Soybean Genome Sequencing: Technologies, Applications, and Future Directions

Soybeans, a cornerstone of global nutrition and biofuel production, serve as a critical source of plant-based protein and oil. Their diverse applications and nutritional richness are pivotal in securing global food supplies and promoting sustainable energy solutions. With the rapid advancement of science and technology, genome sequencing has emerged as a transformative tool, swiftly finding widespread application in soybean research. This technology has revolutionized traditional soybean research methodologies, presenting unprecedented opportunities for soybean breeding.

By leveraging genome sequencing, researchers can gain profound insights into soybean genetic information, enabling them to pursue objectives such as climate-adaptive breeding and nutritional enhancement. These advancements offer new avenues for addressing global food challenges.

This article delves into the technological breakthroughs in soybean genome sequencing, its specific applications in agriculture, the economic and environmental impacts it has generated, and future directions for research and development, aiming to comprehensively showcase the academic and practical significance of soybean genome sequencing.

Technologies for Soybean Genome Sequencing

The evolution of soybean genome sequencing technology, from its early exploratory stages to the widespread adoption of high-precision, long-read sequencing techniques, has consistently injected new momentum into the in-depth analysis of the soybean genome, laying a solid foundation for subsequent exploration of its genetic mysteries.

Early Sequencing Milestones

During the early stages of genome sequencing technology development, soybean genome research achieved landmark accomplishments. In 2008, researchers successfully utilized Sanger technology to complete a draft genome sequence of cultivated soybean (Williams 82 variety). This achievement marked a new era in soybean genome research, providing a robust foundation for subsequent in-depth investigations into soybean's genetic mechanisms. In 2010, the genome of wild soybean (Glycine soja) was also successfully decoded. By studying the wild soybean genome, researchers uncovered the loss of relevant genes during the domestication process. This insight not only enhances our understanding of soybean's evolutionary journey from wild to cultivated forms but also offers crucial genetic resources for breeding soybean varieties with superior traits.

Soybean genome sequenced for the first time(Schmutz et al., 2010)

Technological Advancements

Continuous innovations in sequencing technology have significantly enhanced the precision and completeness of soybean genome sequencing. The emergence of PacBio SMRT sequencing technology has marked a new breakthrough in soybean genome research. This technology enables the decoding of up to 98% of the soybean genome, including previously challenging-to-sequence repetitive centromeric regions. Centromeres play a crucial role in chromosome segregation and genetic stability, and their accurate decoding helps us gain a deeper understanding of the structure and function of soybean chromosomes.

Moreover, the application of Hi-C chromatin interaction mapping technology has further improved the accuracy of chromosome-level assembly. By constructing high-resolution chromatin interaction maps, researchers can more clearly elucidate the spatial positioning and interactions of genes on chromosomes, providing a vital foundation for studying gene expression regulation and genetic variations.

Soybean Sequencing Technology

Applications of Soybean Genome Sequencing

The accumulation of soybean genome data has opened up unprecedented opportunities and challenges for the agricultural sector. This data holds the key to unlocking the genetic secrets behind critical agricultural traits, such as improving seed composition and enhancing resistance to abiotic stresses. These insights facilitate the precise improvement of soybean varieties and boost production efficiency.

Seed Composition Improvement

Genomic insights are revolutionizing soybean oil quality through targeted gene manipulation. Key advancements include:

• Gene Discovery: Functional genomics studies have identified the FAN gene, a key regulator of fatty acid biosynthesis in soybean seeds.
• Targeted Improvement: Editing the FAN gene via CRISPR/Cas9 enables precise modulation of fatty acid profiles, such as increasing oleic acid content for healthier oil production.
• Practical Impact: This approach addresses consumer demand for nutritionally optimized oils while reducing reliance on chemical hydrogenation.

For instance, Zhou et al. employed whole-genome resequencing technology to study 302 wild and cultivated soybean germplasm resources, unveiling key genes associated with domestication and improvement. These genes encompass various agronomic traits, including oil content, plant height, and pubescence morphology. Notably, 96 selective regions were linked to previously reported quantitative trait loci (QTLs) for oil content, and 21 regions contained genes involved in fatty acid biosynthesis. These findings provide crucial genetic resources for future soybean breeding, aiding in the further enhancement of soybean yield and quality.

