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Table 1 Candidate genes for SHR: sources of selection and features for genotyping the association mapping population

From: Association mapping in sunflower for sclerotinia head rot resistance

Source of selection

Target locus

Sunflower gene IDa

Sequence lengthb

SNPs in CSc

Indels in CSd

Haplotypes in CSe

Genotyping methodf

Primers for AMP genotyping

B. napus expression

At1g34580

 HaMT 

580 (191)

8 (8)

3 (11)

3 (2)

FCE

F:5′GAAAGGACATGCTACTTTATGG3′

        

R:5′CTTTACTTGAATTAAAGTTACT3′

profile

At5g51550

HaPRP1

431

0

-

1

  
  

 HaPRP2 

437 (166)

11 (11)

-

3 (2)

dHPLC

F: 5′GGACGGGAACGTAAAATAATG3′

        

R: 5′CCGTCTGTCCGTACAATCG3′

 

At3g48310

HaCYP450A

786

1 (0)

-

2

  
  

HaCYP450B

310

2 (0)

-

2

  
  

 HaCYP450C 

400 (260)

2 (2)

1 (1)

2 (6)

dHPLC

F: 5′AAGTGACTTTAGCAACGTCC3′

        

R: 5′GAGTTGGTATGGGTGGATGAA3′

 

At5g05940

HaROPGEF1

447

12 (11)

3 (50)

4

  
  

 HaROPGEF2 

403 (197)

2 (2)

2 (11)

2 (2)

FCE

F: 5′TGCGTAGTGGTTCTAAAATTGG3′

        

R: 5′CGTCAATCATTACCCCAACC3′

  

HaROPGEF3

801

0

-

1

  
 

At1g48040

 HaPP2C 

514 (398)

4 (4)

-

2 (4)

Direct sequencing

F: 5′ACTGGGACTACGGCATTGAC3′

        

R: 5′TGCTGAATTTCTGGCTCTGA3′

 

At1g04450

 HaRIC_A 

940 (261)

8 (8)

4 (6)

3 (2)

FCE

F: 5′GCACGAATAGTGACATTGAAAC3′

        

R:5′ACATAAAACAGTTTTCGGTCC3′

  

 HaRIC_B 

1424 (537)

12 (0)

2 (15)

3 (3)

FCE

F: 5′GGCTTGCGTTACATCTCTGA3′

        

R: 5′CCCAACTAGGAGCATTGGAA 3′

 

At1g03687

HaHP1

198

0

1(1)

1

  
 

At4g09180

 HaHP2 

309 (256)

1 (1)

-

2 (5)

Direct sequencing

F: 5′CTGCTATCCAGGCTCATTCA3′

        

R: 5′AGAATGGCAGGGCGACCAAG3′

 

At1g13200

HaFbox1

265

11 (11)

-

3

  
  

HaFbox2

262

8 (5)

1 (1)

5

  
 

At1g14687

 HaZFHD 

166 (166)

9 (7)

-

4 (9)

Direct sequencing

F:5′TCATGCCCTCACTAACATGC 3′

        

R: 5′TTTGTCCGGAATCTTTTTCG 3′

Sunflower EST library

TC49193

HaDRP

587

14 (12)

1 (1)

2

  
 

BQ973243

HaCP

542

14 (10)

-

3

  
 

-

 HaGDPDI 

620 (707)

18 (14)

2 (2)

3 (10)

Direct sequencing

F: 5′CAGAAACTGATCAACCCGAAA 3′

        

R: 5′TGCATGCATCTTGGAAAATAG 3′

 

-

 HaCWP 

351 (177)

4 (4)

3 (10)

2 (2)

FCE

F: 5′CAGGAATCACGGTCCCTAGT3′

        

R: 5′TGAAACATGAGGGATGAGCA3′

 

TC42391

 HaPI 

658 (235)

14 (9)

3 (4)

5 (2)

FCE

F: 5′TCCAACAGTGTGTGACCTTTG3′

        

R: 5′CATTAGTTACGTTACAAAGCTAT3′

 

TC57179

 HaPAL 

343 (343)

2 (2)

-

2 (2)

dHPLC

F:5′TGTGGTCTTCAAATTCATTAATAAC3′

        

R: 5′GGCCATTCCTAACAGGATCA3′

Defense responses

CF088675

 HaWRKY5 

1395 (227)

39 (33)

14 (56)

8 (6)

FCE

F: 5′CCGATCAAAGGCTCAATCTA3′

        

R: 5′CACATCCGCTAGTTCACACC3′

 

BU016906

 HaWRKY7 

1163 (174)

1 (1)

2 (22)

3 (2)

FCE

F: 5′CATTGTTGGTCAACCCTGTG3′

        

R: 5′AGGGAAGCATAACCATGACG3′

 

EU112647

HaGLP1

876

0

3 (3)

3

  
 

AJ540203

HaGLP2

794

6 (6)

-

2

  
 

TC17527

HaGLP3

621

13 (9)

-

6

  
 

TC18217

 HaGLP4 

761 (209)

9 (2)

3 (11)

4 (4)

FCE

F: 5′TGGCTGCAACAACTTTCCTT3′

        

R: 5′TTCAATCCAGAAACAAACTTCTAA3′

 

TC17648

HaGLP5

1710

2 (1)

2 (3)

3

  
  1. a Acronyms used throughout this article, candidate genes genotyped in the AMP are underlined.
  2. b Length of PCR products sequenced in the CS. Length of PCR products genotyped in the AMP are given in parentheses.
  3. c Parsimony informative sites are given in parentheses.
  4. d Base pairs of indels are given in parentheses.
  5. e Number of haplotypes detected in the AMP are given in parentheses.
  6. f FCE: fluorescent capillary electrophoresis, dHPLC: denaturing high liquid performance chromatography.
  7. g Primers 5’-end 6-FAM labeled.