fao

forDevelopmentofNational

FarmAnimalGeneticResourcesManagementPlans

Measurementof

DomesticAnimalDiversity(MoDAD):

RecommendedMicrosatelliteMarkers

NewMicrosatellitemarkerts-Recommendations

ofjointISAG/FAOStandingCommittee

(tobeprentedatISAG2004)

Secondary

Guidelines

Initiativepour

laDiversité

desAnimaux

Domestiques

Initiativefor

Domestic

Animal

Diversity

Iniciativapara

laDiversidad

delosAnimales

Domésticos

Food

and

Agriculture

Organization

of

the

United

Nations

Organisation

des

Nations

Unies

pour

l'alimentation

et

l'agriculture

Organización

delas

Naciones

Unidas

parala

Agricultura

yla

Alimentatción

SecondaryGuidelines-Characterization2

TableofContents

uction3

AdvisoryGroup-Members4

atelliteLists6

6

n13

15

19

SecondaryGuidelines-Characterization3

Introduction

uction

ThetaskoftheAdvisoryGroupwastocompilealistofmicrosatellites

fortheanalysisofgeneticdistanceswithineachdomesticanimalspecies,

badontherecommendationsofaworkinggroup(Report"An

integratedglobalprogrammetoestablishthegeneticrelationshipsamong

thebreedsofeachdomesticanimalspecies"ofAnimalProductionand

HealthDivision,FAO,1993,ISBNNo.1863890602).TheWorking

followingcriteriatolectappropriatemicrosatelliteswereissuedbythe

WorkingGroup:

rosatellitemarkersshouldbeinthepublicdomain,

ossible,microsatellitelocithathavebeenidentifiedin

mappingstudiesshouldbeud,andtholectedshould

preferablybeknowntobeunlinked,

rosatellitevariantsshouldbeshowntoexhibitMendelian

inheritance(highlymutablemicrosatellitelocimayshow

departuresfromtheMendeliangregation,andwouldnotbe

suitableforgeneticdistanceanalysis),

crosatellitelocusshouldexhibitatleastfouralleles,

houldbeinformationonthemicrosatellitesinapublished

report,

atellitelocithatcanbeudonveralrelatedspeciessuch

ascattle,sheepandgoatsarepreferable.

Themicrosatellitelistsbelowwerecompiledaccordingtothe

ientmicrosatellitemarkers

areprentlyavailableforcattle,chicken,f

microsatelliteslociforhoranddonkeywillfollow.

SecondaryGuidelines-Characterization4

Introduction

2AdvisoryGroup-Members

y

DepartmentofGenetics

UniversityofDublin

TrinityCollege

Dublin2IRELAND

(dbradley@)

(Chairman)

ChairofAnimalBreeding

TechnicalUniversityofMunich

D-85350Freising-Weihenstephan

GERMANY

(fries@)

ad

InstituteforAnimalHealth

CamptonLaboratory

Campton,y

BeryshireRG16ONN

ENGLAND

(ad@)

as

DepartmentofAnimalScience

UniversityofSydney

NewSouthWales2006

AUSTRALIA

(frankn@)

SecondaryGuidelines-Characterization5

Introduction

n

DepartmentofVeterinaryScience

UniversityofKentucky

101AnimalPathologyBuilding

Lexington,Kentucky40546-0075

USA

(gcothran@)

er

INRA,StationdeGénétique

QuantitativeetAppliquée

F-78352Jouy-en-Josas

FRANCE

(ugenlol@)

rd

AgRearchMolecularBiologyUnit

DepartmentofBiochemistry

UniversityofOtago

POBox56

Dunedin

NEWZEALAND

(crawforda@)

SecondaryGuidelines-Characterization6

MicrosatelliteLists

atelliteLists

(y)

Therecommendationofagroupofmarkersforuniversaluincattle

posaparticularproblemwhichisnotyetencounteredintheother

arealreadythefocusofmuchrearchactivity

andlargebodiesofdatapertainingtogeneticvariationindifferent

,thereislittleoverlapin

markerchoicebetweenlaboratoriesandconquentlyjointanalysof

ektolistatof30markers

whichmayberecommendedforuinsuchworksuchthatjointanalysis

offuturedatawillbepossiblewithasmuchincorporationofprevious

workaspossible.

Thefollowingcriteria(complementarywiththooftheabove

mentionedWorkingGroup),havebeenemployed,butnotabsolutely,in

markerchoice.

nceofpriorpopulationdata

ilityofmarker

ofalleles

ilityforuinanautomatedquencer

ilityofmultiplexing

-speciesutility.

SecondaryGuidelines-Characterization7

MicrosatelliteLists

ThecriteriawereagreedinameetingoftheEUAIRConcertedAction

Group"Analysisofgeneticdiversityincattletoprervefuturebreeding

options"whichwasheldinDublin,st11markersinthelist

belowwerealsoagreedatthatmeetingandconquentlyshouldbe

s12-

16wererecommendedbyBarbaraHarliziusashavingprovedufulin

herstudiesofGermancattlebreeds,markers17-24allfeatureinatof

multiplexreactionswhichwerecommunicatedtomebyJandeRuiter

andmarkers25-30featureinasubtoftheILSTSlociwhichhavebeen

lectedfortheirsuitabilityforapopulationstudyofAfricanbreedsby

ILRI(communicatedbyOlivierHannotte).Itwasnotpossibletomeet

therequirementofcross-speciesutility,mainlybecaupreferencewas

giventomicrosatellitesforwhichtherewerealreadypopulationdata

available.

SecondaryGuidelines-Characterization8

MicrosatelliteLists

Cattle:

sChrPrimerquences(5'-3')Reference

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

ETH225(D9S1)

ETH152(D5S1)

HEL1(D15S10)

ILSTS005

(D10S25)

HEL51(D21S15)

INRA0052

(D12S4)

INRA035

(D16S11)

INRA063

(D18S5)

MM8(D2S29)

MM12(D9S20)

HEL9(D8S4)

CSRM60

(D10S5)

CSSM663

(D14S31)

ETH185(D17S1)

HAUT24

(D22S26)

HAUT27

(D26S21)

ETH3(D19S2)

9

5

15

10

21

12

16

18

2

9

8

10

14

17

22

26

19

GATCACCTTGCCACTATTTCCT

ACATGACAGCCAGCTGCTACT

TACTCGTAGGGCAGGCTGCCTG

GAGACCTCAGGGTTGGTGATCAG

CAACAGCTATTTAACAAGGA

AGGCTACAGTCCATGGGATT

GGAAGCAATGAAATCTATAGCC

TGTTCTGTGAGTTTGTAAGC

GCAGGATCACTTGTTAGGGA

AGACGTTAGTGTACATTAAC

CAATCTGCATGAAGTATAAATAT

CTTCAGGCATACCCTACACC

ATCCTTTGCAGCCTCCACATTG

TTGTGCTTTATGACACTATCCG

ATTTGCACAAGCTAAATCTAACC

AAACCACAGAAATGCTTGGAAG

CCCAAGGACAGAAAAGACT

CTCAAGATAAGACCACACC

CAAGACAGGTGTTTCAATCT

ATCGACTCTGGGGATGATGT

CCCATTCAGTCTTCAGAGGT

CACATCCATGTTCTCACCAC

AAGATGTGATCCAAGAGAGAGGCA

AGGACCAGATCGTGAAAGGCATAG

ACACAAATCCTTTCTGCCAGCTGA

AATTTAATGCACTGAGGAGCTTGG

TGCATGGACAGAGCAGCCTGGC

GCACCCCAACGAAAGCTCCCAG

CTCTCTGCCTTTGTCCCTGT

AATACACTTTAGGAGAAAAATA

TTTTATGTTCATTTTTTGACTGG

AACTGCTGAAATCTCCATCTTA

GAACCTGCCTCTCCTGCATTGG

ACTCTGCCTGTGGCCAAGTAGG

Steffenetal.(1993)

Steffenetal.(1993)

Kaukinen&Varvio

(1993)

Brezinskyetal.

(1993a)

Kaukinen&Varvio

(1993)

Vaimanetal.(1992)

Vaimanetal.(1994)

Vaimanetal.(1994)

Mommental.

(1994)

Mommental.

(1994)

Kaukinen&Varvio

(1993)

Mooreetal.(1994)

Barendetal.(1994)

Steffenetal.(1993)

Harlizius(comm.

pers.)

Harlizius(comm.

pers.)

SolinasToldoetal.

(1993)

1,2,3,4,5Thegeneticdistancebetweenthemarkerpairsonthesamechromosomesisnotknown

Continued

SecondaryGuidelines-Characterization9

MicrosatelliteLists

Cattle:Continued

sChrPrimerquences(5'-3')Reference

18

19

20

21

22

23

24

25

26

27

28

29

30

ETH104(D5S3)

INRA0325

(D11S9)

INRA023

(D3S10)

BM2113

(D2S26)

BM1818

(D23S21)

BM1824

(D1S34)

HEL135

(D11S15)

ILSTS006

(D7S8)

ILSTS030

(D2S44)

ILSTS0344

(D5S54)

ILSTS0332

(D12S31)

ILSTS0113

(D14S16)

ILSTS0541

(D21S44)

5

11

3

2

23

1

11

7

2

5

12

14

21

GTTCAGGACTGGCCCTGCTAACA

CCTCCAGCCCACTTTCTCTTCTC

AAACTGTATTCTCTAATAGCAC

GCAAGACATATCTCCATTCCTTT

GAGTAGAGCTACAAGATAAACTTC

TAACTACAGGGTGTTAGATGAACTCA

GCTGCCTTCTACCAAATACCC

CTTAGACAACAGGGGTTTGG

AGCTGGGAATATAACCAAAGG

AGTGCTTTCAAGGTCCATGC

GAGCAAGGTGTTTTTCCAATC

CATTCTCCAACTGCTTCCTTG

TAAGGACTTGAGATAAGGAG

CCATCTACCTCCATCTTAAC

TGTCTGTATTTCTGCTGTGG

ACACGGAAGCGATCTAAACG

CTGCAGTTCTGCATATGTGG

CTTAGACAACAGGGGTTTGG

AAGGGTCTAAGTCCACTGGC

GACCTGGTTTAGCAGAGAGC

TATTAGAGTGGCTCAGTGCC

ATGCAGACAGTTTTAGAGGG

GCTTGCTACATGGAAAGTGC

CTAAAATGCAGAGCCCTACC

GAGGATCTTGATTTTGATGTCC

AGGGCCACTATGGTACTTCC

SolinasToldoetal.

(1993)

Vaimanetal.(1994)

Vaimanetal.(1994)

Bishopetal.(1994)

Bishopetal.(1994)

Bishopetal.(1994)

Kaukinen&Varvio

(1993)

Brezinskyetal.

(1993b)

Kempetal.(1995)

Kempetal.(1995)

Kempetal.(1995)

Brezinskyetal.

