1 Introduction

Winged bean (Psophocarpus tetragonolobus), a leguminous plant, has actually been cultivated in tropical regions for a long time, but not many people know its value. The whole plant is edible. The protein content of its seeds is particularly high, and its nutritional components are not bad. It has all kinds of vitamins and trace elements. Therefore, it is called "tropical soybean". This type of crop is highly suitable for low-input sustainable agriculture, and its nitrogen fixation capacity is a major advantage. But it's a bit of a pity that despite its considerable potential, the development of the winged bean has not been smooth. On the one hand, its breeding and improvement projects have always started relatively late; On the other hand, the scarcity of its genomic resources, coupled with the interference of anti-nutritional components and unstable growth characteristics, also makes it difficult to advance research work (Gadi et al., 2025).

When it comes to genomics, an important breakthrough in recent years has been the assembly technology at the chromosome level. This not only helps us to more accurately identify genes and locate QTLS, but also can be used in comparative genomic research to view the evolutionary map of crops from a broader perspective. Especially for "orphan crops" like the winged bean, having such a high-quality assembly not only adds a bit more data but also opens a window for a deeper understanding of its genetic diversity, structural variations, and evolutionary relationships with other leguminous plants. This information is crucial for current molecular breeding. For instance, methods such as marker-assisted selection and genomic selection all rely on solid genomic support behind them to breed superior varieties with high protein content, strong stress resistance and stable yield (Singh et al., 2025).

This study will not stop at the summary of techniques. What we aim to do is to systematically sort out the latest progress in chromosome assembly of the winged bean and see what new evolutionary clues have been obtained at the comparative genome and population genome levels. At the same time, we will also explore the significance of these achievements in actual breeding and crop improvement. Finally, through the findings of tandem genomic data, transcriptome analysis and diversity studies, we hope to provide a clearer direction for the breeding of the winged bean and enable it to truly play a role as a promising sustainable food resource.

2 Genome Assembly and Quality in Winged Bean

2.1 Sequencing and scaffolding technologies used

Chromosome-level assembly cannot be accomplished at the very beginning. This process employs a variety of new technologies, among which long-read platforms like PacBio and Nanopore play a crucial role. They can read longer and are more adept at dealing with repetitive sequences and structurally complex areas. Of course, these results usually also require short reads from Illumina to help correct errors. However, merely reading the passage is not enough. In order to assemble these sequences into chromosome-level assemblies, Hi-C is also required (Ho et al., 2024). This technology can help us determine the sequencing and orientation of genomic fragments. Interestingly, this combination of "assembly + error correction + positioning" has actually been verified to be effective in other leguminous plant projects. For instance, in the study by Li et al. (2024), this technical process was fully utilized, and the results were quite good. This time, winged bean actually borrowed this set of ideas as well.

2.2 Assembly quality metrics and validation approaches

Whether the assembly is good or not and whether there is any "padding" can actually be preliminarily judged by looking at a few indicators. The N50 is the most frequently used one. It can roughly tell us how long the spliced segments are. Apart from this, whether the total assembly size is approximately the same as the estimated value is also quite crucial. But more importantly, it is about completeness. The BUSCO assessment method involves comparing the conserved core genes to see if you have matched all the important parts. There are also some other checks, such as whether the original read segments can match, whether there are any abnormalities in the GC content, and the LAI index specifically used to examine the quality of the repetition area (Wang and Wang, 2022). For instance, if the transcriptome has a alignment rate of more than 75% and N50 is similar to the related species, then the overall quality is more reassuring (Figure 1) (Vatanparast et al., 2016). Tools like GenomeQC evaluate these indicators together and can also be compared with known good reference genomes (Manchanda et al., 2019).

Figure 1 Transcription factor family analysis (Adopted from Vatanparast et al., 2016) Image caption: Number of transcription factors determined within the CPP34-7 (Sri Lankan winged bean germplasm) assembly by transcription factor family (Adopted from Vatanparast et al., 2016)

2.3 Functional annotation pipeline and reliability of gene models

When it comes to gene function annotation, being straightforward and brutal won't work. For the non-type species of the winged bean, annotation relies on three approaches: first, from scratch prediction; second, to check if there are similar genes with other species; and third, to see if there is transcriptome support. Often, these three have to be carried out together. MAKER and BRAKER are the software processes that integrate these. But annotations are only the first step. Next, it still depends on whether these predicted gene models are reliable-whether there is transcriptome or homology support? Is the exon-intron structure reasonable? Is BUSCO's score high enough? These indicators can help us judge the credibility of the model (Vuruputoor et al., 2023). Of course, not all predictions can remain. Finally, a structural and functional filter must be carried out to remove those models that might be false positives. Especially for complex types like plant genomes, the filtering step is quite crucial. After all, for the subsequent work such as trait mapping and evolutionary research, it is necessary to rely on these accurate genetic models to support the situation.

