Genes regulating heading and flowering time of common wheat Triticum aestivum L.
PCR-based allele-specific markers
VRN-1 (Vernalization-1)
The VRN-1 genes controlling the wheat vernalization requirement were localized on the chromosome group 5. These genes encode MADS box transcription factors highly homologous to the APETALA-1, CAULIFLOWER, and FRUITFUL factors that regulate the transition from the vegetative phase of development to the generative one. VRN-1 is required for the initiation and mainte- nance of floral meristem on the wheat shoot apex. It was demonstrated that, for the plant transition to flowering, it is necessary that the VRN-1 transcription level reach a certain threshold value. The winter wheat varieties carry recessive alleles vrn-1, the expression of which is blocked before the period of exposure to low temperatures (vernalization). The spring varieties are characterized by dominant Vrn-1 alleles that are constitutively expressed. Mutations in any of homeologous VRN-1 genes lead to the spring type of development and absence of the vernal- ization requirement for the transition to flowering. Several mutant alleles leading to the absence of the vernalization requirement are known for each of the dominant Vrn-1 genes. Combinations of these alleles can lead to differences in the flowering time
Vrn-A1
Vrn-B1
Vrn-D1
997
1671
1671
VRN-A1 promoter and intron 1
Vrn-B1 intron-1
VRN-D1 intron-1
Vrn-B1 intron-1
vrn-A1
Vrn-A1a
Vrn-A1b
Vrn-A1d
Vrn-A1h
Vrn-A1f
Vrn-A1a
Vrn-A1b
Vrn-A1d
Vrn-A1h
Vrn-A1f
734
876 and 965
714
680
734
733
876 and 965
714
680
734
733
Vrn1AF: GAAAGGAAAAATTCTGCTCG
Vrn1-Int1R: GCAGGAAATCGAAATCGAAG
Vrn1-Int1R: GCAGGAAATCGAAATCGAAG
VRN-A1 promoter
Vrn-A1c
Vrn-A1L
Vrn-A1L
522
522
522
Ex1/C/F: GTTCTCCACCGAGTCATGGT
Intr1/A/R3: AAGTAAGACAACACGAATGTGAGA
Intr1/A/R3: AAGTAAGACAACACGAATGTGAGA
Vrn-B1a
Vrn-B1b
Vrn-B1c
Vrn-B1b
Vrn-B1c
vrn-B1
1091
1055
705
1055
705
1531
Ex1/C/F: GTTCTCCACCGAGTCATGGT
Intr1/B/R3: CTCATGCCAAAAATTGAAGATGA
Intr1/B/R3: CTCATGCCAAAAATTGAAGATGA
Ex1/C/F: GTTCTCCACCGAGTCATGGT
Intr1/B/R4: CAAATGAAAAGGAATGAGAGCA
Intr1/B/R4: CAAATGAAAAGGAATGAGAGCA
Intr1/D/F: GTTGTCTGCCTCATCAAATCC
Intr1/D/R3: GGTCACTGGTGGTCTGTGC Intr1/D/R4: AAATGAAAAGGAACGAGAGCG
Intr1/D/R3: GGTCACTGGTGGTCTGTGC Intr1/D/R4: AAATGAAAAGGAACGAGAGCG
vrn-D1
Vrn-D1a
Vrn-D1a
Gene
Product size (bp)
Gene region
Primers: Sequence
Allelic variant
Yan, L., Helguera, M., Kato, K., Fukuyama, S., Sherman, J., & Dubcovsky, J. (2004). Allelic variation at the VRN-1 promoter region in polyploid wheat. Theoretical and applied genetics, 109(8), 1677-1686.
Fu, D., Szűcs, P., Yan, L., Helguera, M., Skinner, J. S., Von Zitzewitz, J., ... & Dubcovsky, J. (2005). Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Molecular genetics and genomics, 273(1), 54-65.
Fu, D., Szűcs, P., Yan, L., Helguera, M., Skinner, J. S., Von Zitzewitz, J., ... & Dubcovsky, J. (2005). Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Molecular genetics and genomics, 273(1), 54-65.
