The profile of SSR development from an alfalfa genomic library and the polymorphism information of SSRs

 

SSR group†

Equivalent SSR classes‡

Number of

Polymorphism

 

PIC§

Type

(5’~3’)

(5’~3’)

SSRs

Polymorphic

%

Total alleles

Alleles/locus

 

Dinucleotide

ct

ag, ga, tc

43

 

44

 

78.6

 

228

 

5.2

 

0.53

ac

ca, gt, tg

10

at

ta

3

 

Trinucleotide

gat

atc, atg, cat, tca, tga

14

 

17

 

77.3

 

82

 

4.8

 

0.43

ggt

acc, cac, cca, gtg, tgg

5

ctt

aag, aga, gaa, tct, ttc

3

Total or average

78

61

78.2

310

5.1

0.50

† The SSR motifs used for making probes for colony hybridization.

‡ Types of SSRs appeared or could appear in sequence data after sequencing of the DNA inserts detected with the relevant probes.

§ PIC = polymorphism information content.

 

 

 

 

 

 

 

 

The simple sequence repeat markers, core motifs and the flanking primer sequences, melting temperatures, allele numbers, expected fragment sizes of the PCR products and their polymorphism information content (PIC). * If you use these SSRs in your research please acknowledge the source of these markers.

Primer

name

Motif

Primer sequence†

(5’ – 3’)

Tm

(°C)

