A high-resolution radiation hybrid map of porcine chromosome 6

doi:10.1111/j.1365-2052.2004.01161.x

A high-resolution radiation hybrid map of porcine chromosome 6

H. Cao*, J. A. B. Robinson*, Z. Jiang†, J. S. Melville*, S. P. Golovan*, M. W. Jones*

and A. M. Verrinder Gibbins*

*Department of Animal and Poultry Science, University of Guelph, Guelph, Ont., Canada. †Department of Animal Science, Washington

State University, Pullman, WA, USA

Summary A high-resolution comprehensive map was constructed for porcine chromosome (SSC) 6,

where quantitative trait loci (QTL) for reproduction and meat quality traits have been

reported to exist. A radiation hybrid (RH) map containing 105 gene-based markers and

15 microsatellite markers was constructed for this chromosome using a 3000-rad porcine/

hamster RH panel. In total, 40 genes from human chromosome (HSA) 1p36.3-p22,

29 from HSA16q12-q24, 17 from HSA18p11.3-q12 and 19 from HSA19q13.1-q13.4 were

assigned to SSC6. All primers for these gene markers were designed based on porcine gene

or EST sequences, and the orthologous status of the gene markers was confirmed by direct

sequencing of PCR products amplified from separate Meishan and Large White genomic

DNA pools. The RH map spans SSC6 and consists of six linkage groups created by using a

LOD score threshold of 4. The boundaries of the conserved segments between SSC6 and

HSA1, 16, 18 and 19 were defined more precisely than previously reported. This represents

the most comprehensive RH map of SSC6 reported to date. Polymorphisms were detected for

38 of 105 gene-based markers placed on the RH map and these are being exploited in

ongoing chromosome wide scans for QTL and eventual fine mapping of genes associated

with prolificacy in a Meishan · Large White multigenerational commercial population.

Keywords porcine chromosome 6, radiation hybrid map, reproduction, sow productivity.

Introduction

Radiation hybrid (RH) mapping, a somatic cell hybrid

technique, was developed as a general approach for con-

structing high-resolution maps of mammalian chromo-

somes (Cox et al. 1990). This method holds several

advantages over other mapping procedures, the most

important being that polymorphism is not required and thus

the mapping of both polymorphic and monomorphic

markers is facilitated (Amarante et al. 2000).

Recently, linkage between economically important traits

and specific chromosomal regions has been analysed

intensively in swine populations. SSC6 has been reported to

harbour QTL associated with reproductive (Wilkie et al.

1999; Cassady et al. 2001) and meat quality traits

(de Koning et al. 1999; Ovilo et al. 2000; Grindflek et al.

2001), but previous maps of SSC6 lacked the resolution

required for further fine mapping of any QTL regions to

enable final identification of the underlying genes. Exploi-

tation of data from the much more detailed human and

murine maps is essential in accelerating the improvement

of livestock maps. Accordingly, numerous genes have

been mapped on the porcine genome to provide a

more detailed correspondence with the human genome

(http://www.toulouse.inra.fr/lgc/pig/compare/HSA.htm).

As a result, a number of breaks in conservation of synteny

between HSA chromosomes and SSC6 have been demon-

strated (Pinton et al. 2000; Karnuah et al. 2001; Sun et al.

2001; Jiang et al. 2002; Kiuchi et al. 2002; Rink et al.

2002). Nevertheless, to facilitate the identification of can-

didate genes within small chromosome segments, the

homologous regions need to be defined more accurately.

Radiation hybrid mapping was utilized in this study to

link both microsatellite and gene-based markers into a

comprehensive high-resolution map with as few break

points as possible. The current draft sequence of the human

genome (http://www.ncbi.nlm.nih.gov/genome/guide/

human/) and the previous comparative mapping between

the human and pig genomes performed by our group (Jiang

Address for correspondence

J. A. B. Robinson, Department of Animal and Poultry Science,

University of Guelph, Guelph, Ont., Canada N1G 2W1.

E-mail: [email protected]

Accepted for publication 26 May 2004

� 2004 International Society for Animal Genetics, Animal Genetics, 35, 367–378 367

et al. 2002) provide a basis for the selection of new markers

from HSA1, 16, 18 and 19 for mapping on SSC6.

Materials and methods

Marker selection and PCR primer design

Orthologous genes were selected at approximately 3 Mb

intervals based on homologous regions of HSA1, 16, 18

and 19 as previously defined using a comparative mapping

approach (Jiang et al. 2002). The selected genes span a

region of approximately 0–93 Mb on HSA1, 39–81 Mb on

HSA16, 0–34 Mb on HSA18 and 34–60 Mb on HSA19.

Porcine gene or EST sequences were selected based on

their potential orthology with genes on HSA1, 16, 18 and

19, as predicted by BLASTN. Polymerase chain reaction

(PCR) primer pairs were designed to amplify regions with

least similarity to the murine orthologous gene sequences,

using the online oligonucleotide design tool Primer 3

(http://www.genome.wi.mit.edu/cgi-bin/primer/primer3_www.

cgi) and were purchased from Laboratory Services Division,

University of Guelph (Guelph, Ont., Canada). A common

tail, 5¢-CCTCGACTGCGTACCAATTCC-3¢, was added to one

of the primers in each pair to simplify direct sequencing of

the PCR products. The primer sequences and their related

information are shown in Table 1. The PCR amplification

products were sequenced and compared with original

sequences in GenBank to confirm orthologous status. These

primer pairs were also tested using hamster DNA, to avoid

using primers that would co-amplify host homologous genes

in the pig/hamster RH panel. Primers for microsatellite

markers previously assigned to SSC6 were designed based

on information from http://www.genome.iastate.edu/maps/

marcmap.html.

Radiation hybrid panel analysis

A whole genome pig/hamster RH 3000 panel that con-

tained 94 clones was purchased from Research Genetics

(Huntsville, AL, USA).

Amplification of the RH clones was carried out in a

10 ll reaction containing 50 ng RH DNA, 7.5 ng of each

primer, 150 nmol of dNTPs, 1.5–2.5 mM MgCl2 and

0.75 units of Taq Gold polymerase (Applied Biosystems,

Foster City, CA, USA). For multiplex PCR reactions, up to

three primer pairs were added to the same reaction

mixture. The PCR conditions were as follows: 95 �C for

10 min, and 32 cycles of 94 �C for 30 s, annealing

temperature (specific for each primer pair; Table 1) for

30 s, and 72 �C for 30 s, followed by a 5-min extension

at 72 �C. PCR products were analysed by electrophoresis

through 2% agarose gels containing ethidium bromide

(0.4 lg/ml) in 1x TBE buffer. Each locus was scored as

either present (1) or absent (0) for each hybrid line. Each

ambiguous locus was re-analysed.

The RHMAP software package (version 3.0, Boehnke

et al. 1991) was used to analyse the data. Markers were

assigned to linkage groups on achieving a minimum two

point LOD score of 4.0, using the RH2PT routine of RHMAP

3.0. A LOD score of 4.0 was used to be consistent with the

objective of minimizing artificial breakpoints. Multipoint

analysis and ordering of markers was performed with the

RHMAXLIK routine (Lunetta et al. 1996). The marker order

with the greatest likelihood was accepted. The RH map

was constructed using Genetic Map Creator (http://www.

wesbarris.com/mapcreator/).