Fu, D., Szűcs, P., Yan, L., Helguera, M., Skinner, J. S., Von Zitzewitz, J., ... & Dubcovsky, J. (2005). Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Molecular genetics and genomics, 273(1), 54-65.
Fu, D., Szűcs, P., Yan, L., Helguera, M., Skinner, J. S., Von Zitzewitz, J., ... & Dubcovsky, J. (2005). Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Molecular genetics and genomics, 273(1), 54-65.
PPD-1 (Photoperiod-1)
Photoperiod sensitivity is an important agronomic trait that influences the wheat heading date, and the Ppd-1 (Photoperiod-1) genes are significant regulators of this process. The Ppd-1 genes are members of the Pseudo- Response Regulator (PRR) gene family. [1] The photoperiod sensitive Ppd-1b alleles are
expressed during the light period, and the peak of the expression occurs 3 to 6 h after dawn; these alleles are not expressed during the dark period. In contrast, all photoperiod insensitive Ppd-1a alleles demonstrate a misexpression throughout the 24 period.
expressed during the light period, and the peak of the expression occurs 3 to 6 h after dawn; these alleles are not expressed during the dark period. In contrast, all photoperiod insensitive Ppd-1a alleles demonstrate a misexpression throughout the 24 period.
Díaz, A., Zikhali, M., Turner, A. S., Isaac, P., & Laurie, D. A. (2012). Copy number variation affecting the Photoperiod-B1 and Vernalization-A1 genes is associated with altered flowering time in wheat (Triticum aestivum). PloS one, 7(3), e33234.
Beales, J., Turner, A., Griffiths, S., Snape, J. W., & Laurie, D. A. (2007). A pseudo-response regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.). Theoretical and Applied Genetics, 115(5), 721-733.
Wilhelm, E. P., Turner, A. S., & Laurie, D. A. (2009). Photoperiod insensitive Ppd-A1a mutations in tetraploid wheat (Triticum durum Desf.). Theoretical and Applied Genetics, 118(2), 285-294.
Ppd-A1
Ppd-B1
Ppd-D1
288
414
414
5' UTR
PPD-D1 promoter
truncated Ppd-B1 in the ‘Chinese Spring’ allele
Ppd-A1a.1 Ppd-A1b.2
338
299
299
TaPpd-A1prodel: FCGTACTCCCTCCGTTTCTTT
TaPpd-A1prodelR3: AATTTACGGGGACCAAATACC TaPpd-A1prodelR2: GTTGGGGTCGTTTGGTGGTG
TaPpd-A1prodelR3: AATTTACGGGGACCAAATACC TaPpd-A1prodelR2: GTTGGGGTCGTTTGGTGGTG
‘Chinese Spring’ allele
425
219H05F2: TAACTGCTCCTCACAAGTGC
97J10R2: CCGGAACCTGAGGATCATC
97J10R2: CCGGAACCTGAGGATCATC
Ppd-D1_F: ACGCCTCCCACTACACTG
Ppd-D1_R1: GTTGGTTCAAACAGAGAGC
Ppd-D1_R2: CACTGGTGGTAGCTGAGATT
Ppd-D1_R1: GTTGGTTCAAACAGAGAGC
Ppd-D1_R2: CACTGGTGGTAGCTGAGATT
Ppd-D1a Ppd-D1b
Gene
Product size (bp)
Gene region
Primers: Sequence
Allelic variant
Nishida, H., Yoshida, T., Kawakami, K., Fujita, M., Long, B., Akashi, Y., ... & Kato, K. (2013). Structural variation in the 5′ upstream region of photoperiod-insensitive alleles Ppd-A1a and Ppd-B1a identified in hexaploid wheat (Triticum aestivum L.), and their effect on heading time. Molecular breeding, 31(1), 27-37.
Díaz, A., Zikhali, M., Turner, A. S., Isaac, P., & Laurie, D. A. (2012). Copy number variation affecting the Photoperiod-B1 and Vernalization-A1 genes is associated with altered flowering time in wheat (Triticum aestivum). PloS one, 7(3), e33234.
