Genetic analysis and molecular mapping of the purple leaf sheath in barley (Hordeum vulgare)

Authors: Bayable, Demeke; Caspersen, Ann; Fiedler, Jason; Hu, Gongshe; Gao, Dongying

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/21/2025
Publication Date: 4/24/2025
Citation: Bayable, D.M., Caspersen, A.M., Fiedler, J.D., Hu, G., Gao, D. 2025. Genetic analysis and molecular mapping of the purple leaf sheath in barley (Hordeum vulgare). The Plant Genome. 18:e70034. https://doi.org/10.1002/tpg2.70034.
DOI: https://doi.org/10.1002/tpg2.70034

Interpretive Summary: Barley is a major cereal crop plant worldwide grown mainly for beverages, feed and food. In the United States, the crop is grown in more than 23 states, Idaho being a major producer. Barley cultivars develop purple pigmentation in different plant parts. The pigment has antioxidant property that can confer health benefits when the grain is consumed. In the vegetative tissue, the pigment might confer tolerance to environmental stresses and contribute to wide adaptation, although the effect on crop productivity is poorly understood. In addition, relationships between the genetic control of the pigment development between the reproductive and vegetative tissue is not clearly known. In this study, we examined the development of purple pigmentation on the leaf sheath of a newly released spring barley cultivar ('GemCraft') and its genetic basis compared to other barley cultivars that do not develop the pigment. 'GemCraft' seedling develops green leaf sheath like the other cultivars, and the purple pigment accumulation begins late in the seedling stage. The pigment development on the reproductive tissue was not stable, and when developed, not clearly visible on the grain. We identified a gene region that controlled >70% of the pigment development on the leaf sheath. The region harbors 79 genes, most of them with an unknown role in barley. Comparative analysis with relatively well studied crop plants of the same grass lineage like rice was used to examine the likely gene (from the 79 genes) responsible for the purple pigment development. A single gene (HORVU.MOREX.r3.2HG0188710) likely controls the purple pigment development in the 'GemCraft' leaf sheath. This finding facilitates use of molecular marker to track the gene in plant breeding and to clone the gene for further studies. Unraveling the tissue-specific regulation of the pigmentation in the barley plant system is essential for effective manipulation of the pigment development for specific end uses.

Technical Abstract: Although anthocyanin is frequently found in various barley organs, the genetic basis of the pigmentation is still poorly understood. In this study, we examined the development of anthocyanin in GemCraft, a malting barley cultivar showing purple leaf sheath (PLS), and found that the pigmentation became visible on the leaf sheath at the early tillering stage. This study employed single nucleotide polymorphism (SNP) array genotyping data in two F2 populations developed using GemCraft and two barley lines with green leaf sheath throughout the plant development. Genetic and quantitative trait locus (QTL) analyses suggested regulation of the purple pigment accumulation by a single major QTL that was inherited as a dominant allele, which was necessary for the phenotype to develop. A major QTL, named qPLS2 (purple leaf sheath2 locus), was found on chromosome 2H and explained >70% of the trait variation. Nonetheless, the genetic model in the two mapping populations resonated between multiple loci and a single locus that determines the trait variation. Accordingly, in one of the populations, three minor QTL were also detected on chromosomes 1H and 5H: each of these QTL explained <5% variation and showed influence in regulation of the purple pigment intensity. In the qPLS2 QTL interval, comparative genomic analysis of annotated genes that are widely known to regulate anthocyanin development in plants identified a single candidate gene encoding a basic helix–loop–helix (bHLH) transcription factor. The study identified a new major QTL associated with the purple leaf sheath and generated further information for validation and cloning the causal gene for effective utilization of anthocyanin in barley genetic improvement.