National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
Wuhan Igenebook Biotechnology Co., Ltd, Wuhan, 430014, China.
Genome Biol. 2023 Apr 4;24(1):65. doi: 10.1186/s13059-023-02908-x.
Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs to the transcriptome, is critical for determining the traits that influence wheat growth and development. Asymmetric transcription of homoeologs has been so far investigated in a tissue or organ-specific manner, which could be misleading due to a mixture of cell types.
Here, we perform single nuclei RNA sequencing and ATAC sequencing of wheat root to study the asymmetric gene transcription, reconstruct cell differentiation trajectories and cell-type-specific gene regulatory networks. We identify 22 cell types. We then reconstruct cell differentiation trajectories that suggest different origins between epidermis/cortex and endodermis, distinguishing bread wheat from Arabidopsis. We show that the ratio of asymmetrically transcribed triads varies greatly when analyzing at the single-cell level. Hub transcription factors determining cell type identity are also identified. In particular, we demonstrate that TaSPL14 participates in vasculature development by regulating the expression of BAM1. Combining single-cell transcription and chromatin accessibility data, we construct the pseudo-time regulatory network driving root hair differentiation. We find MYB3R4, REF6, HDG1, and GATAs as key regulators in this process.
Our findings reveal the transcriptional landscape of root organization and asymmetric gene transcription at single-cell resolution in polyploid wheat.
同源基因是指由异源多倍体形成的同源基因。普通小麦（Triticum aestivum）是一种异源六倍体物种，具有许多同源基因。同源基因表达偏向性是指同源基因对转录组的相对贡献，对于确定影响小麦生长和发育的性状至关重要。迄今为止，同源基因的不对称转录一直是在组织或器官特异性的方式下进行研究的，由于细胞类型的混合，这可能会产生误导。
在这里，我们对小麦根进行了单核 RNA 测序和 ATAC 测序，以研究不对称基因转录、重建细胞分化轨迹和细胞类型特异性基因调控网络。我们鉴定了 22 种细胞类型。然后，我们重建了细胞分化轨迹，这些轨迹表明表皮/皮层和内皮层之间的起源不同，这将普通小麦与拟南芥区分开来。我们表明，在单细胞水平分析时，不对称转录三联体的比例变化很大。确定细胞类型身份的枢纽转录因子也被鉴定出来。特别是，我们证明 TaSPL14 通过调节 BAM1 的表达参与了血管发育。通过结合单细胞转录组和染色质可及性数据，我们构建了驱动根毛分化的拟时调控网络。我们发现 MYB3R4、REF6、HDG1 和 GATAs 是这个过程中的关键调节因子。
我们的研究结果揭示了多倍体小麦中根组织和不对称基因转录的单细胞分辨率转录景观。
