Table 1. Marker information for markers used in the genomic and locus scans.



Name


Chr

Position
(cM)

Heterozygosity
(%)

No. of
alleles

Min allele
size (bp)

Max allele
size (bp)

Unamplified
alleles detected

Annealing temp
& PCR conditionsb


Typec

Companion
Markers
Chr location
of companion
markers
BM643811.6554256268NO56SINGLE
BMS192816.98115138174NO58DOUBLEUWCA461
BMS2321114697138152NO58DOUBLEBMS5271
BMS4015128.2759134158NO58DOUBLEBMS82461
BMS4017134.8857147163NO58DOUBLEBMS5271
TGLA57146.275786102NO58SINGLE
BMS527155.98711165187NO58DOUBLEBMS23211
BM9019167.565591115NO58DOUBLEBMS40021
BM8246176.2798167191NO60SINGLE
URB038180.6878155173NO60DOUBLECSSM191
BMS1170192.8788214228NO58SINGLE
BMS17891100.9837103121NO58SINGLE
CSSM191108.3826141155NO56DOUBLEURB0381
UWCA461113.8939120150NO58DOUBLEBMS40021
BMS5991125.88412112154NO58DOUBLEBMS40141
BMS40141135.57467787NO56DOUBLEBMS5991
URB0141142.1736115125NO60DOUBLESRC407
TGLA4420.89111136170NO58DOUBLETEXAN42
INRA04027.58924161240NO58SINGLE
TEXAN2222.5664116122NO58DOUBLEBMS8032
SRC23 229.18510136166NO58DOUBLETEXAN12
BMS803241766134146NO58DOUBLETEXAN22
BMS1300246.6324163169NO58DOUBLEIDVGA-22
BMS1126256.38110122156NO58DOUBLEBMS25192
TEXAN1268.7747118136NO58DOUBLESRC232
TGLA226280704141147NO58DOUBLEINRA402
TEXAN4288.4757110136NO58DOUBLETGLA442
BMS25192101.5698101127NO58DOUBLEBMS11262
BM21132106.2897125139NO58 END-LABELDOUBLE2
IDVGA-22117.8739119147NO56 2XPRIMERDOUBLEBMS13002
BMS87130603103113NO58DUPLEXBMS9373
INRA006319.5594106114NO58DUPLEXBMS21453
ILSTS096329.7697192204NO58DUPLEXIDVGA-353
BMS482336.2779137157NO58SINGLE
BL41345.2667236250NO58SINGLE
BM4129352.351878102NO54DOUBLEBMS8963
INRA003359.5637166180NO58 END-LABELDOUBLEBM8623
BMS937367.9596133149NO58DUPLEXBMS8713
ILSTS064377.98713142172NO54SINGLE3
TGLA76382.7676124136NO54DOUBLEINRA0033
BMS2145393.9547148164NO58DUPLEXINRA0063
IDVGA-353102.98712221247NO58DUPLEXILSTSO963
BMS8963114.9665130140NO56DOUBLEBM41293


Namea


Chr

Position
(cM)

Heterozygosity
(%)

No. of
alleles

Min allele
size (bp)

Max allele
size (bp)

