Ando Atsumi, Kirkbride Ryan C, Jones Don C, Grimwood Jane, Chen Z Jeffrey
Department of Molecular Biosciences, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA.
Agriculture and Environmental Research, Cotton Incorporated, Cary, NC, USA.
BMC Genomics. 2021 Apr 29;22(1):309. doi: 10.1186/s12864-021-07579-1.
Cotton fibers provide a powerful model for studying cell differentiation and elongation. Each cotton fiber is a singular and elongated cell derived from epidermal-layer cells of a cotton seed. Efforts to understand this dramatic developmental shift have been impeded by the difficulty of separation between fiber and epidermal cells.
Here we employed laser-capture microdissection (LCM) to separate these cell types. RNA-seq analysis revealed transitional differences between fiber and epidermal-layer cells at 0 or 2 days post anthesis. Specifically, down-regulation of putative cell cycle genes was coupled with upregulation of ribosome biosynthesis and translation-related genes, which may suggest their respective roles in fiber cell initiation. Indeed, the amount of fibers in cultured ovules was increased by cell cycle progression inhibitor, Roscovitine, and decreased by ribosome biosynthesis inhibitor, Rbin-1. Moreover, subfunctionalization of homoeologs was pervasive in fiber and epidermal cells, with expression bias towards 10% more D than A homoeologs of cell cycle related genes and 40-50% more D than A homoeologs of ribosomal protein subunit genes. Key cell cycle regulators were predicted to be epialleles in allotetraploid cotton. MYB-transcription factor genes displayed expression divergence between fibers and ovules. Notably, many phytohormone-related genes were upregulated in ovules and down-regulated in fibers, suggesting spatial-temporal effects on fiber cell development.
Fiber cell initiation is accompanied by cell cycle arrest coupled with active ribosome biosynthesis, spatial-temporal regulation of phytohormones and MYB transcription factors, and homoeolog expression bias of cell cycle and ribosome biosynthesis genes. These valuable genomic resources and molecular insights will help develop breeding and biotechnological tools to improve cotton fiber production.
棉纤维为研究细胞分化和伸长提供了一个有力的模型。每根棉纤维都是一个单独的细长细胞，由棉籽表皮层细胞发育而来。由于纤维细胞与表皮细胞难以分离，阻碍了人们对这种显著发育转变的理解。
在此，我们采用激光捕获显微切割技术（LCM）来分离这些细胞类型。RNA测序分析揭示了开花后0天或2天纤维细胞与表皮层细胞之间的过渡差异。具体而言，假定的细胞周期基因下调与核糖体生物合成及翻译相关基因上调相关联，这可能暗示了它们在纤维细胞起始过程中的各自作用。事实上，细胞周期进程抑制剂Roscovitine增加了培养胚珠中的纤维数量，而核糖体生物合成抑制剂Rbin-1则减少了纤维数量。此外，同源基因的亚功能化在纤维细胞和表皮细胞中普遍存在，细胞周期相关基因的D同源基因比A同源基因的表达偏向多10%，核糖体蛋白亚基基因的D同源基因比A同源基因的表达偏向多40 - 50%。关键细胞周期调节因子预计是异源四倍体棉花中的表观等位基因。MYB转录因子基因在纤维细胞和胚珠之间表现出表达差异。值得注意的是，许多植物激素相关基因在胚珠中上调而在纤维细胞中下调，表明对纤维细胞发育存在时空效应。
纤维细胞起始伴随着细胞周期停滞，同时核糖体生物合成活跃、植物激素和MYB转录因子的时空调节以及细胞周期和核糖体生物合成基因的同源基因表达偏向。这些有价值的基因组资源和分子见解将有助于开发育种和生物技术工具，以提高棉花纤维产量。
