4 Discussion
Vegetable soybeans: origin, genetics, breeding importance
Vegetable soybeans, prized for their notable attributes such as large seed size, sweetness, and lack of beany flavor, offer significant nutritional advantages as a vegetable (Carneiro et al. 2020; Kumar et al. 2011; Nair et al. 2023). Understanding their origin, genetic structure, and selection signatures is pivotal for harnessing soybean germplasms in breeding programs. In this study, we integrated phenotypic and genotypic data to establish a core collection from 2,394 Taiwanese soybean accessions. This core collection comprises 244 accessions from 29 countries, preserving over 98% of the allelic coverage. Compared to previous collections based solely on phenotypic traits (Huang et al. 2022; Kao et al. 2021), our approach retains a more diverse germplasm at the molecular level. The inclusion of these diverse accessions enhances our understanding of the interplay between soybean phenomic and genomic characteristics, providing a comprehensive foundation for future breeding efforts.
Breeding goals and genetic diversity in soybeans
Compared to the broader objectives of grain soybeans, such as oil production, animal feed, and human consumption, breeding goals for vegetable soybeans are more specialized (Guo et al. 2022; Nair et al. 2023; Sedivy et al. 2017), resulting in lower variations (Shanmugasundaram and Yan 2001). Previous breeding efforts in Taiwan have utilized grain soybean germplasms to broaden genetic diversity and enhance adaptation and resistance to biotic and abiotic stresses in vegetable soybeans (Chou 2015; Shanmugasundaram and Yan 2001). Our results reflect this breeding strategy, revealing a small proportion of vegetable soybean accessions sharing genetic backgrounds with grain soybeans (Supplementary Tables 3 and 9). Understanding these genetic relationships informs breeding strategies aimed at enhancing desired traits while preserving genetic diversity. The distinct genetic profiles observed in vegetable soybeans compared to grain soybeans indicate the importance of considering population structure and genetic diversity in soybean breeding programs. While grain soybeans exhibited dispersed distributions across multiple groups, vegetable soybeans (Group I) exhibited a more specialized genetic profile with lower diversity and increased differentiation from other groups, suggesting a specialized genetic foundation shaped by breeding practices (Fig. 4A-B). AMOVA results confirm the distinct genetic profiles between vegetable and grain soybeans (Fig. 4F). The slower LD decay rates observed in vegetable soybeans further imply a history of more selective processes compared to grain soybeans (Fig. 4D), consistent with previous studies (Liu et al. 2022).
Genomic scan identifies selection regions
To deepen our understanding of the genetic mechanisms underlying vegetable soybean selection, we conducted a comprehensive genome-wide scan and identified 159 significant signatures within 67 putative selection regions (Fig. 5). The detection of favorable alleles in vegetable soybeans (Group I), associated with a notable increase in 100-seed weight (Fig. 6C), highlights the effectiveness of domestication and improvement efforts. Soybean is a short-day sensitive plant, where flowering time and seed size play crucial roles in determining seed yield (Vogel et al. 2021; Xiong et al. 2023; Zhang et al. 2015). Our investigation pinpointed two chromosomal regions with high selective signals (Fig. 5B-C), harboring GmXXXX and GmXXXX. GmXXXX encodes a protein with the APETALA2 (AP2) domain, governing floral, ovule, and seed development (Jiang et al. 2020; Yu et al. 2023). Over-expression of GmXXXX in Arabidopsis results in significant alterations in seed characteristics, impacting seed size and morphology (Jiang et al. 2020). Recent research has further demonstrated the co-regulatory mechanisms of GmXXXXand GmXXXX under short-day conditions, jointly modulating photoperiodic regulation and influencing seed size (Yu et al. 2023). Additionally, stem growth habit in soybeans profoundly influences the reproductive period and seed development (Liu et al. 2010; Xiong et al. 2023; Zhang et al. 2015). GmXXXX (XXX locus), an Arabidopsis XXX (AtXXX) homolog, is a major regulator of soybean determinacy (Liu et al. 2010). Determinate cultivars (dt1/dt1) exhibit prompt stem termination post-flowering, while indeterminate cultivars (Dt1/Dt1) sustain growth, leading to extended flowering periods. Cultivars with minimal temporal overlap between vegetative and reproductive phases have the potential to enhance pod and seed development (Xiong et al. 2023). Furthermore, a genomic association network study reveals the significant impact of the XXX locus on various soybean traits, such as stem pod density, number of three seeds per pod, and total seed number (Fang et al. 2017), elucidating the roles of GmXXXX and GmXXXX in seed development and reinforcing their importance in emphasizing the reproductive growth of vegetable soybeans.