Unamplified
alleles detected

Annealing temp
& PCR conditionsb


Typec

Companion
Markers
Chr location
of companion
markers
BMC421431237311172196NO56DOUBLEILSTS0643
BMC141040774202224NO58DUPLEXBMS12374
BMS178848.4801189115NO58DOUBLEINRA0724
BMS827424.7624102108NO58DOUBLERM0884
BMS1237430.68718140184NO58DUPLEXBMC14104
BMS1840441.7767165187NO58DUPLEXBMS10744
BMS2172449.66887896NO56DUPLEXBM15004
INRA072459.3709112130NO58DOUBLEBMS17884
ILSTS062468.3737188206NO58DUPLEXAGLA227B4
BMS1074474.9774141157NO58DUPLEXBMS18404
BM1500482.8594135145NO54SINGLE
RM088 494.8477128150NO54DOUBLEBMS8274
AGLA227B4101.5353171177NO58DUPLEXILSTS0624
BMS109550811195117NO56DUPLEXBR29365
BMS610512.87810108126NO54DOUBLEBL45
BP1518.87711302326YES54DUPLEXAGLA2935
RM103528.6798114134NO58DOUBLEBMS13155
AGLA293532487237257NO54DUPLEXBP15
BMS1315532.5616133145NO58DOUBLERM1035
BM321538445110126NO58DOUBLERM0845
BMC1009540.6717265285NO58 END-LABELSINGLE
BMS1898544.171892112NO58SINGLE
BL4551.2787149161NO54DOUBLEBMS6105
RM084555.8768128142NO58 END-LABELDOUBLEBM3215
BR2936564.3705140152NO58SINGLE
BMS1216575.6717139167NO58DOUBLEBMS5975
BMS1248588.47413122162NO58DUPLEXBMC10095
BM315 5100.18913107135NO60SINGLE
BM28305113.58914151179NO58DUPLEXBM81265
BMS5975120584128136NO60DOUBLEBMS12165
BM81265122.1342127129NO58DUPLEXBM28305
ILSTS093607010182201NO58 END-LABELDOUBLEILSTS0356
ILSTS090611.8542145147NO56DUPLEXBMS25086
BM1329635.5666145155NO58TRIPLERM216; BM81249&6
BMS2508644.277797111NO56DUPLEXILSTS0906
BMS518655.2754147159NO58DUPLEXBM81246
BMS470663.67365971NO58DUPLEXBMS22519
BM4621672.3425139155NO56DUPLEXBMS24606
ILSTS0356817217210266NO56DOUBLEILSTS0936
BMS2460686.26956783NO56DUPLEXBM46216
BM8124694.2429121139NO58TRIPLE RM216; BM13299&6
BMC42036112.9576150166NO58DUPLEXBL10386
BL10386122.368699113NO60DOUBLERM3728
BM716070676175189NO58DOUBLEBMS28407
RM012 77.9102106108NO58DOUBLEIL47


Namea


Chr

Position
(cM)

Heterozygosity
(%)

No. of
alleles

Min allele
size (bp)

Max allele
size (bp)

Unamplified
alleles detected

Annealing temp
& PCR conditionsb


Typec

Companion
Markers
Chr location
of companion
markers
BMS713715.2737129157NO58DOUBLEBM7417
IL4730.56168799NO58SINGLE
BM6105735.777889103NO58DOUBLE INRA192INRA1927
BM741 750.452180182YES54DOUBLEBMS7137
BMS2840764.38917217283NO58DOUBLEBM71607
BM8129769.601132132NO58DUPLEXBMS15918
INRA112772.1848158172NO58DOUBLERASA7
INRA192782.4674124134NO58DOUBLEBM61057
BMS1331791.1615132144NO52DOUBLEBMS22097
OARAE129 796.6483136144NO56DOUBLEBL10437
BMS22097103.1751297125NO50 3mM MgCLDOUBLEBMS13317
RASA7103.1564181187NO52DOUBLEINRA1127
ILSTS00671168110281299NO54DOUBLEBP417
BMS19797124.467993111NO58DOUBLEUWCA207
BL10437134.1871493123NO58DOUBLEOARAE1297
BMS186480686145159NO58DUPLEXBMS12909
SRC276814.4656181195NO58DUPLEXBMS26298
BM1227819.1324111119NO58DUPLEXBMS21519
RM372 819.1835126134NO58DOUBLEBL10386
BMS1591828.178878108NO58DOUBLEMCM648
BMS678838.480797111NO58DUPLEXSRC2598
BMS1341851.4534111123NO56DOUBLEHEL98
BMS2072858.8818152168NO56DOUBLEBMS4349
MCM64 862.7768144180NO58SINGLE
HEL9876.7809147165NO52DOUBLEBMS13418
SRC259887.9839130154NO58DUPLEXBMS6788
BMS28478112.28210205223NO58DOUBLEILSTS0356
BMS26298116.3724145151NO58DUPLEXSRC2768
BMS215190748127145NO58DUPLEXBM12279
ETH22598.1757141153NO58DUPLEXBMS22959
RM216 932901096118NO54TRIPLEBM8124; BM13296&6
BMS817938817114128NO58DUPLEXMCM648
TGLA261944.68815255283NO54DOUBLEBMS28748
BMS434951.6819101125NO56DOUBLEBMS20728
BMS129095982897123NO58DUPLEXBMS18648
TGLA73971.4625116124NO58DOUBLEBMS19679
BMS2251980.838594104NO58DUPLEXBMS4706
BMS2295991.5816110128NO58DUPLEXETH2259
BMS19679102.5901081101NO58DOUBLETGLA739
BM3033100412104106NO58DUPLEXBMS94714
CSSM381078816160198NO58DUPLEXBMS274210
BMS26351017.27312146176NO54SINGLE
BMS23491022.1791468110NO58DUPLEXINRA3710
BRN1029.28110236258NO58DUPLEXBM82711
BMS27421038.59413127153NO58DUPLEXCSSM3810


