Temporal-spatial transcriptomics reveals key gene regulation for grain yield and quality in wheat

Cereal grain size and quality are important agronomic traits in crop production. The development of wheat grains is underpinned by complex regulatory networks. The precise spatial and temporal coordination of diverse cell types is essential for the formation of functional compartments. To provide comprehensive spatiotemporal information about biological processes in developing wheat grain, we performed a spatial transcriptomics study during the early grain development stage from 4 to 12 days after pollination. We defined a set of tissue-specific marker genes and discovered that certain genes or gene families exhibit specific spatial expression patterns over time. Weighted gene co-expression network and motif enrichment analyses identified specific groups of genes potentially regulating wheat grain development. The embryo and surrounding endosperm specifically expressed transcription factor TaABI3-3B negatively regulates embryo and grain size. In Chinese breeding programs, a haplotype associated with higher grain weight was identified, linked to altered expression levels of TaABI3-3B. Data and knowledge obtained from the proposed study will provide pivotal insights into yield improvement and serve as important genetic information for future wheat breeding.