Distances (D), in Rays, were calculated as D ¼ )ln(1 ) h), where h is the breakage frequency.

Polymorphism discovery

Primers designed for gene-based markers were used to

amplify two pools of genomic DNA. The pools were created

by combining equal amounts of DNA from13 Large White

pigs or 16 Meishan pigs, including animals from three

generations (F0, F1 and F2) in each case. Direct sequencing

of these PCR products was performed using an ABI 377

automatic sequencer (Applied Biosystems, Foster City, CA,

USA) by Laboratory Service Division (University of Guelph).

Results and discussion

Radiation hybrid map construction

Initially, 181 orthologous genes were selected from HSA1,

16, 18 and 19 based on available information for pig gene

or EST sequences in GenBank. Primers were designed to

amplify unique sequences of these genes and were tested

using pig and hamster DNA as templates; 17% of the primer

pairs amplified both pig and hamster genomic DNA, and

15% of the primer pairs failed to provide specific PCR

products. Thus, 68% of the primer pairs were used for RH

panel typing with the result that 105 gene-based markers

and 15 microsatellite markers were assigned to the SSC6

RH map. The marker symbols, names, corresponding loca-

tions, and start and stop distances on HSA1, 16, 18 or 19

are shown in Table 1.

The complete data set was analysed with the RHMAP

software package version 3.0. The mean retention fre-

quency for gene-based markers was 23.7% (range 5.3–

54.3%), and for microsatellite markers was 57% (range

11.7–68.1%). Using a two-point LOD score of 4.0, two-point

analyses of the 3000-rad panel revealed six linkage groups,

with 23, 7, 20, 14, 33 and 23 loci, respectively (Fig. 1).

These data represent the largest single assignment of

gene-based markers to SSC6. As well as the six linkage

groups shown in Fig. 1, the two-point analysis also revealed

two small linkage groups with only two loci each, leaving

just eight unlinked markers (not shown in Fig. 1 or

Table 1). Nine of the 15 microsatellites examined had been

� 2004 International Society for Animal Genetics, Animal Genetics, 35, 367–378

Cao et al.368

Tab

le1

SSC6RH

map

markers,withdatab

aseinform

ation,regional

localizationofHSA

homologousloci,primer

inform

ation,product

size

andmap

location.

Locus

symbol

Gen

enam

eHSA

location

HSA

distance

(start/stop;Mb)

Accession

no.

Primer

sequen

ces

Tm

(�C)

Product

size

(bp)

LG(AD)

CDH1

Cadherin1,type1,

E-cadherin(epithelial)

16q22.1

59.46/59.55

AW431113,BE2

35473,

BE0

13620an

dBM659150

F:ACCCCACTGCCCCACCTTAT

R:TCCTCACCGCCTCCGTACAT

61

181

1(0.000)

NFAT5

Nuclearfactorof

activatedTcells5,

tonicity-responsive

16q22.1

60.28/60.42

AJ005160

F:CCTCGACTGCGTACCAATTCCGAGCTATGGAACAAGGATG

R:AGCAACCAGAATACCATGGCTACAA

61

254

1(0.589)

ATBF1

AT-binding

transcriptionfactor1

16q22.3-q23.1

63.71/63.76

BI337553,AW785662

andBE2

35417

F:CCTCGACTGCGTACCAATTCCCCCTTCAAGAGTCAGCAAC

R:GATGCAATCATATCTGCCAGCTTCT

61

436

1(1.089)

HPR

Haptoglobin-related

protein

16q22.1

62.99/63.00

AF4

92467

F:CCTCGACTGCGTACCAATTCCGGAGATTGAGAAGGTGATT

R:CAGATGCTCCGTAAAGTTGAGGTTG

61

196

1(1.437)

DHODH

Dihydroorotate

dehydrogenase

16q22

62.94/62.95

BI343408an

dAW

486848

F:CCTCGACTGCGTACCAATTCCGGAGAGGGATGCCTTGAA

R:ACTGTGGTGTTCGTGACAATCAGTC

61

1264

1(1.867)

VPS4A

Vacuolarprotein

sorting4A

(yeast)

16q23.1

60.03/60.04

AW785058,BM484481

andBI346401

F:CCTCGACTGCGTACCAATTCCGCGAATCTATATCCCGTTG

R:GTGAGTTGCTGACTGCACTTTCCTC

61

202

1(2.566)

KATNB1

Katanin

p80

(WD40-containing)

subunitB1

16q13

48.17/48.19

BF1

89878,AW435616,

BF0

78237,BE0

13827

andBF7

10054

F:CCTCGACTGCGTACCAATTCCCCAAGGAGGCAGCAAAG

R:GAGGCCTTCAGCCCGATG

61

309

1(3.009)

GOT2

Glutamic-oxaloacetic

transaminase

2,

mitochondrial(aspartate

aminotransferase

2)

16q21

49.14/49.16

M11732

F:CCTCGACTGCGTACCAATTCCGTCTCTGCCAGTCCTATGC

R:CGTTGACAGGAGGGTTGGAATACAT

61

�1086

1(3.471)

MT3

Metallothionein

3

[growth

inhibitory

Pfactor(neurotrophic)]

16q13

47.01/47.01

BF1

91454

F:CCTCGACTGCGTACCAATTCCTGCGAGGGATGCAAATG

R:AGCTGCACTTCTCTTCCTCAGCTTC

61

788

1(4.002)

KIAA0872

KIAA0872protein

16q22.1

68.15/68.16

BF1

98919

andAW785756

F:CCTCGACTGCGTACCAATTCCTTTCTTCTATGCCTACGTG

R:GATGTCCAGCGGCTTATAGAGGAAG

61

259

1(4.862)

CASPR4

Cellrecognition

protein

CASPR4

16q23.1

67.27/67.52

BF1

90030

andAW415146

F:CCTCGACTGCGTACCAATTCCGTGCATCCATCATTTACAA

R:AAAGGAGCTCACGTAGAGCAGCAAG

61

164

1(5.345)

WW

OX

WW

domain

containing

oxidoreductase

16q23.3-q24.1

69.06/70.18

BC014716

F:GTCCAAGCTCTGCAACATCCTCTT

R:CCTCGACTGCGTACCAATTCCACTTGGTGAAGGGTCTGG

61

167

1(5.551)

DC13

DC13protein

16q23.3

71.94/71.97

BE0

14487

R:CCTCGACTGCGTACCAATTCCAGAAGAGGAACAAGAGCAG

F:ACTCCAAGGATTCTGGAGACCAAGT

61

180

1(6.077)

LOC124359

Sim

ilarto

RIKEN

cDNA

4930453I21

16q23.3

71.57/71.68

AW

360379

F:AGAAACTCTCGCACAGACCCTCAG

R:CCTCGACTGCGTACCAATTCCCCTGTAGGACACCGTCTTG

61

155

1(6.768)

HSD17B2

Hydroxysteroid

(17-beta)

dehydrogenase

2

16q24.1-q24.2

72.91/72.97

AW785511

andAW312396

F:CCTCGACTGCGTACCAATTCCATGCTTTGTCCAAGTATC

R:CATCTCTTATCTGCTGCGAGTTGGT

61

156

1(7.137)

MLYCD

Malonyl-CoA

decarboxylase

16q24

74.78/74.85

BF1

89220,AW415837

andBI343470

F:CCTCGACTGCGTACCAATTCCAAGTCGAAAACCAAGGAG

R:GGTGATGCCCTTGAGGCTGAC

61

309

1(7.655)

� 2004 International Society for Animal Genetics, Animal Genetics, 35, 367–378

High-resolution radiation hybrid map of porcine chromosome 6 369

Tab

le1

Continued

Locus

symbol

Gen

enam

e

HSA

location

HSA

distance

(start/stop;Mb)

Accession

no.

