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Table 1 Summary of results for a subset of primer pairs designed for 60 expressed sequence tag (EST) loci derived from red raspberry (RI) and black raspberry (RO) sequences. Primer pairs were evaluated for the production of polymorphic PCR products and the ability to distinguish between the two species. Amplicon sizes are in base pairs (bp). Those primer pairs with unclear results are indicated as “unk”

From: Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.)

 

Polymorphic in Black Raspberry

Polymorphic in Red Raspberry

Number of alleles in Black Raspberry

Number of alleles in Red Raspberry

Amplicon size range Black Raspberry (bp)

Amplicon size range Red Raspberry (bp)

Distinguish between species?

Comments

RI_CHEa0001J04f

y

y

8

9

129–335

128–334

y

 

RI_CHEa0001K23f

y

y

7

9

101–300

102–300

y

 

RI_CHEa0001M05f

y

y

10

9

138–344

139–343

y

 

RI_CHEa0001N07f

y

y

7

7

124–383

124–386

y

 

RI_CHEa0002A10f

y

y

9

12

127–266

127–269

y

 

RI_CHEa0002G14f

y

y

7

8

127–281

122–277

y

 

RI_CHEa0002J02f

y

unk

3

2

130–233

174–182

y

 

RI_CHEa0002K01f

y

y

18

14

117–395

117–392

y

 

RI_CHEa0002L24f

y

y

8

8

112–264

113–265

y

 

RI_CHEa0002N01f

y

y

3

4

171–372

135–292

y

 

RI_CHEa0003H23f

y

y

11

10

117–321

117–298

y

 

RI_CHEa0003N21f

y

y

10

13

131–295

117–295

y

 

RI_CHEa0003O01f

y

y

22

19

108–393

108–387

y

 

RI_CHEa0004B20f

y

y

7

6

180–297

191–332

y

 

RI_CHEa0004H20f

y

y

17

15

110–390

110–385

y

 

RI_CHEa0004L23f

y

y

10

11

112–403

112–383

y

 

RI_CHEa0004P08f

y

y

5

6

132–153

131–154

y

 

RI_CHEa0005M24f

y

y

11

13

179–402

176–395

y

 

RO_CBEa0002O01f

y

y

6

9

110–330

110–334

y

 

RO_CBEa0004M17f

y

n

4

2

111–331

111–322

y

Polymorphism in black raspberry needs validation

RO_CBEa0005H05f

y

unk

7

7

134–315

142–319

y

Inconsistent amplification for Heritage

RO_CBEa0005I06f

y

y

10

8

102–327

110–284

y

Polymorphism in black raspberry needs validation

RO_CBEa0006A02f

y

y

6

6

110–290

107–292

y

Poor amplification in one Bristol replicate

RO_CBEa0007C05f

y

y

7

12

110–329

109–332

y

Poor amplification in one Bristol replicate

RO_CBEa0007K08f

y

y

3

5

254–317

130–317

y

Inconsistent amplification in ZIH–e1

RO_CBEa0008E02f

y

y

13

12

115–415

117–415

y

 

RO_CBEa0008O22f

y

y

5

5

120–290

122–279

y

Inconsistent amplification in Preston_2; only one replicate of ZIH–e1

RO_CBEa0009K12f

y

y

2

4

160–184

155–355

y

Polymorphism in black raspberry needs validation; inconsistent amplification in Heritage

RO_CBEa0009N10f

y

y

11

11

108–298

108–295

y

 

RO_CBEa0010G06f

y

y

15

15

108–287

115–287

y

Poor amplification in one ZIH–e1 and one Bristol replicate

RO_CBEa0010M20f

y

y

16

14

115–415

115–415

y

 

RI_CHEa0001H16f

n

n

1

4

283

103–286

y

Poor amplification for Bristol, Preston_2, and Heritage

RI_CHEa0003C04f

n

y

1

3

260

254–260

y

Poor amplification for Bristol and Preston_2

RI_CHEa0005E12f

n

n

1

1

278

278

n

 

RI_CHEa0005K13f

n

n

1

1

277

277

n

 

RI_CHEa0005P17f

n

y

2

3

226–256

226–308

y

 

RO_CBEa0001B17f

n

y

2

2

153–160

157–248

y

One replicate of Preston_2 failed

RO_CBEa0003P15f

n

n

7

7

110–318

110–318

n

Poor amplification in one Preston_2 replicate

RO_CBEa0008G23f

n

y

5

6

107–219

107–269

y

 

RI_CHEa0001C22f

unk

n

unk

1

 

151

unk

Poor amplification for Bristol, Preston_2, and ZIH–e1

RI_CHEa0002D18f

unk

unk

unk

unk

unk

unk

unk

Poor amplification for all samples

RI_CHEa0002G20f

unk

n

unk

1

unk

279

unk

Poor amplification for all samples

RI_CHEa0002H09f

unk

unk

unk

unk

unk

unk

unk

Poor amplification for all samples

RI_CHEa0002H15f

unk

unk

unk

unk

unk

unk

unk

Data for Bristol and Heritage only; only one replicate of Heritage amplified; poor amplification.

RI_CHEa0002L16f

unk

unk

unk

unk

unk

unk

unk

Poor amplification for all samples

RI_CHEa0003D14f

unk

n

3

3

172–201

172–201

n

Only one black raspberry replicate (Bristol) was successful; poor amplification for ZIH–e1

RI_CHEa0004B18f

unk

unk

unk

unk

unk

unk

unk

Poor amplification for all samples

RI_CHEa0004N08f

unk

unk

unk

unk

unk

unk

unk

Poor amplification for all samples

RI_CHEa0004P09f

unk

n

7

8

114–384

112–391

y

Only data for black raspberry is Bristol; poor amplification for ZIH–e1

RI_CHEa0005B17f

unk

unk

3

2

281–362

190, 281

y

Poor amplification for Bristol and Heritage.

RI_CHEa0005I04f

unk

unk

10

10

141–395

140–389

unk

Only one black raspberry replicate (Preston_2) was successful; poor amplification for ZIH-e1

RI_CHEa0005P15f

unk

unk

3

3

129–140

129–213

y

Only one red raspberry replicate (ZIH-e1) was successful; poor amplification for Bristol

RO_CBEa0001C08f

unk

unk

3

3

123–291

120–285

y

Both Bristol and one Preston_2 replicates failed; poor amplification for Heritage

RO_CBEa0001L10f

unk

y

14

12

115–298

122–298

y

One replicate of Bristol failed; inconsistent amplification for Preston_2

RO_CBEa0002K20f

unk

unk

5

8

140–315

138–315

y

Poor amplification in both Bristol replicates; inconsistent amplification for Preston_2, Heritage and ZIH-e1

RO_CBEa0002P20f

unk

unk

unk

unk

unk

unk

unk

One replicate of Bristol failed; poor amplification in second Bristol and one Heritage replicate

RO_CBEa0005J12f

unk

y

6

4

123–284

149–179

y

Only one black raspberry sample (Bristol) was successful

RO_CBEa0005J24f

unk

unk

6

7

162–485

159–486

y

Inconsistent amplification for all samples

RO_CBEa0005N17f

unk

y

6

7

110–290

109–293

y

Poor amplification in one Bristol replicate

RO_CBEa0006C18f

unk

y

2

6

133–252

133–256

y

Poor amplification in both Bristol replicate; inconsistent amplification for Preston_2