(1993c)

Kempetal.(1995)

1,2,3,4,5Thegeneticdistancebetweenthemarkerpairsonthesamechromosomesisnotknown

SecondaryGuidelines-Characterization10

MicrosatelliteLists

Cattle:Additionalinformation:Fourmultiplexreactionswhichincludemarkersaboveare:

Marker

nge

ETH10(D5S3)

ETH225(D9S1)

ETH3(D19S2)

INRA005(D12S4)

INRA023(D3S10)

INRA063(D18S5)

HEL13(D11S5)

HEL5(D21S15)

HEL1(D15S10)

BM1818(D23S21)

BM1824(D1S34)

BM2113(D2S26)

210-226bp

140-156bp

117-129bp

119-123bp

197-223bp

176-186bp

198bp

161bp

110bp

270-258bp

178-190bp

125-143bp

Notallcriteriahavebeenfulfilledinthecaofeachmarker,primarily

cas

ll

notbeacomplicationinpopulationgeneticstudyunlesslinkageisclo.

However,therelativemappositionsofsomepairsareunknowntothe

authoratprent.

Additionalandpossiblyimportantinformationisthatatofmarkers

areavailablecommerciallyfromAppliedBiosystemsandthemay

assumeimportanceinpopulationstudyifawidenumberoflaboratories

followinginformationwasforwardedbyStephenBates,PerkinElmer,

AppliedBiosystemsDivision,whoalsoindicatedthat,despitethe

markersbeingpatented,thereshouldbenoproblemwithrearchers

whowantedtomanufacturetheirownprimersfornon-commercialu.

STRsthatareoptimizedforfluorescentmultiplexing;twoquadruplexes

andonetriplex.

SecondaryGuidelines-Characterization11

MicrosatelliteLists

Cattle

MarkerFluorochromeSizeRangeChromosome

TGLA48(D7S26)

TGLA263(D3S34)

TGLA53(D16S3)

MGTG7(D23S5)

TGLA57(D1S8)

TGLA73(D9S3)

MGTG4B(D4S5)

AGLA293(D5S13)

TGLA227(D18S1)

TGLA126(D20S1)

TGLA122(D21S6)

Tet(green)

Tet(green)

Tet(green)

Tet(green)

Fam(blue)

Fam(blue)

Fam(blue)

Fam(blue)

Hex(yellow)

Hex(yellow)

Hex(yellow)

68–86

110–130

144–178

273–300

70–100

102–128

129–164

196–260

80–100

108-129

130-164

7

3

16

23

1

9

4

5

18

20

21

Theprimersareincludedintwopublishedmaps(Bishopetal.1994;

Barendetal1994)Theoriginalreferenceis:J.

rphicDNAmarkersinBovidae(WorldIntellectual

PropertyOrg.,Geneva).92/13102.

Anadditionaldevelopmentwhichmayinfluencemarkerchoiceisthe

resultsfromTheCattleBloodTypingGroupofISAG,whichischaired

evaluating30microsatellitemarkersinan

attempttostandardizeatthatcanbeudbyparentagetesting

laboratoriesworld-wide.

SecondaryGuidelines-Characterization12

MicrosatelliteLists

References

Barend,W.,Armitage,iclinkagemapofthebovine

Genetics6:227-235.

Bishop,M.D.,Kappes,iclinkagemapforcattle.

Genetics136:619-639.

Brezinsky,L.S.,Kemp,J.,Teale,A.J..005:apolymorphic

.24:73.

Brezinsky,L.S.,Kemp,J.,Teale,A.J..006:apolymorphic

.24:73.

Brezinsky,L.S.,Kemp,J.,Teale,lymorphicbovine

microsatellites(ILSTS010-014)..24:75-76.

Fries,R.,Eggen,A.,Womack,.

Genome4:405-428.

Kaukinen,J.,Varvio,olymorphicbovinemicrosatellites.

.24:148.

Kemp,S.J.,Hishida,ofpolymorphicbovine,ovine

.26:299-306.

Mommens,G.W.,Coppieters,eotiderepeat

.25:

368.

Moore,S.S.,Byrne,terizationof65bovinemicrosatellites.

5:84-90.

SolinasToldo,S.,Fries,allymapped,cosmid-derived

.

Genome4:720-727.

Steffen,P.,Eggen,ionandmappingofpolymorphic

.24:121-124.

Vaiman,D.,Osta,terisationoffivenewbovine

.23:537.

Vaiman,D.,Mercier,99cattlemicrosatellites:

characterisation,syntenymapping,

5:288-297.

SecondaryGuidelines-Characterization13

MicrosatelliteLists

n

Chicken:(ad)

quences(5’-3’)nce

MCW41

MCW43

MCW44

MCW48

MCW49

MCW50

MCW51

MCW59

MCW71

MCW73

MCW75

MCW1

MCW2

MCW4

MCW5

C3

E1

?

C4

C6E1

?

C3E6

C1E2

?

C33E46

E

unlinked

C4E28

C4

E2

C11E5

CCCAATGTGCTTGAATAACTTGGG

CCAGATTCTCAATAACAATGGCAG

TGACTACTTTGATACGCATGGAGA

CACCAAGTAGACGAAAACACATTT

AGTCCGAGCTCTGCTCGCCTCATA

ACAGTGGCTCAGTGGGAAGTGACC

CGTATAGGAGGGTTTCTGCAGGGA

AAGGAGGAACGCACCGCACCTTCT

AGCGGCGTTGAGTGAGAGGAGCGA

TCCCCAACCCGCGGAGAGCGCTAT

GGTGTCCGCACCCCGGAGCTTCTT

GCAGCATCGCGCAGCACCGCGGAT

GGAACAAGCTCTTTCTTCTTCCCG

TCATGGAGGTGCTGGTACAAAGAC

AAGTGCCTTTGCTATCCTGATTGG

AACTCCTATTGTGCAGCAGCTTAT

TGGCGTTATTTCAAAACGACCGTA

GCGGTCGTTCGGTCCTTATTTTAA

TATTTCACCCACGGGGACGAATAC

AGGGTGCTGAGAGCTGCCAATGTC

CGTCAAGCCAGATGCTGATGAGTG

ATTCCAACCAGAAGTTTGACTCGC

ACTGTCACAGTGGGGTCATGGACA

ACACGTCCTGTGTCACATGCCTGT

TCCAGAGACAGTTGCTCCACATTC

GCAAGTTAGTTATTGTAGGGGCTC

GGATTACAGCACCTGAAGCCACTA

AAACCAGCCATGGGTGCAGATTGG

ACCTCCTGCTGGCAAATAAATTGC

TCACTTTAGCTCCATCAGGATTCA

55

55

50

55

55

55

50

55

55

55

55

50

50

55

55

Crooijmantal.

(1995)

Crooijmantal.

(1995)

Crooijmantal.

(1995)

Crooijmantal.

(1995)

Crooijmantal.

(1995)

Crooijmantal.

(1995)

Crooijmantal.

(1995)

Crooijmantal.

(1995)

Crooijmantal.

(1995)

Crooijmantal.

(1995)

Crooijmantal.

(1995)

Crooijmantal.

(1995)

Crooijmantal.

(1994)

Crooijmantal.

(1995)

Crooijmantal.

(1994)

Continued

SecondaryGuidelines-Characterization14

MicrosatelliteLists

Chicken:Continued

quences(5’-3’)nce

MCW14

MCW16

ADL102

ADL136

ADL158

ADL171

ADL172

ADL176

ADL210

ADL267

E11

E2

C30E29

E5C10

C30E29

E43

E42

E6

E30

C3E6

AAAATATTGGCTCTAGGAACTGTC

ACCGGAAATGAAGGTAAGACTAGC

ATGGCGCAGAAGGCAAAGCGATAT

TGGCTTCTGAAGCAGTTGCTATGG

TTCCACCTTTCTTTTTTATT

GCTCCACTCCCTTCTAACCC

TGTCAAGCCCATCGTATCAC

CCACCTCCTTCTCCTGTTCA

TGGCATGGTTGAGGAATACA

TAGGTGCTGCACTGGAAATC

ACAGGATTCTTGAGATTTTT

GGTCTTAGCAGTGTTTGTTT

CCCTACAACAAAGAGCAGTG

CTATGGAATAAAATGGAAAT

TTGTGGATTCTGGTGGTAGC

TTCTCCCGTAACACTCGTCA

ACAGGAGGATAGTCACACAT

GCCAAAAAGATGAATGAGTA

AAACCTCGATCAGGAAGCAT

GTTATTCAAAGCCCCACCAC

55

50

47

52

52

46

49

52

46

50

Crooijmantal.

(1994)

Crooijmantal.

(1994)

Chengetal.(1995)

Chengetal.(1995

Chengetal.(1995)

Chengetal.(1995)

Chengetal.(1995)

Chengetal.(1995)

Chengetal.(1995)

Chengetal.(1995)

References

Crooijmans,R.P.M.A.,vanKampen,rosatellite

85:10-413.

Crooijmans,R.P.M.A.,vanderPoel,J.J.,Groenen,M.A.M.1995.

.26:73-78.

Cheng,H.H.,Levin,pingofageneticmapofthechicken

yScience74:1855-1874.

SecondaryGuidelines-Characterization15

MicrosatelliteLists

(rd)

Themarkerhadtohavethefollowingcriteriatobeincludedonthelist:

lowing

"Touchdown"programmeisud:

3cycles

3cycles

3cycles

3cycles

20cycles

95C

60C

95C

57C

95C

54C

95C

51C

92C

48C

45cs

1min

45cs

1min

45cs

1min

45cs

1min

45cs

1min

ferispublishedwiththemarker

reports(e.g.,Edeetal.,1994b).TodetectthePCRproductoneofthe

primersindlabeledwitheitherP33orP32.

inimumoffiveallelesandaPICgreaterthan0.6,

portantlyhaveclean,easilyreadandscoredPCRproducts.

