Comparative Proteomic Atlas of Two Soybean Varieties with Contrasting Seed Oil and Protein Content

As complex quantitative traits, soybean seed oil and protein contents are governed by dynamic proteome networks that remain largely unknown. Here, we investigated the dynamic changes of the proteome during seed maturation across two soybean varieties with contrasting seed oil and protein content. Through optimizing the detectability of low-abundance proteins and utilizing library-free data-independent acquisition (directDIA) mass spectrometry, we unprecedentedly identified 7414 proteins and 3975 protein groups (PGs), substantially expanding the soybean seed proteome. Among the PGs, 1391 differentially accumulated between the two varieties. By comparing the abundance of PGs between the two varieties, we identified the core and periphery proteome of soybean seeds and revealed that variations in the oil and protein content are primarily attributed to the peripheral proteome, which significantly fluctuated across seed developmental stages. Our work presents a quantitative proteomic atlas underlying the variation of seed oil and protein content in soybean varieties and provides insight into the mechanisms regulating the seed oil and protein content in soybean.