Namea


Chr

Position
(cM)

Heterozygosity
(%)

No. of
alleles

Min allele
size (bp)

Max allele
size (bp)

Unamplified
alleles detected

Annealing temp
& PCR conditionsb


Typec

Companion
Markers
Chr location
of companion
markers
BMS5291048.480696106NO56DOUBLEX6782710
BMS4191051.17513140186NO58DUPLEXSRC32310
BR16031059.3806123133NO56DOUBLEILSTS07010
INRA0711059.38511209229NO58DUPLEXBMS264110
INRA0371069.95611118146NO58DUPLEXBMS234910
BMS16201071.74178098NO58SINGLE
ILSTS0701072.37168296YES56DOUBLEBR160310
X678271072.3384103109NO58DOUBLEBMS52910
BMS26411079.1694173179NO58DUPLEXINRA07110
TGLA2721086.8446131151NO58DOUBLEBM61177
BMS6141089.5849131153NO58DOUBLEBMS263510
SRC32310101.47511101125NO58DUPLEXBMS41910
BM827110144208216NO58DUPLEXBRN10
BM9067119.5861399125NO46DOUBLEBMS98911
BM28181120.5667104122NO56DOUBLERM15011
RM0961131.3607102114NO56DOUBLESRC14612
BM716911418612218244NO58DOUBLEHEL1311
BMS17161147.7756183213NO58DUPLEXILSTS03611
ILSTS0361156.9747147159NO58DUPLEXBMS171611
RM1501165.59414143169NO56DOUBLEBM281811
BMS20471173.89218143193NO58DUPLEXBL110311
BMS9891185.480998114NO58DOUBLEBM906711
BL11031190.9869108130NO58DUPLEXBMS204711
BMS46011102.6777118142NO58DOUBLEINRABER16211
INRABER16211102.655893109NO58DOUBLEBMS46011
BMS60711105.38210133167NO58DUPLEXBMS135011
HEL13 11114.5515185197NO52DOUBLEBM716911
BMS410120801282108NO58TRIPLEXBM9248; BMA924813,12
BMS20571220.7801086108NO58DUPLEXBMS272412
RM094 1241.7666146162NO58DUPLEXBMS131612
BMA92481246.6262234240NO58TRIPLEXBMS410; BM924812,13
BMS9751261.26868698NO58DOUBLEBM402812
BM40281279.77113102126YES58DOUBLEBMS97512
BMS13161298.7831196126NO58DUPLEXRM09412
BMS272412105.8546129139NO58DOUBLEBMS99513
TGLA2313065992116NO58DUPLEXILSTS05913
BMS17421314.8665157167NO58DUPLEXBMS99513
ILSTS05913348313162200NO58DUPLEXTGLA2313
BM92481352.88410115145NO58TRIPLEXBMS410; BMA924812,13
RM327 1362.1861081101NO56DOUBLEAGLA23213
AGLA2321379.59014155183NO54DUPLEXBM73725
BMS9951384.1806118134NO58DOUBLEBMS272412
BM150814071799115NO56DUPLEXBMS167814
BMS1678146.2827123135NO56DUPLEXBM150814
RM011 1427.7868101121NO58DUPLEXBL102914


Namea


Chr

Position
(cM)