3 Chromosomal Features and Genome Organization in Winged Bean

3.1 Karyotype structure, centromere/telomere patterns, and repeat content

Psophocarpus tetragonolobus is a diploid with a set of nine chromosomes. This conclusion is not drawn out of thin air but is based on high-density genetic maps and chromosome-level genome assembly. Its genome size is approximately 530 Mb, covering more than 90% of the estimated size (Ho et al., 2022). However, it should be noted that although the overall content of repetitive sequences does not seem high, being lower than that of cowpea (49.5%) and kidney beans (41%), this is likely because the regions with high GC content and repetitive sequences were underestimated during assembly. As for the specific patterns of centromeres and telomeres, they have not been fully clarified yet. However, since assembly has reached the chromosomal level, it should only be a matter of time before these structures are recognized in the future.

3.2 Distribution of gene density, recombination hotspots, and structural organization

Not all genes are evenly distributed in the genome of the winged bean. Some areas have high density, while others are sparse. In the assembly data, the representativeness of the coding regions is quite good, and many SNPS are concentrated in these areas. Quantitative traits such as pod color, anthocyanin content, and seed color often have QTLS that cluster in specific linkage groups, suggesting that this area might be a genetically active "hotspot" (Chankaew et al., 2022). When comparing the winged bean with other leguminous crops, it can be seen that there are quite a few structural changes such as chromosomal rearrangement and gene translocation. However, it's not all chaotic. Direct homologous genes are still distributed throughout every chromosome. Collinear regions can still be seen on multiple chromosomes, indicating that its genomic organization is both regular and slightly dynamic.

3.3 Insights from chromatin interaction maps (Hi-C compartments, 3D architecture)

Hi-C technology has been very popular in recent years, and research on winged beans has not been neglected either. The researchers integrated Hi-C data and pieced the genome from fragments into chromosome-level pseudomolecules, which is quite crucial for clarifying the three-dimensional structure. Although the division of its A/B compartments has not yet been clarified and the advanced chromatin structure has not been fully mapped, these basic data alone can already pave the way for subsequent exploration of chromatin organization, gene regulation, and even the spatial distribution of functional elements.

4 Comparative Genomics and Evolutionary Insights in Winged Bean

4.1 Synteny and collinearity with related legumes

There are actually many similarities in gene arrangement between Psophocarpus tetragonolobus and other leguminous plants. Especially for species like soybean (Glycine max) and cowpea (Vigna unguiculata), the collinearity and conserved regions between them are relatively obvious. It is worth noting that over 90% of the sequences in the transcriptome data have a strong similarity to these leguminous members (Vatanparast et al., 2016). This indicates that there is a high degree of consistency among them in terms of gene sequence and quantity. However, not all organ DNA is equally stable. The mitochondrial part shows that winged beans are clustered together with soybeans and green beans (Vigna radiata), forming a close lineage relationship. In addition, leguminous plants like broad beans can also reveal some conserved areas in the analysis. These collinear regions provide a fundamental framework for studying trait localization and evolutionary relationships.

4.2 Genome rearrangements and divergence events shaping evolution

Although the genomes of the winged bean and its close relatives are generally stable, a comparison reveals that there have been many structural adjustments between them. Some rearrangements are quite obvious, such as inversion and transposition. These changes are likely related to the historical background of the winged bean, including early hybridization, cross-regional spread and even more than one domestication attempt (Yang et al., 2018). Interestingly, the core genes in mitochondria seem to have undergone strong purification selection with little change. However, the genes on the chloroplast side show more differences, which also indicates that the evolutionary rhythms of different organelles may not be the same. The areas where collinearity breaks are often those regions where differentiation occurs.

4.3 Conserved and unique gene families highlighting adaptive traits

Some gene families are shared by the winged bean and other leguminous plants. There are also some that are unique to it. For instance, defense-related genes such as Kunitz trypsin inhibitor (KTI) not only exist in the four-lined bean but also show signs of expansion, possibly evolving in response to biological stress. Of course, not only winged beans, but also other leguminous plants such as broad beans have similar phenomena of gene expansion and contraction (Liu et al., 2025). The results of functional annotation and enrichment analysis are also quite interesting, showing that some specific genes in the winged bean are related to metabolism, stress resistance, and even reproduction. Although some of these genes only show their functions in specific environments, they are clearly worthy of attention in the formation of crop traits and future variety improvement.