Díaz, A., Zikhali, M., Turner, A. S., Isaac, P., & Laurie, D. A. (2012). Copy number variation affecting the Photoperiod-B1 and Vernalization-A1 genes is associated with altered flowering time in wheat (Triticum aestivum). PloS one, 7(3), e33234.
Beales, J., Turner, A., Griffiths, S., Snape, J. W., & Laurie, D. A. (2007). A pseudo-response regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.). Theoretical and Applied Genetics, 115(5), 721-733..
junction between intact copies in the ‘CS’ allele
‘Chinese Spring’ allele
994
PpdB1_F25: AAAACATTATGCATATAGCTTGTGTC
PpdB1_R70: CAGACATGGACTCGGAACAC
PpdB1_R70: CAGACATGGACTCGGAACAC
Díaz, A., Zikhali, M., Turner, A. S., Isaac, P., & Laurie, D. A. (2012). Copy number variation affecting the Photoperiod-B1 and Vernalization-A1 genes is associated with altered flowering time in wheat (Triticum aestivum). PloS one, 7(3), e33234.
junction between intact copies of the gene
Ppd-B1a three-copy Sonora64 allele
223
PpdB1_F31: CCAGGCGAGTGATTTACACA
PpdB1_R36: GGGCACGTTAACACACCTTT
PpdB1_R36: GGGCACGTTAACACACCTTT
Ppd-B1 copy number
Ex1/C/F: GTTCTCCACCGAGTCATGGT
Intr1/B/R4: CAAATGAAAAGGAATGAGAGCA
Intr1/B/R4: CAAATGAAAAGGAATGAGAGCA
Cane, K., Eagles, H. A., Laurie, D. A., Trevaskis, B., Vallance, N., Eastwood, R. F., ... & Martin, P. J. (2013). Ppd-B1 and Ppd-D1 and their effects in southern Australian wheat. Crop and Pasture Science, 64(2), 100-114.
Cane, K., Eagles, H. A., Laurie, D. A., Trevaskis, B., Vallance, N., Eastwood, R. F., ... & Martin, P. J. (2013). Ppd-B1 and Ppd-D1 and their effects in southern Australian wheat. Crop and Pasture Science, 64(2), 100-114.
5' UTR
Ppd-B1a.1
620
Ex1/C/F: GTTCTCCACCGAGTCATGGT
Intr1/B/R4: CAAATGAAAAGGAATGAGAGCA
Intr1/B/R4: CAAATGAAAAGGAATGAGAGCA
Ppd-B1 copy number
Ppd-B1a / Ppd-B1b / Ppd-B1c
CNV10 CCCGTCATCAGTAAGCACCCCCTCGCCGC
CAGCAGCAGTAGTATTTCTGAATGATGATACACC
CAGCAGCAGTAGTATTTCTGAATGATGATACACC
Ppd-B1a / Ppd-B1b / Ppd-B1c
Nishida, H., Yoshida, T., Kawakami, K., Fujita, M., Long, B., Akashi, Y., ... & Kato, K. (2013). Structural variation in the 5′ upstream region of photoperiod-insensitive alleles Ppd-A1a and Ppd-B1a identified in hexaploid wheat (Triticum aestivum L.), and their effect on heading time. Molecular breeding, 31(1), 27-37.
VRN-3 (VERNALIZATION-3, Flowering Locus T, TaFT1)
The Vrn-B3 gene (TaFT1) is a key gene acting as an integrator of several autonomous pathways. The common wheat Vrn-B3 gene mapped on chromosome 7B is homologous to the Arabidopsis FT1 gene. aa FT-like genes belong to the PEBP gene family and control flowering time in dicot and monocot plants.aa
This protein is transported to the apical meristem for initiation of floral meristem development. Recently, it was demonstrated that the wheat TaFT1 functions as a flowering inductor not alone, but within a complex. Thus, TaFT1 combines with 14-3-3 proteins in cytoplasm and moves to the nucleus, where it interacts with TaFDL2 (Triticum aestivum FLOWERING LOCUS D-LIKE 2) to produce the “florigen activation complex” (FAC). This complex can bind to the promoters of several genes such as VRN-1 to regulate their expression.
