Comparative transcriptome analysis reveals candidate gene for flowering time QTL HvHeading in barley

TL;DR

This study identifies a candidate gene linked to flowering time in barley, offering insights into how crops adapt and improve productivity.

Contribution

The study identifies HvSpt6 as a candidate gene for HvHeading QTL and reveals promoter mutations affecting flowering time.

Findings

Phenotyping and RNA-sequencing identified a 3.94 Mbs interval with 22 differentially expressed genes.

Promoter mutations in HvSpt6 create a binding site for TEM1, potentially delaying flowering in barley.

The study demonstrates an effective approach for gene identification in complex crop genomes.

Abstract

Identifying genes regulating flowering time enhances understanding mechanisms that improve crop adaptation and productivity. This study aims to identify gene(s) underlying barley flowering time quantitative trait locus (QTL) “HvHeading”.

To investigate the reported delayed-flowering effect of QTL, we selected spring barley MAGIC DH lines with different alleles in HvHeading locus which carry the same alleles in epistatic loci. Phenotyping apex development revealed contrasting effects of two alleles of HvHeading locus. Combining recombination and differential gene expression analyses using RNA-sequencing for apex and leaf tissue pinpointed a 3.94 Mbs interval which carried 22 differently expressed genes. Initial analysis using Morex IBSC v2 reference genome suggested a transcription elongation factor HvSpt6, encoded by HORVU1Hr1G067820, as a possible candidate gene potentially involved in flowering time regulation. Full-length HvSpt6 sequencing found two promoter mutations in the allele from delayed-flowering genotype, creating a binding site for TEM1, a transcription factor known for involvement in suppressing flowering time in Arabidopsis.

The findings provided the first insights for flowering time regulation by HvHeading underlying gene. Though further functional studies are needed to conclusively identify the causal gene. This study showed that leveraging knowledge of epistatic loci to address phenotypic background effects, followed by RNA sequencing can be an effective approach for identifying genes in large regions of suppressed recombination in crops with complex genomes.

The online version contains supplementary material available at 10.1186/s12870-025-06598-4.

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