Genome-wide association study for identification of SNP markers associated with barley spike productivity (Hordeum vulgare L.)
Abstract
Background. Barley (Hordeum vulgare L.) is an important cereal crop with a wide range of uses. Barley yield is a complex indicator consisting of some yield structure components. Identification of molecular markers linked to spike morphology is of great importance for barley breeding improvement. The objective of this study was to search for significant markers and identify loci associated with barley spike traits through a genome-wide association study (GWAS).
Materials and methods. In 2021–2023, 199 accessions of spring barley of different breeding levels from the VIR collection were studied in the fields of Pushkin and Pavlovsk Laboratories of VIR. The set included 103 accessions of six-row and 96 accessions of two-row barley of various origin. Genotyping was conducted using the Barley 50K Illumina Infinium iSELECT chip. GWAS was performed in the R using the mixed linear model with a kinship matrix (MLM).
Results. A wide diversity of yield structure characters: spike length (SL), spikelet number per spike (SN), grain number per spike (GN), grain weight per spike (GW), and thousand-grain weight (TGW), was shown depending on spike row number and environmental impacts. As a result of GWAS, 129 markers associated with yield indicators were identified: 12 for SL, 73 for SN, 19 for GN, 9 for GW, and 16 for TGW. Significant markers were matched with genomic regions on all barley chromosomes. Some of them are associated with already known Vrs genes on the first five chromosomes. A protein–protein interaction analysis with k-means identified three functional clusters, including 19 SNPs linked to orthologous genes for spike development.
Conclusion. The identified markers, loci, and protein interactions are interesting for further studies of the spike architecture and quantitative traits contributing to barley yield.
About the Authors
K. A. LukinaRussian Federation
Kseniia A. Lukina, Postgraduate Student, Associate Researcher, VIR
42, 44 Bolshaya Morskaya Street, St. Petersburg 190000, Russia
I. V. Rozanova
Russian Federation
Irina V. Rozanova, Cand. Sci. (Biology), Senior Researcher, Sirius University of Science and Technology, Research Center of Genetics and Life Sciences
1 Olimpiysky Ave., Sirius Settlem., Sirius Federal Territory, Krasnodar Territory 354340, Russia
O. N. Kovaleva
Russian Federation
Olga N. Kovaleva, Cand. Sci. (Biology), Leading Researcher, VIR
42, 44 Bolshaya Morskaya Street, St. Petersburg 190000, Russia
N. A. Shvachko
Russian Federation
Nataliya A. Shvachko, Cand. Sci. (Biology), Leading Researcher, VIR
42, 44 Bolshaya Morskaya Street, St. Petersburg 190000, Russia
I. G. Loskutov
Russian Federation
Igor G. Loskutov, Dr. Sci. (Biology), Chief Researcher, Head of a Department, VIR
42, 44 Bolshaya Morskaya Street, St. Petersburg 190000, Russia
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For citations:
Lukina K.A., Rozanova I.V., Kovaleva O.N., Shvachko N.A., Loskutov I.G. Genome-wide association study for identification of SNP markers associated with barley spike productivity (Hordeum vulgare L.). Proceedings on applied botany, genetics and breeding.
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