Legume Genomics and Genetics 2025, Vol.16, No.1, 23-32 http://cropscipublisher.com/index.php/lgg 26 gibberellin synthesis genes (Hu et al., 2023). In fact, these regulatory mechanisms are more complex than we imagine. The same transcription factor may play completely different roles at different stages of development, and sometimes it may also "string" with other signaling pathways. For example, a transcription factor responsible for drought resistance may also affect flowering time. This characteristic of "specialization and versatility" not only brings challenges to breeding work, but also provides new opportunities. After all, if a key regulatory node can be found, it may be possible to improve multiple agronomic traits simultaneously. 3.3 Impact of environmental interactions on genetic pathways The growth performance of soybeans is like an "environmental detector", and the same genes may be completely different in different places-this land is a high-yield variety, and changing land may cause wilting (Rani et al., 2023b). Interestingly, some varieties are particularly selective and can only reach their maximum potential in specific environments. Through GWAS analysis, it was found that certain genomic regions act as "environmental sensors" that adjust trait performance based on different planting conditions (Ravelombola et al., 2021; Fu et al., 2022). For example, drought resistant genes are particularly active in arid areas, but may become lazy in humid areas. These findings make breeding work more like 'precise matching'. Not only do we need to consider the genes themselves, but we also need to consider their "temperaments" in different environments. Now we know that soybeans are regulated by a triple network of genes, transcription factors, and environmental signals from flowering time to disease resistance. Sometimes a gene needs to "listen" to both internal developmental signals and external environmental signals before deciding how to express it. Although this complexity is a headache, it also provides new ideas for cultivating varieties with stronger adaptability, such as finding key regulatory nodes that can stably function in multiple environments. 4 Advances in Genomics and Bioinformatics Tools 4.1 High-throughput sequencing technologies in soybean genomics Nowadays, conducting soybean research is not as difficult as it used to be. New technologies have made genomic analysis both fast and accurate. Take the SoySNP50K chip for example. It screened out 51 important markers from various soybean materials at once, and these markers were all linked to visible and tangible traits such as plant height and grain weight (Rani et al., 2023a). What's more interesting is that through whole genome sequencing of 250 soybean samples from different sources, new genes such as GSTT1 and CKX3 were unexpectedly discovered. Surprisingly, they are related to the complex trait of yield (Yang et al., 2021). However, on the other hand, although finding so many SNP loci and candidate genes is a good thing, it still depends on their performance in different varieties when they are actually applied to breeding (Ravelombola et al., 2021). Just as it was recently discovered, some genes that perform well in the south are completely different when planted in the north. 4.2 Functional genomics approaches to unravel genetic interactions Nowadays, the methods for studying the functions of soybean genes are getting more and more advanced. Take this TILLING-by-Sequencing+ technology for example. It can precisely identify the mutations we need from tens of thousands of mutants like a sieve (Lakhssassi et al., 2021). What is particularly interesting is that for some mutants found by this method, the fatty acid composition in the seeds has completely changed, which provides a new idea for improving the quality of soybean oil. Even more amazing is the CRISPR/Cas9 "gene scissors", combined with the transformation technology of Agrobacterium roots, which makes the study of soybean root systems particularly convenient. In the past, studying root system genes was very troublesome. Now, we can precisely edit the target genes directly and modify them however we want. For instance, recently someone used this method to knock out the genes that control root growth. As a result, it was found that not only did the root system change, but the drought resistance of the entire plant was also affected. The greatest advantage of this technology is its speed. It can verify the function of a gene within just a few months, which is much more time-saving than traditional methods. However, it should be noted that although technology has advanced, the complex interactions among soybean genes still often leave people confused. Sometimes, modifying one gene can affect several unexpected traits.
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