This protein is transported to the apical meristem for initiation of floral meristem development. Recently, it was demonstrated that the wheat TaFT1 functions as a flowering inductor not alone, but within a complex. Thus, TaFT1 combines with 14-3-3 proteins in cytoplasm and moves to the nucleus, where it interacts with TaFDL2 (Triticum aestivum FLOWERING LOCUS D-LIKE 2) to produce the “florigen activation complex” (FAC). This complex can bind to the promoters of several genes such as VRN-1 to regulate their expression.
Yan, L., Fu, D., Li, C., Blechl, A., Tranquilli, G., Bonafede, M. A. R. C. O. S., ... & Dubcovsky, J. (2006). The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proceedings of the National Academy of Sciences, 103(51), 19581-19586.
Turck, F., Fornara, F., & Coupland, G. (2008). Regulation and identity of florigen: FLOWERING LOCUS T moves center stage. Annual review of plant biology, 59, 573-594.
Li, C., Lin, H., & Dubcovsky, J. (2015). Factorial combinations of protein interactions generate a multiplicity of florigen activation complexes in wheat and barley. The Plant Journal, 84(1), 70-82.
VRN-B3
VRN-D3
after NcoI: 375+27
after NcoI: 401
after NcoI: 401
SNP in coding region
VRN-B3 promoter
Vrn-B3c
1401
Vrn-P14-F: GCTTTGAACTCCAAGGAGAA
Vrn-P14-R: ATAATCAGCAGGTGAACCAG
Vrn-P14-R: ATAATCAGCAGGTGAACCAG
Ppd-D1_F: ACGCCTCCCACTACACTG
Ppd-D1_R1: GTTGGTTCAAACAGAGAGC
Ppd-D1_R1: GTTGGTTCAAACAGAGAGC
Intrada Allele Cimarron Allele
Gene
Product size (bp)
Gene region
Primers: Sequence
Allelic variant
Yan, L., Fu, D., Li, C., Blechl, A., Tranquilli, G., Bonafede, M. A. R. C. O. S., ... & Dubcovsky, J. (2006). The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proceedings of the National Academy of Sciences, 103(51), 19581-19586.
Yan, L., Fu, D., Li, C., Blechl, A., Tranquilli, G., Bonafede, M. A. R. C. O. S., ... & Dubcovsky, J. (2006). The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proceedings of the National Academy of Sciences, 103(51), 19581-19586.
Chen, F., Gao, M., Zhang, J., Zuo, A., Shang, X., & Cui, D. (2013). Molecular characterization of vernalization and response genes in bread wheat from the Yellow and Huai Valley of China. BMC Plant Biology, 13(1), 1-12.
Wang, S., Carver, B., & Yan, L. (2009). Genetic loci in the photoperiod pathway interactively modulate reproductive development of winter wheat. Theoretical and Applied Genetics, 118(7), 1339-1349.
VRN-B3 promoter
vrn-B3
Vrn-B3e
Vrn-B3d
Vrn-B3e
Vrn-B3d
1384
1544
3001
1544
3001
FTpr-F: CGAAAGCGGAGGGTATATTAAA
FTpr-R: CCCGAACATAGAAGAAGCATAG
FTpr-R: CCCGAACATAGAAGAAGCATAG
Berezhnaya, A., Kiseleva, A., Leonova, I., & Salina, E. (2021). Allelic variation analysis at the vernalization response and photoperiod genes in Russian wheat varieties identified two novel alleles of Vrn-B3. Biomolecules, 11(12), 1897.
VRN-B3 promoter
Vrn-B3a
1200
FT-B-INS-F: CATAATGCCAAGCCGGTGAGTAC
FT-B-INS-R: ATGTCTGCCAATTAGCTAGC
FT-B-INS-R: ATGTCTGCCAATTAGCTAGC
VRN-B3 promoter
Vrn-B3d-F: GTTACACCACATCCACAGAAC
Vrn-B3d-R: CCAATACTACCGGCCACTAA
Vrn-B3d-R: CCAATACTACCGGCCACTAA
Berezhnaya, A., Kiseleva, A., Leonova, I., & Salina, E. (2021). Allelic variation analysis at the vernalization response and photoperiod genes in Russian wheat varieties identified two novel alleles of Vrn-B3. Biomolecules, 11(12), 1897.
