# Genetic analysis of the single internode dwarf 1 mutant in barley

## TL;DR

This study identifies a gene responsible for dwarf barley plants with single internode stems, offering insights into stem development in cereals.

## Contribution

The study maps the Sid1 gene to a 429-kb region on chromosome 4H and identifies a mutation in an EPF-coding gene as a candidate for the dwarf phenotype.

## Key findings

- The Sid1 gene was mapped to a 429-kb region on chromosome 4H in barley.
- A C → T transition in an EPF-coding gene introduces a premature stop codon in the sid1 mutant.
- The EPF-encoding gene is a promising candidate for the Sid1 locus.

## Abstract

Stem development is crucial for plant lodging, nutrients and water transport, and structural support for other organs. Understanding stem development and growth is essential for ensuring global food security. Although numerous lodging-resilient and high-yielding crop varieties have been developed in the Green Revolution by controlling plant height, the molecular mechanism underlying stem development, particularly for cereals, is not fully understood. The allelic stem mutants in barley (Hordeum vulgare subsp. vulgare), single internode dwarf 1 (sid1), provide a model system for genetic studies on stem development.

We characterized and genetically analyzed the sid1.b mutation. To determine the precise position of Sid1, a high-resolution genetic map was constructed. Segregating F2 plants derived from a cross between wild type (WT) and the mutant were genotyped with the barley 50 k iSelect SNP Array, and the detected SNPs were converted to PCR-based markers for fine mapping. The Sid1 gene was mapped to a 429-kb region on chromosome 4H. Illumina sequencing of WT and sid1 identified a C → T transition in an epidermal pattern factor (EPF)-coding gene, which introduces a premature stop codon in the mutant allele.

In the present study, we genetically characterized and mapped the sid1.a mutation, which causes a dwarfed phenotype with single internode stems in barley. The EPF-encoding gene in the delimited region is a promising candidate for Sid1. Therefore, our study provides a foundation for cloning of Sid1, which will enhance our understanding of the molecular mechanisms underlying stem development, particularly in monocot plants.

The online version contains supplementary material available at 10.1186/s12870-025-06790-6.