by somatic cell genetics
or in situ hybridization (Le Beau et al. 1993; Overhauser et al.
1993; van Kessel et al. 1994). They include pituitary adenylcyclase
activating peptide (ADCYAP1), laminin a chain (LAMA1), and
mitochondrial NADH-ubiquinone reductase, 24 kDa subunit
(NDUFV2) on the short arm, and transthyretin (TTR), B-cell lymphoma 2 (BCL2), plasminogen activator inhibitor type 2 (PAI2),
n-cadherin (CDH2), desmocollin type 2 (DSC2), ferrochelatase
(FECH), cytochrome b5 (CYB5) and myelin basic protein (MBP)
on the long arm (Fig. 1a). The murine homologs of HSA18 genes
have been mapped to at least four chromosomes as follows: Bcl-2
and Planh2 genes are on MMU1, thymidylate synthase (Ts1) gene
is on MMU5, Lama1 is on MMU17, and the rest are on MMU18
(Mouse Genome Database 3.1, 1996).
Two bovine genes—Yamaguchi sarcoma viral oncogene homolog 1 (YES1) and desmocollin type 1 (DSC1)—homologous to
HSA18 loci have been mapped by in situ hybridization to Chr 24
(Chowdhary et al. 1996), and ZOO-FISH analyses show that
HSA18 loci are located entirely on BTA24 (Hayes 1995; Toldo et
al. 1995; Chowdhary et al. 1996). We report here the genomic
localization of eight bovine genes homologous to HSA18 genes
Correspondence to: A. Teale
ADCYAP1, CDH2, CYB5, DSC2, FECH, NDUFV2, PAI2, and
TTR, using somatic cell genetics and linkage analysis in the International Bovine Reference Panel (IBRP).
Oligonucleotide primers for PCR were designed on the basis
of the published nucleotide sequences of sheep or cattle genes
ADCYAP1, CDH2, CYB5, DSC2, FECH, NDUFV2 and TTR, and
were used to amplify the corresponding DNA fragments from
bovine total genomic DNA. Primers for PAI2 gene fragments were
designed on the basis of a consensus sequence of the human and
murine genes. PCR amplification and single-strand conformation
polymorphism (SSCP) analysis were performed as described previously (Agaba et al. 1996) except that the annealing and gel
temperatures were optimized for each DNA fragment as shown in
Table 1. The primers for PAI2 were allelic; that is, under optimum
PCR conditions amplification of one allele from some individuals
was favored over the alternative (null) allele, and, as expected,
dominant inheritance was observed in informative IBRP families.
Somatic cell hybrid mapping was achieved by PCR amplification of bovine sequences in a panel of 27 bovine × rodent somatic
cell hybrids kindly provided by J. Womack of Texas A & M
University. In the case of the PAI2 gene, bovine fragments were
differentiated from rodent fragments by SSCP analysis. Seven
genes, ADCYAP1, CDH2, CYB5, DSC2, FECH, PAI2 and TTR,
segregated 100% concordantly with each other and with Chr 24,
while the NDUFV2 gene segregated 100% concordantly with
BTA5.
Fig. 1. (A) Location of some of the genes on
human Chr 18 determined by in situ hybridization
(from Le Beau et al. 1993; van Kessel et al.
1994); (B) assignment of eight of the genes to
bovine Chrs 5 and 24 by somatic cell hybrid
analysis; (C) location of the genes on the linkage
map of Chr 24. Some loci are at the bottom of the
multipoint map because they cannot be ordered
with odds greater than 1000:1; instead, they are
listed as being at a distance relative to an ordered
locus.
M.K. Agaba et al.: Human Chr 18 genes located in cattle
531
Table 1. List of the HSA18 genes mapped in cattle showing the primer sequences, SSCP analysis conditions, number of alleles, and meioses informative for linkage analysis.
