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Table 1 Allelic variability in the promoter region and 1st intron of VRN1 genes of wheat

From: Evolution of VRN-1 homoeologous loci in allopolyploids of Triticum and their diploid precursors

Loci

Alleles

Status of regulatory regions/changes

Level of ploidy, genomes, species

References

Promoter

1st intron

2n

4n

6n

BBAA

GGAA

BBAADD

VRN-A1

vrn-A1

vrn-A1/ 8 bp insertion vs. vrn-A1 or VRN-A1 of all diploids

vrn-A1/no changes

 

T. dicoccoides

T. dicoccum

T. durum

 

T. aestivum

[21, 22, 26, 27, 29, 56]

vrn-A1u

vrn-A1u/ SNPs vs. vrn-A1 or VRN-A1 of other diploids

vrn-A1u/ 1.4 kb deletion vs. vrn-A1 or VRN-A1 of other diploids

T. urartu (AA)

   

[27]

vrn-A1f

vrn-A1f/ 50 bp deletion vs. vrn-A1

vrn-A1/ in some cases large indels were found (see below)

  

T. araraticum, T. timopheevii

 

[26.49]

vrn-A1f-del

vrn-A1f/ 50 bp deletion

vrn-A1f-del/ 2.7 kb deletion

  

T. araraticum

 

[49]

Vrn-A1f-ins

vrn-A1f/ 50 bp deletion

Vrn-A1f-ins/ 0.4 kb insertion

  

T. timopheevii

 

[49]

Vrn-A1f-del/ins

vrn-A1f/ 50 bp deletion

Vrn-A1f-del/ins / 0.4 kb insertion, 2.7 kb deletion

  

T. timopheevii

 

[49]

Vrn-A1a

Vrn-A1a.1-a.3/231 or 211 or 52 bp insertions

vrn-A1/no changes

 

T. dicoccum

T. durum

 

T. aestivum

[21, 26, 29, 56]

VRN-A1b

VRN-A1b/19 bp deletion

vrn-A1/no changes

 

T. dicoccoides

T. dicoccum

T. durum

 

T. aestivum

[21, 26, 27, 29, 56]

Vrn-A1c

vrn-A1/no changes

Vrn-A1c / 5.5 kb deletion

 

T. turgidum

 

T. aestivum

[3, 21]

Vrn-A1d

Vrn-A1d/ 19 and 32 bp deletions

vrn-A1/no changes

 

T. dicoccoides

  

[21, 26, 27]

Vrn-A1e

Vrn-A1e/ 54 bp deletion

vrn-A1/no changes

 

T. dicoccum

T. durum

  

[21, 26, 29]

VRN-A1f1

VRN-A1f1/ 1 bp deletion

vrn-A1/no changes or Vrn-A1ins

T. monococcum (AA)

   

[25, 27]

Vrn-A1ins

vrn-A1/no changes or VRN-A1f1

Vrn-A1ins/ 0.5 kb insertion

T. monococcum (AA)

   

[25, 27]

Vrn-A1g

Vrn-A1g/ 34 bp deletion

vrn-A1/no changes

T. monococcum, T.boeoticum (AA)

   

[26]

VRN-A1h

VRN-A1h/ 20 bp deletion

vrn-A1/no changes

T.boeoticum (AA)

   

[27]

Vrn-A1i

Vrn-A1i / SNP

vrn-A1/no changes

 

T. durum

  

[29, 56]

Vrn-A1k

Vrn-A1k/ 42 bp insertion

vrn-A1/no changes

 

T. durum

  

KX874608

Vrn-A1L

vrn-A1/no changes

Vrn-A1L / 7.2 kb deletion

 

T. dicoccoides

T. carthlicum,

T. polonicum

T. durum

  

[22, 27]

VRN-B1/G1

vrn-B1

vrn-B1/no changes

vrn-B1/no changes

 

T. dicoccoides

T. dicoccum

T. durum

 

T. aestivum

[21, 22, 26, 27, 29, 56]

vrn-B1sp

vrn-B1sp/ minor changes vs. vrn-B1

vrn-B1sp/no large changes

Ae. speltoides (BB/GG)

   

[27]

VRN-B1dic

VRN-B1dic/ 11% dissimilarity vs. vrn-B1

vrn-B1/no changes

 

T. dicoccoides

  

[28]

Vrn-B1a

vrn-B1/no changes

Vrn-B1a/ 6.8 kb deletion

 

T. durum

 

T. aestivum

[22, 29, 56]

Vrn-B1b

vrn-B1/no changes

Vrn-B1b/ Vrn-B1a + additional 36 bp deletion and SNP

   

T. aestivum

[57, 58]

Vrn-B1c

vrn-B1/no changes

Vrn-B1c / 7.6 kb deletion, 0.4 kb duplication

 

T. durum

 

T. spelta

T. aestivum

[34, 58, 56]

Vrn-B1ins

Vrn-B1ins/ 5.4 kb insertion

vrn-B1/no changes

 

T. carthlicum

  

[53]

VRN-B1a

VRN-B1a/ 127 bp insertion

vrn-B1/no changes

 

T. turanicum

  

[26]

vrn-G1a

vrn-G1a/ 220 bp insertion

vrn-B1/no changes

  

T. araraticum,

T. timopheevii

 

[26, 49]

VRN-D1

vrn-D1

vrn-D1/no changes

vrn-D1/no changes

Ae. tauschii (DD)

 

T. aestivum

[21, 22, 29]

Vrn-D1a

vrn-D1/no changes

Vrn-D1a / 4.2 kb deletion

 

T. aestivum

[22]

Vrn-D1b

Vrn-D1b/ SNP

Vrn-D1a / 4.2 kb deletion

 

T. aestivum

[63]

Vrn-D1с

Vrn-D1с/ 174 bp insertion

vrn-D1/no changes

 

T. aestivum

[64]

Vrn-D1s

vrn-D1/no changes

Vrn-D1s / 0.8 kb insertion

 

T. aestivum

[65]

Vrn-D(t)1

vrn-D1/no changes

Vrn-D(t)1/ 5.4 kb deletion

Ae. tauschii (DD)

 

[50]