Unveiling the molecular pathways of foxtail millet inflorescence development

The findings provide vital genetic resources for enhancing foxtail millet productivity, which could significantly contribute to global food systems.

Inflorescence development directly influences crop yield by determining the number of grains per panicle, which is shaped by the structure of the inflorescence itself. Key factors such as panicle branching, spikelet number, and the growth pattern of florets all impact final grain numbers. Understanding the molecular basis of inflorescence development is therefore critical for improving crop yield stability. Previous studies on major cereals have identified several families of genes, particularly from the MADS-box family, which regulate floral organ differentiation and inflorescence meristem identity. However, the genetic regulation of inflorescence development in foxtail millet, a vital C4 crop, remains less understood. The current study offers a comprehensive analysis of the transcriptome at different stages of foxtail millet inflorescence development, with a focus on uncovering the molecular pathways involved.

A study (DOI: 10.48130/seedbio-0025-0024) published in Seed Biology on 17 December 2025 by Xiaoqian Chu’s & Jia-Gang Wang’s team, Shanxi Agricultural University, sheds light on the transcriptome dynamics of foxtail millet inflorescence development, offering insights into the genetic regulation of panicle formation, flower organ development, and grain yield.

In this study, researchers employed RNA sequencing (RNA-seq) to investigate the gene expression patterns associated with inflorescence development in foxtail millet. RNA samples were collected from three key developmental stages: the double ridge meristem (DR), bristle primordium meristem (BP), and green anther (GrA), and compared to a control of two-week-old seedling leaves (SE). A total of 12 RNA-seq samples were analyzed, with over 30 million clean reads mapping successfully to the foxtail millet reference genome, ensuring reliable gene expression data. Principal component analysis (PCA) confirmed the high reproducibility of the biological replicates. The study identified a significant variation in gene expression across the stages, with 30,618 genes detected in total, and a large portion of genes (14,609) co-expressed in all stages. Notably, 270 genes were specifically expressed during the DR stage, 172 during the BP stage, and 1,088 during the GrA stage. Further analysis revealed that genes associated with key biological processes like transcription factor regulation, transporter activity, and reactive oxygen species (ROS) responses were highly expressed in the GrA stage, indicating active floral organ growth and differentiation. A deep dive into the MADS-box gene family, which regulates floral organ identity, showed that SiMADS1 was particularly abundant in the GrA stage and was essential for proper floral organ formation. Knockout of SiMADS1 using CRISPR/Cas9 led to defective floral organs, including stigma and anther malformations, confirming its critical role in inflorescence development. Additionally, downstream regulatory genes of SiMADS1 were identified through combined RNA-seq and DAP-seq analyses, uncovering genes involved in carpel and floral organ development. These findings suggest that SiMADS1 governs inflorescence development by regulating a network of genes crucial for floral organ morphogenesis and panicle formation. This research provides essential genetic resources for future studies on inflorescence development in foxtail millet, offering insights into improving crop yield through genetic manipulation of key regulatory genes.

This study represents a significant step forward in understanding the molecular mechanisms of inflorescence development in foxtail millet. The identification of key genes like SiMADS1 offers new opportunities for improving crop yield through genetic manipulation. By expanding the molecular toolkit available for breeding, this research has the potential to contribute to global food security efforts by enhancing the productivity and resilience of foxtail millet and other cereal crops.

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References

DOI

10.48130/seedbio-0025-0025

Original Source URL

https://doi.org/10.48130/seedbio-0025-0025

Funding information

This work was supported by the National Key Research and Development Program of China (2023YFD1202702-6), the National Natural Science Foundation (32400217, and 32200222), and the Start-up Fund of Shanxi Agricultural University (2021BQ84).

About Seed Biology

Seed Biology (e-ISSN 2834-5495) is published by Maximum Academic Press in partnership with Yazhou Bay Seed Laboratory. Seed Biology is an open access, online-only journal focusing on research related to all aspects of the biology of seeds, including but not limited to: evolution of seeds; developmental processes including sporogenesis and gametogenesis, pollination and fertilization; apomixis and artificial seed technologies; regulation and manipulation of seed yield; nutrition and health-related quality of the endosperm, cotyledons, and the seed coat; seed dormancy and germination; seed interactions with the biotic and abiotic environment; and roles of seeds in fruit development. Seed biology publishes a wide range of research approaches, such as omics, genetics, biotechnology, genome editing, cellular and molecular biology, physiology, and environmental biology. Seed Biology publishes high-quality original research, reviews, perspectives, and opinions in open access mode, promoting fast submission, review, and dissemination freely to the global research community.