Gene symbol
Primer sequences
Ta (°C)a
Product
size (bp)
SSCP conditions
(power)(Tg)b
Alleles
Meioses
Reference for nucleotide sequence
ADCYAP1
acctctgtaataaccaccgg
aaaagtttgacgacgctcgg
tgactatgaaggcagtggc
attggatcaccgatattccc
aagataaccaagccttcgg
agaagacattgacagacacc
ctcaagactatgtcctgacc
gctatttacagcatccctcg
ggttggcccgatgccctggc
tcactggctagaacttgag
agttgaatgtttaggggcc
ccactgacatatttacagcg
actcaacaagtggaccagc
tctgctacaaactgtgggc
gctggtgaatccaagtgtcc
tccctgaggcaaatggctcc
56
349
5W, 4°C
2
110
Kimura et al. 1990
55
320
5W, 4°C
2
83
Liaw et al. 1990
53
388
5W, 4°C
4
138
Cristiano et al. 1993
56
326
5W, 4°C
2
85
Koch et al. 1992
56
165
5W, 4°C
3
243
Shibuya et al. 1995
53
260
5W, 4°C or 25°C
2
162
Pilkington and Walker 1989
56
303
—
2
68
Belin et al. 1989; Ahern et al. 1989
56
130
5W, 4°C or 25°C
1
0
Tu et al. 1989
CDH2
CYB5
DCS2
FECH
NDUFV2
PAI2c
TTR
a
b
c
Ta 4 annealing temperature.
Tg 4 gel temperature.
PAI2 was genotyped by an allele-specific amplification assay.
Table 2. Two-point linkage analyses showing recombination fractions and the Lod scores.
FECH
FECH
PAI2
TGLA351
CSSM31
CDH2
CYB5
ILSTS101
DSC2
ADCYAP1
CSSM23
INRA90
BM315
PAI2
TGLA351
CSSM31
CDH2
CYB5
ILSTS101
DSC2
ADCYAP1
CSSM23
INRA90
—
—
—
—
0.19; 4.87
0.20; 9.02
—
—
—
0.05; 10.60
—
—
0.05; 6.47
0.06; 5.45
—
0.21;
—
—
0.11;
0.05;
0.18;
—
—
0.04;
0.00;
—
0.13;
0.06;
—
—
—
0.17; 3.75
0.04; 4.54
—
0.09; 4.67
—
—
0.13;
0.18;
0.10;
0.18;
—
0.20;
—
—
0.13; 13.98
—
—
—
—
—
0.18; 7.61
0.19; 3.84
—
—
The PCR-generated fragments were screened for polymorphism in the IBRP by SSCP analysis, and informative families
were genotyped (Table 1). Mendelian inheritance was demonstrated and genotype data were analyzed for linkage against the
Cattle Genotypic Database (CGD) markers with CRI-MAP v2.4
SunOs as described by Barendse and associates (1994). Two-point
analyses revealed genetic linkage as shown in Table 2. The loci
CSSM31 and CSSM23 have previously been mapped to BTA24
(Barendse et al. 1994), and BM315 to BTA5 (Bishop et al. 1994).
The order of three loci FECH–ADCYAP1—CYB5 on BTA24 is
rearranged compared with the order ADCYAP1-FECH-CYB5 on
HSA18 (Fig. 1c).
These data provide further information on the bovine equivalents of HSA18 and reveal extensive conservation of synteny between human and cattle similar to that previously observed for
other genomic regions (Threadgill et al. 1990, 1994; Zhang et al.
1992). Unlike the situation in the mouse genome, synteny of the
PAI2 gene with other HSA18 homologous loci is conserved in
cattle. However, syntenic conservation between BTA24 and
HSA18 loci was disrupted by the translocation of the NDUFV2
locus to BTA5. The size of the HSA18 homolog represented by
NDUFV2 that is located on BTA5 will become clearer as additional type I loci in the vicinity of NDUFV2 on HSA18 are
mapped in cattle. Since ZOO-FISH analyses of the bovine chromosomes do not show homology between HSA18 and BTA5
(Hayes 1995; Toldo et al. 1995; Chowdhary et al. 1996), we conclude that the HSA18 homolog represented by NDUFV2 on BTA5
is probably smaller than 7 million base pairs, the lower detection
limit of ZOO-FISH (Scherthan et al. 1994).
4.51
3.07
8.83
3.50
4.23
11.14
4.90
9.77
5.69
7.45
22.49
5.01
5.36
NDUFV2
0.09; 20.98
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