Heterozygosity
(%)

No. of
alleles

Min allele
size (bp)

Max allele
size (bp)

Unamplified
alleles detected

Annealing temp
& PCR conditionsb


Typec

Companion
Markers
Chr location
of companion
markers
BL10291442.87010138174NO58DUPLEXRM01114
BMS9471452.87811112136NO58SINGLE
BM43051466.4868150168NO58DUPLEXBMS42915
BMS20551484.1738147171NO58DOUBLEINRA05015
MGTG13B150483135141NO58DOUBLEBMS20949
BMS2533155.28611128160NO56SINGLE
JAB81520.8483220224NO56DOUBLEBMS20949
INRA0501531.1798132152NO54DOUBLEBMS205514
BMS26841534.970980110NO58DUPLEXMGTG13B15
IDVGA-101551.6808161175NO56DUPLEXBMS81215
BMS8121568.88611111133NO56DUPLEXIDVGA-1015
BMS8201581.6809106134NO56DUPLEXSRC407
BMS4291593.4737125143NO58DUPLEXBM430514
TGLA245166.58611129161NO56DUPLEXBMS60119
BM121 1624.46012118158NO56DUPLEXTGLA22718
BR65041651.2839121145NO56SINGLE
INRA04816737312265303NO58DUPLEXCSSM4327
BM35091684.5952596158NO54DUPLEXBMC421625
BMS4621693.2517108130NO58DUPLEXBMS227024
BMS1825173.87714148202NO58SINGLE
VH981712.87810141163NO52DOUBLEMAF3626
CSSM9 1731.4747147161NO60SINGLE
BM305 1751.98514101135NO58DUPLEXBMS135518
HUJ2231774.8576150168NO56DUPLEXBOLA-DRB123
BM18621786.3878194220NO56DUPLEXBM123317
BM12331798.6788166180NO58DOUBLEBMS238221
BMS1355182.8758149165NO58DUPLEXBM30517
BR4206188.8537104118NO58DUPLEXBMS252624
BMS22131826.2749130146NO58DUPLEXBMS94117
INRA1851842.3553137143NO58DUPLEXBMS263918
BMS26391857909157185NO58DUPLEXINRA18518
BM20781877.8681192114NO56DUPLEXBR650416
TGLA2271884.7841176102NO56 2XPRIMERDUPLEXBM12116
BM920219073885115NO56DUPLEXBMS192624
HEL10 1915.961698112NO58DUPLEXTGLA12221
X822611919.4758123141NO58DUPLEXBMS214219
RM222 1939.4627118136NO56SINGLE
BMS21421944.771987113NO58DUPLEXX8226119
BMS6501956.58713134174NO60DUPLEXIDVGA-4419
IDVGA-441978.6786203215NO60DUPLEXBMS65019
BMS6011999.5656177187YES56DUPLEXTGLA24516
HEL12 200.7697145163NO58DUPLEXBMS49917
TGLA30420207348694NO56DUPLEXBM73725
BMS11282033.950791103NO58DUPLEXBM500420
BM41072052.4549157183NO58DOUBLEBMS64127


Namea


Chr

Position
(cM)

Heterozygosity
(%)

No. of
alleles

Min allele
size (bp)

Max allele
size (bp)

