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

## TL;DR

This study explores how Tartary buckwheat responds to high ammonium stress, identifying key genes and mechanisms that could help breed more tolerant plants.

## Contribution

The study integrates physiological, transcriptomic, and genomic data to uncover novel genes and pathways involved in Tartary buckwheat's response to high ammonium.

## Key findings

- High ammonium stress inhibits root growth by affecting antioxidant enzyme activities in Tartary buckwheat.
- 426 differentially expressed genes were identified, with many related to antioxidant systems and hormone signaling being down-regulated.
- Candidate genes like FtCLE7 and FtCEP3 are suggested to help plants adapt to high ammonium conditions.

## Abstract

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.