No. of alleles

Expected size (bp)‡

PIC

Aac001

(ac)12

f: act acg act cta gac act tta tta g

r: ctt ctc tct ttc tca tac tct tc

47.7

46.6

10

138

0.92

Aac002

(ac)16(at)6

f: ttg aaa ttg gca aac cca c

r: aaa ggt gca gaa acc ctc

50.7

46.2

11

112

0.91

Aac003

(ac)12

f: agc aac aaa ctt taa ggc ag

r: ggg acc cat tct tat tta ag

46.9

45.1

4

121

0.67

Aac004

(ac)10

f: aag gca aat aag cta gac cca

r: agc tcg gga ccc att ctt at

58.0

59.9

9

246

0.83

Aac005

(tcc)3(ca)2+(ac)9

f: aca caa tag caa cca ggg tg

r: tcg gtt gcg tgt gta act c

49.8

49.1

4

234

0.48

Aac006

(ac)7+5

f: gat tca ctt gcc att cga gct tgc

r: tcc tgg ccg ttg atg tgt gtt g

60.9

60.2

5

170

0.33

Aac007

(ac)6+5+4

f: cat acc att aca tgc tcc ac

r: ggt acc cac gtg taa tat aat tg

45.1

48.0

3

157

0.50

Aac008

 (ac)15(ta)4

f: act ctt agg agc agg atc ac

r: gca gaa gct cta gtg gta tg

46.7

46.7

11

231

0.91

Aac009

 (ac)11(ca)2

f: tgt tga ggt cat ggt ggc ta

r: agc tcg gga ccc cta aaa t

60.1

59.9

9

220

0.80

Aac010

 (ac)4+4+5+7

f: atg ttg tga ggt gtc taa ttt atg g

r: ata taa att agg gac tcc act ttg g

51.2

51.4

8

201

0.45

Aat001

(tc)2+(at)5

f: gca tac tcc cag cta atc cg

r: cga gct cgg tac cga ttc

64.3

62.3

5

236

0.65

Aat002

(at)8+(ca)4

f: aat taa tgg att gac acc c

r: tgt gtg tgt gtg tgt ggg

43.5

45.3

9

143

0.90

Aat003

(at)2+(ca)2(at)4

f: cac cct aga taa gat tgt aaa g

r: gga tcg ccc tgt tag tag

44.1

45.2

3

111

0.50

Act001

(ct)25

f: tac aca agc aat tca agg aag g

r: cac acg act att gcg ctt atg

51.4

51.2

4

172

0.22

Act002

(ct)8+(ca)8

f: tcc tat ctt acc tac aat gcg aac

r: ccc aca tct cac tcc atc c

51.6

49.4

3

167

0.12

Act003

(ta)4+(ct)9

f: taa ctt cca ttc ttc caa cct g

r: ttc tac atc tgc tct ctg ttg aat c

50.4

51.5

5

163

0.32

Act004

(ct)10+2+20

f: aca tga ttt aag gtt gag aca gag

r: ttt agg gtg tta cag gag gaa c

49.0

49.5

4

 146

0.56

Act005

(ct)25

 
f: caa tcc gtg agt ggt gag aa
r: ttg gac cga act ggg taa ac

59.7

59.8

3

111

0.23

Act006

(ctt)5+(ct)6

 
f: ctg gaa cat gga acc tgg at
r: gtt ttg cgt tga cct tgg ta

59.8

58.7

2

255

0.42

Act007

(ct)4+3+(ct)3(ggt)2

 
f: ctt ccc ctt cgt ttt tct cc
r: gat gca aac atg tgc cag ac

60.0

60.1

3

221

0.56

Act008

(ct)13+4

 
f: cac ttc acc aac cca aaa ca
r: ccc tct ata cac ctc cca cg

59.4

59.4

4

239

0.43

Act009

(ct)12+5

 
f: aag caa ccg aac aac gat tt
r: agt gac agt tat ggg ggt gg

59.6

59.7

10

203

0.62

Act010

(tccc)3(ct)20

 
f: atc ttg aaa gcc aga cac cg
r: cca ttg tat tcc cta agt ttg cc

60.3

60.9

6

268

0.48

Act011

(ct)12

 
f: gca tga tca agc tag aaa ccc t
r: tct cag act cga att atc caa gc
 
59.8
59.9

6

288

0.89

Act012

(ct)10

 
f: gtt tgt gca gcc ctt tga tt
r: atg caa acc aag att aag gc

60.1

56.9

3

130

0.70

Act013

(ct)20

 
f: aca tgc cat tta gcc cat tc
r: aag ttc act cgc gaa aga gg

59.8

59.6

4

224

0.56

Act014

(ct)19

 
f: aat tta tta tgg ccc ctc cg
r: cca cct tca atg taa gcc gt

60.0

60.0

2

295

0.12

Act015

(ct)11

 
f: act ccc tcc ttg ctc cat tt
r: cat gga tgg att cgt gaa ga

60.1

59.5

1

101

 

Act016

(ct)4+7+4

f: atg tgt aga cct tga ctc ttg atg

r: gtt tca cct ttg tca cct gc

49.5

49.4

2

160

0.12

Act017

(ct)10

 
f: cgg gcc tct ttt cac tta ca
r: ctt ctc tca cca ctt tcc cg

60.2

59.8

4

293

0.61

Act018

(ct)19(ta)6+(ct)7

f: agt gtg tga taa ata agt ttg tgg

r: cgt aat tgt tac tgg ttt gaa ag

61.1

62.0

5

242

0.48

Act019

(ct)14+(ta)4

 
f: ccg gat ttc ttt cat tgt gg
r: gaa aca atg gat ttt tgc cg

60.3

60.3

6

218

0.71

Act020

(ct)19

 
f: tgt tca gag tta agt gca gcg
r: tca agt gct cac cca aac aa

59.3

60.3

7

276

0.92

Act021

(ct)9

 
f: gca tgt gca gtg gaa gaa ga
r: aat ggt acg cgt gta tgc aa

60.0

60.0

2

235

0.23

Act022

(ct)6+8

 
f: gct caa att tca cgt cac ga
r: tcc att cac ttc aac atc gc

59.9

59.7

1

288

 

Act023

(ct)16

f: tgc att gta tac tta cct ttc att g

r: ccc aca cac tca aat ctc ctt ac

50.4

52.0

1

171

 

