# Genomic variation induced by a low concentration of ethyl methanesulfonate (EMS) in quinoa ‘Longli-4’ variety

## TL;DR

This study shows how a low concentration of EMS causes uneven mutations in the quinoa genome, offering insights for breeding.

## Contribution

The study provides the first detailed analysis of EMS-induced genomic variation in quinoa using a low concentration.

## Key findings

- EMS induced SNPs unevenly across all 18 quinoa chromosomes with an average of 91.2 SNPs per Mb.
- G/C to A/T transitions dominated mutations, and SNPs were mostly found in intergenic regions.
- A positive correlation was found between chromosome length and the number of SNPs.

## Abstract

Quinoa (Chenopodium quinoa, 2n = 4x = 36), a super pseudocereal crop, has been introduced into China nearly 60 years. Many excellent varieties have been developed through massive selection; however, few are developed through mutagenesis breeding. In this study, the ‘Longli-4’ variety, locally cultivated in Gansu province, Northwest China, was selected for experimentation. The grains of ‘Longli-4’ were treated with ethyl methanesulfonate (EMS) at a concentration of 0.8% for 8 h. Nine plants from independent M2 families were randomly selected to investigate the mutagenesis effect of EMS on the quinoa genome. The results indicated that the single nucleotide polymorphisms (SNPs) induced by EMS were unevenly distributed across all 18 chromosomes, with an average mutation frequency of 91.2 SNPs/Mb, ranging from 4.5 to 203.5 SNPs/Mb. A significant positive correlation between the number of SNPs and chromosome length was identified through linear model analysis. Transitions from G/C to A/T were the most predominated in all variant categories, accounting for 34.4–67.2% of the mutations, and SNPs were significantly enriched in intergenic regions, representing 69.2–75.1% of the total mutations. This study provides empirical support for the application of low concentration EMS treatment in quinoa breeding.

The online version contains supplementary material available at 10.1186/s40529-024-00427-x.