Identification of Informative Microsatellite Markers in the Avena Chloroplast Genome Provides New Insights into Oat Phylogeny
Svetlana Goryunova1,2,*, Margarita Lebedeva1, Aya Trifonova1, Denis Goryunov2,3, Anastasia Sivolapova2, Aleksey Troitsky3, Igor Loskutov4, Vitalii Pukhalskiy1
1 Laboratory of Plant Genetics, Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russia
2 Laboratory of Cell and Genomic Technologies, Russian Potato Research Center, Kraskovo, Russia
3 Department of Evolutional Biochemistry, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
4 Department Genetic Resources of Oat, Barley, Rye, Federal Research Center N. I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
* Corresponding Author: Svetlana Goryunova. Email: 
Phyton-International Journal of Experimental Botany https://doi.org/10.32604/phyton.2026.077294
Received 06 December 2025; Accepted 12 March 2026; Published online 05 June 2026
Abstract
Twenty-six cultivated and wild oat species with genomes of varying ploidy levels are currently known worldwide. The search for informative markers, as well as the analysis of variability and phylogeny of oat species, represents a key research directions with both fundamental and applied significance. Chloroplast microsatellites are promising markers for studying groups of closely related species, particularly in the context of allopolyploid origin analyses. The transferability of chloroplast microsatellite markers among species belonging to different “core pooids” supertribes within the Pooideae subfamily of Poaceae has been demonstrated. Following preliminary screening, twelve primer pairs were selected for further analysis. Using these markers, 70 samples representing 25
Avena species were evaluated. The number of alleles per locus ranged from 2 to 9, with an average genetic diversity value (H) of 0.479. Based on allele length variation, 45 haplotypes were distinguished. Considerable differences in gene diversity were observed among the oat species studied. The highest levels of polymorphism were detected in the diploid species
A. eriantha and
A. ventricosa (C-genome), one diploid species with the As-genome (
A. atlantica), and the tetraploid species
A. insularis (AC-genome) and
A. agadiriana (AaBa-genome). The absence of 50 bp-deletion in the intergenic region
ndhF–
rpl32 suggests that
A. insularis is unlikely to be the maternal progenitor of hexaploid oats. Overall, this study enabled the identification of novel informative markers for the analysis of the
Avena chloroplast genome and contributed to refining current understanding of phylogenetic relationships among oat species.
Keywords
Chloroplast microsatellite; phylogeny;
Avena; intraspecific variability
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