Whole genome resequencing technology to study soybean genes(Zhou et al., 2015)

Kim and colleagues employed whole-genome resequencing techniques to investigate 781 soybean germplasm resources, encompassing cultivated, wild, and naturally hybridized soybeans. This research led to the construction of a comprehensive genome-wide variation map, featuring 10.6 million single nucleotide polymorphisms (SNPs) and 1.4 million insertions/deletions (indels). The study revealed that cultivated soybeans exhibited a 7.1% overall reduction in harmful mutations, with an additional 1.4% reduction observed in improved varieties. This suggests that artificial selection may have intensified the elimination of deleterious alleles, particularly within linkage regions associated with specific gene selections.

Furthermore, the application of genotype imputation methods enhanced the genome-wide association study (GWAS) resolution for traits related to soybean seed protein and oil content. These findings lay a crucial genomic foundation for future soybean breeding efforts, facilitating the optimization of breeding strategies to enhance both yield and quality.

Whole genome resequencing to study soybean protein and oil traits(Kim et al., 2021)

Abiotic Stress Resistance

During its growth cycle, soybean often encounters various abiotic stresses, such as drought and salinity, which can severely impact its yield and quality. The application of genome data has provided robust support for breeding soybean varieties that exhibit resistance to these abiotic stresses.

For instance, Yano and colleagues utilized nanopore long-read sequencing technology to assemble the genomes of 11 soybean strains from Japan and other countries. They developed the Asm2sv method to identify structural variations (SVs) at the gene level. The study revealed significant genomic differentiation between Japanese and American soybeans, particularly around the selective sweep region near the PDH1 gene, which controls pod shattering resistance. Additionally, multiple quantitative trait loci (QTLs) associated with the large-seed phenotype in Japanese soybeans were identified through genome-wide association studies (GWAS). These findings lay a crucial genomic foundation for future soybean breeding, facilitating the optimization of breeding strategies to enhance yield, quality, stress resistance, and adaptability.

Application of Soybean Sequencing Technology in Controlling Pod Shedding Resistance (Yano et al., 2025)

Zhang and colleagues, through gene function research, have unveiled the role of the soybean ferritin gene, GmFER1, in enhancing stress resistance and boosting yield. GmFER1 significantly bolsters soybean's resistance to salt stress and root rot by elevating antioxidant enzyme activity and Na⁺ efflux capacity, thereby improving salt tolerance. Additionally, it enhances disease resistance by strengthening antioxidant capabilities.Moreover, overexpression of GmFER1 has been shown to increase the net photosynthetic rate and yield of soybeans. Natural variations of this gene, such as the Hap2 haplotype, notably enhance salt tolerance, disease resistance, pod number, hundred-seed weight, as well as oil and isoflavone content.

This study provides novel genetic resources and theoretical foundations for molecular breeding of stress-resistant soybeans, paving the way for the development of salt-tolerant, disease-resistant, and high-yielding soybean varieties.

Application of Gene Sequencing to Soybean Resistance to Salt Stress and Root Rot (Zhang et al., 2025)

Economic and Environmental Implications of Soybean Genome Sequencing

As a vital component of the global agricultural economy, the soybean industry's production methods and genetic improvements have profound economic and environmental implications. The widespread application of soybean genome sequencing and related technologies has not only reshaped the cost-effectiveness structure of soybean production but also demonstrated immense potential in resource-efficient utilization and ecological environmental protection.

Genomics-Driven Reduction of Nitrogen Inputs

In soybean cultivation, the excessive use of nitrogen fertilizers not only escalates production costs but also causes severe environmental pollution, such as water eutrophication. The advent of genomic breeding technologies offers an effective pathway towards sustainable intensification of soybean farming. Through optimized research on soybean Nod genes, researchers have developed soybean varieties capable of more efficiently forming symbiotic nitrogen-fixing relationships with rhizobia. These varieties can fix more nitrogen from the atmosphere during growth, thereby reducing reliance on chemical nitrogen fertilizers.

Practical production data indicates that genomic breeding has led to a 30% reduction in nitrogen fertilizer use during soybean cultivation, effectively alleviating environmental pressure while lowering production costs. Furthermore, genome-edited varieties exhibit more efficient resource utilization during growth, with a 25% lower carbon footprint compared to traditional varieties. This achievement holds significant importance for promoting green agricultural development and addressing climate change.

