Soybean functional genomics: bridging theory and application

Soybean is one of the world’s most important crops, providing a significant source of plant-based protein and oil for humanity. With the global population continuously increasing, the demand for soybean as both a food and feed source has been rapidly increasing. Therefore, it is crucial to study how to enhance soybean yield and quality to meet food security demands. Soybean production has significantly increased over the past few decades. According to the data from the Food and Agriculture Organization (FAO) of the United Nations, global soybean production has risen from relatively low levels in the 1950s to millions of tons today. The USA, Brazil, and Argentina are the leading countries in global soybean production, collectively contributing to the majority of the world’s soybean output. The increase in soybean production can be attributed to continuous advancements in agricultural technology, including the development of superior soybean varieties, efficient agricultural management practices, and modern mechanization in agriculture. In this special issue, we have invited experts in the field of soybean research to present the latest developments in soybean functional genomics. Across the 17 papers published in this journal, various aspects of soybean genomics, genetic improvements and adaptation, genetic basis of agronomic traits, genetic basis of biotic and abiotic stress tolerance, and regulation of nodulation have been reviewed. Future insights and breeding technologies have also been proposed. Here, we summarize some of the highlights from these articles.

Genomic research on soybean

In recent years, significant progress has been made in soybean genomics research, unveiling the role of epigenetics in soybean regulation, the occurrence of polyploidy and diploidization, and the three-dimensional structure of the soybean genome. These advancements have not only deepened our understanding of soybean biology but have also provided valuable resources for soybean breeding and genetic improvement. The review by Ni and Tian (2023) provides an overview of the application of the 3D genome in soybeans. The importance and research techniques of 3D genomics are described, with a particular focus on the advancements and applications of the 3D genome in soybeans, including the identification of open chromatin regions and the role of gene regulatory elements. The article also outlines several promising directions for future research in 3D functional genomics to advance molecular breeding in crops. Yuan and Song (2023) provide a comprehensive review of polyploidy and diploidization in soybeans. They introduce the occurrences of polyploidy and diploidization in soybeans and their impact on genome structure and epigenetic modifications. The potential applications and challenges of polyploidy in soybean breeding are also discussed.

Genetic improvement and adaptation

Soybean is a typical short-day, temperate crop that is sensitive to photoperiod and temperature. Soybean’s response to photothermal conditions determines plant growth and development, subsequently impacting its architecture, yield formation, and geographical adaptation. Traits related to photothermal adaptation, such as flowering time and maturity, are controlled by multiple major and minor genes, as well as the interaction between genotype and environment. The exquisite review by Hou et al. (2023) on the origin, variation, and selection of natural alleles controlling flowering and adaptation in soybeans provides a detailed exploration of the molecular and genetic basis of photoperiodic flowering in soybean, as well as the differences in molecular and evolutionary mechanisms between wild and cultivated soybeans. Additionally, the paper discusses the practical foundations for enhancing soybean adaptation and yield through molecular breeding. A review by Wu et al. (2023) discusses the research progress on soybean photothermal adaptability and its molecular breeding progress. Through genetic and molecular cloning studies of soybean’s photoperiod-dependent flowering pathway, it elucidates the impact of photothermal conditions on soybean growth and development, as well as their influence on yield formation and geographical adaptation. The article also introduces the role of photoreceptor genes and components of the circadian clock complex in regulating soybean flowering time and explores the prospects of molecular breeding techniques in enhancing soybean adaptation to different photothermal conditions. A review by Lyu et al. (2023) focuses on soybean shade avoidance syndrome and shade tolerance. The article introduces the concept of soybean shade avoidance syndrome, the mechanisms affecting soybean yield, and the breeding strategies for soybean shade tolerance. Finally, the article proposes an ideal planting structure suitable for high-yield breeding.

Genetic basis of agronomic traits

This section extensively highlights the latest advances in the genetic mapping and genome-wide association studies of agronomic traits in soybeans. It focuses on key traits such as soybean seed protein content, biomass accumulation, plant height, and nodulation. Additionally, it delves into the genetic diversity across various soybean germplasm resources and the genetic basis of these traits, along with the pivotal genes associated with them. The review published by Liu et al. (2023) primarily provides insights into the genetic characteristics of soybean seed proteins, encompassing molecular markers, genomic analysis, and the properties and genetic control of seed proteins. The article discusses key factors that affect soybean seed protein content and how recent advancements in soybean genomics have enhanced our understanding of molecular mechanisms related to seed quality. Furthermore, the paper explores the challenges associated with breeding high-protein soybeans and strategies for overcoming these challenges. The genome-wide association studies on soybean biomass accumulation characteristics published by Wang et al. (2023) used diverse germplasm populations to investigate the genetic basis of soybean biomass, identifying 10 loci and 47 potential candidate genes. This research provides valuable insights for future soybean breeding and improvement. A research paper by Yu et al. (2023) investigated the genetic basis of plant height in soybean germplasm from Northeast China. Researchers employed a comprehensive approach of genome-wide association studies, haplotype, and candidate gene analysis, identifying superior and rare haplotypes for plant height. The researchers identified major stable QTLs, haplotypes, and candidate genes associated with plant height and explored their genetic basis in natural soybean populations. These QTLs and haplotypes can be used to breed soybean crops with desired plant height, while the identified candidate genes can be used for soybean crop improvement after appropriate functional validation. The review by Gresshoff et al. (2023) provides a functional genomics dissection of the nodulation autoregulation pathway (AON) in soybean. The article discusses molecular markers, signal transduction, and symbiosis in legumes, and explores the role of combined mutation genetics and functional genomics in dissecting nodulation induction and AON pathways.

