Triticeae Genomics and Genetics, 2025, Vol.16, No.3, 138-147 http://cropscipublisher.com/index.php/tgg 138 Feature Review Open Access Spatiotemporal Transcriptome Atlas of Wheat Grain Filling Stage Xingzhu Feng Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding email: xingzhu.feng@hibio.org Triticeae Genomics and Genetics, 2025, Vol.16, No.3 doi: 10.5376/tgg.2025.16.0020 Received: 30 Apr., 2025 Accepted: 11 Jun., 2025 Published: 29 Jun., 2025 Copyright © 2025 Feng, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Feng X.Z., 2025, Spatiotemporal transcriptome atlas of wheat grain filling stage, Triticeae Genomics and Genetics, 16(3): 138-147 (doi: 10.5376/tgg.2025.16.0020) Abstract The grain-filling period is a crucial stage that determines the yield and quality formation of wheat grains, involving a complex spatio-temporal regulation process. To gain a deeper understanding of the dynamic changes in gene expression and their molecular mechanisms during grain development, this study, based on multiple time points and multiple tissues, constructed a spatio-temporal transcriptome map of wheat grains covering the entire grain-filling period. Three key periods - early, middle, and late grain-filling - were selected, and the main tissues such as endosperm, embryo, and aleurone layer were collected respectively. High-quality transcriptome data were obtained by using high-throughput RNA sequencing technology. Through differential expression analysis, time series clustering, tissue-specific expression analysis and functional annotation, a large number of key genes and transcription factors related to carbon and nitrogen metabolism, starch synthesis, hormone regulation, stress resistance response, etc. were identified. This study also constructed multiple regulatory networks closely related to grain development and revealed the potential roles of non-coding Rnas and epigenetic factors in regulation, providing resource support for the analysis of the complex regulatory networks of grain development. This research will lay a solid foundation for the improvement of wheat quality, molecular breeding and the functional study of key regulatory genes during the grain-filling period. Keywords Wheat; Grouting period; Transcriptome; Spatio-temporal map; Grain development 1 Introduction Wheat (Triticum aestivum L.) feeds nearly one-third of the world’s population, not only because it is grown in large quantities - with a global planting area of approximately 230 million hectares, but more importantly, it provides a crucial source of heat and nutrients. But when it comes to output and quality, it depends on the grouting period. During this period, whether the grains are ultimately large or small, whether they can be ground well and roasted fragrant all depend on this stage (Zhang et al., 2023). The structures such as the embryo, endosperm and seed coat are not independent of each other. Instead, they jointly regulate the accumulation process of nutrients through the coordinated expression of genes and also influence the formation of various functional areas within the grain (Li et al., 2025). Of course, to understand these processes clearly is not about thinking. In recent years, technological advancements in transcriptomics, proteomics, metabolomics and other fields have indeed deepened our understanding of the molecular networks of wheat grain development, especially in grain filling (Rangan et al., 2017). After applying high-throughput RNA sequencing and spatial transcriptomics technologies, researchers can identify thousands of differentially expressed genes at one time and also clearly understand the respective roles played by different cell types in regulation. But then again, most of the early studies focused on the "whole", such as the entire grain or a certain organ. Although this approach has reference value, it obviously lacks "partitioning operations", especially being far from sufficient at the cell type and spatial levels (Zhang et al., 2021; 2023). This makes it very difficult for us to truly figure out exactly which cells, at what point in time and through what mechanism are promoting grain development and quality formation. This study integrated high-resolution gene expression data from multiple cell types and developmental time points, constructed a spatiotemporal transcriptome map of wheat grains during the grain-filling period, classified wheat grains into different cell types, identified marker genes, and mapped the regulatory network driving grain development and quality formation. By providing a detailed molecular map, this map fills the key knowledge gap
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