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Solovyova M.V., Brykova A.N., Zuev E.V., Shvachko N.A. The use of genome-wide association analysis to identify markers associated with the duration of the growing season of spring soft wheat (Triticum aestivum L.). Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2026, Vol. 61, № 3, p. 422-434.
(how to cite this article)

doi: 10.15389/agrobiology.2026.3.422eng

UDC: 633.11:581.14:577.2

Acknowledgements:
Supported financially by the Russian Science Foundation, project No. 24-16-00284

 

THE USE OF GENOME-WIDE ASSOCIATION ANALYSIS TO IDENTIFY MARKERS ASSOCIATED WITH THE DURATION OF THE GROWING SEASON OF SPRING SOFT WHEAT (Triticum aestivum L.)

M.V. Solovyova ✉, A.N. Brykova, E.V. Zuev, N.A. Shvachko

Federal Research Center Vavilov All-Russian Institute of Plant Genetic Resources, 42, ul. Bol’shaya Morskaya, St. Petersburg, 190031 Russia, e-mail maria.soloveva.97@mail.ru (✉ corresponding author), a.brykova@vir.nw.ru, e.zuev@vir.nw.ru, n.shvachko@vir.nw.ru

ORCID:
Solovyova M.V. orcid.org/0000-0002-6904-4488
Zuev E.V. orcid.org/0000-0001-9259-4384
Brykova A.N. orcid.org/0000-0002-2215-5068
Shvachko N.A. orcid.org/0000-0002-1958-5008

Final revision received September 19, 2025
Accepted February 02, 2026

Wheat (Triticum aestivum L.) is the most widely cultivated grain crop in the world, so its yield affects the global economy. Wheat breeding in the Russian Federation should be aimed not only at high adaptability, plasticity and grain quality, but also at creating early-ripening varieties with optimal growing season duration, reflecting the territorial features of the environment. Genome-Wide Association Study (GWAS) is a modern statistical method for studying the genetic foundations of important agronomic traits of plants (disease resistance, yield, stress adaptation); it allows identifying genetic loci and candidate genes associated with quantitative traits, and thereby accelerates the selection of adaptive varieties with the specified characteristics. In this work, using genome-wide association analysis (GWAS) on the VIR spring soft wheat collection, markers were identified for the first time on chromosome 5A, 2A and 6A associated with the duration of the growing season and its interphase intervals and not previously described for these signs. They are proposed as new candidates for marker-based selection (MAS) of precocity. The aim of the work was to identify genetic markers associated with the phenological characteristics of spring soft wheat using the method of genome-wide association analysis (GWAS). The material for the work was 184 samples of spring soft wheat from the collection of the All-Russian Institute of Plant Genetic Resources named after N.I. Vavilov (VIR) of various origins (92 samples from Germany, 84 from Russia, 7 from Kazakhstan, 1 from the Netherlands) and different breeding periods (local varieties, varieties before 1950 of the year, varieties of the period 1951-1991 and modern varieties). Field phenotyping was performed in 2021-2023 in the fields of the Pushkin and Pavlovsky Laboratories of the Russian Academy of Medical Sciences (Pushkin, Leningrad Region). For each sample, the duration of the sprouting-earing, earing—ripening and sprouting—ripening periods was determined. The generally accepted agricultural techniques for cultivating spring soft wheat were used in field experiments. The sample under study was genotyped at TraitGenetics GmbH (Germany) using a 20K Wheat Illumina SNP chip (www.traitgenetics.com). According to the results of genotyping, 17267 polymorphic SNPs were obtained. Subsequently, SNP filtering was performed and a final set of 13,375 polymorphic SNP markers was obtained. The population structure was determined using the STRUCTURE v 2.3.4 program. To search for associations between genotype and phenotype, the GWAS statistical method was used in the TASSEL 5.0 program using a mixed linear model (MLM+K) taking into account the kinship matrix, which reduces the proportion of false positive associations, with Bonferroni significance. Additionally, a meta-analysis was performed in the R environment, combining p-values over three years using the Fisher method. A high genetic diversity of the sample was found, the samples were divided into six groups, which mostly combined varieties from similar breeding periods (Russian varieties in two, German varieties in four). The total growing season (shoots—waxy ripeness) has lengthened from 78.7 days in 2021 to 87.1 days in 2023. According to the results of GWAS for individual years and meta-analysis, a total of 98 significant markers associated with wheat growth phases and localized in 10 chromosomes with the dominant role of chromosome 5A were identified. Some of the markers are associated with well-known wheat phenology genes (Vrn on chromosomes of the 5th homeological group, Ppd-D1 on 2D, Vrn-3/FT1 on 7A), along with which new markers have been identified. It turned out that the key role in the genetic control of the duration of the growing season is played by chromosome 5A, which has been steadily evolving for three years, which confirms the correctness of the analysis model and the quality of phenotyping.

Keywords: Triticum aestivum L., phases of plant development, phenotyping, GWAS, meta-analysis, significant markers.

 

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