SecondaryGuidelines-Characterization16

MicrosatelliteLists

Sheep:

MarkerChrPrimerquences(5'-3')*Reference

BM1314*

BM6506*

BM6526*

BM757*

BM8125*

BM827*

CSSM31*

CSSM47*

HUJ616*

ILSTS002*

OarAE129

OarCP20

OarCP34

OarCP38

OarFCB128

OarFCB20

OarFCB48

22

1

26

9

17

3

23

2

13

14

5

21

3

10

2

2

17

TTCCTCCTCTTCTCTCCAAAC

ATCTCAAACGCCAGTGTGG

GCACGTGGTAAAGAGATGGC

AGCAACTTGAGCATGGCAC

CATGCCAAACAATATCCAGC

TGAAGGTAGAGAGCAAGCAGC

TGGAAACAATGTAAACCTGGG

TTGAGCCACCAAGGAACC

CTCTATCTGTGGAAAAGGTGGG

GGGGGTTAGACTTCAACATACG

GGGCTGGTCGTATGCTGAG

GTTGGACTTGCTGAAGTGACC

CCAAGTTTAGTACTTGTAAGTAGA

GACTCTCTAGCACTTTATCTGTGT

TCTCTGTCTCTATCACTATATGGC

CTGGGCACCTGAAACTATCATCAT

TTCAAACTACACATTGACAGGG

GGACCTTTGGCAATGGAAGG

TCTATACACATGTGCTGTGC

CTTAGGGGTGAAGTGACACG

AATCCAGTGTGTGAAAGACTAATCCAG

GTAGATCAAGATATAGAATATTTTTCAACACC

GATCCCCTGGAGGAGGAAACGG

GGCATTTCATGGCTTTAGCAGG

GCTGAACAATGTGATATGTTCAGG

GGGACAATACTGTCTTAGATGCTGC

CAACTTTGGTGCATATTCAAGGTTGC

GCAGTCGCAGCAGGCTGAAGAGG

CAGCTGAGCAACTAAGACATACATGCG

ATTAAAGCATCTTCTCTTTATTTCCTCGC

AAATGTGTTTAAGATTCCATACAGTG

GGAAAACCCCCATATATACCTATAC

GAGTTAGTACAAGGATGACAAGAGGCAC

GACTCTAGAGGATCGCAAAGAACCAG

Bishopetal.(1994)

Bishopetal.(1994)

Bishopetal.(1994)

Bishopetal.(1994)

Bishopetal.(1994)

Bishopetal.(1994)

Mooreetal.(1994)

Mooreetal.(1994)

Barendetal.

(1994)

Kempetal.(1992)

Pentyetal.(1993)

Edeetal.(1994a)

Edeetal.(1994b)

Edeetal.(1994b)

Buchanan&

Crawford(1993)

Buchananetal

(1994)

Buchananetal.

(1994)

Continued

SecondaryGuidelines-Characterization17

MicrosatelliteLists

Sheep:Continued

MarkerChrPrimerquences(5'-3')*Reference

OarHH35

OarHH41

OarHH47

OarHH64

OarJMP29

OarJMP8

OarVH72

OMHC1

RM4*

TGLA137*/**

4

10

18

4

24

6

25

20

15

5

AATTGCATTCAGTATCTTTAACATCTGGC

ATGAAAATATAAAGAGAATGAACCACACGG

TCCACAGGCTTAAATCTATATAGCAACC

CCAGCTAAAGATAAAAGATGATGTGGGAG

TTTATTGACAAACTCTCTTCCTAACTCCACC

GTAGTTATTTAAAAAAATATCATACCTCTTAAGG

CGTTCCCTCACTATGGAAAGTTATATATGC

CACTCTATTGTAAGAATTTGAATGAGAGC

GTATACACGTGGACACCGCTTTGTAC

GAAGTGGCAAGATTCAGAGGGGAAG

CGGGATGATCTTCTGTCCAAATATGC

CATTTGCTTTGGCTTCAGAACCAGAG

CTCTAGAGGATCTGGAATGCAAAGCTC

GGCCTCTCAAGGGGCAAGAGCAGG

ATCTGGTGGGCTACAGTCCATG

GCAATGCTTTCTAAATTCTGAGGAA

CAGCAAAATATCAGCAAACCT

CCACCTGGGAAGGCCTTTA

GTTGACTTGTTAATCACTGACAGCC

CCTTAGACACACGTGAAGTCCAC

Henryetal.(1993)

Henryetal.(1993)

Henryetal.(1993)

Henryetal.(1993)

Pentyetal.(in

prep.)

Pentyetal.(in

prep.)

Piersonetal.(1993)

Groth&Wetherall

(1994)

Kossareketal.

(1993)

Georges&Masy

(1992)

*Bovinemicrosatellite

**TheprimerquencesfortheTGLAmarkersweredesignedfromthequenceprovidedinthepatent

(Georges&Masy,1992)sotheymaybedifferentfromthepublishedbovineprimerquencesforthesame

marker.

References

Barend,W.,Armitage,iclinkagemapofthebovine

.6:227-235.

Bishop,M.D.,Kappes,iclinkagemapforcattle.

Genetics136:619-639.

Buchanan,wford,icrosatellitesatthe

OarFCB11,OarFCB128,OarFCB193,OarFCB266andOarFCB304loci.

.24:145.

SecondaryGuidelines-Characterization18

MicrosatelliteLists

Buchanan,F.C.,Galloway,wford,

microsatellitesattheOarFCB5,OarFCB19,OarFCB20,OarFCB48,

.25:60.

Ede,A.J.,Pierson,wford,icrosatellites

attheOarCP9,OarCP16,OarCP20,OarCP21,OarCP23andOarCP26

.26:129-130.

Ede,A.J.,Pierson,wford,icrosatellites

attheOarCP34,OarCP38,OarCP43,OarCP49,OarCP73andOarCP79

.26:130-131.

Georges,y,J.1992:PolymorphicDNAmarkersinBovidae,

(WorldIntellectualPropertyOrg.,Geneva).92/13120.

Groth,therall,eotiderepeat

polymorphismwithintheovinemajorhistocompatibilitycomplexclassI

.25:61.

Henry,H.M.,Penty,icrosatellitesatthe

OarHH35,OarHH41,OarHH44,.

Genet.24:223.

Kemp,S.J.,Brezinsky,LandTeale,002:apolymorphic

.23:184.

Kossarek,L.M.,Gros,dinucleotiderepeat

.71:3175.

Moore,S.S.,Byrne,terisationof65bovinemicrosatellites.

5:84-90.

Penty,J.M.,Henry,icrosatellitesattheOarAE16,

OarAE54,OarAE57,.24:

219.

Pierson,C.A.,Hanrahan,icrosatellitesatthe

OarVH34,OarVH41,OarVH58,.

Genet.24:224.

SecondaryGuidelines-Characterization19

MicrosatelliteLists

(,INRA,.,F-31326,Castanet

Tolosan,FRANCE(milan@)withthehelpof

n,WageningenAgriculturalUniversity,Departmentof

AnimalBreeding,NL-6701BHWageningen,THENETHERLANDS

(n@))

-ven***(highquality)or**(mediumquality)markers

re2additionalmarkerstotherequested25,

ence

wasgiventohighlypolymorphicmarkers.

kerwaslectedoneachchromosome(except

chromosome18),andifpossibleonemarkeroneacharmofthe

ersarefoundatadistanceofless

than35cm.

sforwhichnullalleleshavebeenreportedandmarkers

whichyieldedpatternswhichcouldnotbeunambiguously

interpretedwereavoided.

encewasgiventomarkersthatcanbeanalydonautomatic

quencers(testedonABIquencerinatleastonelaboratory).It

meansthatnoartifactualbandsareamplifiedandthatthemarkers

canbemultiloaded(thisshouldbepossibleeitherusingmanualor

automaticquencers).

kershavebeengroupedin9tsofmarkersanalysableon3

ferenceinsizebetweentwo

adjacentmarkersisatleast30bp(inordertoallowthe

identificationofnewallelesoutsideofthefragmentminimum-

maximumsizerange).

SecondaryGuidelines-Characterization20

MicrosatelliteLists

lDNAforcorrectsizingofallelesmaybeobtainedthrough

.

Swine:Sortedbyt:

PropodbyQualitySizeMarkerSetChr.

TWTWMinMax

Difference

CGA

S0101

S0215

S0355

SW911

SW936

S0068

SW632

SW24

S0227

S0225

SW122

S0090

S0226

SW951

S0228

S0218

S0178

S0005

S0386

SW72

S0002

SW857

S0026

IGF1

S0155

SW240

1

1

1

2

2

2

3

3

3

4

4

4

5

5

5

6

6

6

7

7

7

8

8

8

9

9

9

1p

7

13

15

9

15

13

7

17

4

8

6

12

2q

10

6

X

8

5

11

3p

3q

14

16

5

1q

2p

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

***

***

***

***

***

***

***

**

***

***

***

**

**

***

***

***

**

***

***

***

***

***

***

***

***

***

***

**

***

***

***

***

***

***

**

***

***

250

197

135

243

153

80

211

159

96

231

170

110

244

181

125

222

164

110

205

156

100

190

144

92

197

150

96

320

216

169

277

177

117

260

180

121

256

196

122

251

205

133

249

184

124

248

174

116

216

160

106

209

166

115

34

28

66

36

31

38

35

48

45

48

38

31

40

30

38

35

31

35

T:Toulou;W:Wageningen.

Difference:Differenceinbpbetweentwoadjacentmarkersbelongingtothesamet.

SecondaryGuidelines-Characterization21

MicrosatelliteLists

Swine:Sortedbychromosome:

TWTWMinMaxcM

CGA

S0155

SW240

S0226

SW72

S0002

S0227

IGF1

S0005

SW122

S0228

S0101

SW632

S0225

S0178

SW911

Sw951

S0386

S0090

S0215

S0068

SW857

S0355

SW936

S0026

SW24

S0218

1p

1q

2p

2q

3p

3q

4

5

5

6

6

7

7

8

8

9

10

11

12

13

13

14

15

15

16

17

X

1

9

9

5

7

8

4

9

7

4

6

1

3

4

6

2

5

7

5

1

3

8

2

2

8

3

6

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

***

***

***

***

**

***

***

**

***

***

***

***

***

**

**

***

***

***

***

***

***

***

***

***

***

***

**

***

***

***

***

***

***

***

***

***

**

250

150

96

181

100

190

231

197

205

110

222

197

159

170

110

153

125

156

244

135

211

144

243

80

92

96

164

320

166

115

205

116

216

256

209

248

122

249

216

180

196

124

177

133

174

251

169

260

160

277

117

106

121

184

-

50

-

50

-

105

-

-

40

35

–

-

60

-

>50

-

-

-

-

-

55

-

-

70

–

-

-

T:ToulouW:Wageningen

SecondaryGuidelines-Characterization22

MicrosatelliteLists

Swine:

MarkerSequenceofprimers(5’-3’)Fluorochrome

labelling

./

MgC12(mM)

