According to the Cotton Research Institute of the Chinese Academy of Agricultural Sciences, the team led by researcher Ma Xiongfeng has successfully constructed the first cotton fiber initiation and development map that combines single-cell transcriptome, spatial transcriptome, and spatial metabolome. This map can identify the expression patterns of key genes in cotton and their relationship with metabolic pathways, analyze the core regulatory mechanisms during fiber development, and provide new ideas for further improving cotton fiber quality and increasing fiber yield. The relevant research results have been published in the internationally renowned journal Nature Communications.

　　Cotton is the main raw material for the textile industry. Cotton fibers are developed from single cells on the surface of the outer epidermis of seeds. In the early stages of seed development, about 25% of ovule epidermal cells differentiate into cotton fibers, which go through four different stages: initiation, elongation and primary wall formation, secondary wall thickening, and fiber maturation. The first two stages determine the amount and length of fibers produced by each seed, which will directly affect the final cotton fiber yield; The latter two stages are related to cell wall thickening, which determines fiber strength and fineness, and will directly affect the final cotton fiber quality.

　　However, the regulatory mechanisms that determine the above developmental stages are still largely unknown. Therefore, analyzing the mechanisms that determine the fate of cell development and regulate the initiation and elongation of cotton fibers will provide new avenues for improving cotton fiber yield and quality.

　　The research team used the standard strain TM-1 of upland cotton as the research material to draw single-cell transcriptome, spatial transcriptome, and spatial metabolomics maps of early cotton fiber development. They constructed a multi-level dynamic regulatory network for cotton fiber initiation and development, which not only captures gene expression patterns during fiber cell development with high resolution, but also reveals metabolic changes closely related to gene expression, filling the current technical gap in fiber cell development research.

　　It is reported that the team has identified a group of key genes regulating the initiation and development of cotton fibers through further multi omics joint analysis, and selected some of these genes for functional verification. It was found that the BEE3 gene plays a key role in regulating the initiation and development of fibers, and overexpression of this gene can significantly promote the development of ovule epidermal cells into fiber cells.

　　At present, the team is conducting genetic analysis of the functional mechanism of the gene in cotton 113, a high lint percentage material, to discover excellent allelic variations, in order to develop valuable molecular markers for the cultivation of high lint percentage cotton varieties. The single-cell omics data and spatial transcriptome data during the initial development of cotton fibers have been shared.