Act024

(ct)7(ctcc)3

 
f: tgt cga aag cac ttg gaa tg
r: tgc aat cta gca tcg gag aa

59.8

59.5

5

200

0.71

Act025

(ct)6+5

 
f: atc ggt tct gag atc gcc ta
r: caa acc ctt caa aac cct ca

59.8

59.9

4

207

0.35

Act026

(ct)9

 
f: aaa cca ccc ttc cat ctt cc
r: agg gtg gag aag aag cat ga

60.2

59.8

7

222

0.58

Act027

(ct)13

f: gtg gat gac ctt ggt gaa g

r: ttc aat taa tca caa gca ata tc

47.0

46.4

1

168

 

Act028

(ct)4+5

f: ttc att tct tct tcg tct tc

r: gct att aaa tca aac gaa cg

43.6

45.0

2

123

0.38

Act029

(ct)10

 
f: cct ctc gtt tac ctc cct tg
r: tcc aat cat aat tgt ccg ca

58.8

59.9

6

282

0.66

Act030

(ct)15

 
f: agg agc atc tgc cca tag tg
r: agg gag atc gag gga caa gt

60.2

60.1

1

254

 

Act031

(ct)4+5+4

 
f: gga aaa agg gga agg caa ta
r: tgt ttt cct ttt tgc tta att c

60.3

55.5

1

225

 

Act032

(ga)8+(ct)20+9

 
f: gac acc tgt ttt tga acc cg
r: ggc gag aaa cac ttg tgt gg

60.4

61.7

1

281

 

Act033

(ct)10+3

 
f: ggg ctc aga aac aca gat cc
r: aac ccg tta aca att ccc aa

59.7

59.2

1

175

 

Act034

(ct)4t(ct)3t(ct)4t(ct)2

 
f: gaa aga ctt gtg tgg acc agg
r: tgt aga cca ggg acc aaa cc

59.6

59.8

1

163

 

Act035

(ct)11

 
f: cgc aat gaa tta ggt cga ttt
r: tgg att acc ttg gtg aag gc

59.1

59.9

4

226

0.23

Act036

(ct)10

f: gga ttg tgg atg gaa cct g

r: atc aga gtt cag agt ctt atg cag

49.6

49.2

1

100

 

Act037

(ct)8at(ct)10at(ct)9

 
f: gcc aca gat caa caa ttt gc
r: act tct tac cca ccg gaa cc

59.1

60.2

3

242

0.41

Act038

(ct)15

 
f: att ccc atg agt gcc aag ac
r: tgt gtt tga gca ttc cat cc

59.9

59.5

2

296

0.12

Act039

(ct)25

 
f: ttc agg atc cct aaa tga gtg aa
r: gtt ttg gat gca caa cat gg

56.0

59.8

3

189

0.48

Act040

(ct)5(cca)4+(at)3

f: cgg tgg gtg aga gat gga tat g

r: ccc gca tga atg cat ata ttg

55.6

53.1

8

233

0.50

Act041

(ct)4+4+(cct)3

f: atg agt cca tgg gtg ata act g

r: tac ttt gtg tct tgt gaa tat cct c

50.5

49.2

1

213

 

Act042

(tct)3+(ct)4+(cca)3

f: gtt aat ctc tgt tct ctt ctt ctg

r: ttg ttc gtc gaa gaa gat g

46.0

45.6

8

298

0.75

Act043

(ct)4+4+(tg)3

f: tgg aat tga aac act taa acc tct c

r: gat aca tag tgc gaa aga tta aag g

52.8

50.8

1

222

 