Primer

sequen

ces

Tm

(�C)

Product

size

(bp)

LG(AD)

S0035

DNA

segment,

microsatellite

F:GGCCGTCTTATACTCTCAGCATA

R:CCAAATAAACAGCAGGCAGCCT

57

186

1(8.277)

MC1R

Melanocortin

1receptor

(alphamelanocyte

stim

ulatinghorm

one

receptor)

16q24.3

81.30/81.31

AF3

26520

F:CCTCGACTGCGTACCAATTCCCCATGTACTACTTCGTCTG

R:GTGTGGTGGTAGTAGGCGATGAAGA

61

343

1(8.767)

CYBA

Cytochromeb-245,

alphapolypeptide

16q24

80.15/80.15

U02477

F:GTGTTGGTCTGCCTGCTGGAGTA

R:CCTCGACTGCGTACCAATTCCCCCGGATGTAGTAGTTCCT

61

255

1(9.242)

APRT

Adenine

phosphoribosyltransferase

16q24

80.44/80.45

BI342595an

dBI343520

F:CCTCGACTGCGTACCAATTCCCTGGAGATCCAGAGAGA

R:ACTCGAACTGCAGAAGGGAGAAGAA

61

358

1(9.559)

DPEP1

Dipeptidase

1(renal)

16q24.3

81.01/81.03

X53730

F:CCTCGACTGCGTACCAATTCCCACTCCATCGACAGCAG

R:CGTGTCCACCAGCCAGTTGT

61

213

1(9.910)

ZDHHC7

Zincfinger,DHHC

domain

containing7

16q23.3

75.55/75.59

BI185968an

dBI184335

F:AGTGGACTGAGTGCAGTGGTTTCTC

R:CCTCGACTGCGTACCAATTCCCACTCTTGAGCCTCTCGAT

61

653

1(10.490)

NOC4

NeighbourofCOX4

16q24

77.03/77.06

AW

312595

F:CCTCGACTGCGTACCAATTCCCGAACACGATGAGAACAA

R:GAATGTCATCCAGGTGGTTATCAAA

61

662

1(10.683)

TNRC9

Trinucleotiderepeat

containing9

16q12.2

42.90/43.00

F15073

F:CTCGGGGATGAGGAGTTTGAAATAC

R:CCTCGACTGCGTACCAATTCCAGATTCCTTGAGATGGTAA

61

191

2(0.000)

RBL2

retinoblastoma-like2

(p130)

16q12.2

43.88/43.94

BI304691,BI132957

andBI404578

F:TGCTATAGGACTCAGCCACAAGC

R:CCTCGACTGCGTACCAATTCCACTATCACTGCTGCCAGAAT

61

492

2(0.188)

LYPLA

3Lysophospholipase

3

(lysosomal

phospholipase

A2)

16q22.2

58.97/58.99

BF4

42148

F:CCTCGACTGCGTACCAATTCCCAACCGTATCCCGGTCAT

R:ATGAGCCAGCCATCTTTGAAGC

61

195

2(1.032)

LCAT

Lecithin-cholesterol

acyltransferase

16q22.1

58.66/58.67

BG384679,AW

346632

andAW

786443

F:CCTCGACTGCGTACCAATTCCGGCTGGTACATGTGGCTA

R:AAAACCATATTGAGGTGCTGTGTCC

61

278

2(1.336)

CDH5

Cadherin5,type2,

VE-cadherin

(vascularepithelium)

16q22.1

56.98/57.02

Y13919

F:CCTCGACTGCGTACCAATTCCTCTCCCTCCTCGTGTACCT

R:CAAAGATATGCAGCGTGTCGTAGG

61

351

2(1.794)

CDH11

Cadherin11,type2,

OB-cadherin(osteoblast)

16q22.1

55.36/55.47

BF0

78663

F:CGAGGAAGAAGATGTCCGTGAGA

R:CCTCGACTGCGTACCAATTCCTGATGAAATCATCCACATC

61

212

2(2.269)

SW

R2149

DNA

segment,

microsatellite

AF2

53918

F:TAACCTGCTGAGCCACAATG

R:GGGGGTTAAAAGTCCCTATTC

56

171

2(2.670)

U2AF65

U2sm

allnuclear

ribonucleoprotein

auxiliary

factor(65kD)

19q13.43

57.04/57.07

BI182545

F:CCTCGACTGCGTACCAATTCCAAGAAGAAGGTCCGCAAGT

R:AGTGATGCCAAAGGGGATGTTG

61

429

3(0.000)

S0300

DNA

segment,

microsatellite

U11544

F:TCCTCGGAAAGATGTAACTGC

R:CTGTCACCAACAGGGCACTA

56

160

3(0.737)

� 2004 International Society for Animal Genetics, Animal Genetics, 35, 367–378

Cao et al.370

PPP2R1A

Protein

phosphatase

2(form

erly2A),

regulatory

subunit

A(PR65),alphaisoform

19q13.41

53.32/53.36

Z34955

F:ACGGTGGAGGAGACGGTGGT

R:CTGTCGAAGCTCCGCCTTGA

61

213

3(0.938)

NKG7

Naturalkillercellgroup

7sequence

19q13.41

52.50/52.51

BF1

89226an

dBI186983

F:CCTCGACTGCGTACCAATTCCCTGTCTTGGTTGCCCTGAG

R:ACATGACCAGGAAGCTCACAGAGAC

61

263

3(1.061)

BAX

BCL2-associatedXprotein

19q13.3-q13.4

50.12/50.12

BG732698an

dBI359754

F:CCTCGACTGCGTACCAATTCCCAGGATGCATCTACCAAGA

R:CGCCACTCGGAAAAAGACTTCTC

61

488

3(1.409)

FUT2

Fucosyltransferase

2(secretorstatus

included)

19q13.3

49.90/49.92

U70881an

dU70882

F:CCTCGACTGCGTACCAATTCCACTACCACCTGAACGACT

R:ATGGTCTCTCCACCAGCAAGGTAG

61

535

3(1.623)

ZIN

Zinedin

19q13.2

47.87/47.89

BI346856,

BI343376,

BI345694an

dBG733587

F:CCTCGACTGCGTACCAATTCCCCTCCTTACACTGGACTC

R:GAAGCGGATGCCTCTGTCGT

61

506

3(2.023)

FOSB

FBJmurineosteosarcoma

viraloncogene

homologueB

19q13.32

46.61/46.62

AF1

20155

F:CCTCGACTGCGTACCAATTCCGCCAGGAACCAGTTACTCC

R:GAACCCTTCTCTTCTCCTCCTCCTC

61

435

3(2.188)

