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Although soybean and chickpea belong to the legume family, their seed starch content is very different. Currently, many studies focus on the molecular mechanisms of starch synthesis within a single species. However, the key genes and regulatory relationships responsible for the difference in seed starch content between the two species remain unknown. To elucidate the molecular mechanisms responsible for the above difference, multi-omics and bioinformatics analyses were used here to analyze gene expression patterns, protein–protein interaction networks, gene-transcription factor co-expression networks, and miRNA–gene regulatory relationships based on reported sucrose and starch metabolic genes in Arabidopsis. The results were as follows. First, seven differential expression genes of the two species in starch synthesis metabolism, including GBSS1, APL3, APS1, SS2, PTST, SBE2, and ISA, and the starch degradation gene BMY in soybean and chickpea, may contribute to their seed starch content differences. Then, the protein–protein interaction between DPEs and PHS may facilitate seed starch synthesis in chickpea. Finally, the positive regulation of two starch degradation genes (GmBMY and GmPHS) and four sucrose metabolism genes (GmHXK, GmPFK, GmTPS, and GmFRK) by transcription factors may lead to lower seed starch content in soybean. This study elucidates the possible molecular mechanisms underlying the difference in seed starch content between the two species and addresses the scientific problem of why soybean seeds have lower starch content than chickpea seeds. [ABSTRACT FROM AUTHOR]