State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, China.
Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, Shandong, China.
Plant Cell Rep. 2024 Oct 7;43(11):254. doi: 10.1007/s00299-024-03339-z.
The genomic organization, phylogenetic relationship, expression patterns, and genetic variations of m6A-related genes were systematically investigated in wild emmer wheat and the function of TdFIP37 regulating salt tolerance was preliminarily determined. m6A modification is one of the most abundant and crucial RNA modifications in eukaryotics, playing the indispensable role in growth and development as well as stress response in plants. However, its significance in wild emmer wheat remains elusive. Here, a genome-wide search of m6A-related genes was conducted in wild emmer wheat to obtain 64 candidates, including 21 writers, 17 erasers, and 26 readers. Phylogenetic and collinearity analysis demonstrated that segmental duplication and polyploidization contributed mainly to the expansion of m6A-related genes in wild emmer. A number of cis-acting elements involving in stress and hormonal regulation were found in the promoter regions of them, such as MBS, LTR, and ABRE. Genetic variation of them was also investigated using resequencing data and obvious genetic bottleneck was occurred on them during wild emmer wheat domestication process. Furthermore, the salt-responsive candidates were investigated through RNA-seq data and qRT-PCR validation using the salt-tolerant and -sensitive genotypes and the co-expression analysis showed that they played the hub role in regulating salt stress response. Finally, the loss-function mutant of Tdfip37 displayed the significantly higher salt-sensitive compared to WT and then RNA-seq analysis demonstrated that FIP37 mediated the MAPK pathway, hormone signal transduction, as well as transcription factor to regulate salt tolerance. This study provided the potential m6A genes for functional analysis, which will contribute to better understand the regulatory roles of m6A modification and also improve the salt tolerance from the perspective of epigenetic approach in emmer wheat and other crops.
系统研究了野生二粒小麦中 m6A 相关基因的基因组组织、系统发育关系、表达模式和遗传变异，并初步确定了 TdFIP37 调节耐盐性的功能。m6A 修饰是真核生物中最丰富和最重要的 RNA 修饰之一，在植物的生长发育以及应对胁迫中发挥着不可或缺的作用。然而，其在野生二粒小麦中的意义尚不清楚。本研究在野生二粒小麦中进行了 m6A 相关基因的全基因组搜索，获得了 64 个候选基因，包括 21 个写入器、17 个擦除器和 26 个读取器。系统发育和共线性分析表明，片段复制和多倍化主要导致野生二粒小麦 m6A 相关基因的扩张。在它们的启动子区域发现了许多涉及应激和激素调节的顺式作用元件，如 MBS、LTR 和 ABRE。利用重测序数据对它们的遗传变异进行了研究，发现它们在野生二粒小麦驯化过程中发生了明显的遗传瓶颈。此外，通过 RNA-seq 数据和使用耐盐和敏感基因型的 qRT-PCR 验证研究了盐响应候选基因，共表达分析表明它们在调节盐胁迫反应中发挥着核心作用。最后，Tdfip37 的功能丧失突变体与 WT 相比表现出明显的盐敏感，然后 RNA-seq 分析表明 FIP37 介导了 MAPK 途径、激素信号转导以及转录因子来调节耐盐性。本研究为功能分析提供了潜在的 m6A 基因，这将有助于更好地理解 m6A 修饰的调控作用，并从二粒小麦和其他作物的表观遗传角度提高耐盐性。