SCN1B

Sodium

channel,

voltage-gated,typeI,

beta

polypeptide

19q13.1

36.14/36.15

BI341129an

dBF1

929998

F:CCTCGACTGCGTACCAATTCCTGGCGGAGATGGTTTACT

R:CCCGTACAGTTCTCTTTGCTTTCTG

61

611

3(3.456)

SW

1067

DNA

segment,

microsatellite

AF2

35183

F:GCCAGTGACTCTGCCTCTGT

R:ACCGGGGGATTAAACAAAAA

56

170

3(5.029)

SLC7A9

Solute

carrierfamily

7(cationic

amino

acidtransporter,

y+system),member9

19q13.1

33.94/33.98

BI34327,BE0

14016

and

BG384838

F:CCTCGACTGCGTACCAATTCCGGGATTCTTGCGACACTG

R:CTCGGAGAAGCTGAGACAGATGATG

61

483

3(5.564)

GPI

Glucose

phosphate

isomerase

19q13.1

35.47/35.51

X07382

F:CCTCGACTGCGTACCAATTCCGCGAATGGAAAGGGTACT

R:CATCAATGTTGGAGACGAACCAGAC

61

309

3(6.059)

UPK1A

Uroplakin

1A

19q13.13

36.80/36.81

BF1

92610an

dBG609475

F:CCTCGACTGCGTACCAATTCCTGGTGCTCATGCTCATCG

R:TTGGTGATCAGGGACGGGTTA

61

241

3(6.426)

COX7A1

Cytochromecoxidase

subunitVIIapolypeptide

1(m

uscle)

19q13.1

37.28/37.28

CA780468

F:GGTCCGCTCCTTTAGCTCAACC

R:CCTCGACTGCGTACCAATTCCGACACAGAGTCATAGTCAC

61

289

3(6.662)

SPINT2

Serineprotease

inhibitor,

Kunitztype,2

19q13.1

39.37/39.40

BI338215an

dBF0

79374

F:CCTCGACTGCGTACCAATTCCGCAGGATTCTGATGACCT

R:CGGCATCCTCCGTAGATGAACTTAT

61

555

3(7.213)

TGFB1

Transform

inggrowth

factor,beta

1

(Camurati–Engelm

ann

disease)

19q13.1

42.45/42.50

M23703

F:CCTCGACTGCGTACCAATTCCGCCCACTGTTCCTGTGAC

R:GGTTCATGCCGTGAATGGTG

61

295

3(7.615)

XRCC1

X-rayrepaircomplementing

defectiverepairin

Chinese

hamstercells1

19q13.2

44.69/44.73

BE0

12688,

AW

353742,

BI337673an

dBE0

12458

F:CCTCGACTGCGTACCAATTCCAGTTCCCAGGGGACGAG

R:CACCAGGGAGGGGTTGTCC

61

601

3(8.010)

� 2004 International Society for Animal Genetics, Animal Genetics, 35, 367–378

High-resolution radiation hybrid map of porcine chromosome 6 371

Tab

le1

Continued

Locus

symbol

Gen

enam

e

HSA

location

HSA

distance

(start/stop;Mb)

Accession

no.

Primer

sequen

ces

Tm

(�C)

Product

size

(bp)

LG(AD)

SIRT2

Sirtuin

(silentmatingtype

inform

ationregulation

2homologue)2

(S.cerevisiae)

19q13

39.98/40.00

AW

657450,AW

346910,

BE2

34094an

dBI184249

F:CCTCGACTGCGTACCAATTCCAAGAAGGAGCTGGAGGAC

R:GAGCTCCCCAGAAAAGAGCTGTAAG

61

255

3(8.791)

SW

193

DNA

segment,

microsatellite

AF2

35233

F:GCAATTTGCCTGATGCTCTT

R:TTCACTCTGAGGGGTCCTGA

57

184

3(9.327)

SUPT5H

SuppressorofTy5

homologue(S.cerevisiae)

19q13

40.58/40.61

AW

619853,AW

785911,

BI343372an

dBI400129

F:CCTCGACTGCGTACCAATTCCCAGGTCAACCCACAGTA

R:GCGAGGGTGTGGGGTGATAG

61

316

3(9.555)

STK13

Serine/threoninekinase

13(aurora/IPL1-like)

19q13.43

58.64/58.65

AW477959an

d

CA778485

F:CCTCGACTGCGTACCAATTCCATAGAGAAGGAAGGACTGG

R:GCATTTCTGCAGTTCCTTGTAGAGC

61

814

4(0.000)

ISG15

Interferon-stimulated

protein,15kDa

1p36.33

0.48/0.48

BI183574

F:CCTCGACTGCGTACCAATTCCGGTGCAAAGCTTCAGAGAC

R:GGTGCACATAGGCTTGAGGTCATAC

61

220

4(0.620)

BC-2

Putativebreast

adenocarcinoma

marker(32kD)

19q

59.96/59.96

BI338403

F:CCTCGACTGCGTACCAATTCCGCTCAAGTCTAACAACTCC

R:CATCGTTCATCATCTCCTCCTTCAT

61

235

4(0.956)

ARPM2

Actin-relatedprotein

M2

1p36.3

2.38/2.38

BF1

94602an

d

AW

430875

F:CCTCGACTGCGTACCAATTCCAGGTCTTGCACCTGCACT

R:AGGGAGTAGCCCTCGAAGATGG

61

325

4(1.388)

ICMT

Isoprenylcysteine

carboxylmethyltransferase

1p36.21

5.86/5.87

BE0

32550

F:GCAGATCACCTGGCTCAGTGC

R:CCGGAACCAGGCGTAGACTC

61

166

4(2.089)

ENO1

Enolase

1(alpha)

1p36.3-p36.2

8.54/8.56

AW

619583

F:AAGGCTGGCGCTGTTGAGAAG

R:CCTCGACTGCGTACCAATTCCCCGTATTTCTCCTTGATG

61

593

4(2.858)

RERE

Arginine-glutamic

acid

dipeptide(RE)repeats

1p36.1-p36.2

7.99/8.14

Z84142

F:CCAACCCCATGGAGCATTTC

R:CCTCGACTGCGTACCAATTCCTCCGGGTAGCTCATTTCT

61

159

4(3.008)

SW

4DNA

segment,

microsatellite

AF2

53862

F:CCTGGGGCACACTCACACCT

R:CCGTCGTGTGTGCCAAAGAT

61

144

4(3.357)

NPPA

Natriureticpeptide

precursorA

1p36.21

11.75/1175

X54669

F:AGGCTATGCCCCCACAAGTACTAAG

R:CCTCGACTGCGTACCAATTCCCAGCCCAGTCCACTCTGTG

61

271

4(3.836)

NPPB

Natriureticpeptide

precursorB

1p36.2

11.98/11.98

M23596

F:GAGCGGACGGACCTGGAG

R:CCAAAGCAGCCAGAGTCACG

61

164

4(3.899)

MTHFR

5,10-m

ethylenetetra

hydrofolate

reductase

1p36.3

11.69/11.71

BG835531,BG384323

andAW436969

F:CCTCGACTGCGTACCAATTCCATCATCACCCAGCTTTTCT

R:CTCGATCACGTCCTTGATCTGCT

61

1035

4(4.037)