Reference

CGA

IGF1

S0002

S0005

S0026

S0068

S0090

S0101

S0155

S0178

S0215

S0218

S0225

S0226

S0227

S0228

S0355

ATAGACATTATGTCCGTTGCTGAT

GAACTTTCACATCCCTAAGGTCGT

GCTTGGATGGACCATGTTG

CATATTTTTCTGCATAACTTGAACCT

GAAGCCCAAAGAGACAACTGC

GTTCTTTACCCACTGAGCCA

TCCTTCCCTCCTGGTAACTA

GCACTTCCTGATTCTGGGTA

AACCTTCCCTTCCCAATCAC

CACAGACTGCTTTTTACTCC

AGTGGTCTCTCTCCCTCTTGCT

CCTTCAACCTTTGAGCAAGAAC

CCAAGACTGCCTTGTAGGTGAATA

GCTATCAAGTATTGTACCATTAGG

GAATGCAAAGAGTTCAGTGTAGG

GTCTCCCTCACACTTACCGCAG

TGTTCTCTGTTTCTCCTCTGTTTG

AAAGTGGAAAGAGTCAATGGCTAT

TAGCCTGGGAACCTCCACACGCTG

GGCACCAGGAATCTGCAATCCAGT

TAGGCTCAGACCCTGCTGCAT

TGGGAGGCTGAAGGATTGGGT

GTGTAGGCTGGCGGTTGT

CCCTGAAACCTAAAGCAAAG

GCTAATGCCAGAGAAATGCAGA

CAGGTGGAAAGAATGGAATGAA

GCACTTTTAACTTTCATGATACTCC

GGTTAAACTTTTNCCCCAATACA

GATCCATTTATAATTTTAGCACAAAGT

GCATGGTGTGATGCTATGTCAAGC

GGCATAGGCTGGCAGCAACA

AGCCCACCTCATCTTATCTACACT

TCTGGCTCCTACACTCCTTCTTGATG

TTGGGTGGGTGCTGAAAAATAGGA

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

62/1.5

58/1.5

62/1.5

58/1.5

55/1.5

62/1.5

58/1.5

60/1.5

55/1.5

58/1.5

55/4.0

55/2.0

55/4.0

55/4.0

55/4.0

55/4.0

55/4.0

(1,2)

(3,1,2,4)

(5,4,2,6)

(5,1,4,2)

(2,7)

(5,1,4,2)

(8,4,2)

(1)

(1,2)

(1)

(9,2)

(9,2)

(9,2)

(9,2)

(9,2)

(9,2)

(10)

Continued

SecondaryGuidelines-Characterization23

MicrosatelliteLists

Swine:Continued

MarkerSequenceofprimers(5’-3’)Fluorochrome

labelling

./

MgC12(mM)

Reference

S0386

SW24

SW122

SW857

SW240

SW632

SW72

SW911

SW936

SW951

TCCTGGGTCTTATTTTCTA

TTTTTATCTCCAACAGTAT

CTTTGGGTGGAGTGTGTGC

ATCCAAATGCTGCAAGCG

TTGTCTTTTTATTTTGCTTTTGG

CAAAAAAGGCAAAAGATTGACA

AGAAATTAGTGCCTCAAATTGG

AAACCATTAAGTCCCTAGCAAA

TGGGTTGAAAGATTTCCCAA

GGAGTCAGTACTTTGGCTTGA

ATCAGAACAGTGCGCCGT

TTTGAAAATGGGGTGTTTCC

TGAGAGGTCAGTTACAGAAGACC

GATCCTCCTCCAAATCCCAT

CTCAGTTCTTTGGGACTGAACC

CATCTGTGGAAAAAAAAAGCC

TCTGGAGCTAGCATAAGTGCC

GTGCAAGTACACATGCAGGG

TTTCACAACTCTGGCACCAG

GATCGTGCCCAAATGGAC

X

X

X

X

X

X

X

X

X

48/3.0

58/1.5

58/1.5

58/1.5

58/1.5

58/1.5

58/1.5

60/1.5

58/1.5

58/1.5

(11)

(4)

(4)

(4)

(4)

(4)

(4)

(4)

(4,10)

(4)

References

en,H.,Chowdhary,rylinkagemapofthe

cs137:

1089-1100.

ald,A.,Brown,MaPconsortiumlinkagemapof

thepig(susscrofa).6:157-175.

o,A.,Fredholm,M.,Andersson,mentofthe

geneforporcineinsulinlikegrowthfactor(IGF1)tochromosome5by

.25:37-39.

,G.A.,Alexander,satellitelinkagemapofthe

cs136:231-245.

SecondaryGuidelines-Characterization24

MicrosatelliteLists

lm,M.,Wintero,terizationof24porcine(dA-

dC)n-(dT-dG)nmicrosatellites:genotypingofunrelatedanimalsfromfour

4:187-192.

,M.,Lahbib-Mansais,MaPconsortium

cytogeneticmapofthedomesticpig(SusScrofa).6:176-

186.

ters,W.,,terizationofporcine

.24:163-170.

en,H.,Johansson,mentof20microsatellite

cs16:431-439.

,A.,Dalens,ionof28newporcinemicrosatellites

5:580-583.

,D.,Woloszyn,teMappingoftheacidmeatRN

7:

,J.,Milan,gemapwithmicrosatellitesisolated

6:623-628.

BuffalosDonkeys

HorsGoats

PigsSheep

ChickenDucks

CamelidsCattle

/~uatz/FAO/09/09/200416:48:51

NrNameChr*Map

Primer

quence(5'->

3')

ForwardRever

Annealing

temperature

GenBank

(Accession

Number

Multiplex

known

alleles,

and

allele

range

Diversity

studies

033

17

(17)

CACTGT

GAATGC

ATGTGTGTG

AGC

CCCATG

ATAAGA

GTGCAG

ATGACT

65U03805

11

154-

175

R1,R2

R3,

038

11

(10)

TTCATATAA

GCAGTTTAT

AAACGC

ATAGGA

TCTGGTAAC

TTACAGATG

55U03817

13

163-

187

R1,R2

R3,

043

1p

(27)

AAAACT

CTGGGA

ACTTGA

AAACTA

GTTACA

AATTTA

AGAGAC

AGAGTT

55U03824

12

222-

258

R1,R2

R3,

047

3q

(8)

TCTCTGTCT

CTATCACTA

TATGGC

CTGGGC

ACCTGA

AACTATCAT

CAT

55U03821

20

127-

162

R1,R2

R3,

/~uatz/FAO/(1of7)09/09/200416:50:39

036

1p

(27)

GGATAA

CTCAAC

CACACGTCT

CTG

AAGAAG

TACTGGTTG

CCAATCGTG

55U03827

7

162-

176

R1,R2

R3,

019

1q

(1)

TTGTCAGCA

ACTTCTTGT

ATCTTT

TGTTTTAAG

CCACCC

AATTATTTG

55U03794

15

131-

161

R1,R3,

060

11

(10)

AAGATG

TGATCC

AAGAGA

GAGGCA

AGGACC

AGATCG

TGAAAG

GCATAG

60AF232758

15

95-135

R1,R2

0299(7)

CGTGAG

AACCGA

AAGTCA

CACATTC

GCTCCATTA

TGCACA

TGCCATGCT

55U03807

11

174-

196

R1,R3,

041

21

(22)

AATTTC

AAAGAA

CCGTTACAC

AGC

AAGGGA

CTTGCA

GGGACT

AAAACA

55U03816

11

129-

147

R1,R3,

/~uatz/FAO/(2of7)09/09/200416:50:39

0579(7)

GTCGCT

GGATAA

ACAATT

TAAAGT

TGTGGTGTT

TAACCCTTG

TAATCT

60U03840

11

102-

130

R1,R3,

11

(10)

CCTCCACAC

AGGCTTCTC

TGACTT

CCTAACTTG

CTTGAGTTA

TTGCCC

60X59767

10

121-

147

R1,R3,

032

1q

(1)

TTATTTTCA

GTGTTTCTA

GAAAAC

TATAATATT

GCTATCTGG

AAATCC

55U03811

9

208-

224

R1,R3,

008-

CTTGGTGTT

ACTAGCCCT

GGG

GATATATTT

GCCAGA

GATTCTGCA

55U03796

7

179-

193

R1,R3,

14CSSM045

2q

(2)

TAGAGG

CACAAG

CAAACC

TAACAC

TTGGAA

AGATGC

AGTAGA

ACTCAT

60U03830

7

102-

122

R1,R3,

022

4q

(5)

TCTCTCTAA

TGGAGT

TGGTTTTTG

ATATCCCAC

TGAGGA

TAAGAATTC

55-60U03806

6

203-

213

R1,R3,

/~uatz/FAO/(3of7)09/09/200416:50:39

046

11

(10)

GGCTAT

TAACTGTTT

TCTAGG

AAT

TGCACA

ATCGGA

ACCTAG

AATATT

55U03834

6

152-

160

R1,R3,

013

5p

(29)

ATAAGA

GATTACCCT

TCCTGACTG

AGGTAA

ATGTTCCTA

TTTGCTAAC

55U03841

5

162-

172

R1,R3,

003

3p

(19)

GAACCT

GCCTCTCCT

GCATTGG

ACTCTGCCT

GTGGCC

AAGTAGG

65Z22744

19

96-192

R2R4,

061-

AGGCCA

TATAGG

AGGCAA

GCTTAC

TTCAGA

AGAGGG

CAGAGA

ATACAC

60-

12

100-

126

R1,

1013

3p

(19)

AAAAAT

GATGCC

AACCAA

ATT

TAGGTA

GTGTTCCTT

ATTTCTCTG

G

54G18560

10

217-

239

R2

/~uatz/FAO/(4of7)09/09/200416:50:39

3

2p

(23)

GAGAGT

TTCACTGTG

CAG

CGCGAA

TTCCCA

GAGTGA

GTGAAG

TATCT

50-55M30012

9

142-

198

R2

062-

GTTTAAACC

CCAGATTCT

CCCTTG

AGATGT

AACAGC

ATCATGACT

GAA

55-

8

124-

136

R1,

070

3p

(19)

TTCTAACAG

CTGTCACTC

AGGC

ATACAG

ATTAAA

TACCCACCT

G

50-55Af004364

8

119-

139

R2

121

2q

(2)

CCAACTCCT

TACAGG

AAATGTC

ATTTAG

AGCTGG

CTGGTA

AGTG

59Z14037

7

182-

198

R2

33

13

(12)

TATTAGAGT

GGCTCA

GTGCC

ATGCAG

ACAGTTTTA

GAGGG

55L37213

6

126-

138

R3,

/~uatz/FAO/(5of7)09/09/200416:50:39

005

11

(10)

GGAAGC

AATGAA

ATCTATAGC

C

TGTTCTGTG

AGTTTGTAA

GC

55L23481

5

173-

186

R2R3,

R4,

030

2q

(2)

CTGCAGTTC

TGCATATGT

GG

CTTAGA

CAACAG

GGGTTTGG

55L37212

5

146-

158

R3,

008

15

(14)

GAATCA

TGGATTTTC

TGGGG

TAGCAG

TGAGTG

AGGTTGGC

58L23483

4

168-

176

R3,

099

3p

(19)

CCAAAG

AGTCTA

ACACAA

CTGAG

ATCCGA

ACCAAA

ATCCCATCA

AG

60G29087

4

87-119

R2,

1R

21

(22)

GGCTTC

AACTCA

CTGTAA

CACATT

TTCTTCAAG

TATCACCTC

TGTGGCC

60D10197

3

169-

187

R1,

*Cattlechromosomeassignments(inparenthes)-asgivenat

/cgi-bin/cgdlo,andconvertedtoRiverBuffalochromosome

assignments

accordingtoDiBerardinoandIannuzzi(1984):ForSwampBuffalo,2n=

48,duetotranslocationofchromosome9tochromosome4.

