NF-YB1-YC12-bHLH144 complex directly activates Wx to regulate grain quality in rice (Oryza sativa L.)

Plant Biotechnol J. 2019 Jul;17(7):1222-1235. doi: 10.1111/pbi.13048. Epub 2019 Jan 4.


Identification of seed development regulatory genes is the key for the genetic improvement in rice grain quality. NF-Ys are the important transcription factors, but their roles in rice grain quality control and the underlying molecular mechanism remain largely unknown. Here, we report the functional characterization a rice NF-Y heterotrimer complex NF-YB1-YC12-bHLH144, which is formed by the binding of NF-YB1 to NF-YC12 and then bHLH144 in a sequential order. Knock-out of each of the complex genes resulted in alteration of grain qualities in all the mutants as well as reduced grain size in crnf-yb1 and crnf-yc12. RNA-seq analysis identified 1496 genes that were commonly regulated by NF-YB1 and NF-YC12, including the key granule-bound starch synthase gene Wx. NF-YC12 and bHLH144 maintain NF-YB1 stability from the degradation mediated by ubiquitin/26S proteasome, while NF-YB1 directly binds to the 'G-box' domain of Wx promoter and activates Wx transcription, hence to regulate rice grain quality. Finally, we revealed a novel grain quality regulatory pathway controlled by NF-YB1-YC12-bHLH144 complex, which has great potential for rice genetic improvement.

Keywords: G-box; Wx gene; grain quality; heterotrimer complex; nuclear factor Y; rice (Oryza sativa L.).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Basic Helix-Loop-Helix Transcription Factors / metabolism
  • Edible Grain
  • Gene Expression Regulation, Plant*
  • Oryza / enzymology*
  • Oryza / genetics
  • Plant Proteins / genetics
  • Plant Proteins / metabolism*
  • Seeds
  • Starch Synthase / genetics
  • Starch Synthase / metabolism*


  • Basic Helix-Loop-Helix Transcription Factors
  • Plant Proteins
  • Starch Synthase