SW

122

DNA

segment,

microsatellite

AF2

35206

F:TTAGAAGACAAATTTTAGAAGCTCTTT

R:AAAAAGGCAAAAGATTGACACA

56

201

4(4.408)

SDR1

Short-chain

dehydrogenase/reductase

1

1p36.1

12.66/12.71

BG834113

F:AATGGCTGGGAGCGTTGGTA

R:CGCGTTCTGCGAACTCCCTA

61

174

4(4.674)

PGD

Phosphogluconate

dehydrogenase

1p36.3-p36.13

10.42/10.44

X16638

F:CCTCGACTGCGTACCAATTCCAGTCTTTGCTCGATGCTTA

R:CATGAAGCCCTGAGTGTAGGAGATG

61

348

4(5.045)

� 2004 International Society for Animal Genetics, Animal Genetics, 35, 367–378

Cao et al.372

CAC-1

CAC-1

1p35-p34

33.18/33.19

BF1

89480

F:CCTCGACTGCGTACCAATTCCGTGTTGTCACGCTACCT

R:ACTCTCTGCCACGCAGAACAGTAA

61

557

5(0.000)

GJB5

Gapjunctionprotein,beta

5

(connexin

31.1)

1p35.1

35.04/35.05

AW786361

andBE2

35692

F:CCTCGACTGCGTACCAATTCCCTGCTACGACGAGTTCTT

R:GAGGGTGTACTTGGGGTAGAACAGG

61

286

5(0.507)

MTF1

Metal-regulatory

transcrip-

tionfactor1

1p33

38.11/38.16

Z84162,BE2

35677,

AW312370an

dZ84098

F:CCTCGACTGCGTACCAATTCCACAGTCCAGACAACAGCAT

R:AGTGAGGGTTGCACCTTCGATATTT

61

362

5(1.014)

PABPC4

Poly(A)bindingprotein,

cytoplasm

ic4(inducible

form

)

1p32-p36

39.94/39.96

AW436678an

d

BI185581

F:ACTCATCCAGACCATGCACTCAAAC

R:CCTCGACTGCGTACCAATTCCTGGCATGATGAGCCTGTAG

61

388

5(1.554)

MC5R

Melanocortin

5receptor

18p11.2

13.92/13.92

AF1

33793

F:CCTCGACTGCGTACCAATTCCGAGAACATCTTGGTCATTG

R:AGTGCGTAGAAGATGGTCACGTAGC

61

287

5(1.843)

MC2R

Melanocortin

2receptor

(adrenocorticotropic

hor-

mone)

18p11.2

13.96/13.96

AF0

64077

F:CCTCGACTGCGTACCAATTCCGCCTTCACAGCACTGTTC

R:AAGGGGTCGATGATAGCATTACACA

61

290

5(2.054)

PPT1

Palm

itoyl-protein

thioesterase

1

(ceroid-lipofuscinosis,

neuronal1,infantile)

1p32

40.57/40.59

BE2

34609an

dBI340400

F:CCTCGACTGCGTACCAATTCCTGTAATCCCTTAAGCATGG

R:TGGGAGTTGACATTCAAAAAGAAGC

61

317

5(2.538)

GALNAC4ST-2

GalNAc-4-sulphotransf-

erase

2

18q11.2

24.43/24.70

BI337921

andAW

670338

F:CCTCGACTGCGTACCAATTCCCTACATTAGCTACAACTGC

R:ATAAAAAGCCATTGCCTCATCTGGT

61

290

5(3.936)

DSG2

Desm

oglein

218q12.1

29.10/29.15

BE2

32087,BG382012

andBG733433

F:CCTCGACTGCGTACCAATTCCCAAACCTTTGCCTGAAGTA

R:AAGGAGGAAGCTGGGGCATAGAC

61

249

5(5.290)

TTR

Transthyretin(pre-albumin,

amyloidosistypeI)

18q12.1

29.19/29.20

X82258

F:CCTCGACTGCGTACCAATTCCGCTTAGCCCCTACTCTTAC

R:TGTTTTATTGTCTCTGCCCGAGTTT

61

168

5(5.751)

SS18

Synovialsarcomatransloca-

tion,chromosome18

18q11.2

23.57/23.64

BU946845,BU946839

andBF7

02330

F:CCTCGACTGCGTACCAATTCCTCTGCCTGATTGTTTTAGC

R:CAAATTTATGGCACCCCTTCTGTTT

61

232

5(6.366)

OAZ

OLF-1/EBF-associatedzinc

fingergene

16q12

39.94/40.18

BI184377an

d

AU059448

F:CCTCGACTGCGTACCAATTCCGCACACCTTTGTCTTCTTT

R:GAAGGCTTTGCTACAGAACTTGCAG

61

307

5(6.669)

LAMA3

Laminin,alpha3[nicein

(150kD),kalinin

(165kD),

BM600(150kD),epilegrin]

18q11.2

21.34/21.43

AW

787099,BG385235

andBE2

32484

F:CCTCGACTGCGTACCAATTCCGGAACTTTCAGTTGGATCT

R:CTTCCAATGTGAATGAGGATTCCAG

61

340

5(7.228)

GATA6

GATA

bindingprotein

618q11.1-q11.2

19.63/19.66

AF2

95687an

dBI181578

F:CCTCGACTGCGTACCAATTCCGAGGGAATTCAGACCAGGA

R:GCTGCAATCGTCTGAGTTAGAAGAGG

61

221

5(8.054)

CETN1

Centrin,EF-handprotein,1

18p11.32

0.86/0.87

BF1

91379

F:CCTCGACTGCGTACCAATTCCGGAGGAGATGAAGAGGAT

R:CCACGCGTTTTAGATTTTTGAATGA

61

191

5(9.232)

ROCK1

Rho-associated,coiled-coil

containingprotein

kinase

1

18q11.1

18.39/18.57

D89493

F:ATTAAAGTCTCAAGGTGGCGATGGT

R:CCTCGACTGCGTACCAATTCCAAGAATCTGCATAAAATGG

61

428

5(9.948)

ADCYAP1

Adenylate

cyclase

activating

polypeptide1(pituitary)

18p11

0.89/0.90

AF0

47007

F:CCTCGACTGCGTACCAATTCCGAAACAAATGGCTGTTAAG

R:TTTGGATAGAACACATGAGCGATGA

61

195

5(10.253)

EMILIN-2

Extracellularglycoprotein

EMILIN-2

precursor

18p11.3

3.12/3.14

BI340897an

d

AW

479974

F:CCTCGACTGCGTACCAATTCCGCGCTACCTGATCACAG

R:CTTCAAGTGCACGACCAGGTG

61

194

5(10.727)

EPB41L3

Erythrocyte

membrane

protein

band4.1-like3

18p11.32

5.43/5.55

CA779909

F:CCTCGACTGCGTACCAATTCCCCGAATCAGCATCACTAAA

R:AATAAGCTACGAAAGGCATGGATTG

61

180

5(11.202)

High-resolution radiation hybrid map of porcine chromosome 6 373

� 2004 International Society for Animal Genetics, Animal Genetics, 35, 367–378

Tab

le1

Continued

Locus

symbol

Gen

enam

e

HSA

location

HSA

distance

(start/stop;Mb)

Accession

no.

