A joint team from Peking University Institute of Advanced Agricultural Sciences / State Key Laboratory of Wheat Improvement / Shandong Laboratory of Advanced Agricultural Sciences today published the study “Spatiotemporal transcriptomics reveals key gene regulation for grain yield and quality in wheat” in Genome Biology. Using state-of-the-art spatial transcriptomics, the authors dissected gene expression together with positional information to define functionally distinct cell populations and produced the first three-dimensional gene-expression atlas of the developing wheat grain.

 

Bread wheat (Triticum aestivum L.) is grown on ~230 million hectares and feeds more than one-third of humanity. A mature grain comprises three genetically distinct tissues—the diploid embryo, the triploid endosperm and the maternal pericarp/testa—that display pronounced spatiotemporal gene-expression patterns and form specialized developmental niches. Yet conventional bulk RNA-seq cannot resolve these patterns, hampering discovery of the molecular circuits that ultimately determine grain yield and quality.

 

Here, spatially resolved transcriptomes were generated for whole grains at 4, 8 and 12 days after pollination (DAP). The dataset visualizes the expression of nearly 80,000 genes across space and time, identifies ten well-characterized cell sub-populations and uncovers 190 grain-specific marker genes (Fig. 1). Dynamic expression trajectories of tissue-specific genes—particularly transcription factors (TFs)—were reconstructed. Integrative co-expression and cis-regulatory analyses revealed TaABI3-B1, a B3-domain TF specifically expressed in the embryo and surrounding endosperm tissues, as a negative regulator of embryo and grain size. Allelic variants and transgenic lines confirmed that reduced TaABI3-B1 expression increases grain dimensions, providing a new breeding target for higher yield.

 

Fig. 1. Overview of the wheat-grain spatial-transcriptomics workflow.

 

This study delivers an unprecedented spatiotemporal resource for wheat-grain biology and highlights a novel mechanism controlling grain size, laying a theoretical foundation for molecular-design breeding and yield improvement in wheat.

Dr. Yuan Chen and Dr. Xue Han (State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences) are co-corresponding authors. Dr. Xiaohui Li, a joint PhD student between Peking University Institute of Advanced Agricultural Sciences and Northwest Agriculture and Forestry University, is the first author. Other contributors include joint PhD student Yiman Wan; Prof. Xingguo Li and Prof. Jiajie Wu (Shandong Agricultural University); Dr. Jun Xiao and Dr. Dongzhi Wang (Institute of Genetics and Developmental Biology, Chinese Academy of Sciences); and Prof. Kunming Chen (Northwest Agriculture and Forestry University). The work was supported by the Shandong Provincial Key R&D Program, the Taishan Scholars Program and the Shandong Provincial Natural Science Foundation.