Seeds, which result from fertilization, serve both as propagules that enable the establishment of a new generation and as vectors for the transmission of parental genetic information. They also represent the primary economic output of crops, directly influencing crop productivity, quality, and global food security. Over the past decade, the rapid advancement of multi-omics technologies—including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and phenomics—has greatly promoted research in the field of seed biology. Reference genomes and pan-genomes of an increasing number of species now underpin the dissection of quantitative trait loci (QTLs) governing seed weight, protein content, and other agronomically critical traits.

The field of seed biology and functional genomics is entering a new era, driven by single-cell and single-nucleus omics, spatial transcriptomics, and chromatin accessibility profiling. These technologies enable high-resolution characterization of seed development and germination at the single-cell level, revealing dynamic transcriptional reprogramming during endosperm development and embryogenesis. Meanwhile, the integration of multi-omics data with genome-wide association studies, machine learning, and artificial intelligence is accelerating the translation of molecular insights into molecular design breeding.

Despite rapid technological advancements, progress in seed biology and functional genomics remains highly fragmented. Omics datasets are dispersed across different species, platforms, and journals; standards for data integration are lacking; and for many important crop and wild species, multi-layer omics resources for seeds are still unavailable. Therefore, a special issue to consolidate these advances is urgently needed.

This Special Issue of Seed Biology aims to compile the latest advances in seed omics, highlight how multi-omics integration promotes our understanding of seed biology, and encourage the translation of omics discoveries into improvements in seed quality and breeding innovation. We warmly invite submissions of research articles, reviews, and perspectives related to the topics listed below. Please note that the topics provided may not encompass all research areas in this field. If your topic is related but not included here, please contact us.

Topics of interest：

l  Multi-omics dissection of seed development: embryogenesis, endosperm and seed coat formation, and seed maturation

l  Omics of seed dormancy and germination: transcriptional, translational, hormonal, and metabolic regulation of dormancy release and germination timing

l  Seed quality and nutritional composition: proteomics, metabolomics, and lipidomics of storage reserves, vitamins, and health-related compounds

l  Seed vigor, longevity, and storability: omics of desiccation tolerance, seed aging, and priming

l  Omics of seed responses to abiotic and biotic stress, and of seed–microbiome interactions

l  Population genomics, pan-genomics, GWAS/TWAS, and evolutionary omics of seed traits and domestication

l  Single-cell, single-nucleus, and spatial omics of seeds: cell-type-resolved atlases of embryo, endosperm, and surrounding tissues

l  Epigenomics and non-coding RNA regulation of seed development, maturation, and germination

l  Multi-omics data integration, databases, AI and machine learning approaches for predicting and engineering seed traits

l  From omics to application: molecular design breeding, genome editing, and seed quality and yield improvement

Guest Editors

Dr. Liangsheng Zhang, Zhejiang University, China

Dr. Peng Zhao, Wuhan University, China

Dr. Giorgio Perrella, University of Milan, Italy

Dr. Chenjiang You, South China Agricultural University, China

Submission Deadline

The deadline for submitting manuscripts is June 30, 2027; however, we are open to considering extensions on a case-by-case basis. Accepted papers will be published as open-access articles.

Submission Instructions

To submit your full manuscript, kindly use the online submission system at Seed Biology (mc03.manuscriptcentral.com/seedbio). Additionally, please select a topic relevant to this Special Issue during submission and explicitly reference it in your cover letter. For any additional inquiries, please reach out to the Guest Editors:

Liangsheng Zhang (zls83@zju.edu.cn)

Peng Zhao (pzhao2000@whu.edu.cn)

Giorgio Perrella (giorgio.perrella@unimi.it)

Chenjiang You (cjyou@scau.edu.cn)