Cotton, the primary source of natural fibers for the textile industry, is one of the most important cash crops and has long been domesticated worldwide. Of various cultivated species of cotton, two allotetraploids, Gossypium hirsutum (upland cotton) and Gossypium barbadense (extra-long staple, Pima, Egyptian, or Sea Island cotton) contribute over 90% of global fiber production [1]. While G. hirsutum possesses extensive adaptability and predominance yield, G. barbadense produces long and strong fibers with higher quality [2].Elucidating the relationship among cultivated cotton species is necessary to breed cotton more suited to agricultural needs. Genomic studies have provided high-quality assembled genomes and clarified the phylogenetic relationship between G. hirsutum and G. barbadense, associated with specific features such as fiber elongation and stress response [3]. Comparative investigations have been done involving G. hirsutum and G. barbadense, for example, characterizing heat shock proteins [4], identifying candidate genes for fiber quality, and exploring the mechanism of Verticillium wilt resistance [5].

Seed germination is the first process in the life cycle of higher plants, both in time and significance, as its success determines the proliferation of individuals and propagation of species. During seed germination, a sophisticated signaling network is evolved to regulate downstream metabolic processes and sense endogenous and exogenous signals, including phytohormones and other factors [6]. For instance, as abscisic acid (ABA) positively affects seed dormancy, it inhibits the process of seed germination adversely by directly delaying radicle expansion and activating transcription factors [7]. Gibberellins (GA) release seeds from dormancy and stimulate germination [8]. Defense mechanisms are also pivotal for the stress response of seed germination, such as reactive oxygen species (ROS) scavenging pathways, osmotic modulating system, and pathogen defense system [9].

In cotton, seed germination is of great significance and attracts the attention of botanists as well. Melatonin was found to promote seed germination by increasing antioxidant enzymes and regulating phytohormones, especially under drought and salt stress [[10], [11], [12]]. The previous study analyzed and compared the transcriptome profiles of the cold-tolerant cotton variety KN27–3 and the susceptible variety XLZ38 for tolerance and found that in KN27–3, IAA, CTK, GA, and ABA cooperate to alter energy metabolism to maintain nitrogen and carbon homeostasis, thereby promoting seed germination [13]. In addition, it was found that when seeds were subjected to varying degrees of chilling, the hydration rate of G. hirsutum was lower than that of G. narnadense [14]. However, given their specific features, the divergence of mechanisms underlying seed germination between G. hirsutum and G. barbadense has not been discussed.

Proteomics approaches have been used to reveal dynamic changes in cotton proteome responses to environmental conditions and developmental processes [15]. To better understand the different characteristics of two heterozygous polyploid kinds of cotton, we carried out a proteomic study to compare proteomes between them during seed germination. We found that although there was no significant difference in their morphology during germination, the difference in gene expression had already been demonstrated. For instance, there were more proteins related to stress and detoxification in G. hirsutum. In these two cotton species, expression patterns of some proteins related to carbon metabolism showed opposite trends. This study helps to elucidate the evolution and domestication history of cotton polyploids and may allow breeders to understand their domestication history better and improve fiber quality and adaptability.