Berezhnaya, A., Kiseleva, A., Leonova, I., & Salina, E. (2021). Allelic variation analysis at the vernalization response and photoperiod genes in Russian wheat varieties identified two novel alleles of Vrn-B3. Biomolecules, 11(12), 1897.
SNP in coding region
FAM Allele G HEX Allele C
FT-B1 assay: GCCAACCACCAGCGGGTC
GCCAACCACCAGCGGGTG
GGGCTAATGGCCGGTAGGGATA
GCCAACCACCAGCGGGTG
GGGCTAATGGCCGGTAGGGATA
VRN-B3 promoter
Vrn-B3e
Vrn-B3e-F: CGCCAGACAGCATTCCTATTA
Vrn-B3e-R: TACTGGTGTCTCTTGCCATTC
Vrn-B3e-R: TACTGGTGTCTCTTGCCATTC
Vrn-B3d
Brassac, J., Muqaddasi, Q. H., Plieske, J., Ganal, M. W., & Röder, M. S. (2021). Linkage mapping identifies a non-synonymous mutation in FLOWERING LOCUS T (FT-B1) increasing spikelet number per spike. Scientific reports, 11(1), 1-12.
VRN-B3 promoter
vrn-B3
Vrn-B3b
Vrn-B3b
1140 or 691 1581 (with F2)
FT-B-NOINS-F: ATGCTTTCGCTTGCCATCC
FT-B-NOINS-F2: GCTGTGTGATCTTGCTCTCC
FT-B-NOINS-R: CTATCCCTACCGGCCATTAG
FT-B-NOINS-F2: GCTGTGTGATCTTGCTCTCC
FT-B-NOINS-R: CTATCCCTACCGGCCATTAG
SNP in coding region
Ppd-D1_F: ACGCCTCCCACTACACTG
Ppd-D1_R1: GTTGGTTCAAACAGAGAGC
Ppd-D1_R2: CACTGGTGGTAGCTGAGATT
Ppd-D1_R1: GTTGGTTCAAACAGAGAGC
Ppd-D1_R2: CACTGGTGGTAGCTGAGATT
302
243
Liu, H., Zhang, X., Xu, Y., Ma, F., Zhang, J., Cao, Y., ... & An, D. (2020). Identification and validation of quantitative trait loci for kernel traits in common wheat (Triticum aestivum L.). BMC plant biology, 20(1), 1-15.
TaELF3 (EARLY FLOWERING 3)
ELF3 was found in T. monococcum as a candidate gene for the Eps-Am1 locus. It was demonstrated that, although the identified gene manifested no differences in the expression level, changes in four amino acids were detected, and the wheat lines with such mutations were characterized by changed expression patterns of the PIF-like, Ppd-1, and FT1 genes. aaa ELF3 was also identified in T. aestivum according to the homology with barley and rice sequences. aaa The genes were mapped on homeologous chromosomes of the first group. The plants with dominant TaELF3-1DLa allele moved to flowering later than the plants with null-allele of this gene.aaa It was demonstrated that TaELF3 negatively affects the TaGI expression, which corresponds to the function of the homologous Arabidopsis gene.
Alvarez, M.A., Tranquilli, G., Lewis, S., et al., Genetic and physical mapping of the earliness per se locus Eps-Am1 in Triticum monococcum identifies EARLY FLOWERING 3 (ELF3) as a candidate gene, Funct. Integr. Genomics, 2016, vol. 16, pp. 365–382.
Zikhali, M., Leverington-Waite, M., Fish, L., et al., Validation of a 1DL earliness per se (eps) flowering QTL in bread wheat (Triticum aestivum), Mol. Breed., 2014, vol. 34, pp. 1023–1033.
Wang, J., Wen, W., Hanif, M., et al., TaELF3-1DL, a homolog of ELF3, is associated with heading date in bread wheat, Mol. Breed., 2016, vol. 36, p. 161.
