Legume Genomics and Genetics 2025, Vol.16, No.2, 54-62 http://cropscipublisher.com/index.php/lgg 59 pathways such as fatty acid synthesis, lignin biosynthesis, and phenylpropanoid metabolism, many gene regions overlap with structural variations (SVS) and SNPS, and this is precisely where selective clearance occurs intensively. During the domestication process, these genes were strongly screened. In fact, it was not only for agronomic purposes. Some variations simultaneously affected seed composition, plant morphology and even stress response (Jia et al., 2024). Looking at the overall trend, the total number of SVS in cultivated populations is far lower than that in wild species, and there is also a significant loss of private variations. This difference itself indirectly confirms the genetic bottleneck brought about by domestication. 6.2 Differences in adaptive genes between wild and cultivated types Not every type of mung bean can remain calm in the face of environmental changes. Cultivated mung beans often seem "picky", while wild mung beans are much more flexible. From the comparative genomic data, it can be seen that the genetic diversity of wild populations is higher, and they carry more adaptive genes. Moreover, these differences are often hidden in regulatory regions rather than directly acting on coding sequences. Proteins with EF-hand domains associated with calcium signaling pathways occur more frequently and sometimes more complex in wild mung beans, which may be one of the reasons why they can cope with complex environments (Jia et al., 2024). In contrast, for cultivated types, in some metabolic pathways, the number of gene families has even decreased. However, it is not a one-sided weakening. For instance, the genes in the pathways related to plant-pathogen interaction and isoflavone synthesis show signs of expansion, which to some extent indicates that they are gradually finding their own rhythm in the artificial cultivation system (Liu et al., 2022). 6.3 Reconstruction of gene regulatory networks during domestication Behind many domesticated traits, it is not merely a simple change in genetic coding. The adjustment at the regulatory level is the decisive link. Minor changes in the promoter sequence and the accumulation of PAV events often affect the arrangement of the entire regulatory network. Some genes, such as PDH1 which controls pod cracking, not only have changes occurred in the coding region, but its upstream regulatory region has also been simultaneously "rewritten", which has been repeatedly mentioned in multiple transcriptome and genomic studies (Liu et al., 2022; Li et al., 2024). For instance, gene families such as B-box (BBX) that are involved in stress responses have undergone repeated expansion during the domestication process. Although most of the repetitive genes were eventually screened out by purification selection and retained the core function, these expansion phenomena themselves are sufficient to show that the regulatory system is not imstatic and it is also quietly reconstructed during the domestication process (Yin et al., 2024). 7 Applications of Comparative Genomics in Mung Bean Breeding 7.1 Development and utilization of molecular markers from domestication-related genes The breakthroughs made in molecular breeding of mung beans in recent years are inseparable from the promotion of comparative genomics. This field has identified many types of variations related to domestication and agronomic traits, such as SNPS, InDel and PAV, involving a wide range of traits, including flowering time, grain size, disease resistance, and even nutritional quality. It is worth noting that these markers are no longer just on paper; they are increasingly being used in molecular marker-assisted selection (MAS) and population genetic diversity assessment (Chen et al., 2022; Rohilla et al., 2022). However, markers are merely entry points. Tools such as high-density genetic maps and GWAS are the "Bridges" that establish clear connections between markers and traits, especially playing an accelerator role in enhancing yield and resistance. In addition, markers such as SSR, SNP and transposon-derived markers have also begun to be used for genetic assessment of interspecific hybrid offspring, with a straightforward aim - to broaden the genetic basis of breeding materials (Fatmawati et al., 2021; 2023). 7.2 Potential of genomic selection and molecular design breeding If we talk about something further than MAS, it all depends on genomic selection. Now, with the addition of GWAS, high-throughput typing technology and the pan-genome, molecular design breeding of mung beans has also begun to truly "take root". The advantage of this type of method lies in the fact that it can predict the
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