Single-cell RNA-seq reveals fate determination control of an individual fiber cell initiation in cotton (Gossypium hirsutum)

Abstract

Cotton fiber is a unicellular seed trichome, and lint fiber initials per seed as a factor determines fiber yield. However, the mechanisms controlling fiber initiation from ovule epidermis are not understood well enough. Here, with single-cell RNA sequencing (scRNA-seq), a total of 14,535 cells were identified from cotton ovule outer integument of Xu142_LF line at four developmental stages (1.5, 1, 0.5 days before anthesis and the day of anthesis). Three major cell types, fiber, non-fiber epidermis and outer pigment layer were identified and then verified by RNA in situ hybridization. A comparative analysis on scRNA-seq data between Xu142 and its fiberless mutant Xu142 fl further confirmed fiber cluster definition. The developmental trajectory of fiber cell was reconstructed, and fiber cell was identified differentiated at 1 day before anthesis. Gene regulatory networks at four stages revealed the spatiotemporal pattern of core transcription factors, and MYB25-like and HOX3 were demonstrated played key roles as commanders in fiber differentiation and tip-biased diffuse growth, respectively. A model for early development of a single fiber cell was proposed here, which sheds light on further deciphering mechanism of plant trichome and the improvement of cotton fiber yield.