COP1 and ELF3 control circadian function and photoperiodic flowering by regulating GI stability, Mol. Cell, 2008, vol. 32, pp. 617–630.
TaELF3-B1
TaELF3-D1
SNP in exon 4
SNP in exon 4
TaELF3-B1a
TaELF3-B1b
TaELF3-B1b
TaELF3-B1_Kasp_F: gaaggtgaccaagttcatgctCCCTTGCAGCTCGCT
TaELF3-B1 Kasp_V: gaaggtcggagtcaacggattCCCTTGCAGCTCGCC
TaELF3-B1 Kasp2_generic: CGACCCAACACTCACG
TaELF3-B1 Kasp_V: gaaggtcggagtcaacggattCCCTTGCAGCTCGCC
TaELF3-B1 Kasp2_generic: CGACCCAACACTCACG
TaELF3-D1_ Kasp1_F: gaaggtgaccaagttcatgctTGGAGACATGACGGGAACA
TaELF3-D1_Kasp1_V: gaaggtcggagtcaacggattTGGAGACATGACGGGAACG
TaELF3-D1_Kasp1_generic: GGAAACCAGGCTTCACG
TaELF3-D1_Kasp1_V: gaaggtcggagtcaacggattTGGAGACATGACGGGAACG
TaELF3-D1_Kasp1_generic: GGAAACCAGGCTTCACG
TaELF3-D1a TaELF3-D1b
Gene
Product size (bp)
Gene region
Primers: Sequence
Allelic variant
Zikhali, M., Wingen, L. U., & Griffiths, S. (2016). Delimitation of the Earliness per se D1 (Eps-D1) flowering gene to a subtelomeric chromosomal deletion in bread wheat (Triticum aestivum). Journal of experimental botany, 67(1), 287-299.
Zikhali, M., Wingen, L. U., & Griffiths, S. (2016). Delimitation of the Earliness per se D1 (Eps-D1) flowering gene to a subtelomeric chromosomal deletion in bread wheat (Triticum aestivum). Journal of experimental botany, 67(1), 287-299.
WAPO1 (WHEAT ORTHOLOG OF APO1)
WAPO1 is an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1 (APO1). Plants with additional WAPO1 copies show delayed heading time.
Kuzay, S., Lin, H., Li, C., Chen, S., Woods, D. P., Zhang, J., ... & Dubcovsky, J. (2022). WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat. PLoS genetics, 18(1), e1009747.
WAPO1-A1
WAPO1 Promoter
WAPO1
C47F
C47F
WAPO-A1a
WAPO-A1b/c/d
WAPO-A1b/c/d
WAPO1_pro_Fwd: ACGGTTCCTCTTCCTGCTCAT
WAPO1_pro_Rvs: CGGAGGCGAGGACGAGT
WAPO1_pro_Rvs: CGGAGGCGAGGACGAGT
WAPO1_C47F_Fwd: agctcactcactctcActccA
WAPO1_C47F_Rvs: GAAGGTCGGAGTCAACGGATT gaggaaggacggcgtcgggatg
WAPO1_C47F_Rvs: GAAGGTCGGAGTCAACGGATT gaggaaggacggcgtcgggatg
Gene
Product size (bp)
Gene region
Primers: Sequence
Allelic variant
Kuzay, S., Xu, Y., Zhang, J., Katz, A., Pearce, S., Su, Z., ... & Dubcovsky, J. (2019). Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping. Theoretical and Applied Genetics, 132(9), 2689-2705.
Kuzay, S., Xu, Y., Zhang, J., Katz, A., Pearce, S., Su, Z., ... & Dubcovsky, J. (2019). Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping. Theoretical and Applied Genetics, 132(9), 2689-2705.
WAPO-A1b
WAPO-A1a/c/d
WAPO-A1a/c/d
100
200
200
after HypCH4V: 200
after HypCH4V: 180
after HypCH4V: 180
TaZIM-1 (ZINC-FINGER PROTEIN EXPRESSED IN INFLORESCENCE MERISTEM)
TaZIM-1 is a GATA-like transcription factor. This gene is a negative regulator of flowering in wheat. TaZIM-A1 expression has circadian pattern. TaZIM-A1 directly bound to the promoters of TaCO-1 and TaFT-1 and downregulated their expression.