Primer

sequen

ces

Tm

(�C)

Product

size

(bp)

LG(AD)

PTPRM

Protein

tyrosine

phosphatase,receptor

type,M

18p11.2

8.57/8.68

BI183364,

AW656688

andBE0

13858

F:CCTCGACTGCGTACCAATTCCAACTCCAGCCAGATTAAA

R:ATGAGAGCGGCGTTGATGTAGTT

61

847

5(11.571)

PPP4R1

Protein

phosphatase

4,

regulatory

subunit1

18p11.21

9.65/9.72

BF1

89573an

d

AW

436288

F:CCTCGACTGCGTACCAATTCCCCTGCTGGATCAGTATC

R:CGTAGGTCTCCCTGAGGCAGTG

61

146

5(11.909)

HMCS

Molybdenum

cofactor

sulphurase

18q12

33.80/33.88

BI403162,BI403428an

d

BG384067

F:CCTCGACTGCGTACCAATTCCTGGGAGTCGGTTCTGTTA

R:GGAGCAGTACGATTATTCACCAGCA

61

428

5(12.837)

MAPRE2

Microtubule-associated

protein,RP/EBfamily,

member2

18q12.1

32.59/32.76

BE0

13298an

d

AW

657451

F:CCTCGACTGCGTACCAATTCCATAGGAGCCTAAGCCCAAG

R:GGCGAAGATTTGGAAAGATACTAAGA

57

258

5(13.125)

LAPTM5

Lysosomal-associated

multispanningmembrane

protein-5

1p34

31.00/31.02

BI304807an

dBE2

36206

F:CCTCGACTGCGTACCAATTCCTGAGCACTCAGTGGAAGTG

R:TGATGACAAAGAGCATGGTGATGAG

61

1010

5(13.778)

SFRS4

Splicingfactor,arginine/

serine-rich4

1p35.2

29.48/29.51

BF7

10794an

dBI400329

F:CCTCGACTGCGTACCAATTCCAGCCGTAGCACAAGTGATT

R:CCATCCAGGTACTGAGCTCCTTGTA

61

252

5(14.073)

SECP43

tRNA

selenocysteine-

associatedprotein

1p35.2

28.89/28.91

BE0

31048an

d

BG609066

F:CCTCGACTGCGTACCAATTCCTAAAACCGGTGGAATATAG

R:GCATGGTGCTCTGAGTATAGCCGTA

61

153

5(14.347)

FGR

Gardner-Rasheedfeline

sarcomaviral(v-fgr)

oncogenehomologue

1p36.2-p36.1

27.51/27.53

AW670343an

d

BI335994

F:CCTCGACTGCGTACCAATTCCACTGAACTCATCAACAAGG

R:CCAGAAAGGACTGCAGATACTCGAA

61

303

5(14.553)

SW2505

DNA

segment,

microsatellite

AF2

25168

F:CTGCAAGGAGGCAGGGGATT

R:CCTGCAGAGGCACAGTTTGG

61

207

5(14.936)

DJ465N24.2.1

Hypotheticalprotein

dJ465N24.2.1

1p36.13-p35.1

25.09/25.10

BI399694,BF7

04492an

d

BE0

30569

F:CCTCGACTGCGTACCAATTCCTACGTGAACGATCTGTGG

R:GCGCGAGTAGGACCTCGAGTAG

61

256

5(15.092)

HTR1D

5-hydroxytryptamine

(serotonin)receptor1

1p36.3-p34.3

23.09/23.09

AF1

17655

F:CCTCGACTGCGTACCAATTCCCCACAGAAACTCCAAAAG

R:GCGTTTACTATACTCCAGGGCATCC

61

383

5(15.692)

WNT4

Wingless-typeMMTV

integrationsite

family,

member4

1p36.23-p35.1

22.02/22.04

AW

415026an

d

CA997682

F:CCTCGACTGCGTACCAATTCCACTCAAGGAGAAGTTTGAC

R:CAATGGCCTTGGACGTCTTGTT

61

212

5(15.820)

S0444

F:GACAGTGACTTGCAGGGTGA

R:GCCCACAATCTTGAGCCTAT

56

219

5(16.330)

PLA2G2A

Phospholipase

A2,groupIIA

(platelets,synovialfluid)

1p35

19.87/19.88

BI359586

F:CCTCGACTGCGTACCAATTCCTGGCAGTGATCATGGCATT

R:TAGCAACCATAGAAGGCGTAATTGG

61

324

5(17.043)

PRKACB

Protein

kinase,

cAMP-dependent,

catalytic,

beta

1p36.1

84.94/85.10

F:CCTCGACTGCGTACCAATTCCAAAAGAGTTTTGCGAATTT

R:CCTTCCAATGTCACAGAGGCATAAC

61

392

6(0.000)

CTBS

Chitobiase,di-N-acetyl-

1p22

85.52/85.54

AW

619352an

d

BE2

32595

F:CCTCGACTGCGTACCAATTCCGTTGGCCATAAAACTTGGA

R:GGCCTGCTTAATTTGTTGAGCTATC

61

831

6(0.199)

Cao et al.374

� 2004 International Society for Animal Genetics, Animal Genetics, 35, 367–378

ETL

EGF-TM7-latrophilin-related

protein

1p33-p32

79.52/79.63

BI359886an

dBF1

91028

F:CCTCGACTGCGTACCAATTCCTCCACCTCTACCTCATTGT

R:TGATGCTGAAAATCCAACTACCACA

61

168

6(0.994)

MGC3184

Sim

ilarto

sialyltransferase

7

[(alpha-N

-acetylneuraminyl

2,3-betagalactosyl-1,3)-N-

acetylgalactosaminide

alpha-2,6-sialyltransferase]E

1p31.1

77.46/77.66

BI182122

F:CTGAAAATGCACTGCAGGGACTG

R:CCTCGACTGCGTACCAATTCCTGCAGGTTGTTGTAGACCT

61

304

6(1.698)

PTGER3

Prostaglandin

Ereceptor3

(subtypeEP3)

1p31.2

71.44/71.64

AJ001201

F:CCTCGACTGCGTACCAATTCCGTCATCGTCCTGTACCTGT

R:AAGGCAGAAGCGAAGAAAATGTTG

61

374

6(2.082)

CTH

Cystathionase

(cystathionine

gamma-lyase)

1p31.1

71.00/71.03

BQ600852

F:CCTCGACTGCGTACCAATTCCGACTCTCTGTGGGCTTAG

R:GAAAGGTTATGAGGTGCCTTGGAAT

61

764

6(2.256)

S0121

DNA

segment,microsatellite

L30152

F:GGAAGGCCCAAAGAGTTGTA

R:ATAGGGCATGAGGGTGTTTG

56

187

6(2.505)

ARHI

Rashomologuegene

family,memberI

1p31

68.47/68.48

AW784881,BE2

33242

andBI342139

F:CCTCGACTGCGTACCAATTCCCTATCGAAGATACCTACC

R:ACAGCTCCTGCACGTTGATATTCAT

61

369

6(2.789)

SW824

DNA

segment,microsatellite

AF2

35377

F:TTGCGTGTGTGTGTGTGTGTG

R:TGCCTTCTACCAAAGCCTCGTT

61

170

6(3.149)

