Physiological, transcriptomic, and genomic analysis unravels the response of Tatary buckwheat root to high ammonium stress

Toxicity caused by high ammonium severely affects plant growth and crop production, it is urgent to breed high NH₄ ⁺-tolerant and high-yield plants. However, the molecular mechanisms on the response and tolerance of plant to high NH₄ ⁺ remain poorly understood. In this study, four different genotypes of Tartary buckwheat (<i>Fagopyrum tataricum</i> Garetn.) were used to investigate the molecular mechanism on high NH₄ ⁺ response by integrating physiological, transcriptome, and genome analysis. The root and shoot growth of Tartary buckwheat (TB) seedlings were significantly inhibited by 50 and 100 mmol/L NH₄ ⁺ treatments. High NH₄ ⁺ inhibits root growth by affecting activities of antioxidant enzymes, thereby suppressing plant growth. In total 426 high NH₄ ⁺-responsive common differentially expressed genes (DEGs) were identified in TB. Most of DEGs involved in antioxidant enzyme system, hormone signaling, and N transport and assimilation were down-regulated by high NH₄ ⁺. Co-expression analysis suggested the possible hub genes in regulating high NH₄ ⁺ response, such as <i>FtNRT1.14</i>, <i>FtMYB61/52</i>, <i>FtbZIP6/34</i>, <i>FtNAC72/73</i>, and <i>FtLTP14.</i> 19 small secreted peptides (SSPs) encoding genes were respond to high NH₄ ⁺, including <i>FtCLE7</i> and <i>FtCEP3</i>. The up-regulation of <i>FtCLE7</i> expression and down-regulation of <i>FtCEP3</i> expression may help plants to optimize root perception and response to high NH₄ ⁺. Additionally, 443 genotype-specific high NH₄ ⁺-responsive DEGs with sequence variation were identified by integrating transcriptome and genome re-sequencing data. The <i>TFs</i> such as <i>MYB</i>, <i>MADS</i>, and <i>LBD</i> genes and the <i>RLKs</i> such as <i>FtBAM1/3</i> may help TB to adapt to high NH₄ ⁺. This work provides useful information for investigating the mechanisms on TB respond to high NH₄ ⁺, and the candidate genes for breeding TB with high NH₄ ⁺ tolerance were suggested.