Genetic basis of abiotic and biotic stress tolerance

The growth and yield of soybeans are often significantly affected by both biotic and abiotic stressors, such as pathogens, pests, drought, high temperatures, and soil salinity. It is expected that these stresses will become more widespread with the arrival of climate change. To ensure the stability and sustainable production of soybeans, understanding the genetic basis of soybean stress tolerance is of paramount importance. In recent years, significant progress has been made in identifying the genes and molecular mechanisms involved in soybean stress responses, thanks to the rapid advancement of genetic genomics and functional genomics tools. This has led to the discovery of new stress-responsive genes and pathways, as well as the development of soybean varieties with improved stress tolerance. A research paper by Yang et al. (2023) describes a study that analyzed the gene expression profiles of soybean cultivars under drought stress using RNA-seq technology. The researchers identified genes involved in drought tolerance mechanisms and revealed significant differences in gene expression between drought-tolerant and sensitive varieties. The findings contribute to a deeper understanding of the drought tolerance mechanisms in soybeans and provide a theoretical basis for soybean breeding. An exquisite review by Leung et al. (2023) focuses on soybean salt tolerance gene mining, which introduces the genes involved in different salt tolerance mechanisms that have been verified in the past 20 years, and discusses the strategy of selecting salt tolerance genes for crop improvement. The article presents a wealth of research findings and data, including studies in genomics, transcriptomics, proteomics, and metabolomics, as well as crop improvement methods based on functional genomics. Furthermore, the paper delves into the challenges and opportunities in future research and how to better utilize these research outcomes to enhance salt tolerance and yield in soybeans.

Rao et al. (2023) provide a comprehensive review of the soybean immune mechanisms, primarily focusing on soybean’s immune mechanisms and interactions with microorganisms. The article discusses the NLR protein family in soybeans and their roles in pathogen infection, as well as the intersection of PTI and ETI signaling pathways in soybeans. In addition, the paper explores disease prevention and control strategies in soybeans and future research directions. A research paper by Zhao et al. (2023) primarily discusses the relationship between necrotic symptoms caused by soybean mosaic virus (SMV) infection and genes associated with the transcriptional mapping of the PR1 protein in soybeans. The study unveils the molecular mechanisms behind the necrotic response induced by SMV, which has been overlooked in soybean genetic research. The research reveals that SMV infection leads to the upregulation of PR1 genes in soybean plants, which is linked to the plant’s necrotic symptoms. Additionally, the study identifies numerous differentially expressed genes associated with SMV infection and delineates the metabolic pathways in which these genes are involved. Meanwhile, another research paper by McDonald et al. (2023) elucidates how to identify the gene Rcs3 responsible for resistance to frog eye leaf spot disease in soybean breeding. The researchers employed genetic analysis and gene mapping techniques to pinpoint Rcs3 to a specific region on chromosome 16 and traced its origins in soybean varieties. Additionally, they identified SNP markers that can be effectively used for marker-assisted selection. These findings hold significant implications for soybean breeding and the management of frog eye leaf spot disease.

Genetic basis and applications of soybean breeding

Breeding crop varieties with high yields and ideal plant architecture is a desirable goal of agricultural science. Compared to crops like rice, wheat, and maize, the soybean’s yield per unit area has not shown significant improvement, indicating that soybean breeding lacks a true “Green Revolution.” The genetic basis and applications of soybean breeding are broad and diverse, encompassing various aspects such as plant architecture, male sterility, and hybrid breeding. The review by Clark and Ma (2023) provides a summary of the current understanding and recent advancements in the genetic control of several key characteristics of soybean stem architecture, including stem growth habit, plant height, branch angle, branch number, petiole angle, and leaf size and shape. The critical genes underlying these traits have been identified as integrators of hormonal, developmental, and environmental signals that regulate the growth and orientation of stem organs. In crop breeding, the manipulation of plant growth using auxin has become a prominent and highly researched area of interest, a comprehensive review by Li and Chen (2023) with a particular focus on soybeans, exploring the application of plant auxin in crop breeding. While the precise regulatory role of auxin in crop development remains somewhat unclear, the practical introduction of auxin pathways in crop breeding is still largely theoretical. Through meticulously crafted schematic diagrams, the review summarizes the roles of auxin in various crops, including rice, maize, and soybeans. These roles primarily involve aspects such as stem height, leaf angle, tillering, seed development, root system architecture, and nutrient uptake. Fang et al. (2023) have provided a comprehensive overview of the latest progress and current status of male sterility and hybrid breeding in soybeans. The authors discuss the breeding programs based on male sterility and the current landscape of hybrid soybean breeding. They also discuss ongoing efforts aimed at making hybrid soybeans a commercial success. Furthermore, the article introduces the molecular mechanisms and related genes involved in soybean development, highlighting their significant roles in soybean reproductive development. In summary, this paper offers valuable insights into soybean hybrid breeding, serving as a valuable resource in the field of plant reproductive biology.

Overall, this special issue on soybeans stands as a valuable repository of knowledge and innovation, unveiling the multifaceted world of soybean research. It showcases the relentless pursuit of excellence by scientists, researchers, and experts in unraveling the mysteries of soybean genetics, genomics, and breeding. The diverse range of topics covered in this special issue underscores the depth and breadth of our exploration into the soybean genome. The insights gained here have far-reaching implications, not only for soybean cultivation but also for global agriculture, food security, and sustainable practices.

Author contribution

All authors contributed to the study conception and design. F. K. designed the letter; Z. S. wrote and revised the manuscript; H.-M. L., S.-H. L., and X. L. modified the letter; and all authors read and approved the final version of the manuscript.

Funding

This work was supported by the National Natural Science Foundation of China (Grant 32090064 to F.K.) and National Natural Science Foundation of China (32072086).

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Conflicts of interest

The authors declare no competing interests.