C8A

Complementcomponent8,

alphapolypeptide

1p32

57.24/57.30

AB008156

F:CCTCGACTGCGTACCAATTCCAGGATTTCCAGTGTAAGGA

R:TTACACACGAGGTGGCGTTTCAG

61

965

6(4.009)

CYP2J2

CytochromeP450,

subfamilyIIJ(arachidonic

acidepoxygenase)

polypeptide2

1p31.3-p31.2

60.28/60.32

BI359857,BE0

14607an

d

BF1

91621

F:CCTCGACTGCGTACCAATTCCTTAGAGGAACGCATTCAGG

R:AGCTCCTGGAACTGATTATCCTGGT

61

540

6(4.731)

JAK1

Januskinase

1

(aprotein

tyrosinekinase)

1p32.3-p31.3

65.25/65.38

AB036335

F:TGCTCCGGAGTGTTTAATTCAGTGT

R:CCTCGACTGCGTACCAATTCCTCTGGACAGTTAGGTGGAC

61

488

6(5.396)

DG93

DNA

segment,

microsatellite

U26957

F:GGCAGCTCATGTTGAGTGAA

R:CCCCACTCTGTCCTTCAAAA

57

152

6(5.620)

PDE4B

Phosphodiesterase

4B,

cAMP-specific

(phosphodiesterase

E4

dunce

homologue,

Drosophila)

1p31

66.34/66.80

BM083204,

AW431490

andBI400362

F:CCTCGACTGCGTACCAATTCCCAATGTGGCTGGCTATTC

R:GTTATGATAGGCCACGTCGGAATG

61

304

6(5.852)

DJ167A19.1

Hypothetical

protein

DJ167A19.1

1p33-p32.1

54.15/54.18

BI346501,BF4

43761an

d

BI402089

F:CCTCGACTGCGTACCAATTCCCTGGACAGAAGAAAAGCTC

R:TTTTCCTGGTATTGGTAGAAGAGACC

57

1081

6(6.424)

SCP2

Sterolcarrierprotein

21p32

52.94/53.15

F14816

F:GGCAGTTTTGGCTAGTGAAGTGTTT

R:CCTCGACTGCGTACCAATTCCAATCATGCTGTTTTCTTCA

61

121

6(6.598)

SW

1069

DNA

segment,

microsatellite

AF2

43574

F:CTGTGTCATCACCAGGCTGT

R:AACCACAATGGTGGAGGTTC

57

195

6(6.713)

GPX6

Glutathioneperoxidase

61p32

52.43/52.43

BI184046

F:CCTCGACTGCGTACCAATTCCTGAATGTGGCTAGCGAGTG

R:ATCTTGCTGAACATGGGGAAAGAGA

61

202

6(6.918)

SIAT6

Sialyltransferase

6(N

-acetyllacosaminide

alpha2,3-sialyltransferase)

1p34.1

44.01/44.24

BG383416,BI341911

andBE0

31094

F:CCTCGACTGCGTACCAATTCCTCAACAATGGCCTCATGG

R:CATGCGCACGGTCTCGTAGTAGT

61

340

6(8.133)

High-resolution radiation hybrid map of porcine chromosome 6 375

� 2004 International Society for Animal Genetics, Animal Genetics, 35, 367–378

mapped previously to SSC6 (INRA-UMN RH map; http://

www.toulouse.inra.fr/lgc/pig/RH/Menuchr.htm), but the

order of some of these loci differed slightly in our study. In

addition, in our results, linkage group III includes loci

SW193, S0300 and SW1067 as part of a single linkage

group, which were previously reported to map to two small

groups (INRA-UMN RH map).

Comparative map

Of the 105 gene-based markers, 40 spanned a region of

approximately 0–86 Mb on HSA1p36.3-p22, 29 spanned

40–81 Mb on HSA16q12-q24, 17 spanned 1–34 Mb on

HSA18p11.3-q12 and 19 spanned 34–60 Mb on

HSA19q13.1-q13.4. The previous mapping of 29 of the 120

markers to SSC6 by cytogenetic mapping (http://

www.toulouse.inra.fr/lgc/pig/compare/SSC.htm and Lah-

bib-Mansais et al. 2000) and of 16 of the 120 by linkage

mapping (http://www.toulouse.inra.fr/lgc/pig/RH/Menuchr.

htm) was used in determining linkage group order and

orientation (Fig. 1).

While large regions of conserved segments have been

reported between SSC6 and HSA1, 16, 18 and 19 (Goureau

et al. 1996), one potential inconsistency was found. The

human genome position for OAZ is reported to be on

HSA16q12 (accession no. NM_015069), therefore this gene

was expected to map to SSC6p in linkage group I or II. In

our RH map, OAZ is located in group V on SSC6q2.8–3.1.

Repeated analyses of this marker confirmed our results; no

other inconsistencies have emerged.

Sixty-four genes expressed in a28-day-old pig embryohave

been assigned to an RH map (Karnuah et al. 2001), nine of

the genes being placed on SSC6. Our results support the

homologies reported between SSC6 and HSA1, 16 or 18 for

six of these genes. Although RH mapping can provide higher

resolution, of the 62 genes or ESTs physicallymapped to SSC6

(http://www.toulouse.inra.fr/lgc/pig/cyto/gene/chromo/

SSCG6.htm) only RYR1, UOX and HMG17 have been map-

ped previously using an RH panel (IMpRH panel; Hawken

et al. 1999; Karnuah et al. 2001). Thus, overall the assign-

ment of the 105 genes/ESTs in the present study significantly

increases the density of type I markers on the SSC6 RH map.

Polymorphism discovery and QTL location

A total of 137 gene-based markers were amplified from

Large White and Meishan pools and sequenced. Polymor-

Tab

le1

Continued

Locus

symbol

Gen

enam

e

HSA

location

HSA

distance

(start/stop;Mb)

Accession

no.

Primer

sequen

ces

Tm

(�C)

Product

size

(bp)

LG(AD)

SW607

DNAsegment,

microsatellite

AF2

35332

F:CATCTTGCTCATTGCTGCAT

R:GGACCTTCCAGGCTCTTAGC

56

242

6(8.344)

SW

2466

DNAsegment,

microsatellite

AF2

53824

F:CCTTCCCCCACACAATCTC

R:TGAGTGCAACCGTGGTTAGG

56

150

6(8.477)

SLC2A1(G

LUT1)

Solute

carrier

family2(facilitatedglucose

transporter),member1

1p35-p31.3

43.38/43.42

X17058

F:CCTCGACTGCGTACCAATTCCCTGCTGGCCTTCATATCT

R:ATGAGGATGCCGACGACGAT

61

209

6(8.554)

GUCA2B

Guanylate

cyclase

activator2B(uroguanylin)

1p34-p33

42.65/42.65

Z83746

F:CTTCCGGGTCCAGCTGAAAT

R:TCAAGGCCTGGAAGATGCTG

61

179

6(8.656)

LG,linkagegroup;AD,accumulative

distance

(inrays).