References:

,J.S.F.,Moore,S.S.,Hetzel,D.J.S.,Evans,D.,Tan,ne,K.(1997)Geneticdiversity

/~uatz/FAO/(6of7)09/09/200416:50:39

ofAsianwaterbuffalo(Bubalusbubalis)

:Genetics28:103-115.

,B.,Georgoudis,A.,Napolitano,F.,Catillo,G.,Giubilei,E.,Ligda,sanane,M.

(2001)GeneticdiversitybetweenItalian,Greekand

ockProductionScience70:203-211

,.(@)

,L.R.,Glowatzki,M-L.,MacHugh,llard,C.(2000)Phylogeneticanalysisofthetribe

Boviniusingmicrosatellites.

AnimalGenetics31:178-185.

rdino,nuzzi,L.(1984)DetaileddescriptionofRBA-bandedchromosomesofriver

buffalo(BubalusbubalisL.).Génét.Sé.

16:249-260

s,S.M.,deHondt,ack,J.E.(2001)Currentstatusoftheriverbuffalo(Bubalus

bubalisL.)lofHeredity

92:221-225.

Multiplex:

nonedeveloped.

/~uatz/FAO/(7of7)09/09/200416:50:39

Nr

MarkerList

forthe

Donkey

ap

Primerquence

(5’->3’)

Forward

Rever

Annealing

temperature

Genbank

(Accession

Number)

Multiplex

Allele

range

Diversity

studies

071

M1

CAGGAAACTCATGTTGATACCATC

TGTTGTTGAAACATACCTTGACTGT

58°C

X74636X1

165–

183

R1,R3

064

M4

GAAGCTGCCAGTATTCAACCATTG

CTCCATCTTGTGAAGTGTAACTCA

58°C

X74635X1

153–

169

R1,R3

3.

HTG074

M4

CCTGAAGCAGAACATCCCTCCTTG

ATAAAGTGTCTGGGCAGAGCTGCT

58°C

AF142607X4

272–

297

R1,R3

4.

AHT058

M8

ACGGACACATCCCTGCCTGC

GCAGGCTAAGGGGGCTCAGC

58°CNone

X1

130–

146

R1,R3

5.

HMS039

M9

CCAACTCTTTGTCACATAACAAGA

CCATCCTCACTTTTTCACTTTGTT

58°C

X74632X2

150–

170

R1,R3

6.

HMS0210

M10

ACGGTGGCAACTGCCAAGGAAG

CTTGCAGTCGAATGTGTATTAAATG

58°C

X74631

218–

238

R1,R3

7.

HTG0615

M15

CCTGCTTGGAGGCTGTGATAAGAT

GTTCACTGAATGTCAAATTCTGCT

58°CNone

84–

106

R1,R3

8.

HTG1021

M21

CAATTCCCGCCCCACCCCCGGCA

TTTTTATTCTGATCTGTCACATTT

54°C

AF169294X2

93–

113

R1,R3

9.

AHT0424

M24

AACCGCCTGAGCAAGGAAGT

CCCAGAGAGTTTACCCT

58°CNone

X1

148–

164

R1,R3

10.

ASB172M2

GAGGGCGGTACCTTTGTACC

ACCAGTCAGGATCTCCACCG

58°CX93531X1

91–

109

R1,R3

11.

ASB233

M3

GAGGTTTGTAATTGGAATG

GAGAAGTCATTTTTAACACCT

58°C

X93537X1

128–

154

12.

LEX334

M4

TTTAATCAAAGGATTCAGTTG

TTTCTCTTCAGGTGTCCTC

58°C

AF075635X2

203–

217

13.

LEX345

M5

GCGGAGGTAAGAAGTGGTAG

GGCCTAAGATGAGGGTGAA

54°C

AF075636X3

245–

255

14.

SGCV287

M7

CTGTGGCAGCTGTCATCTTGG

CCCAATTCCAGCCCAGCTTGC

60°C

U90604

151–

163

15.

LEX6811

M11

AAATCCCGAGCTAAAATGTA

TAGGAAGATAGGATCACAAGG

54°CNone

162–

174

16.

COR05812

M12

GGGAAGGACGATGAGTGAC

CACCAGGCTAAGTAGCCAAAG

56°C

AF108375X4

210–

230

17.

COR06913

M13

AGCCACCAGTCTGTTCTCTG

AATGTCCTTTGGTGGATGAAC

56°C

AF142606X3

273–

279

18.

VHL20914

M14

TCTTACATCCTTCCATTACAACTA

TGATACATATGTACGTGAAAGGAT

56°C

Y08451X5

84–96

19.

ASB0215

M15

CCTTCCGTAGTTTAAGCTTCTG

CACAACTGAGTTCTCTGATAGG

54°C

X93516X2

222–

254

R1,R2,R3

20.

HMS2016

M16

TGGGAGAGGTACCTGAAATGTAC

GTTGCTATAAAAAATTGTCTCCCTAC

58°CNone

116–

140

21.

COR00717

M17

GTGTTGGATGAAGCGAATGA

GACTTGCCTGGCTTTGAGTC

56°C

AF083450

156–

170

22.

LEX5418

M18

TGCATGAGCCAATTCCTTAT

TGGACAGATGACAGCAGTTC

55°C

AF075656X5

165–

177

/~uatz/FAO/(1of2)09/09/200416:50:51

Nr

23.

LEX7319

M19

CCCTAGAGCCATCTCTTTACA

CAGATCCAGACTCAGGACAG

54°CAF213359234–

264

24.

COR02222

M22

AAGACGTGATGGGAAATCAA

AGAAAGTTTTCAAATGTGCCA

56°C

AF101391

254–

264

25.

LEX6323

M23

CGGGGTGTGCATCTCTTAGG

TGGCGAATGCTGAATCTGG

54°C

AF075663

241–

249

26.

COR01825

M25

AGTCTGGCAATATTGAGGATGT

AGCAGCTACCCTTTGAATACTG

56°C

AF083461X6

249–

271

27.

COR07126

M26

CTTGGGCTACAACAGGGAATA

CTGCTATTTCAAACACTTGGA

56°C

AF142608X6

190–

202

28.

HMS4527

M27

TGTTACAGGTATTGGTAAACTGTGC

GGAACAAGAAGAAATCACTAATGTC

58°C

U89813

185–

197

29.

NVHEQ05428

M28

AGATGTCCACCTTCTCGCTG

CGGGGCTTTTAGGAGGTAACTA

62°C

AJ245763

172–

186

30.

COR08229

M29

GCTTTTGTTTCTCAATCCTAGC

TGAAGTCAAATCCCTGCTTC

58°CAF154935

192–

226

References:

ren-Mendez,J.,a,cdiversityinSpanishdonkeybreedsusingmicrosatelliteDNA

.33:433-442.

vic,A.,,,,,.2002,Geneticdiversityofthreedonkeypopulationsinthe

Genetics33:169-177.

a,J.,,.

.118:57-63.

Multiplexes:

lexMasterMix:AHT04+AHT05+ASB17+ASB23+HMS06+HMS07

lexMasterMix:ASB02+HTG10+HMS03+LEX33

lexMasterMix:LEX34+COR069

lexMasterMix:COR070+COR058

5.

MultiplexMasterMix:VHL209+LEX54

lexMasterMix:COR018+COR071

/~uatz/FAO/(2of2)09/09/200416:50:51

Nr

MarkerList

fortheHor

.

Primerquence

(5’->3’)

Forward

Rever

Annealing

temperature

Genbank

(Accession

Number)

Multiplex

Allele

range

Diversity

studies

071

M1

CAGGAAACTCATGTTGATACCATC

TGTTGTTGAAACATACCTTGACTGT

60°C

X74636

[SW1]

X1

165–

183

R1,R2,R3,

R4,R5,R6,

R7,R8

064

M4

GAAGCTGCCAGTATTCAACCATTG

CTCCATCTTGTGAAGTGTAACTCA

60°C

X74635X1

153–

169

R1,R2,R3,

R4,R5,R6,R7

074

M4

CCTGAAGCAGAACATCCCTCCTTG

ATAAAGTGTCTGGGCAGAGCTGCT

60°CNone

120–

130

R1,R2,R3,

R4,R5,R6,

R7,R8

058

M8

ACGGACACATCCCTGCCTGC

GCAGGCTAAGGGGGCTCAGC

60°CNone

X1

130–

146

R1,R2,R3,

R4,R6,R7

049

M9

CTATCTCAGTCTTCATTGCAGGAC

CTCCCTCCCTCCCTCTGTTCTC

55°CNone

X1

127–

141

R1,R2,R3,

R4,R5,R6,

R7,R8

0210

M10

ACGGTGGCAACTGCCAAGGAAG

CTTGCAGTCGAATGTGTATTAAATG

60°C

X74631

218–

238

R1,R2,R3,

R4,R5,R6,

R7,R8

0215

M15

CCTTCCGTAGTTTAAGCTTCTG

CACAACTGAGTTCTCTGATAGG

55°C

X93516X2

222–

254

039

M9

CCAACTCTTTGTCACATAACAAGA

CCATCCTCACTTTTTCACTTTGTT

60°C

X74632X2

150–

170

R4,R5,R6,

R7,R8

0615

M15

CCTGCTTGGAGGCTGTGATAAGAT

GTTCACTGAATGTCAAATTCTGCT

60°CNone

1021

M21

CAATTCCCGCCCCACCCCCGGCA

TTTTTATTCTGATCTGTCACATTT

55°C

AF169294X2

0424

M24

AACCGCCTGAGCAAGGAAGT

CCCAGAGAGTTTACCCT

60°CNone

X1

2030

M30

CAAGTCCTCTTACTTGAAGACTAG

AACTCAGGGAGAATCTTCCTCAG

60°CNone

X1

13.

ASB172M2

GAGGGCGGTACCTTTGTACC

ACCAGTCAGGATCTCCACCG

60°CX93531X1

91–

109

R1,R2,

R3,R7

14.

ASB233

M3

GAGGTTTGTAATTGGAATG

GAGAAGTCATTTTTAACACCT

60°C

X93537X1

128–

154

R7

15.

LEX334

M4

TTTAATCAAAGGATTCAGTTG

TTTCTCTTCAGGTGTCCTC

60°C

AF075635X2

203–

217

R7

16.

UCDEQ42528

M28

AGCTGCCTCGTTAATTCA

CTCATGTCCGCTTGTCTC

60°C

U67406

17.

LEX345

M5

GCGGAGGTAAGAAGTGGTAG

GGCCTAAGATGAGGGTGAA

55°C

AF075636X3

245–

255

18.

SGCV287

M7

CTGTGGCAGCTGTCATCTTGG

CCCAATTCCAGCCCAGCTTGC

62°C

U90604

151–

163

19.

COR05812

M12

GGGAAGGACGATGAGTGAC

CACCAGGCTAAGTAGCCAAAG

58°C

AF108375X4

210–

230

20.

COR06913

M13

AGCCACCAGTCTGTTCTCTG

AATGTCCTTTGGTGGATGAAC

58°C

AF142606X3

273–

279

/~uatz/FAO/(1of3)09/09/200416:51:01

Nr

21.

