WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat

PLoS Genet. 2022 Jan 13;18(1):e1009747. doi: 10.1371/journal.pgen.1009747. eCollection 2022 Jan.


Improving our understanding of the genes regulating grain yield can contribute to the development of more productive wheat varieties. Previously, a highly significant QTL affecting spikelet number per spike (SNS), grain number per spike (GNS) and grain yield was detected on chromosome arm 7AL in multiple genome-wide association studies. Using a high-resolution genetic map, we established that the A-genome homeolog of WHEAT ORTHOLOG OF APO1 (WAPO-A1) was a leading candidate gene for this QTL. Using mutants and transgenic plants, we demonstrate in this study that WAPO-A1 is the causal gene underpinning this QTL. Loss-of-function mutants wapo-A1 and wapo-B1 showed reduced SNS in tetraploid wheat, and the effect was exacerbated in wapo1 combining both mutations. By contrast, spikes of transgenic wheat plants carrying extra copies of WAPO-A1 driven by its native promoter had higher SNS, a more compact spike apical region and a smaller terminal spikelet than the wild type. Taken together, these results indicate that WAPO1 affects SNS by regulating the timing of terminal spikelet formation. Both transgenic and wapo1 mutant plants showed a wide range of floral abnormalities, indicating additional roles of WAPO1 on wheat floral development. Previously, we found three widespread haplotypes in the QTL region (H1, H2 and H3), each associated with particular WAPO-A1 alleles. Results from this and our previous study show that the WAPO-A1 allele in the H1 haplotype (115-bp deletion in the promoter) is expressed at significantly lower levels in the developing spikes than the alleles in the H2 and H3 haplotypes, resulting in reduced SNS. Field experiments also showed that the H2 haplotype is associated with the strongest effects in increasing SNS and GNS (H2>H3>H1). The H2 haplotype is already present in most modern common wheat varieties but is rare in durum wheat, where it might be particularly useful to improve grain yield.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping / methods*
  • Flowers / genetics
  • Flowers / growth & development
  • Genetic Linkage
  • Haplotypes
  • Loss of Function Mutation
  • Plant Proteins / genetics*
  • Quantitative Trait Loci*
  • Sequence Deletion
  • Triticum / genetics
  • Triticum / growth & development*


  • Plant Proteins

Grants and funding

JD received support for this project from the Agriculture and Food Research Initiative Competitive Grants 2017-67007-25939 (WheatCAP), USDA National Institute of Food and Agriculture (NIFA, https://nifa.usda.gov/) and from the Howard Hughes Medical Institute (https://www.hhmi.org/). The USDA-NIFA grant supported the salaries of SK, JZ and SC. The Howard Hughes Medical Institute supported the salaries of JD, HL, CL and DW. DW is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation (http://www.lsrf.org/) that paid his salary for three years. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.