Allelic diversity of the barley semidwarfing genes HvGA20ox2, Sln1, HvBRI1, and HvDep1: integrating published data and results of the in silico pangenome analysis
https://doi.org/10.30901/2227-8834-2026-1-o12
Abstract
This review is focused on analyzing the polymorphism of the dwarfing genes HvGA20ox2, HvBRI1, and HvDep1 in cultivated barley, as well as the Sln1 gene, which is promising in this regard. Data on the mechanism of action and the role of their natural and induced alleles in barley breeding are summarized. To expand our understanding of the polymorphism of HvGA20ox2, Sln1, HvBRI1, and HvDep1, this review integrates the results of the in silico analysis of their sequences in the cultivated barley pangenome, which includes 53 genotypes. This approach revealed a spectrum of previously uncharacterized haplotypes and mutations potentially associated with plant height. For HvGA20ox2, 10 promoter haplotypes and 6 protein types were identified, including the known alleles sdw1.c, sdw1.d, sdw1.ins, and sdw1.ZU9, with the latter two differentiated into subtypes. The Sln1 gene was characterized by a highly conserved coding region (changes were detected in only three genotypes), whereas the promoter region exhibited considerable variability, with 13 haplotypes. For HvBRI1, the uzu1.a dwarfism allele was identified; however, this gene is characterized by the lowest polymorphism of both the promoter and coding regions. The highest promoter variability (81% of the accessions differed from the wild type) with highly conserved protein was demonstrated for HvDep1. Thus, these data expand opportunities for the targeted application of the identified genetic diversity in further fundamental and applied research in barley breeding.
Supporting agencies: The study was supported by a grant from the Russian Science Foundation (No. 25-26-00341, https://rscf.ru/project/25-26-00341/).
About the Authors
I. V. Porotnikov
N.I. Vavilov All-Russian Institute of Plant Genetic Resources
Russian Federation
Russian Federation
Igor V. Porotnikov, Researcher, VIR
42, 44 Bolshaya Morskaya Street, St. Petersburg 190000, Russia
K. A. Lukina
N.I. Vavilov All-Russian Institute of Plant Genetic Resources
Russian Federation
Russian Federation
Kseniia A. Lukina, Researcher, VIR
42, 44 Bolshaya Morskaya Street, St. Petersburg 190000, Russia
O. Yu. Antonova
N.I. Vavilov All-Russian Institute of Plant Genetic Resources
Russian Federation
Russian Federation
Olga Yu. Antonova, Cand. Sci. (Biology), Leading Researcher, VIR
42, 44 Bolshaya Morskaya Street, St. Petersburg 190000, Russia
O. N. Kovaleva
N.I. Vavilov All-Russian Institute of Plant Genetic Resources
Russian Federation
Russian Federation
Olga N. Kovaleva, Cand. Sci. (Biology), Leading Researcher, VIR
42, 44 Bolshaya Morskaya Street, St. Petersburg 190000, Russia
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Supplementary files
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1. Приложение_Рисунок S1_Appendix_Fig S1 | |
| Subject | A circular dendrogram constructed based on the sequence analysis of the Sln1 gene promoter region. | |
| Type | Исследовательские инструменты | |
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2. Приложение_Рисунок S2_Appendix_Fig S2 | |
| Subject | . A circular dendrogram constructed based on the sequence analysis of the HvDEP1 gene promoter region. | |
| Type | Исследовательские инструменты | |
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3. Приложение_таблица 1_Appendix_Table S1 | |
| Subject | Identification numbers for the genes HvGA20ox2, Sln1, HvBRI1 and HvDEP1 in 53 accessoins of cultivated barley from the pangenome | |
| Type | Исследовательские инструменты | |
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4. Приложение_таблица 2_Appendix_Table S2 | |
| Subject | Characteristics of haplotypes isolated from 53 accessions of cultivated barley based on the analysis of polymorphism of the promoter region of the HvGA20ox2 gene | |
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5. Приложение_таблица 3_Appendix_Table S3 | |
| Subject | Characteristics of haplotypes isolated from 53 accessions of cultivated barley based on the analysis of polymorphism of the promoter region of the Sln1 gene | |
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6. Приложение_таблица 4_Appendix_Table S4 | |
| Subject | Characteristics of haplotypes isolated from 53 accessions of cultivated barley based on the analysis of polymorphism of the promoter region of the HvBRI1 gene | |
| Type | Исследовательские инструменты | |
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7. Приложение_таблица 5_Appendix_Table S5 | |
| Subject | Characteristics of haplotypes isolated from 53 accessions of cultivated barley based on the analysis of polymorphism of the promoter region of the HvDEP1 gene | |
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For citations:
Porotnikov I.V., Lukina K.A., Antonova O.Yu., Kovaleva O.N. Allelic diversity of the barley semidwarfing genes HvGA20ox2, Sln1, HvBRI1, and HvDep1: integrating published data and results of the in silico pangenome analysis. Proceedings on applied botany, genetics and breeding. 2026;187(1):262-276. (In Russ.) https://doi.org/10.30901/2227-8834-2026-1-o12
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