5 Gene Family Evolution and Functional Adaptation in Winged Bean

5.1 Expansion of stress-response and defense-related gene families

The ability of the winged bean to cope with external stress is very likely related to the expansion of some special gene families in its body. Transcriptome studies have found that some genes related to plant defense, such as Kunitz trypsin inhibitor (KTI), are significantly increased in quantity in the winged bean. This gene plays a significant role in defending against pathogens and herbivorous insects. Moreover, this kind of expansion is not an isolated case in the winged bean. In closely related plants such as green beans and common beans, gene families related to lignin synthesis and abiotic stress tolerance, such as lassase and B-box protein, can also be observed. Some have expanded, while others have decreased (Yin et al., 2021; Cheng et al., 2024; Yin et al., 2024). Although the mechanisms may not be exactly the same, these changes roughly indicate one direction-the winged bean has indeed made many adjustments at the genetic level to adapt to the environment.

5.2 Diversification of nutritional and metabolite biosynthesis pathways

High protein content is one of the reasons why winged beans have attracted widespread attention. But what supports its nutritional value behind the scenes is not just the visible words "high content". Many gene families involved in nutrient synthesis show a certain degree of diversity in the winged bean. Some genomic and transcriptomic alignment data show that its transcript is highly similar to that of other leguminous crops, but it also has its own "personality". In plants such as broad beans and kidney beans, researchers have found that some gene families related to nutrient accumulation are significantly enriched in metabolic regulation (Vlasova et al., 2016). In other words, the winged bean may have also been subjected to similar selective pressure, which makes its nutritional structure more complex and rich.

5.3 Evolutionary patterns of nodulation and symbiotic genes

The winged bean can efficiently fix nitrogen, and this is inseparable from the genetic support of its tumor-forming symbiotic system. Although there is no very clear and systematic organization of its tumor-forming gene family at present, some comparative analyses from other leguminous plants have provided clues: genes related to symbiosis and tumor-forming remain highly conserved in these plants. This conservatism reflects their functional significance. Looking at the mitochondria side, on the core genes that maintain energy metabolism, the winged bean shows a strong purification selection pressure (Singh et al., 2025), which usually means that these genes cannot be changed easily. Based on this information, the fact that the winged bean can grow well in tropical environments and has the ability to fix nitrogen is closely related to the stable evolution of these genes.

6 Case Study

6.1 Discovery of an inversion linked to pod size and development traits

So far, no one has directly proved that there is a clear relationship between chromosomal inversion and the size of the pod of the winged bean. However, QTL analysis and high-density linkage mapping have identified some genomic regions related to pod length, color, and anthocyanin content (Figure 2) (Chankaew et al., 2022). Although these findings cannot provide a conclusion that "inversion leads to a certain trait", they do offer directions worth further exploration. In other plants, inversion is often associated with organ development. They inhibit recombination and retain allele combinations beneficial to growth (Huang and Rieseberg, 2020). Therefore, it is worth further exploration whether the QTL regions of some important pod traits are also related to similar structural variations.

Figure 2 The phenotypes, parental and progenies, of the W054×TPT9 cross. The pods and seeds of W054, TPT9, and F1 progeny are shown in (A), the pod colors of W054, TPT9, F1 progeny, and diversity of eight types are located in the surrounding F2 population (B), and the wing and banner colors of W054, TPT9, F1 progeny, and six types of F2 population are shown in (C) (Adopted from Chankaew et al., 2022)

6.2 Supporting evidence from synteny breaks, allele variation, and expression analysis

The QTLS such as pod length, anthocyanin content and color are precisely located at the same position. This "overlap" is no coincidence and usually indicates the possible existence of pleiotropy or close linkage phenomena. And such aggregations may also be related to chromosomal inversions. In other species, the "divergent islands" formed by inversion often present as collinear breaks, abnormal allele frequencies or linkage disequilibrium (Wellenreuther and Bernatchez, 2018). Although no exact inversion breakpoint has been found in the winged bean, the concentrated trend of QTL and the strong allelic effect seem to support the possibility that structural variations may be affecting pod development. Interestingly, studies on other plants have also found that the inversion region is often accompanied by changes in the expression regulation of related genes. Whether this phenomenon also occurs in the winged beans still needs to be verified through experiments.

6.3 Implications for marker-assisted breeding and yield improvement

If you are considering how to improve the yield or pod quality of winged beans, these QTLS are indeed good entry points. They are closely related to pod traits and can serve as markers to guide breeding directions. If it is further confirmed in the future that these regions contain chromosomal inversions, then the selection of haplotypes for these inversions may make marker-assisted breeding more efficient. Inversion regions have an advantage: they can protect favorable allele combinations from being broken up by recombination (Berdan et al., 2021). In other crops, this strategy has already been employed to increase yield or resistance. For the winged bean, it might be a path worth trying.

