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Background High temperature shock is becoming increasingly common in our climate, affecting plant growth and productivity. The ability of a plant to survive stress is a complex phenomenon. One of the essential tissues for plant performance under various environmental stimuli is the crown. However, the molecular characterization of this region remains poorly investigated. Gibberellins play a fundamental role in whole-plant stature formation. This study identified plant stature modifications and crown-specific transcriptome re-modeling in gibberellin-deficient barley  sdw1 . a  (BW827) and  sdw1.d  (BW828) mutants exposed to increased temperature. Results The deletion around the  sdw1  gene in BW827 was found to encompass at least 13 genes with primarily regulatory functions. A bigger genetic polymorphism of BW828 than of BW827 in relation to wild type was revealed. Transcriptome-wide sequencing (RNA-seq) revealed several differentially expressed genes involved in gibberellin metabolism and heat response located outside of introgression regions. It was found that  HvGA20ox4 , a paralogue of the  HvGA20ox2  gene, was upregulated in BW828 relative to other genotypes, which manifested as basal internode elongation. The transcriptome response to elevated temperature differed in the crown of  sdw1.a  and  sdw1.d  mutants; it was most contrasting for  HvHsf  genes upregulated under elevated temperature in BW828, whereas those specific to BW827 were downregulated. In-depth examination of  sdw1  mutants revealed also some differences in their phenotypes and physiology. Conclusions We concluded that despite the studied  sdw1  mutants being genetically related, their heat response seemed to be genotype-specific and observed differences resulted from genetic background diversity rather than single gene mutation, multiple gene deletion, or allele-specific expression of the  HvGA20ox2  gene. Differences in the expressional reaction of genes to heat in different  sdw1  mutants, found to be independent of the polymorphism, could be further explained by in-depth studies of the regulatory factors acting in the studied system. Our findings are particularly important in genetic research area since molecular response of crown tissue has been marginally investigated, and can be useful for wide genetic research of crops since barley has become a model plant for them.

High-throughput sequencing data revealed genotype-specific changes evoked by heat stress in crown tissue of barley sdw1 near-isogenic lines