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 (Fagopyrum tataricum 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 FtNRT1.14, FtMYB61/52, FtbZIP6/34, FtNAC72/73, and FtLTP14. 19 small secreted peptides (SSPs) encoding genes were respond to high NH4 +, including FtCLE7 and FtCEP3. The up-regulation of FtCLE7 expression and down-regulation of FtCEP3 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 TFs such as MYB, MADS, and LBD genes and the RLKs such as FtBAM1/3 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.