Unamplified
alleles detected

Annealing temp
& PCR conditionsb


Typec

Companion
Markers
Chr location
of companion
markers
BM50042064.38610120148NO58DUPLEXBMS112820
BMS5212075684134142NO58DUPLEXBMS238221
BM8115210839119139NO52DUPLEXMAF3626
RM1512111.7749111133NO54SINGLE
BM1032130.5729146162NO56DUPLEXTGLA32530
BMS8682147.98311124156NO58DUPLEXBMS161630
TGLA1222167.38612141181NO58DUPLEXHEL1019
OY32183.2394148160NO50DOUBLEBMS6624
BMS23822187.653183187NO58DOUBLEBMS272412
CSSM262208311238276NO58DUPLEXBL109830
INRA1942221.8665145165NO56SINGLE
BMS25732240.4757117131NO58TRIPLEXBMS875; RME4022,26
BMS8752261.153597105NO58TRIPLEXBMS2573; RME4022,26
BM41022281.1715137173NO58DUPLEXBMS238221
INRA064230587177186NO58DOUBLEBM123317
BM47239.175996126NO56 END-LABELSINGLE
RM0332317.3644150156NO58DOUBLEBMS238221
UWCA12322.1737108120NO58SINGLE
BOLA-DRB12335.4859208229NO56DUPLEXHUJ22317
BM72332349.1806104124NO56DUPLEXBM144323
BM14432367.1889145165NO56DUPLEXBM723323
BL6 240345149163NO54DUPLEXAGLA25730
BMS2526246869139155NO58DUPLEXBR420618
BMS22702421.27097896NO58DUPLEXBMS46216
BMS662438.2727132146NO60DOUBLEOY321
BMS19262457.4757124146NO56DUPLEXBM920219
BMC4216250513163167NO54DUPLEXBM350916
BM40052512.3809102122NO58DOUBLERM40425
BMS1302512.3526146234NO58SINGLE
BM7372527.87910110134NO52DOUBLEAF5(L6038)25
BMS13532545.37010100128NO58DUPLEXBMS174324
AF5(L6038)2560.67710132156NO56DOUBLEBM73725
BM18642564.9625125142NO56DUPLEXILSTS08129
BMS651262.5898117133NO58DOUBLEILSTS07220
HEL112620.78112181211NO58DUPLEXBM80426
RME402641.38714145189NO58TRIPLEXBMS875; BMS257322,22
BM8042659.6676142152NO58DUPLEXHEL1126
BM72372664.354594102NO56DUPLEXBMC220828
MAF36 2672.6514151157NO54SINGLE
BM3507270849161185NO58DUPLEXINRA13427
BMS6412714.3891082104NO58DOUBLEBM410720
CSSM432734.1769249265NO58DUPLEXINRA04816
INRA1342745.5607123143NO58DUPLEXBMS279830
BM203 2764.17114203231NO58DUPLEXINRA04816
BMS20602804968799NO58DUPLEXAF5(L6038)25


Namea


Chr

Position
(cM)

Heterozygosity
(%)

No. of
alleles

Min allele
size (bp)

Max allele
size (bp)

Unamplified
alleles detected

Annealing temp
& PCR conditionsb


Typec

Companion
Markers
Chr location
of companion
markers
IDVGA-29288.7737136152NO56DUPLEXBM4723
BMS5102822.1861083107NO58DUPLEXRBP328
BMS17142842.1547121139NO58DUPLEXBMS206028
BMC22082852.4314143151NO56DUPLEXBM723726
RBP32852.4224132142NO58DUPLEXBMS51028
BM46022908210112144NO58DUPLEXBL110029
BMS764299.775794108NO58DUPLEXBMS160029
BMS16002928.4565139153NO58DUPLEXBMS76429
BL11002946.66457785NO58DUPLEXBM460229
ILSTS081296584988114NO56DUPLEXBM186425
BMS631X0413313958DUPLEXBMS91130
BM6017X4.71111714358DUPLEXBMS279830
URB010X25.5619220254SINGLE
BMS1616X45.979310758DUPLEXBMS86821
BL1098X52.8620121758DUPLEXCSSM2622
ILSTS017X73.5711512958DUPLEXBMC602130
BMC6021X91.3513915958DUPLEXILSTS01730
BMS2798X104.3616917958DOUBLEINRA13223
TGLA325X119.562109612256DUPLEXBM10321
BMS911X136.279411658DUPLEXBMS63130
XBM16 X143.9914016056DUPLEXURB01030
XBM451X150.572510612058DUPLEXAF5(L6038)25

aMarkers listed in bold were only used in the secondary scan and not in the genomic scan.
bThe standard PCR mix and thermocycling protocol was the same as Kappes et al. (1997) except where the primer concentration or MgCL concentration was indicated. All reactions were labeled by random incorporation except for the 6 markers that were end-labeled, as indicated.
cTriplexed and duplexed markers were ran in the same PCR reaction. Triple and double loaded markers were amplified in separate PCR reactions but load on the same polyacrylamide gel.