VHL20914

M14

TCTTACATCCTTCCATTACAACTA

TGATACATATGTACGTGAAAGGAT

57°C

Y08451X5

84–96

22.

COR00717

M17

GTGTTGGATGAAGCGAATGA

GACTTGCCTGGCTTTGAGTC

58°C

AF083450

156–

170

23.

LEX5418

M18

TGCATGAGCCAATTCCTTAT

TGGACAGATGACAGCAGTTC

55°C

AF075656X5

165–

177

24.

LEX7319M19

CCCTAGAGCCATCTCTTTACA

CAGATCCAGACTCAGGACAG

55°CAF213359234–

264

25.

COR02222

M22

AAGACGTGATGGGAAATCAA

AGAAAGTTTTCAAATGTGCCA

58°C

AF101391

254–

264

26.

LEX6323

M23

CGGGGTGTGCATCTCTTAGG

TGGCGAATGCTGAATCTGG

55°C

AF075663

241–

249

27.

COR01825

M25

AGTCTGGCAATATTGAGGATGT

AGCAGCTACCCTTTGAATACTG

58°C

AF083461X6

249–

271

28.

COR07126

M26

CTTGGGCTACAACAGGGAATA

CTGCTATTTCAAACACTTGGA

58°C

AF142608X6

190–

202

29.

HMS4527

M27

TGTTACAGGTATTGGTAAACTGTGC

GGAACAAGAAGAAATCACTAATGTC

60°C

U89813

185–

197

30.

COR08229M29

GCTTTTGTTTCTCAATCCTAGC

TGAAGTCAAATCCCTGCTTC

59°CAF154935

192–

226

References:

tad,,.

117:307-317.

tad,G.,.2003,GeneticrelationshipbetweenMongolianandNorwegianhors?

AnimalGenetics34:55-58.

tad,emarcationandpotentialforbreedallocationofhorsassdby

Genetics.32:59-65.

,J.,,s,-Pla,o,eticstructureofSpanish

Genetics31:39-48.

,M.L,,-Atance,o,buciondelavariabilidadgeneticaen

poblacionesdeponisEspanolis:.47:169-174.

,P.,n,a,,,,it,rphism

ofOldKladruberhors,genet.25:357-363.

,R.,n,ric.

Scand.,SectionA.,52:180-185.

,T.,ki,wa,,wa,,,ma.2003.

MicrosatellitevariationinJapaneandAsianhorsandtheirphylogeneticrelationshipusingaEuropeanhoroutgroup.

ty94:374-380.

Multiplexes:

lexMasterMix:AHT04+AHT05+ASB17+ASB23+HMS06+HMS07+HTG04+VHL20

lexMasterMix:ASB02+HTG10+HMS03+LEX33

lexMasterMix:LEX34+COR069

lexMasterMix:COR070+COR058

lexMasterMix:VHL209+LEX54

lexMasterMix:COR018+COR071

/~uatz/FAO/(2of3)09/09/200416:51:01

Nr

Seite:1

[SW1]Hattehierfalschenlinkgeschickt.–Hierwüeallelinksgeä://www.

/cgi-bin/emblfetch?G01593

/~uatz/FAO/(3of3)09/09/200416:51:01

RankNameOrigin

Map

Info

Primerquence(5'->3')

ForwardRever

Annealing

temperature

Genbank

(Accession

Number)

Allele

range

Multiplex

Diversity

studies

1SRCRSP5

CHI21

M1

GGACTCTACCAACTGAGCTACAAG

TGAAATGAAGCTAAAGCAATGC

55°C

L22197

156-

178

D1,D2

2MAF065

OAR15

M2

AAAGGCCAGAGTATGCAATTAGGAG

CCACTCCTCCTGAGAATATAACATG

58°C

M67437

116-

158

VIC8mp

D1,D2

3MAF70

BTA4

M3

CACGGAGTCACAAAGAGTCAGACC

GCAGGACTCTACGGGGCCTTTGC

65°C

M77199

134-

168

D1,D4

4SRCRSP23unknown

M4

TGAACGGGTAAAGATGTG

TGTTTTTAATGGCTGAGTAG

58°C

81-

119

FAM

8mp

D2

5OarFCB48

OAR17

M5

GAGTTAGTACAAGGATGACAAGAGGCAC

GACTCTAGAGGATCGCAAAGAACCAG

58°C

M82875

149-

173

FAM

7mp

D2,D4,

D5

6INRA023

BTA3

M6

GAGTAGAGCTACAAGATAAACTTC

TAACTACAGGGTGTTAGATGAACT

58°C

X80215

196-

215

FAM

8mp

D1

7SRCRSP9

CHI12

M7

AGAGGATCTGGAAATGGAATC

GCACTCTTTTCAGCCCTAATG

58°C

L22200

99-

135

NED

7mp

D2,D5

8OarAE54

OAR25

M8

TACTAAAGAAACATGAAGCTCCCA

GGAAACATTTATTCTTATTCCTCAGTG

58°C

L11048

115-

138

VIC7mp

D2,D5

9SRCRSP8

Unknown

M9

TGCGGTCTGGTTCTGATTTCAC

GTTTCTTCCTGCATGAGAAAGTCGATGCTTAG

55°C

L22200

215-

255

D1,D2,

D5

10SPS113BTA10

CCTCCACACAGGCTTCTCTGACTT

CCTAACTTGCTTGAGTTATTGCCC

58°C

134-

158

PET7mp

11INRABERN172BTA26

CCACTTCCCTGTATCCTCCT

GGTGCTCCCATTGTGTAGAC

58°C

234-

256

FAM

7mp

12

OarFCB20

OAR2

M12

GGAAAACCCCCATATATACCTATAC

AAATGTGTTTAAGATTCCATACATGTG

58°C

L20004

93-

112

NED

8mp

D1,D2

13CSRD247

OAR14

M13

GGACTTGCCAGAACTCTGCAAT

CACTGTGGTTTGTATTAGTCAGG

58°C

220-

247

PET8mp

14

McM527

OAR5

M14

GTCCATTGCCTCAAATCAATTC

AAACCACTTGACTACTCCCCAA

58°C

L34277

165-

187

PET8mp

/~uatz/FAO/(1of3)09/09/200416:51:08

15ILSTS087BTA6

M15

AGCAGACATGATGACTCAGC

CTGCCTCTTTTCTTGAGAG

58°C

L37279

135-

155

FAM

8mp

16

INRA063

CHI18

M16

GACCACAAAGGGATTTGCACAAGC

AAACCACAGAAATGCTTGGAAG

58°C

X71507

164-

186

VIC8mp

D2,D3,

D4

17ILSTS011

BTA14

M17

GCTTGCTACATGGAAAGTGC58°C

L23485

256-

294

FAM

7mp

D1,D2

18SRCRSP7

CHI6

M18

TCTCAGCACCTTAATTGCTCT

GGTCAACACTCCAATGGTGAG

55°C

L22199

117-

131

D2

19ILSTS005

BTA10

M19

GGAAGCAATTGAAATCTATAGCC

TGTTCTGTGAGTTTGTAAGC

55°C

L23481

172-

218

D1,D2;

D3,D4

20SRCRSP15Unknown

M20

CTTTACTTCTGACATGGTATTTCC

TGCCACTCAATTTAGCAAGC

55°C

172-

198

D2,D5

21SRCRSP3

CHI10

M21

CGGGGATCTGTTCTATGAAC

TGATTAGCTGGCTGAATGTCC

55°C

L22195

98-

122

D2

22ILSTS029

BTA3

M22

TGTTTTGATGGAACACAG

TGGATTTAGACCAGGGTTGG

55°C

L37252

148-

170

D2,D3,

D5

23TGLA53

BTA16

M23

GCTTTCAGAAATAGTTTGCATTCA

ATCTTCACATGATATTACAGCAGA

55°C

126-

160

D1,D2

24ETH10

CHI5

M24

GTTCAGGACTGGCCCTGCTAACA

CCTCCAGCCCACTTTCTCTTCTC

55°C

Z22739

200-

210

D2,D3,

D5

25MAF209

CHI17

M25

GATCACAAAAAGTTGGATACAACCGTG

TCATGCACTTAAGTATGTAGGATGCTG

55°C

M80358

100-

104

D2

26INRABERN185CHI18

M26

CAATCTTGCTCCCACTATGC

CTCCTAAAACACTCCCACACTA

55°C

X73937

261-

289

D2,D3,

D5

27BM6444

BTA2

M27

CTCTGGGTACAACACTGAGTCC

TAGAGAGTTTCCCTGTCCATCC

65°C

G18444

118-

200

28P19(DYA)Unknown

AACACCATCAAACAGTAAGAG

CATAGTAACAGATCTTCCTACA

55°C

AJ621046

160-

196

29TCRVB6BTA10

GAGTCCTCAGCAAGCAGGTC

CCAGGAATTGGATCACACCT

55

L18953

217-

255

/~uatz/FAO/(2of3)09/09/200416:51:08

30DRBP1BTA23

ATGGTGCAGCAGCAAGGTGAGCA

GGGACTCAGTCTCTCTATCTCTTTG

58°C

M55069

195-

229

FAM

7mp

D2

Diversitystudies

,ZhaoSH,BianC,WangHS,WeiH,LiuB,YuM,FanB,ChenSL,ZhuMJ,LiSJ,XiongTA,crelationshipsamongtwelve

elEvol.2002Nov-Dec;34(6):729-44.

tG,Biju-DuvalMP,ErtugrulO,ZagdsurenY,MaudetC,f22microsatellitemarkersinfluorescentmultiplexesforparentage

testingingoats(Caprahircus).AnimGenet.1999Dec;30(6):431-8.

kovaN,GaillardC,Obexer-RuffG,net.1999Feb;30

(1):36-41.