Furthermore, we identified overlaps between selection regions in vegetable soybean and previously reported GWAS QTLs influencing key agronomic traits (Fig. 6A). The convergence may indicate regions of the genome under selective pressure due to their association with crucial agronomic traits. For instance, selection region 14-3 aligns with traits related to 100 pod fresh weight and 100 seed fresh weight (Li et al. 2019). This evidence further underscores that the identified selection regions are of interest for vegetable soybean improvement, particularly in enhancing seed size and weight. In addition, selection region 1-1 is associated with seed coat color, while regions 19-5 and 19-6 are linked to leaflet width and area (Fang et al. 2017). To meet market preferences, vegetable soybeans are typically green or yellow-green, unlike the varied colors observed in grain soybeans (Nair et al. 2023; Sedivy et al. 2017). Previous studies have highlighted variations in leaflet morphology, correlating with differences in seed size and seed number per pod (Jeong et al. 2011). Thus, in breeding efforts for vegetable soybeans, genomic regions associated with both ‘seed coat color’ and ‘leaflet-related traits’ may have been specifically targeted, further emphasizing the importance of these genomic regions in breeding programs aimed at improving vegetable soybean cultivars.
Core collection optimizes germplasm analysis
Our study highlights the effectiveness of the core collection framework for analyzing large-scale crop germplasm data, ensuring that observed genetic variations accurately reflect true genetic diversity rather than sampling biases. By reducing the number of accessions to manage and maintain, core collections optimize resource allocation in efficient utilization, germplasm-related research, and conservation efforts. Through exploring population structure and genome-wide selection scans within a diverse panel of soybean germplasm genomes, we identified loci showing significant differences between vegetable and grain soybeans. Validating core collection results against a larger population enhances the credibility of this approach, offering a practical and resource-efficient strategy for researchers handling extensive germplasm datasets. The positive and significant correlation observed between accumulated favorable alleles and 100-seed weight supports their contribution to observed phenotypic variation (Fig. 7A-B), highlighting the genetic basis of seed weight and the potential for marker-assisted selection in yield improvement breeding programs. The robustness of the core collection framework in identifying significant genomic regions further sheds light on its utility in advancing genetic studies and accelerating crop improvement efforts.
Limitations and future directions
While our study offers valuable insights into the genetic underpinnings of vegetable soybean selection, it is essential to acknowledge limitations that may constrain the generalizability and practicality of our findings. Firstly, although our core collection is extensive, it may not fully represent the global diversity of soybeans. Despite efforts to include accessions from 29 countries, limitations in germplasms may result in overlooked or underrepresented genetic variations, particularly from regions not covered in this study. This could impact the generalizability of the study findings to the broader vegetable soybean population. Additionally, our focus on specific trait, may bias the overall genetic variations, neglecting other potentially significant genomic regions related associated with agronomic traits. Future studies could broaden the scope of phenogenomic analysis to encompass a broader range of agronomic traits and provide a more comprehensive understanding of the genetic basis of vegetable soybean adaptation and resilience to environmental challenges. Finally, our reliance on historical data and existing germplasm collections may not fully capture the dynamic evolution of soybean genetics in response to changing environmental conditions and emerging challenges (Singer et al. 2023). Despite these constraints, our study serves as a stepping stone for further research and underscores the importance of the ongoing need to explore and incorporate diverse genetic resources to unravel the complexities of vegetable soybean genetics and advance breeding endeavors.
Conclusion
In conclusion, our investigation on vegetable soybeans reveals distinct genetic profiles compared to grain soybeans, emphasizing the importance of targeted breeding efforts aimed at specific traits such as seed size and weight. The establishment of a diverse core collection, integrating phenotypic and genotypic data, enriches our understanding of soybean characteristics. We identified significant selection signatures and potential selection regions associated with vegetable soybean improvement, highlighting candidate genes crucial for seed development and flowering time regulation. The positive correlation between favorable alleles and 100-seed weight emphasizes the potential for the breeding program. Overall, within the framework of the core collection, our study contributes to a deep understanding of the genetic basis of vegetable soybean selection, offering valuable insights for further functional investigations and the advancement of improvement efforts.