The impact of asymmetrical gene expression on the development of spike morphology in Triticum aestivum

Wheat yield is primarily determined by panicle density per unit area, grain count per spike, and grain weight. The proliferation of wheat spikes affects both the number of grains per spike and grain weight. However, the molecular regulatory mechanisms of wheat spike development are still largely elusive. In this study, we acquired high-quality sequencing data from 5989 cells derived from the double-ridge stage spike of a common wheat variety Jimai 22. The data revealed the presence of 10 distinct cell types, which were validated using RNA in situ hybridization and cell type-specific gene expression. The transition from promeristem to protoxylem and protophloem cells signifies the initiation of differentiation for protoxylem and primary protophloem cells within the promeristem. This process results in five distinct cellular differentiation states that correspond to the expression of 1410 genes. In wheat spikes, differential gene expression across eight developmental stages revealed seven unique expression patterns. Specifically, genes differentially expressed in stages C3, C4, C5, and C7 were identified as being uniquely active during the anther meristem, double ridge, floral meristem, and pistil primordium stages, respectively. Furthermore, the differential genes in stage C2 are likely to encompass critical genes that regulate the reproductive growth of wheat spikes, while those in stage C1 may significantly influence floret creation and development. Additionally, the transition of gene triplets between suppressed and balanced types represents a key element affecting spike differentiation. In this context, dominant gene triplets primarily fulfill functions associated with housekeeping genes. This study explores the impact of asymmetrical gene triplet expression during spike development on the regulation of wheat yield traits, utilizing the single-cell transcriptome atlas of the wheat spike. Our analysis of homologous gene asymmetrical expression throughout development, coupled with single-cell resolution, suggests this asymmetry could be a pivotal factor in cell differentiation.