,Tan,Moore,Mukherjee,Matheson,SelvarajGeneticvariationwithinandrelationshipsamongpopulationsofAsiangoats(Caprahircus)

JournalofAnimalBreedingandGeneticsVolume118,Issue4,Page213-233,Aug2001

nmor-WütMicrosatelliteDNAand

recentstatisticalmethodsinwildlifeconrvationmanagement:applicationsinAlpineibex[Capraibex(ibex)]MolecularEcologyVolume11Issue3Page

421-March2002

/~uatz/FAO/(3of3)09/09/200416:51:08

RankNameOriginMap

Primerquence(5'->3')

ForwardRever

Annealing

temperature

Genbank

(Accession

Number)

Allele

range

Multiplex

Diversity

studies

1MAF65OAR15

M1

AAAGGCCAGAGTATGCAATTAGGAG

CCACTCCTCCTGAGAATATAACATG

60°C

M67437

123-

127

bp

4.16-

FAM

D3,D4,

D5

2OarFCB193OAR11

M2

TTCATCTCAGACTGGGATTCAGAAAGGC

GCTTGGAAATAACCCTCCTGCATCCC

54°C

L01533

96-

136

bp

5.16-

FAM

D5

3OarJMP29OAR24

M3

GTATACACGTGGACACCGCTTTGTAC

GAAGTGGCAAGATTCAGAGGGGAAG

56°C

U30893

96-

150

bp

4.2NED

D5

4OarJMP58OAR26

M4

GAAGTCATTGAGGGGTCGCTAACC

CTTCATGTTCACAGGACTTTCTCTG

58°C

U35058

145-

169

bp

4.3HEX

5OarFCB304OAR19

M5

CCCTAGGAGCTTTCAATAAAGAATCGG

CGCTGCTGTCAACTGGGTCAGGG

56°C

L01535

150-

188

bp

5.3NED

D1,D2,

D6

6BM8125OAR17

M6

CTCTATCTGTGGAAAAGGTGGG

GGGGGTTAGACTTCAACATACG

50°C

G18475

110-

130

bp

3.1NED

D1

7

OarFCB128

OAR2

M7

ATTAAAGCATCTTCTCTTTATTTCCTCGC

CAGCTGAGCAACTAAGACATACATGCG

55°C

L01532

96-

130

bp

1.16-

FAM

D1,D5,

D6

8OarCP34OAR3

M8

GCTGAACAATGTGATATGTTCAGG

GGGACAATACTGTCTTAGATGCTGC

50°C

U15699

112-

130

bp

3.2VIC

D1,D3,

D4,D5,

D6

9OarVH72OAR25

M9

GGCCTCTCAAGGGGCAAGAGCAGG

CTCTAGAGGATCTGGAATGCAAAGCTC

57°C

L12548

121-

145

bp

2.16-

FAM

D1

10OarHH47OAR18

M10

TTTATTGACAAACTCTCTTCCTAACTCCACC

GTAGTTATTTAAAAAAATATCATACCTCTTAAGG

58°C

L12557

130-

152

bp

2.2VIC

D2

/~uatz/FAO/(1of4)09/09/200416:52:03

11DYMS1OAR20M11

AACAACATCAAACAGTAAGAG

CATAGTAACAGATCTTCCTACA

59°C

AJ621046

159-

211

bp

2.3NED

12SRCRSP1CHI13

M12

TGCAAGAAGTTTTTCCAGAGC

ACCCTGGTTTCACAAAAGG

54°C

L22192

116-

148

bp

3.1NED

13

SRCRSP5

OAR18

M13

GGACTCTACCAACTGAGCTACAAG

GTTTCTTTGAAATGAAGCTAAAGCAATGC

56°C

L22197

126-

158

bp

2.36-

FAM

14SRCRSP9CHI12

M14

AGAGGATCTGGAAATGGAATC

GCACTCTTTTCAGCCCTAATG

55°C

L22201

99-

135

bp

1.16-

FAM

15MCM140OAR6

M15

GTTCGTACTTCTGGGTACTGGTCTC

GTCCATGGATTTGCAGAGTCAG

60°C

L38979

167-

193

bp

3.36-

FAM

16MAF33OAR9

M16

GATCTTTGTTTCAATCTATTCCAATTTC

GATCATCTGAGTGTGAGTATATACAG

60°C

M77200

121-

141

bp

3.2HEX

D3,D4

17MAF209OAR17

M17

GATCACAAAAAGTTGGATACAACCGTGG

TCATGCACTTAAGTATGTAGGATGCTG

63°C

M80358

109-

135

bp

5.2NED

D5,D6

18INRA063OAR14

M18

ATTTGCACAAGCTAAATCTAACC

AAACCACAGAAATGCTTGGAAG

58°C

X71507

163-

199

bp

4.46-

FAM

D7

19OarFCB20OAR2

M19

AAATGTGTTTAAGATTCCATACAGTG

GGAAAACCCCCATATATACCTATAC

56°C

L20004

95-

120

bp

4.5HEX

D5,D6

20BM1329

OAR6

M20

TTGTTTAGGCAAGTCCAAAGTC

AACACCGCAGCTTCATCC

50°C

G18422

160-

182

bp

3.36-

FAM

21MAF214OAR16

M21

GGGTGATCTTAGGGAGGTTTTGGAGG

AATGCAGGAGATCTGAGGCAGGGACG

58°C

M88160

174-

282

bp

2.1HEX

D2,D5,

D6

/~uatz/FAO/(2of4)09/09/200416:52:03

22ILSTS11OAR9

M22

GCTTGCTACATGGAAAGTGC

CTAAAATGCAGAGCCCTACC

55°C

L23485

256-

294

bp

1.36-

FAM

D2

23MCM527OAR5

M23

GTCCATTGCCTCAAATCAATTC

AAACCACTTGACTACTCCCCAA

58°C

L34277

165-

187

bp

4.26-

FAM

D2

24OarFCB226OAR2

M24

CTATATGTTGCCTTTCCCTTCCTGC

GTGAGTCCCATAGAGCATAAGCTC

60°C

L20006

119-

153

bp

4.1HEX

25ILSTS28OAR3

M25

TCCAGATTTTGTACCAGACC

GTCATGTCATACCTTTGAGC

53°C

L37211

105-

177

bp

2.2NED

D2

26MAF70OAR4

M26

CACGGAGTCACAAAGAGTCAGACC

GCAGGACTCTACGGGGCCTTTGC

60°C

M77199

124-

166

bp

5.4HEX

D3,D4,

D5

27BM1824OAR1

M27

GAGCAAGGTGTTTTTCCAATC

CATTCTCCAACTGCTTCCTTG

58°C

G18394

5.5FAM

D6,D7

28OarAE129OAR5

M28

AATCCAGTGTGTGAAAGACTAATCCAG

GTAGATCAAGATATAGAATATTTTTCAACACC

54°C

L11051

133-

159

bp

1.2NED

D1,D5

29

HUJ616

OAR13

M29

TTCAAACTACACATTGACAGGG

GGACCTTTGGCAATGGAAGG

54°C

M88250

114-

160

bp

1.3VIC

30OarCP38OAR10

M30

CAACTTTGGTGCATATTCAAGGTTGC

GCAGTCGCAGCAGGCTGAAGAGG

52°C

U15700

117-

129

bp

6-FAM

D5

31ILSTS5OAR7

M31

GGAAGCAATGAAATCTATAGCC

TGTTCTGTGAGTTTGTAAGC

55°C

L23481

174-

218

bp

1.2NED

D2,D7

Diversitystudies

,MiceikieneI,VilkkiJ,isonofmicrosatelliteandbloodproteindiversityinsheep:inconsistenciesinfragmented

/~uatz/FAO/(3of4)09/09/200416:52:03

l.2003Aug;12(8):2045-56.

tL.,BavareM.C.,CappuccioI.,iniUofmicrosatellitesforgeneticvariationandinbreedinganalysisinSardasheepflocksof

.2003120:425-432.

JJ,BayonY,net.1998Dec;29(6):435-40.

JJ,BayonY,elEvol.2001Sep-Oct;33(5):529-

42.

erger-SaitbekovaN.,ShlapferJ.,DolfG.,.

.2001,118:379-387.

-TasconC,LittlejohnRP,AlmeidaPA,cvariationwithintheMerinosheepbreed:analysisofclolyrelatedpopulations

net.2000Aug;31(4):243-51.

-BurrielI,Garcia-MuroE,cdivenet.1999

Jun;30(3):177-82.

/~uatz/FAO/(4of4)09/09/200416:52:03

Nr

Map

Primerquence(5’->3’)

D-indicatesDyelabelledprimer

Annealing

temperature

Genbank

(Accession

Number)

Multiplex

Allele

range

Diversity

studies

1.S002616

D1M1

D-AACCTTCCCTTCCCAATCAC

CACAGACTGCTTTTTACTCC55°C

L30152

X1

87-

105

R1,R2,

R3,

R4,R6

2.S01551

D1M2

D-TGTTCTCTGTTTCTCCTCTGTTTG

AAAGTGGAAAGAGTCAATGGCTAT

55°C

NAX1

142-

162

R1,R2,R3,

R4,R6

3.S00055

D1M3

D-TCCTTCCCTCCTGGTAACTA

GCACTTCCTGATTCTGGGTA55°C

NAX1

203-

267

R1,R2,

R3,

R4,R6

24108

D2M4

D-ATTTGCCCCCAAGGTATTTC

CAGGGTGTGGAGGGTAGAAG

50°C

AF207836X2

90-

131

R5,R6

83010

D2M5

D-AAGTACCATGGAGAGGGAAATG

ACATGGTTCCAAAGACCTGTG

50°C

AF235378X2

168-

203

R6

6.S035515

D1M6

D-

TCTGGCTCCTACACTCCTTCTTGATG

TTGGGTGGGTGCTGAAAAATAGGA

50°C

L29049X2

244-

271

R1,R2,

R3,

R4,R6

2417

D1M7

D-CTTTGGGTGGAGTGTGTGC

ATCCAAATGCTGCAAGCG

55°C

AF235245X3

95-

124

R1,R2,R3,

R4,R6

6327

D1M8

D-TGGGTTGAAAGATTTCCCAA

GGAGTCAGTACTTTGGCTTGA

55°C

AF225099X3

148-

178

R1,R2,R3,

R4,R6

194113

D2M9

D-AGAAAGCAATTTGATTTGCATAATC

ACAAGGACCTACTGTATAGCACAGG

55°C

AF253904X3

202-

224

R6

93615

D1M10

D-TCTGGAGCTAGCATAAGTGCC

GTGCAAGTACACATGCAGGG55°C

AF225107X4

90-

116

R1,R2,

R3,

R4,R6

11.S0218X

D1M11

D-GTGTAGGCTGGCGGTTGT

CCCTGAAACCTAAAGCAAAG55°C

L29048X4

158-

205

R1,R2,

R3,

R4,R6

12.S02286

D1M12

D-GGCATAGGCTGGCAGCAACA

AGCCCACCTCATCTTATCTACACT55°C

L29195X4

220-

246

R1,R2,

R3,

R4,R6

1226

D1M13

D-CAAAAAAGGCAAAAGATTGACA

TTGTCTTTTTATTTTGCTTTTGG55°C

AF235206X5

106-

128

R1,R2,

R3,

R4,R6

85714

D1M14

D-TGAGAGGTCAGTTACAGAAGACC

GATCCTCCTCCAAATCCCAT55°C

AF225105X5

141-

159

R1,R2,

R3,

R4,R6

15.S00974

D2M15

D-GACCTATCTAATGTCATTATAGT

TTCCTCCTAGAGTTGACAAACTT

55°C

M95020X5

209-

250

R6

2402

D1M16

D-AGAAATTAGTGCCTCAAATTGG

AAACCATTAAGTCCCTAGCAAA55°C

AF235246X6

92-

124

R1,R2,

R3,

R4,R6

15

D1M17

D-GCTTGGATGGACCATGTTG

CATATTTTTCTGCATAACTTGAACCT55°C

NAX6

193-

209

R1,R2,

R3,

R4,R6

24066

D2M18

D-AATGTCACCTTTAAGACGTGGG

AATGCGAAACTCCTGAATTAGC

55°C

AF225140X6

222-

262

R6

723

D1M19

D-ATCAGAACAGTGCGCCGT

TTTGAAAATGGGGTGTTTCC55°C

AF235346X7

97-

114

R1,R2,

R3,

R4,R6

20.S02262

D1M20

D-GCACTTTTAACTTTCATGATACTCC

GGTTAAACTTTTNCCCCAATACA55°C

L29230X7

180-

210

R1,R2,

R3,

R4,R6

/~uatz/FAO/(1of4)09/09/200416:52:25

EditedbyFoxitReader

Copyright(C)byFoxitSoftwareCompany,2005-2007

ForEvaluationOnly.