Liu, H., Li, T., Wang, Y., Zheng, J., Li, H., Hao, C., & Zhang, X. (2019). TaZIM‐A1 negatively regulates flowering time in common wheat (Triticum aestivum L.). Journal of integrative plant biology, 61(3), 359-376.
TaZIM-A1 coding region
First PCR (product is used as template)
TaZIM-A1-del79
TaZIM-A1-nodel79
TaZIM-A1-nodel79
TaZIM-A1-X1-F1: ATGGCACAGCACGACGGCAAGCCATAC
TaZIM-A1-X1-R1: CACTAGTATTACAACTGAGTGAACT
TaZIM-A1-X1-R1: CACTAGTATTACAACTGAGTGAACT
Gene
Product size (bp)
Gene region
Primers: Sequence
Allelic variant
Liu, H., Li, T., Wang, Y., Zheng, J., Li, H., Hao, C., & Zhang, X. (2019). TaZIM‐A1 negatively regulates flowering time in common wheat (Triticum aestivum L.). Journal of integrative plant biology, 61(3), 359-376.
>1000 bp
lower
higher
higher
TaZIM1-A-Ind79-F1: AGCACGACGGCAAGCCATAC
TaZIM1-A-Ind79-R1: GTCAATCACGGCGTCCGCT
TaZIM-A1
Liu, H., Li, T., Wang, Y., Zheng, J., Li, H., Hao, C., & Zhang, X. (2019). TaZIM‐A1 negatively regulates flowering time in common wheat (Triticum aestivum L.). Journal of integrative plant biology, 61(3), 359-376.
First PCR (product is used as template)
TaZIM-A1-X3-F1: GGATGTATCTAACACTAAAATG
TaZIM-A1-X3-R2: GAAAGAACAAATAATCGCTTCA
TaZIM-A1-X3-R2: GAAAGAACAAATAATCGCTTCA
Liu, H., Li, T., Wang, Y., Zheng, J., Li, H., Hao, C., & Zhang, X. (2019). TaZIM‐A1 negatively regulates flowering time in common wheat (Triticum aestivum L.). Journal of integrative plant biology, 61(3), 359-376.
TaZIM-A1-del2258 TaZIM-A1-nodel2258
<3000 bp
lower
higher
higher
TaZIM-A1-2270-F1: AAAGTATCGTGATTCTATGATATGA TaZIM-A1-2270-R2: AAATCAAAGAATGTTAGTATCAGAA
Liu, H., Li, T., Wang, Y., Zheng, J., Li, H., Hao, C., & Zhang, X. (2019). TaZIM‐A1 negatively regulates flowering time in common wheat (Triticum aestivum L.). Journal of integrative plant biology, 61(3), 359-376.
TaZIM-B1 coding region
First PCR (product is used as template)
TaZIM-A1-X1-F1: ATGGCACAGCACGACGGCAAGCCATAC
TaZIM-A1-X1-R1: CACTAGTATTACAACTGAGTGAACT
TaZIM-A1-X1-R1: CACTAGTATTACAACTGAGTGAACT
Liu, H., Li, T., Wang, Y., Zheng, J., Li, H., Hao, C., & Zhang, X. (2019). TaZIM‐A1 negatively regulates flowering time in common wheat (Triticum aestivum L.). Journal of integrative plant biology, 61(3), 359-376.
TaZIM-B1-hapI TaZIM-B1-hapII
>1000 bp
NheI: no restriction
NheI: restricted
NheI: restricted
TaZIM1-A-Ind79-F1: AGCACGACGGCAAGCCATAC
TaZIM1-A-Ind79-R1: GTCAATCACGGCGTCCGCT
TaZIM-B1
Liu, H., Li, T., Wang, Y., Zheng, J., Li, H., Hao, C., & Zhang, X. (2019). TaZIM‐A1 negatively regulates flowering time in common wheat (Triticum aestivum L.). Journal of integrative plant biology, 61(3), 359-376.