Figure 1 A comprehensive RH map for SSC6 with 120 markers in six

linkage groups. On the left of the SSC6 RH map are shown the

cytogenetic locations of 29 and linkage assignments of 16 previously

published markers; on the right of the SSC6 RH map are the human RH

(GB4: http://www.ncbi.nlm.nih.gov/genemap99/) and human cyto-

genetic positions of the genes mapped using the pig/hamster RH panel.

Cao et al.376

� 2004 International Society for Animal Genetics, Animal Genetics, 35, 367–378

High-resolution radiation hybrid map of porcine chromosome 6 377

� 2004 International Society for Animal Genetics, Animal Genetics, 35, 367–378

phisms were detected for 52 of these markers, and included

SNPs (single nucleotide polymorphisms) and indels (inser-

tion deletion polymorphisms) for 45 and 10 of these

markers, respectively, with three genes having both SNP

and indel polymorphisms. Of these polymorphisms, 23 were

in the coding region of the gene, 36 in non-coding region

with seven genes having polymorphisms in both coding and

non-coding regions. Thirty-eight of these polymorphic loci

are located on the RH map.

The Chinese Meishan breed is one of the most prolific pig

breeds known, with the genetic potential to enhance pro-

duction efficiency of European breeds (Haley & Lee 1993). A

putative QTL for the number of piglets born per litter was

identified on SSC6 at position 104 cM (P-value ¼ 0.0075)

in a Meishan · Yorkshire population (Wilkie et al. 1999).

Evidence also exists for a QTL associated with the number

of nipples, which has been mapped to SSC6 at position

145 cM (P < 0.10) in a Meishan · Large White population

(Cassady et al. 2001). Figure 1 shows that these two QTL

could be associated with markers in linkage group V or VI.

In summary, we have constructed a high-resolution RH

map of SSC6, which we are using currently in a chromo-

some-wide analysis for QTL and candidate genes associated

with prolificacy traits in a Meishan · Large White multi-

generational commercial population.

Acknowledgements

This research was supported by the Genex Swine Group

(Canada), the Natural Sciences and Engineering Research

Council of Canada (NSERC), the Food System Biotechnology

Centre (FSBC) at the University of Guelph, and the Ontario

Ministry of Agriculture and Food (OMAF).

References

Amarante M.R.V., Yang Y.P., Kata S.R., Lopes C.R. & Womack J.E.

(2000) RH maps of bovine chromosomes 15 and 29: conserva-

tion of human chromosomes 11 and 5. Mammalian Genome 11,

364–8.

Boehnke M., Lange K. & Cox D.R. (1991) Statistical methods for

multipoint radiation hybrid mapping. The American Journal of

Human Genetics 49, 1174–88.

Cassady J.P., Johnson R.K., Pomp D., Rohrer G.A., Van Vleck L.D.,

Spiegel E.K. & Gilson K.M. (2001) Identification of quantitative

trait loci affecting reproduction in pigs. Journal of Animal Science

79, 623–33.

Cox D.R., Burmeister M., Price E.R., Kim S. & Myers R.M. (1990)

Radiation hybrid mapping: a somatic cell genetic method for

constructing high-resolution maps of mammalian chromosomes.

Science 250, 245–50.

de Koning D.J., Janss L.L.G., Rattink A.P., Van Oers P.A.M., de Vries

B.J., Groenen M.A.M., van der Poel J.J., de Groot P.N., Brascamp

E.W. & van Arendonk J.A.M. (1999) Detection of quantitative

trait loci for backfat thickness and intramuscular fat content in

pigs (Sus scrofa). Genetics 152, 1679–90.

Goureau A., Yerle M., Schmitz A., Riquet J., Milan D., Pinton P.,

Frelat G. & Gellin J. (1996) Human and porcine correspondence

of chromosome segments using bi-directional chromosome

painting. Genomics 36, 252–62.

Grindflek E., Szyda J., Liu Z. & Lien S. (2001) Detection of quanti-

tative trait loci for meat quality in a commercial slaughter pig

cross. Mammalian Genome 12, 299–304.

Haley C.S. & Lee G.J. (1993) Genetic basis of prolificacy in

Meishan pigs. Journal of Reproduction and Fertility (Suppl.) 48,

247–59.

Hawken R.J., Murtaugh J., Flickinger G.H., Yerle M., Robic A.,

Milan D., Gellin J., Beattie C.W., Schook L.B. & Alexander L.J.

(1999) A first-generation porcine whole-genome radiation hybrid

map. Mammalian Genome 10, 824–30.

Jiang Z., Melville J.S., Cao H., Kumar S., Filipski A. & Gibbins A.M.V.

(2002) Measuring conservation of contiguous sets of autosomal

markers on bovine and porcine genomes in relation to the map of

the human genome. Genome 45, 1–7.

Karnuah A.B., Uenishi H., Kiuchi S., Kojima M., Onishi A., Yasue H.

& Mitsuhashi T. (2001) Assignment of 64 genes expressed in 28-

day-old pig embryo to radiation hybrid map. Mammalian. Genome

12, 518–23.

Kiuchi S., Chen Y.Z., Uenishi H., Hayashi Y., Soeda E. & Yasue H.

(2002) Construction of a dense comparative map between hu-

man chromosome 1p36-p35 and swine chromosome 6 by using

human sequence-tagged sites. Cytogenetic and Genome Research

98, 67–70.

Lahbib-Mansais Y., Leroux S., Milan D., Yerle M., Robic A., Jiang Z.

& Gellin J. (2000) Comparative mapping between humans and

pigs: localization of 58 anchorage markers (TOASTs) by use of

porcine somatic cell and radiation hybrid panels. Mammalian

Genome 11, 1098–106.

Lunetta K.L., Boehnke M., Lange K. & Cox D.R. (1996) Selected

locus and multiple panel models for radiation hybrid mapping.

The American Journal of Human Genetics 59, 717–25.

Ovilo C., Perez-Enciso M., Barragan C., Clop A., Rodriguez C. Oliver

M.A., Toro M.A. & Noguera J.L. (2000) A QTL for intramuscular

fat and backfat thickness is located on porcine chromosome 6.

Mammalian Genome 11, 344–6.

Pinton P., Schibler L., Cribiu E., Gellin J. & Yerle M. (2000) Loca-

lization of 113 anchor loci in pigs: improvement of the com-

parative map for humans, pigs, and goats. Mammalian Genome

11, 306–15.

Rink A., Santschi E.M., Eyer K.M., Roelofs B., Hess M. Godfrey M.,

Karajusuf E.K., Yerle M., Milan D. & Beattie C.W. (2002) A first-

generation EST EH comparative map of the porcine and human

genome. Mammalian Genome 13, 578–87.

Sun H.S., Tuggle C.K., Goureau A., Fitzsimmons C.J., Pinton P.,

Chardon P. & Yerle M. (2001) Precise mapping of breakpoints in

conserved synteny between human chromosome 1 and pig

chromosomes 4, 6 and 9. Animal Genetics 33, 91–6.

Wilkie P.J., Paszek A.A., Beattie C.W., Alexander L.J., Wheeler M.B.

& Schook L.B. (1999) A genomic scan of porcine reproductive

traits reveals possible quantitative trait loci (QTLs) for number of

corpora lutea. Mammalian Genome 10, 573–8.

Cao et al.378

� 2004 International Society for Animal Genetics, Animal Genetics, 35, 367–378