7 Genomic Applications in Winged Bean Breeding and Biotechnology

7.1 Use of genomic data in marker-assisted selection and genomic prediction

Some key strains, such as B73 and Palomero, have completed genome sequencing, which is an important advancement. Now, researchers can identify tens of thousands of SNP and SSR markers through the chromosome-level assembly and genetic mapping of the winged bean. These markers are being used in the selection of traits such as pod length, color, protein content and phytonutrients. Not all traits are easy to screen, but with the help of QTL mapping and association studies, some important regions have been identified, which is indeed helpful for screening genotypes. As in other leguminous plants, genomic prediction methods have also begun to play a role in the winged bean, especially in terms of increasing yield and resistance, with significantly higher efficiency (Keller et al., 2020; 2022).

7.2 Genome editing targets for nutritional quality and stress tolerance

Not all genes can move. Those that can be modified need to be identified first. At present, researchers have identified several candidate genes related to nutrition and stress responses, such as those that control protein synthesis or affect the expression of anti-nutritional factors (such as trypsin inhibitors and tannins). These have become the goals of CRISPR/Cas editing. Gene families like Kunitz inhibitors, as well as loci that control pod structure and seed composition, have also begun to enter the breeding toolkit, providing a foundation for subsequent targeted improvements.

7.3 Integration of genomic tools with pre-breeding and crop improvement efforts

Current breeding work is hard to do without genomic data. Genomic tools have already been employed in many steps when screening global germplasm, analyzing genetic diversity, and developing specialized markers (Tribhuvan et al., 2023). These tools not only help manage germplasm resources but also optimize hybrid combinations, making the speed of genetic improvement faster. For instance, in the case of the winged bean, the research team not only improved the yield but also enhanced the nutritional quality through this integration approach, and made it more adaptable to tropical conditions (Tanzi et al., 2019). Although the winged bean is not yet a mainstream crop, the current approach that combines molecular breeding with phenotypic analysis is accelerating its domestication and promotion.

8 Conclusions and Future Perspectives in Winged Bean Genomics and Breeding

8.1 Key insights gained from the chromosome-level assembly

Not all leguminous plants reach their "high point" so quickly. The genome of the winged bean has finally achieved chromosome-level assembly, which can be regarded as a breakthrough for this species that has received less research before. This achievement enables us to directly identify areas related to certain important agronomic traits, such as those that affect plant type, protein content, and phytonutrient levels. More importantly, this is also the first time we have a high-resolution genetic map of the winged bean. The following events then fell into place naturally: With this foundation in place, molecular markers could be developed, traits could be located, and gene selection in breeding could also be made more quickly. Meanwhile, during the assembly process, many genetic differences in global germplasm resources that have not been fully utilized were also discovered-which is of great significance for future variety improvement.

8.2 Remaining challenges and knowledge gaps in winged bean genomics

Of course, things were not all smooth sailing. Although the genome has been assembled, the problems inherent in cultivating winged beans have not disappeared due to technological progress. Weak breeding foundation, narrow diversity and high cross-pollination rate are all realities (Dieu et al., 2021; Laosatit et al., 2021). Some problems have existed for a long time. For instance, the understanding of anti-nutritional factors is still not clear enough, and the genetic mechanisms behind many key traits (such as limited growth, early maturity, and stress resistance) have not been fully grasped. Moreover, the germplasm materials we currently possess are not abundant or comprehensive enough (Lepcha et al., 2017). Another underestimated difficulty is that the integration of data is still very limited-the integration of genomic data, phenotypic expression, high-throughput data and environmental variables is just getting started (Varshney et al., 2021).

8.3 Strategic priorities for research and breeding over the next decade

The potential of the winged bean has been recognized by all, but to truly bring it into play, systematic promotion is still needed. The collection and screening of global germplasm banks need to be expanded, with a focus on identifying the diversity that has not yet been utilized. Afterwards, tools such as molecular markers related to traits and genomic selection models need to be established and utilized (Wang et al., 2024a; 2024b). Genome editing should also be put on the agenda, with goals including improving nutrition, reducing anti-nutritional factors, and enhancing stress resistance. Don't forget that it is also necessary to integrate genetic data, phenotypic data and environmental information. Only in this way can truly adaptive precision breeding be achieved. Finally, the infrastructure for research and breeding should also be given due attention-funds, cooperation networks, and international platforms are all indispensable. If these efforts are well done, the winged bean is very likely to become a key crop with high protein content and resistance to climate stress, especially in tropical regions, and its supporting role in sustainable food systems should not be underestimated.

Acknowledgments

We are grateful to colleagues for their critically reading the manuscript and providing valuable feedback that improved the clarity of the text. We also thank to the two anonymous peer reviewers for their revision suggestions on this study.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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