Actt001

(ctt)24+(tct)5

f: aat tgt gag ctt tcc tct tcc

r: tac gac tct aga cac ttt att agg c

49.5

48.6

11

235

0.86

Actt002

(ct)6+(ctt)3+6

f: aga tgc tct gga gga tga ttc ac

r: cac aca ctt agg gta agc att g

53.8

49.4

9

223

0.67

Actt003

(ctt)4+(tc)3

f: aca cac aca cac aca cac tta g

r: gac aag gtg ttg caa tct c

45.2

44.5

11

189

0.88

Agat001

 (gat)5(ag)2

f: tat ctg att cca act tgg gta tg

r: tac aaa gca tgc aac gaa ac

50.3

49.0

4

231

 

0.48

Agat002

(gat)6

 
f: tca agt tcc gta acc taa ttt cc

r: aga aca tcc tac aaa caa aca aca c

51.4

51.2

4

228

0.73

Agat003

(gat)8

 
f: acc tag taa caa taa tgt tgg tgg

r: tac gcc att tct tct ctt tga c

49.2

50.7

2

236

0.12

Agat004

(gat)7

 
f: caa tag atg cag tat cag gta tc

r: gtt aca cct ttg aag aat cca g

45.5

47.6

2

232

0.22

Agat005

(gat)8

 
f: agg gta aca aac atg gtc tat g

r: cca cac cat aca ata atg aac c

47.8

48.8

1

108

 

Agat006

(gat)7

 
f: aac agt ctc att caa atc cag tc

r: ctt gtt gat gtt att gac ctg g

49.3

49.0

4

100

0.63

Agat007

(gat)10

 
f: ggc tgc aaa gga ttc ttc tga ag

r: ggt cca tga tgt tga tcc ttc tta tg

56.2

56.8

1

102

 

Agat008

(gat)2gac(gat)4

f: aac aga agc cac cgt aag cga c

r: aag tgt tca tgc ctg acc aat ctc

57.2

56.1

3

104

0.12

Agat009

(gat)8

f: cgt tcg agt tat tgt tgt tgg tg

r: cac tga aac tga atc gga aag aag

53.9

54.0

2

207

0.12

Agat010

(gga)5+(ggt)3(gat)5

f: atc tag cag tac cac cac cat atg

r: ttg cac aga cac aga ttg tac ata g

51.8

51.5

1

172

 

Agat011

(gat)8+(gtt)2(att)7

f: cga gga ggt gag ata ata gag g

r: ccc ttc tac aat atc tca tcc tc

49.3

48.4

1

184

 

Agat012

(gat)3+5

f: gat agt ccg tac ctt ggc tct g

r: tgt tca gct ctt cat cta cat ctt c

52.3

51.5

6

106

0.23

Agat013

(gat)6+(ga)4

f: cat tac agt atc tct aaa caa gtt cct g

r: tta tag cca cta tcc tcg ttc c

51.6

49.9

1

150

 

Agat014

(gat)3(tc)2+(ct)3

f: ttt gct tgt ttg aac tca ttg c

r: gtt aca tgc agg gtc gac tc

52.3

49.3

2

141

0.12

Aggt001

(ggt)6+4

f: cct gtt ggt tgt tgt aga tat gg

r: agt tcg cca cca aat gta atc

50.7

50.9

4

177

0.37

Aggt002

(ggt)3+6

f: gga gct cag atg gtg gtg gtt gta g

r: ctc cag tgt tcc ttc tct cac ctc

59.8

55.1

3

238

0.23

Aggt003

(gct)3+(ggt)6

f: ggt gct gca act tct tca aat tc

r: tga tac gct gaa ccc aat tgt aaa c

54.7

56.2

3

221

0.48

Aggt004

(ggt)2+(caa)2(tcc)3

f: aaa tga tat tgt agg aag atc gtg c

r: agt tat gag gga gca ccg ag

52.8

50.9

10

164

0.86

Aggt005

(ggt)4+(ga)3(ttg)4

f: aac taa cac att aca ttt gag ag

r: cta tgt tcc aat gtt cca tc

43.0

44.1

2

114

 

0.12

† f = forward primer; r = reverse primer. ‡ Expected size is the expected PCR fragment length of the alfalfa cultivar ‘W10’.