WPCL1 (PHYTOCLOCK 1 )
WPCL1 is an ortholog of the LUX ARRHYTHMO (LUX)/PHYTOCLOCK 1 (PCL1) gene found of Arabidopsis, which regulates the circadian clock and flowering time.
Loss-of-function mutation in WPCL1 may accelerate and adjust flowering time due to the combination of vernalization gene activities in common wheat.
Loss-of-function mutation in WPCL1 may accelerate and adjust flowering time due to the combination of vernalization gene activities in common wheat.
Mizuno, N., Nitta, M., Sato, K., & Nasuda, S. (2012). A wheat homologue of PHYTOCLOCK 1 is a candidate gene conferring the early heading phenotype to einkorn wheat. Genes & genetic systems, 87(6), 357-367.
Mizuno, N., Kinoshita, M., Kinoshita, S., Nishida, H., Fujita, M., Kato, K., ... & Nasuda, S. (2016). Loss-of-function mutations in three homoeologous PHYTOCLOCK 1 genes in common wheat are associated with the extra-early flowering phenotype. PLoS One, 11(10), e0165618
WPCL-A1 coding region
WPCL-A1
wpcl-A1
wpcl-A1
WPCL-B1
wpcl-B1 (deletion 142 bp)
wpcl-B1 (deletion 142 bp)
WPCL-A1-F: CCACGCCAACGGCGGC
WPCL-A1-R: TGAATCCGGGATGGATGGTTATC
WPCL-A1-R: TGAATCCGGGATGGATGGTTATC
Gene
Product size (bp)
Gene region
Primers: Sequence
Allelic variant
Mizuno, N., Kinoshita, M., Kinoshita, S., Nishida, H., Fujita, M., Kato, K., ... & Nasuda, S. (2016). Loss-of-function mutations in three homoeologous PHYTOCLOCK 1 genes in common wheat are associated with the extra-early flowering phenotype. PLoS One, 11(10), e0165618.
after RsaI: ? after RsaI: ?
?
?
?
WPCL-B1-F1: TCGGATTGGTGTTGCGAGG
WPCL-B1-R1: CATGATGGTCTTGGGCACC
WPCL-B1-F2: ACGTAGTACTCCCTTGGTCC
WPCL-B1-R2: CAACCGAACCTATGAACACCA
WPCL-B1-R1: CATGATGGTCTTGGGCACC
WPCL-B1-F2: ACGTAGTACTCCCTTGGTCC
WPCL-B1-R2: CAACCGAACCTATGAACACCA
WPCL-A1
WPCL-A1 coding region
WPCL-D1
wpcl-D1
wpcl-D1
TWPCL-D1-F: CGGCGGCTGGGGATGAC
WPCL-D1-R: TTGATGACTGAACTGGACCGATCT
WPCL-D1-R: TTGATGACTGAACTGGACCGATCT
after BspT107I: ? after BspT107I: ?
WPCL-D1
WPCL-B1 promoter and intron 1
WPCL-B1
Mizuno, N., Kinoshita, M., Kinoshita, S., Nishida, H., Fujita, M., Kato, K., ... & Nasuda, S. (2016). Loss-of-function mutations in three homoeologous PHYTOCLOCK 1 genes in common wheat are associated with the extra-early flowering phenotype. PLoS One, 11(10), e0165618.
Mizuno, N., Kinoshita, M., Kinoshita, S., Nishida, H., Fujita, M., Kato, K., ... & Nasuda, S. (2016). Loss-of-function mutations in three homoeologous PHYTOCLOCK 1 genes in common wheat are associated with the extra-early flowering phenotype. PLoS One, 11(10), e0165618.
This work was funded by RFBR, project number 20-016-00059
ResearchGate
Contacts:
Antonina Kiseleva, PhD
Antonina Kiseleva, PhD
Google Scholar
Institute of Cytology and Genetics
Siberian Branch of Russian Academy of Sciences
Laboratory of Plant Molecular Genetics and Cytogenetics (Prof. Elena Salina)
Siberian Branch of Russian Academy of Sciences
Laboratory of Plant Molecular Genetics and Cytogenetics (Prof. Elena Salina)
