Zhongyin Deng, Qihang Chen, Shuoxun Wang, Yuqing Che, Shaoshuai Liu , Xiuzhi Wei, Wei Liu, Wanxin Xu, Dada Cui, Guoliang Chen, Xinyu Zou1, Ziying Wang, Tianhua Chen, Tingting Li, Zixu Zhao, Ziyi Yan, Danmei Liu, Xigang Liu, Dengcai Liu, Shuaifeng Geng, Xiangdong Fu, Aili Li, Long Mao

Plant Communications; 2026; IF: 13.7

DOI: 10.1016/j.xplc.2026.101968

Abstract

Elevating intrinsic yield capacity by augmenting spikelet number per spike (SPS) represents a pivotal strategy for sustainable wheat production beyond the Green Revolution. Through a genome-wide association study of 188 accessions across two environments using 3.8 million SNPs, we identified a prominent linkage disequilibrium block on chromosome 4B underpinning SPS. We prioritized TaKNOX1 (TaKNOX-B1), a class I KNOX homeodomain transcription factor, as the causal gene. The underlying polymorphism is a G/A SNP causing an L84F substitution within the KNOX2 domain; structural modeling predicts this alters protein conformation. The elite allele TaKNOX-B1-Hap2 (Phe84) exhibits significant positive selection during modern breeding, co-segregating with enhanced SPS and grain number per spike. CRISPR-Cas9 editing and EMS mutagenesis confirmed TaKNOX1 positively regulates spikelet meristem development in a dose-dependent manner, with transcriptome analysis linking it to gibberellin signaling and meristem identity. Mechanistically, we uncovered a tripartite feedback module where Rht-B1b physically interacts with and represses TaKNOX1, whereas the L84F variant evades this inhibition. Conversely, TaKNOX1 directly activates TaAPO1, a conserved inflorescence regulator. Importantly, TaAPO1 competitively binds Rht-B1b, thereby releasing TaKNOX1 from repression and forming a self-reinforcing positive feedback loop (TaKNOX1→TaAPO1→Rht-B1b→TaKNOX1). Pyramiding the elite TaKNOX-B1-Hap2 and TaAPO-B1-Hap2 alleles synergistically improves yield-related traits. Our findings delineate a master regulatory circuit controlling spike architecture and provide precise targets for marker-assisted selection and genome editing to sustainably increase wheat yield potential.