Legume Genomics and Genetics 2025, Vol.16, No.1, 23-32 http://cropscipublisher.com/index.php/lgg 29 6.2 Complexity of polygenic traits in soybean Those important characteristics of soybeans-such as yield, maturity time and plant height-are not determined by just one or two genes. This is like a group of people having a meeting to make a decision, each expressing some opinions, and finally combining them to form the result (Diers et al., 2018). When conducting previous research using the NAM population, although many related gene markers were found, it is still not fully understood how these genes "meet" with each other. What is more complicated is that some gene loci are particularly "meddlesome" and can affect several traits simultaneously (Fu et al., 2022). For instance, for the same QTL, both plant height and flowering time might be managed, which makes breeding work seem like solving a series of problems-moving one might lead to a whole series. Although technology has advanced nowadays, it is still not an easy task to fully understand the "interpersonal relationships" among these genes. 6.3 Translating genetic insights into practical breeding programs Applying the discoveries from genetic research to breeding is no easy task. Although GWAS and GS technologies have identified many important markers, they always encounter various troubles when applied in practice. For instance, a new gene locus discovered in early-maturing varieties, which theoretically can improve the maturity period and yield, is found to be unstable when applied to the field-if it works well in one plot, it may fail in another. What is even more troublesome is that the genetic differences between cultivated soybeans and wild germplasm are too large, making it particularly difficult to select alleles (Diers et al., 2018). Now even those factors that regulate small Rnas and epigenetics have to be taken into account (Ku et al., 2022), but these mechanisms themselves are like a black box, and it is not clear exactly how they operate. Ultimately, the current challenges mainly come from three aspects: the limitations of the experimental methods themselves, the complexity of trait inheritance, and the bottleneck of transformation from the laboratory to the field. To break through these, it is probably necessary to put more effort into genotyping technology, draw the genetic map more precisely, and at the same time, find ways to truly integrate and utilize various omics data. After all, breeding is not about conducting experiments; ultimately, it is necessary to grow truly good varieties. 7 Future Directions and Applications 7.1 Integrating multi-omics data for deeper genetic insights The study of soybeans has become increasingly sophisticated nowadays. Analyzing genomic, transcriptomic and proteomic data together is like piecing together the pieces of a jigsaw puzzle-the recent HypWAS method is quite interesting. It can predict grain yield by analyzing spectral data (Yoosefzadeh-Najafabadi et al., 2021). In fact, the experimental data accumulated over the years has piled up like a mountain. The key is how to string them together. For instance, some genes have very high expression levels, but the corresponding protein activities are very low. This contradictory phenomenon precisely indicates that multi-omics joint analysis is needed. However, to be fair, although the technology is getting more and more sophisticated, the ultimate goal is very simple: to help breeders avoid detours and cultivate good varieties more quickly. After all, compared with the previous "blind men touching the elephant" style of breeding, at least more clues can be seen now. 7.2 CRISPR/Cas9 and genome-editing tools for targeted genetic interaction studies Gene editing technology has truly brought about earth-shaking changes to soybean research in recent years. Take the "gene scissors" CRISPR/Cas9 for example. After editing the GmEOD1 gene with it, not only did the soybean grains become larger, but also the protein and oil contents increased (Yu et al., 2023). Even more astonishingly, by fiddling with the GmAITR gene, soybeans can actually grow better in saline-alkali land (Wang et al., 2021). Now even the delivery system has been upgraded, using Agrobacterium rhizopus for transformation, and the efficiency is much higher than before (Chen et al., 2019; Niazian et al., 2022). To be honest, although the technology is very advanced, various unexpected situations still occur in actual operation-sometimes editing a gene can also affect other unexpected traits. However, in any case, these new tools have indeed put breeding work on a fast track. Varieties that used to take over a decade to complete can now be accomplished in just a few years.
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