Nr

21.S009012

D1M21

D-CCAAGACTGCCTTGTAGGTGAATA

GCTATCAAGTATTGTACCATTAGG55°C

M95002X7

227-

249

R1,R2,

R3,

R4,R6

200811

D2M22

D-CAGGCCAGAGTAGCGTGC

CAGTCCTCCCAAAAATAACATG

55°C

AF253773X8

95-

108

R5,R6

10676

D2M23

D-TGCTGGCCAGTGACTCTG

CCGGGGGATTAAACAAAAAG

55°C

AF235183X8

136-

176

R6

24.S01017

D1M24

D-GAATGCAAAGAGTTCAGTGTAGG

GTCTCCCTCACACTTACCGCAG58°C

NAX8

197-

221

R1,R2,

R3,

R4,R6

18281

D2M25

D-AATGCATTGTCTTCATTCAACC

TTAACCGGGGCACTTGTG

55°C

AF253712X9

82-

110

R6

26.S014312

D2M26

D-ACTCACAGCTTGTCCTGGGTGT

CAGTCAGCAGGCTGACAAAAAC

55°C

NAX9

150-

167

R6

27.S006813

D1M27

D-CCTTCAACCTTTGAGCAAGAAC

AGTGGTCTCTCTCCCTCTTGCT55°C

NAX9

211-

262

R1,R2,

R3,

R4,R6

28.S01788

D1M28

D-TAGCCTGGGAACCTCCACACGCTG

GGCACCAGGAATCTGCAATCCAGT60°C

NAX10

101-

128

R1,R2,

R3,

R4,R6

9119

D1M29

D-CTCAGTTCTTTGGGACTGAACC

CATCTGTGGAAAAAAAAAGCC60°C

AF225106X10

149-

173

R1,R2,

R3,

R4,R6

30.S00023

D1M30

D-GAAGCCAAAGAGACAACTGC

GTTCTTTACCCACTGAGCCA60°C

NAX10

186-

216

R1,R2,

R3,

R4,R6

Beforetheuofthislistwerecommendtolookat/lgc/pig/panel/

tocheckfortheavailabilityofpossibleadditionalorupdatedinformation

Multiplexesandannealingtemperature:

Multiplexindicatedhereshouldonlybeconsideredaspropositionsoftsofmarkerscompatibleinsize(whichcouldthusbe

labelledwiththesamedye)themarkerswerealsosuccessfully

amplifiedinverydifferentconditions(annealingconditionsdifferingofupto10°C),wehoweverstronglyrecommendyouto

ectedmarkershavebeensuccessfullymultiplexed

withothers,howevermultiplexPCRconditionshavenotbeendefineduptonowforthisupdatedlistofmarkers(ealsohow

wherelecteddiversitymarkers).Multiplexconditionsforfirstgenerationdiversitymarkershavebeensuccessfullydeterminedby

YvesAmiguesfromLabogenaandbyMartienGroenenteam.

Diversityts:

1Twentyone

markers(indicatedasD1)werefromtheoriginaltofISAG-FAOdiversitymarkersoriginallytupintheframe

arkerswerealsoanalydintheframeofthelargescalePigBiodivEUproject.

rkers(indicatedasD2)wereanalydintheframeofthelargescalePigBiodivEUproject.

MarkersfromcurrentdiversitytwerelectedamongthemarkersanalydintheframeofthelargescalePigBiodivEUproject

(includingISAG-FAOfirstgenerationtofmarkers).Markershavebeenlectedamongmarkersthathavebeensuccessfully

analydonalargenumberofbreeds,forwhichtheheterozygositywasofatleast64%andforwhichonaverage9alleleshave

beenobrved.

.

/~uatz/FAO/(2of4)09/09/200416:52:25

EditedbyFoxitReader

Copyright(C)byFoxitSoftwareCompany,2005-2007

ForEvaluationOnly.

Nr

Miscellaneousinformation

D-:indicatesdyelabelledprimer

NA:notavailable

References

R1LavalG,IannuccelliN,LegaultC,MilanD,GroenenMA,GiuffraE,AnderssonL,NisnPH,JorgennCB,

BeeckmannP,GeldermannH,FoulleyJL,ChevaletC,

SelEvol.2000.32(2):187-203.

R2.

FanB.,WangZ.G.,LiY.J.,ZhaoX.L.,LiuB.,ZhaoS.H.,YuM.,LiM.H.,XiongT.A.,LiK.,Geneticvariation

analysiswithinandamongChineindigenousswinepopulationusingmicrosatellitemarkers,.33(2002)222-

227.

Shu-LinYang,Zhi-GangWang,BangLiu,Gui-XiangZhang,Shu-hongZhao,MeiYu,BinFan,Meng-HuaLi,Tong-An

Xiong,KuiLi,GeneticvariationandrelationshipsofeighteenChineindigenouspigbreeds,GeneticsSelectionEvolution,

(2003)35(6):657-71

,,,,,,,,,,,Genetic

VariationandGeneticRelationshipofSeventeenChineIndigenousPigBreedsUsingTenSerumProteinLoci,Asian-

AustralasianJournalofAnimalScience(2003)inpress

KuiL.,ChenY.,MoranC.,FanB.,ZhaoS.H.,PengZ.Z.,Analysisofdiversityandgeneticrelationshipsbetweenfour

ChineindigenouspigbreedsandoneAustraliancommercialpigbreed,.31(2000)322-325.

YangJ.E.,WangJ.,KijasJ.,LiuB.,HanH.,YuM.,YangH.M.,ZhaoS.H.,LiK.,Alowlevelofgeneticdiversityprent

withinthenearcompletemtDNAgenomeof17breedsofindigenousChinepigs,.(2003inpress).

,,,,,,ThegeneticdiversityofvenpigbreedsinChina,estimatedby

meansofmicrosatellites,AsianAustralasianJournalofAnimalGenetics,2000,9:1193-11957.

Fan,,,,,,CharacterizationofthegeneticdiversityonnaturepopulationofChine

.(submited)

KLi,CMoran,YChen,BFan,JLee,SZhao,BLiu,KKim,HWei,AsssmentofgeneticdiversityoffourChineand

oneKoreanindigenouspigbreedsbymicrosatellites,Proceedingsof7thWorldCongressonGeneticsAppliedtoLivestock

Production,2002

YangSL,WangZG,LiuB,ZhangGX,ZhaoSH,YuM,FanB,LiMH,XiongTA,cvariationandrelationships

elEvol.200335(6):657-71

R3Martínez,A.M.,Delgado,J.V.,Rodero,A.&Vega-Pla,J.L.(2000a).GeneticstructureoftheIberianpigbreedusing

Genetics.31,295-301.

Martínez,A.M.,Peinado,B.,Barba,J.V.,Delgado,J.L.&Vega-Pla,J.L.(2000b).GeneticanalysisoftheChatoMurciano

abstractsof27thInternationalConferenceon

polis.

Martínez,M.,Barba,C.,Peinado,B.,Lobera,J.B.,Delgado,J.V.&Poto,A.(1998a).Conrvationprogrammeinthe

ChatoMurcianopigbreed:ia.

Barba,C.,Peinado,B.,Martínez,M.,MaríaDolores,E.,Lobera,J.B.,Delgado,J.V.&Poto,A.(1998).Influenceofthe

recipientgeometryintheconrvationbyfreezeofminaldosoftheChatoMurcianopigbreed.49thMeetingEAAP,

Varsovia.

Delgado,J.V.,Vega-Pla,J.L.,Barba,C.,Martínez,A.M.&Zamorano,M.J.(1998).Caracterizaciónmorfológicay

genéticadelasvariedadesdelTroncoIbérdoIbé.27-43.

/~uatz/FAO/(3of4)09/09/200416:52:25

Nr

R4ZHANGGui-Xiang,WANGZhi-Gang,SUNFei-Zhou,CHENWei-Sheng,YANGGuo-Yi,GUOShi-Jian,LI

Yong-Jun,ZHAOXiao-Li,ZHANGYuan,SUNJun,FANBin,YANGShu-Lin,:GeneticDiversityof

hedinActaGeneticaSinica,March2003,30(3):225-233.

Languageoffulltext:Chine.

R5AntoinetteKotze,ARCAnimalImprovementInstitute,alcommunicationtoDrRoswithaBaumung

R6SanCristobalM.,and26others,(2002)inaryresultson58Europeanbreedsandlines.

Proc.7thWorldCongressonGeneticsAppliedtoLivestockProduction,33,523-528,2002,english.

SanCristobalM.,ChevaletC.,HaleyC.,JoostenR.,RattinkA.,Harlizius,,GroenenM.,AmiguesY.,BoscherM.Y.,Rusl

G.,LawA.,DavoliR.,RussoV.,DesautesC.,AlderssonL.,FimlandE.,BaggaM.,DelgadoJ.,Vega-PlaJ.L.,MartinezA.,

RamosM.,GlodeckP.,MeyerJ.,inoD.,PlastowG.,SiggensK.,LavalG.,ArchibaldA.,MilanD.,

HammondK.,CardelinoR.,FoulleyJ.L.,OllivierL.(2004)GeneticdiversitywithinandbetweenEuropeanpigbreedsusing

microsatellitemarkersandpreliminaryinferencesonevolutionaryforces(submittedtoGenetics)

/~uatz/FAO/(4of4)09/09/200416:52:25

Microsatellitelistforbiodiversitystudiesinchickens

NrNameChrMap

Primerquence(5'->3')

ForwardReverr

Annealing

temperature

Genbank

(Accession

Number)

Multiplex

Allele

range

Diversity

studies

1ADL0268

1

M1

CTCCACCCCTCTCAGAACTA

CAACTTCCCATCTACCTACT

60°C

G01688X1

102-

116

R1,R2,

R4,R5

2MCW0206

2

M2

ACATCTAGAATTGACTGTTCAC

CTTGACAGTGATGCATTAAATG

60°C

AF030579X7

221-

249

R2,R4,

R5

3LEI0166

3

M3

CTCCTGCCCTTAGCTACGCA

TATCCCCTGGCTGGGAGTTT

60°C

X85531X1

354-

370

R2,R4

4MCW0295