Spikelet number per spike gene bZIPC1

Contributed by Priscilla Glenn and Jorge Dubcovsky

Grain yield per surface unit in wheat is a trait composed of several other traits, such as number of spikes per surface unit, spikelet number per spike (SNS), grains per spikelet and thousand kernel weight. Among these SNS has the higher heritability because it is determined early in the reproductive process, which limits environmental effects. However, increases in SNS or in grain number per spike are not translated into increases in total grain yield unless the plants have the resources to fill the extra grains. Optimum environments and cultivars with high-biomass (excess source and limited sink) are more likely to translate increases in SNS or grain number into increases in total grain yield  (1).

Another factor modulating wheat SNS is flowering time. Genotypes flowering earlier tend to have lower SNS than those flowering later (2). In turn, there are two factors regulating flowering time: vernalization and photoperiod requirements. Both processes converge on the FLOWERING LOCUS 1 gene (FT1), which encodes the florigen protein (3). FT-2 is the closest paralog to FT1 and has a significant effect on SNS with limited effects on heading time  (4,5).

Glenn et al. (6) used a yeast-two-hybrid system to find proteins that could interact with the FT-2 gene product. Among others, they found a bZIP-containing transcription factor from the grass-specific C-group (henceforth bZIPC).  The interaction between these two proteins in yeast was validated using bimolecular fluorescence complementation (BiFC) in wheat protoplasts. A phylogenetic analysis of proteins related to this transcription factor from several species revealed the existence of four groups, with the bZIPC interactor of FT2 belonging to group 1. Therefore, the gene was designated bZIPC1. Loss-of-function mutations of both bZIPC1 homoeologs (bzipc-A1 and bzipc-B1) in tetraploid wheat Kronos showed a highly significant reduction in SNS. Finally, they found natural variants of bZIPC-B1 associated with changes in SNS. Three frequent haplotypes were found in the bZIPC-B1 region (H1, H2, H3), with the H1 haplotype associated with higher SNS, grain number per spike and grain weight per spike. The derived haplotype H1 carries the favorable bZIPC-B1b allele (amino acids 151K and 166M), and haplotypes H2 and H3 share the ancestral bZIPC-B1a allele (amino acids 151N and 166V). 

There are significant epistatic interactions between the bZIPC-B1 alleles and the FT-A2 natural alleles (D10A), with the combination between the bZIPC-B1b allele (H1, 151K 166M) and the FT-A2 allele with the amino acid 10A showing the highest SNS. In the population analyzed in Glenn et al. (6), the effect of bZIPC-B1 on SNS was significant in the presence of the FT-A2 A10 allele but not in the presence of the D10, so it is important to combine the two positive alleles.  

Other SNS pages in MASWheat:

KASP markers for bZIPC-B1 (6)

Several modern cultivars have the H1 haplotype carrying the bZIPC-B1b allele, which has two missense SNPs at positions 616,654,272 (N151K) and 616,654,229 (V166M) of chromosome 5B that differentiate H1 from the other haplotypes, which carry the ancestral allele bZIPC-B1a. Glenn et al (6) developed two SNPs KASP markers that can be used to follow the transfer of the bZIPC-B1b allele in breeding programs:










Primer sequences:

Primers for bZIPC1-4229:

    bZIPC-B1b (FAM)           ctgTtggcgcaagtgggA

    bZIPC-B1a (VIC)             ctgTtggcgcaagtgggG

    common                         ccccattcccagtgatctcG

Primers for bZIPC1-4272

    bZIPC-B1b (FAM)            gcttttggacacatattaggCaaG

    bZIPC-B1a (VIC)              gcttttggacacatattaggCaaT  

    common                         gacaTcccacttgcgccaA 

PCR conditions

  • Denaturing step: 94 °C for 15 min
  • Touchdown (10 cycles)
    • 94 °C 20 s
    • -0.6 °C touchdown from 61 to 55 °C 1 min,
  • Amplification (30 cycles)
    • 94 °C 20s
    • 55 °C 1 min
Conditions presented here should be consider only as a starting point of the method optimization at individual laboratories.



  1. Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping. Kuzay S, Xu Y, Zhang J, Katz A, Pearce S, Su Z, Fraser M, Anderson JA, Brown-Guedira G, DeWitt N, Peters Haugrud A. In: Theorical and Applied Genetics, 2019, 132:2689-2705. DOI: 10.1007/s00122-019-03382-5
  2. Mutant alleles of Photoperiod-1 in Wheat (Triticum aestivum L.) that confer a late flowering phenotype in long days. Shaw LM, Turner AS, Herry L, Griffiths S, Laurie DA. In:  PLoS ONE, 2013, 8(11):e79459. DOI: 10.1371/journal.pone.0079459
  3. Regulation of flowering in temperate cereals. Distelfeld A, Li C, Dubcovsky J. In: Current opinion in plant biology, 2009, 12(2):178-184. DOI: 10.1016/j.pbi.2008.12.010
  4. Identification and characterization of a natural polymorphism in FT-A2 associated with increased number of grains per spike in wheat. Glenn P, Zhang J, Brown-Guedira G, DeWitt N, Cook JP, Li K, Akhunov E, Dubcovsky J. In: Theoretical and Applied Genetics, 2022, 135:679-692. DOI: 10.1007/s00122-021-03992-y
  5. FLOWERING LOCUS T2 regulates spike development and fertility in temperate cereals. Shaw LM, Lyu B, Turner R, Li C, Chen F, Han X, Fu D, Dubcovsky J. In: Journal of Experimental Botany, 2019, 70:193-204. DOI: 10.1093/jxb/ery350
  6. Wheat bZIPC1 interacts with FT2 and contributes to the regulation of spikelet number per spike. Glenn P, Woods DP, Zhang J, Gabay G, Odle N, Dubcovsky J. In: Theoretical and Applied Genetics, 2023, 136(11):237. DOI: 10.1007/s00122-023-04484-x