Triticeae Genomics and Genetics, 2025, Vol.16, No.6, 262-268 http://cropscipublisher.com/index.php/tgg 262 Feature Review Open Access Co-expression Network Analysis Reveals Modules Linked to Spike Development in Wheat Zhengqi Ma, Wei Wang Institute of Life Sciences, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding email: wei.wang@jicat.org Triticeae Genomics and Genetics, 2025, Vol.16, No.6 doi: 10.5376/tgg.2025.16.0029 Received: 12 Oct., 2025 Accepted: 27 Nov., 2025 Published: 17 Dec., 2025 Copyright © 2025 Ma and Wang, 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: Ma Z.Q., and Wang W., 2025, Co-expression network analysis reveals modules linked to spike development in wheat, Triticeae Genomics and Genetics, 16(6): 262-268 (doi: 10.5376/tgg.2025.16.0029) Abstract Panicle development of wheat (Triticum aestivumL.) is a key process determining yield potential, which is jointly acted by a complex molecular regulatory network and a large number of developmental genes. In this study, weighted gene co-expression network analysis (WGCNA) was utilized to identify gene modules related to wheat ear development based on a multi-stage high-resolution RNA-seq data system. The results showed that multiple co-expression modules were significantly correlated with key agronomic traits such as panicle length, number of flowers, and branch formation. GO and KEGG enrichment analyses indicated that these modules were mainly involved in biological processes such as flower meristem maintenance, plant hormone signal transduction, and transcriptional regulation. In the study, key hub genes such as TaFUL2 and several important transcription factors belonging to families like MADS-box and bHLH were identified, which may play a core regulatory role in panicle morphogenesis. Module - Trait correlation analysis revealed multiple trait specific gene sets and reflected the spatiotemporal expression patterns of these key regulatory factors. This study not only deepened the understanding of the molecular network of wheat ear development, but also provided important genetic resources and theoretical basis for subsequent functional gene research and molecular breeding. Keywords Wheat ear development; Co-expression network; WGCNA; Transcription factor; hub gene screening 1 Introduction When it comes to the "core role" influencing wheat yield, the development of panicles undoubtedly ranks among the top. After all, the appearance traits such as the length of the ear, the number of small flowers, and the density of grains per ear are directly related to how much grain can be harvested in the end. The differences in the developmental stages of the panicles not only affect whether they look good or not, but also determine the potential for the yield of individual wheat plants. Especially in the current situation where global attention to food security is increasing, even a slight increase in grain count per grain may bring considerable potential for increased production (Wang et al., 2017; VanGessel et al., 2022; Wei et al., 2022). However, relying solely on phenotypic observation is clearly insufficient. The genetic background of wheat is complex, and the hexaploid genome makes it difficult for traditional methods to clearly understand the regulatory details. At this point, co-expression network analysis becomes particularly crucial. It does not directly target a single gene to "fight alone", but rather explores groups of genes that "appear" together in the same developmental sequence. Through the integration of transcriptome data, such methods can sort out several "meaningful" modules from a large amount of expression information, and then identify key pathways and hub genes. Many studies have successfully established the connection between spike development and yield traits using this approach, providing a new perspective for breeding (Li et al., 2022). This study employed weighted gene co-expression network analysis (WGCNA) to identify gene modules related to wheat spike development, aiming to reveal candidate genes and regulatory networks that affect spike formation and yield. By integrating the transcriptome data during the development of wheat ears, this study aims to clarify the molecular mechanism of ear morphogenesis and provide genetic targets for breeding programs. The research results are expected to enhance the understanding of wheat inflorescence biology and increase wheat yield through molecular breeding strategies.
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