A Wild Emmer Wheat B3 Transcription Factor Regulates Seed Growth and Nutrient Allocation

Seed weight (SW) and nutrient allocation are key determinants of yield and grain quality in wheat, yet the regulatory basis of naturally occurring variation in these traits remains poorly resolved. Wild emmer wheat (Triticum dicoccoides), the progenitor of modern wheat, retains extensive eco-geographically structured genetic diversity that was largely eroded during domestication. Here, we identify a B3-domain transcription factor (B3TF) as a key regulator of seed growth and metabolic partitioning in wheat. Genome-wide association analysis of ~460 wild emmer accessions reveals a major locus on chromosome 2BL associated with SW, seed area and nitrogen (N) content, displaying pronounced climatic differentiation across environmental gradients. Introgression of the 2BL wild segment into the hexaploid wheat cultivars Chinese Spring and Bethlehem increases SW in cultivated backgrounds. Independent loss-of-function alleles generated by EMS mutagenesis in the tetraploid wheat cultivar Kronos produce larger seeds. Further, RNA-seq of EMS mutants revealed metabolic reprogramming with upregulated fatty acid, nitrogen and phenylpropanoid pathways and downregulated carbohydrate metabolism and sugar transport. Metabolomic, lipidomic and ICP-MS data showed increased essential amino acids, sugars, lipids, N content and minerals (Zn, Fe, Mo). Furthermore, CRISPR/Cas9-mediated editing in the hexaploid wheat cultivar Fielder produced similar increases in SW and N content as observed in the EMS mutants, establishing this gene as a negative regulator of seed growth across ploidy levels. In addition, natural haplotypes show reciprocal climatic distributions, linking regulatory variation to environmental adaptation. Our findings uncover a TF underlying natural seed trait variation in wild wheat, providing a framework for exploiting regulatory alleles to enhance yield and nutritional quality in modern wheat.