Liang Qiaoxia, Rehman Hafiz M, Zhang Jizhou, Lam Hon-Ming, Chan Ting-Fung
School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, Pakistan.
Plant Cell Environ. 2024 Oct 27. doi: 10.1111/pce.15238.
Soybean (Glycine max) is an important crop for its nutritional value. Its wild relative, Glycine soja, provides a valuable genetic resource for improving soybean productivity. Root development and differentiation are essential for soybean plants to take up water and nutrients, store energy and anchor themselves. Long noncoding RNAs (lncRNAs) have been reported to play critical roles in various biological processes. However, the spatiotemporal landscape of lncRNAs during early root development and differentiation in soybeans is scarcely characterized. Using RNA sequencing and transcriptome assembly, we identified 1578 lncRNAs in G. max and 1454 in G. soja, spanning various root portions and time points. Differential expression analysis revealed 82 and 69 lncRNAs exhibiting spatiotemporally differential expression patterns in G. max and G. soja, respectively, indicating their involvement in the early stage of root architecture formation. By elucidating multiple competitive endogenous RNA (ceRNA) networks involving lncRNAs, microRNAs and protein-coding RNAs, we unveiled intricate regulatory mechanisms of lncRNA in early root development and differentiation. Our efforts significantly expand the transcriptome annotations of soybeans, unravel the dynamic landscapes of lncRNAs during early root development and differentiation, and provide valuable resources into the field of soybean root research.
大豆（Glycine max）因其营养价值而成为一种重要作物。其野生近缘种野生大豆（Glycine soja）为提高大豆产量提供了宝贵的遗传资源。根系发育和分化对于大豆植株吸收水分和养分、储存能量以及固定自身至关重要。据报道，长链非编码RNA（lncRNAs）在各种生物学过程中发挥着关键作用。然而，大豆早期根系发育和分化过程中lncRNAs的时空图谱几乎未被描述。利用RNA测序和转录组组装，我们在栽培大豆中鉴定出1578个lncRNAs，在野生大豆中鉴定出1454个lncRNAs，涵盖了不同的根部分和时间点。差异表达分析显示，分别有82个和69个lncRNAs在栽培大豆和野生大豆中呈现时空差异表达模式，表明它们参与了根系结构形成的早期阶段。通过阐明涉及lncRNAs、微小RNA和蛋白质编码RNA的多个竞争性内源RNA（ceRNA）网络，我们揭示了lncRNA在早期根系发育和分化中的复杂调控机制。我们的工作显著扩展了大豆的转录组注释，揭示了早期根系发育和分化过程中lncRNAs的动态图谱，并为大豆根系研究领域提供了宝贵资源。