Harnessing Wild Soybeans for Climate Resilience

Wild soybean conservation is pivotal for preserving genetic diversity and addressing climate challenges. Key strategies include:

• Role of Genetic Reservoirs: Wild soybeans harbor critical genes for disease resistance, stress tolerance, and nutritional quality, serving as a natural gene bank for cultivated soybean improvement.
• Global Genome Initiative: The Global Soybean Genome Initiative aims to sequence 3,000 wild soybean accessions to identify climate-resilient genes.
• Breeding Applications: Integrating these genes into elite cultivars enables the development of climate-adapted varieties, enhancing global soybean production stability.

This initiative not only enhances the adaptability and stability of soybeans, ensuring the sustainable development of the global soybean industry but also holds great significance for biodiversity conservation. By protecting and utilizing wild soybean resources, we can maintain the genetic diversity of soybean populations, providing ample genetic reserves to address future challenges.

Future Prospects in Soybean Genomics

Despite the remarkable achievements in soybean genome sequencing technology, the field of soybean genomics still demands continuous exploration and innovation to address major global challenges such as food security and climate change. Emerging frontiers like the advancement of gene editing technologies and the deep integration of digital agriculture are paving new paths for the sustainable development of the soybean industry.

Precision Gene Editing in Soybean Breeding

Gene editing technology, as a cornerstone of modern biotechnology, holds vast application potential in soybean genome research. In the future, prime editing technology is expected to play a pivotal role in soybean gene editing. This technology offers enhanced precision and flexibility, enabling the precise integration of specific genes. For instance, by precisely integrating the Bt insect-resistant gene into the soybean genome using prime editing, we can breed soybean varieties with high insect resistance, reducing the reliance on chemical pesticides, lowering production costs, and ensuring the quality and safety of agricultural products.

Additionally, base editing technology provides a new tool for soybean gene function research and variety improvement. Editing the GmFT gene using base editing can regulate the flowering time and growth cycle of soybeans, thereby extending the growing season in temperate regions and enhancing soybean yield and adaptability.

Integration with Digital Agriculture

With the rapid advancement of information technology, digital agriculture has emerged as a significant trend in modern agricultural development. Combining AI-driven genotype-phenotype models with soybean genome data holds promise for real-time field optimization in soybean cultivation. By deploying various sensors in soybean fields, we can collect real-time environmental information such as soil moisture, nutrient content, and meteorological conditions, as well as phenotypic data on the growth status and pest/disease incidence of soybean plants.

The integration of AI and genomic data is revolutionizing soybean farming through precision agriculture:

• Data-Driven Models: AI algorithms analyze genomic and environmental data to build genotype-phenotype models, predicting crop performance under varying conditions.
• Tailored Farming Strategies: Farmers receive customized recommendations (e.g., fertilizer dosage, irrigation schedules, pest management) based on real-time field data and genetic profiles.
• Sustainability Gains: This approach boosts yield by 20% while minimizing resource waste, aligning with sustainable agriculture goals.

 Moreover, digital agriculture technologies enable full-process monitoring and traceability of soybean cultivation, enhancing the quality and safety of agricultural products and their market competitiveness.

Conclusion

The advancement of soybean genome sequencing technology has ushered in unprecedented opportunities and challenges for soybean research. From achieving early sequencing milestones to enhancing genome assembly precision through technological progress, the application of genomic data in agriculture has continuously expanded and deepened. Notable achievements have been made in improving seed composition and cultivating resistance to abiotic stresses, with positive economic and environmental impacts.

Looking ahead, innovations in gene editing and the integration of digital agriculture will further propel the development of soybean genomics, transitioning it from the gene discovery phase to practical application. Through ongoing exploration and innovation, soybean genomics holds promise for making substantial contributions to addressing global food challenges, ensuring food security, and promoting sustainable agricultural development.

In our practical research and application endeavors, it is imperative to strengthen interdisciplinary collaboration, integrating knowledge and technologies from biology, information technology, agricultural science, and other fields. By working together, we can collectively advance the development and application of soybean genome sequencing technology, creating greater value for the well-being of human society.

References

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