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

• Published in: Plant biotechnology journal Vol. 20; no. 12; pp. 2372 - 2388
• Main Authors: Qin, Yuan, Sun, Mengling, Li, Weiwen, Xu, Mingqi, Shao, Lei, Liu, Yuqi, Zhao, Guannan, Liu, Zhenping, Xu, Zhongping, You, Jiaqi, Ye, Zhengxiu, Xu, Jiawen, Yang, Xiyan, Wang, Maojun, Lindsey, Keith, Zhang, Xianlong, Tu, Lili
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01.12.2022; John Wiley and Sons Inc
• Subjects: biotechnology; Cell differentiation; cell fate determination; Comparative analysis; Cotton; Cotton Fiber; Cotton fibers; cotton fibre initiation; Crop yield; Developmental stages; early development; Epidermis; flowering; Gene expression; Gene sequencing; genes; Genomics; Genotype & phenotype; Gossypium - genetics; Gossypium hirsutum; Hybridization; Integument; lint cotton; mutants; Ovule - genetics; ovules; regulatory network; Ribonucleic acid; RNA; RNA-Seq; Scanning electron microscopy; sequence analysis; single cell transcriptomic atlas; Transcription factors; trichomes; Trichomes - genetics; cell fate determination; Gossypium hirsutum; regulatory network; cotton fibre initiation; single cell transcriptomic atlas
• ISSN: 1467-7644; 1467-7652; 1467-7652
• DOI: 10.1111/pbi.13918

Summary Cotton fibre is a unicellular seed trichome, and lint fibre initials per seed as a factor determines fibre yield. However, the mechanisms controlling fibre 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, fibre, non‐fibre 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 fibreless mutant Xu142 fl further confirmed fibre cluster definition. The developmental trajectory of fibre cell was reconstructed, and fibre 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 fibre differentiation and tip‐biased diffuse growth respectively. A model for early development of a single fibre cell was proposed here, which sheds light on further deciphering mechanism of plant trichome and the improvement of cotton fibre yield. With scRNA‐seq, cotton fibre cell was identified differentiated at −1 DPA. It further refines the spatiotemporal patterns of two command genes, MYB25‐like and HOX3, who determine fibre differentiation and tip‐biased diffuse growth respectively.