Novel HD-Zip transcription factor PCD8 integrates developmental gene networks to shape rice panicle morphogenesis

BACKGROUND: Panicle architecture is a key agronomic trait determining rice yield. Identifying and characterizing the regulatory genes controlling panicle morphogenesis is essential for breeding improved rice varieties. RESULTS: To clarify the regulatory pathways underlying panicle architecture and identify novel candidate genes, we performed RNA sequencing (RNA-seq) of 1 cm and 15 cm young panicles from Zhonghua 11 (ZH11). Numerous differentially expressed genes were identified, primarily enriched in metabolic and cellular processes. Among the differentially expressed transcription factors, we identified a previously uncharacterized Homeodomain-Leucine Zipper (HD-Zip) family gene, PaniCle Development 8 (PCD8; LOC_Os08g37580), which was highly expressed in young panicles. CRISPR/Cas9-mediated knockout of PCD8 (PCD8-KO) significantly reduced grain number per panicle, seed setting rate, and grain width while increasing grain length, grain length-to-width ratio, and chalkiness, indicating that PCD8 regulates panicle morphogenesis. Analysis of the 3,000 Rice Genomes (3 K-RG) population identified four major PCD8 haplotypes. Haplotype4 (Hap4), a temperate japonica-specific haplotype associated with long grains, carries a G/A substitution at - 2464 bp in the promoter. Haplotype3 (Hap3) and Hap4 likely evolved from Haplotype1 (Hap1), and all four haplotypes are closely related. PCD8 showed lower nucleotide diversity in temperate japonica and indica than in wild rice. Neutrality tests indicated balancing selection in wild rice and positive selection in indica, whereas reduced diversity in temperate japonica mainly reflects domestication bottlenecks rather than strong locus-specific selection. DNA affinity purification sequencing (DAP‑seq) identified candidate downstream targets of PCD8, and electrophoretic mobility shift assays (EMSA) confirmed direct binding to selected targets. CONCLUSIONS: Multi-omics analyses demonstrate that PCD8 is a novel transcription factor regulating panicle morphogenesis through downstream gene networks, providing a promising candidate for high-yield rice breeding.