Luo Chuping, He Bing, Shi Pibiao, Xi Jinlong, Gui Hongbing, Pang Bingwen, Cheng Junjie, Hu Fengqin, Chen Xi, Lv Yuanda
School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China.
Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
Front Plant Sci. 2022 Sep 20;13:988845. doi: 10.3389/fpls.2022.988845. eCollection 2022.
Chenopodium quinoa is a crop with outstanding tolerance to saline soil, but long non-coding RNAs (LncRNAs) expression profile driven by salt stress in quinoa has rarely been observed yet. Based on the high-quality quinoa reference genome and high-throughput RNA sequencing (RNA-seq), genome-wide identification of LncRNAs was performed, and their dynamic response under salt stress was then investigated. In total, 153,751 high-confidence LncRNAs were discovered and dispersed intensively in chromosomes. Expression profile analysis demonstrated significant differences between LncRNAs and coding RNAs. Under salt stress conditions, 4,460 differentially expressed LncRNAs were discovered, of which only 54 were differentially expressed at all the stress time points. Besides, strongly significantly correlation was observed between salt-responsive LncRNAs and their closest neighboring genes ( = 0.346, -value < 2.2e-16). Furthermore, a weighted co-expression network was then constructed to infer the potential biological functions of LncRNAs. Seven modules were significantly correlated with salt treatments, resulting in 210 hub genes, including 22 transcription factors and 70 LncRNAs. These results indicated that LncRNAs might interact with transcription factors to respond to salinity stress. Gene ontology enrichment of the coding genes of these modules showed that they were highly related to regulating metabolic processes, biological regulation and response to stress. This study is the genome-wide analysis of the LncRNAs responding to salt stress in quinoa. The findings will provide a solid framework for further functional research of salt responsive LncRNAs, contributing to quinoa genetic improvement.
藜麦是一种对盐碱土壤具有出色耐受性的作物，但盐胁迫驱动下藜麦中长链非编码RNA（LncRNAs）的表达谱尚未得到充分研究。基于高质量的藜麦参考基因组和高通量RNA测序（RNA-seq），对LncRNAs进行了全基因组鉴定，并研究了它们在盐胁迫下的动态响应。总共发现了153,751个高可信度的LncRNAs，它们密集地分布在染色体上。表达谱分析表明LncRNAs和编码RNA之间存在显著差异。在盐胁迫条件下，发现了4,460个差异表达的LncRNAs，其中只有54个在所有胁迫时间点均有差异表达。此外，盐响应LncRNAs与其最邻近基因之间存在极显著的相关性（ = 0.346， -值 < 2.2e-16）。此外，构建了一个加权共表达网络来推断LncRNAs的潜在生物学功能。七个模块与盐处理显著相关，产生了210个枢纽基因，包括22个转录因子和70个LncRNAs。这些结果表明LncRNAs可能与转录因子相互作用以响应盐胁迫。这些模块的编码基因的基因本体富集表明，它们与调节代谢过程、生物调节和应激反应高度相关。本研究是对藜麦中响应盐胁迫的LncRNAs进行的全基因组分析。这些发现将为盐响应LncRNAs的进一步功能研究提供坚实的框架，有助于藜麦的遗传改良。
