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Table 1 PCR markers for determining the presence of different alleles of VRN-A1 , VRN-B1 in diploid and polyploid wheats

From: VRN-1 gene- associated prerequisites of spring growth habit in wild tetraploid wheat T. dicoccoides and the diploid A genome species

PCR marker

Name

Primer (5′→3′)

Target allele(s)

Expected product size (bp)

Annealing temp. (ºC)

Reference.

VRN-A1 marker*

Vrn1AF

GAAAGGAAAAATTCTGCTCG

VRN-A1a

876 and 965

55.0

[16,23,31]

 

Int1R

GCAGGAAATCGAAATCGAAG

VRN-A1b

694

  
   

VRN-A1d

662

  
   

VRN-A1h

684

  
   

VRN-A1f

703

  
   

VRN-A1

704

  
   

VRN-A1u

705

  
   

VRN-A1u

713

  

T. monococcum VRN-A1

Indel(-)F

CGCTCTTATATTTGTTTACCAGGG

VRN-A1

1025

50.0

_

Indel(-)R

GGGTCAACTATTCTGTGGAG

VRN-A1u, VRN-A1u’

no product

  

VRN-A1 deletion of 1.4 kb

Intr1/C/F

GCACTCCTAACCCACTAACC

VRN-A1u, VRN-A1u’

1068

56.0

[24]

Intr1/AB/R

TCATCCATCATCAAGGCAAA

    

VRN-A1 insertion of 0.5 kb

Intr 1

ATCATCTTCTCCACCAAGGG

VRN-A1ins

1980

50.0

_

Intr1insR

AATGAACAGCACGGAAACAG

VRN-A1

1476

  

VRN-A1 deletion of 7,2 kb

Ex1/C/F

GTTCTCCACCGAGTCATGGT

VRN-A1L

522

55.6

[24]

Intr1/A/R3

AAGTAAGACAACACGAATGTGAGA

    

VRN-B1 marker*

P2

TCATGCACGCACACACGGTA

VRN-B1

814

55.0

[25]

P5

GGCCAACCCTACACCCCAAG

    

VRN-B1 Non-deletion

Intr1/B/F

CAAGTGGAACGGTTAGGACA

VRN-B1

1149

56.4

[24]

Intr1/B/R4

CAAATGAAAAGGAATGAGAGCA

    
  1. *These diagnostic markers detect allelic variation at the promoter regions. In other cases variation within intron 1 of corresponding genes is detected.