vir-nwТруды по прикладной ботанике, генетике и селекцииProceedings on applied botany, genetics and breeding2227-88342619-0982N.I. Vavilov All-Russian Institute of Plant Genetic Resources10.30901/2227-8834-2025-4-182-194vir-nw-2374Research ArticleИДЕНТИФИКАЦИЯ ГЕНЕТИЧЕСКОГО РАЗНООБРАЗИЯ КУЛЬТУРНЫХ РАСТЕНИЙ И ИХ ДИКИХ РОДИЧЕЙ ДЛЯ РЕШЕНИЯ ФУНДАМЕНТАЛЬНЫХ И ПРИКЛАДНЫХ ПРОБЛЕМIDENTIFICATION OF THE DIVERSITY OF CULTIVATED PLANTS AND THEIR WILD RELATIVES FOR SOLVING FUNDAMENTAL AND APPLIED PROBLEMSПолногеномный анализ ассоциаций для идентификации SNP-маркеров, связанных с продуктивностью колоса ячменя (Hordeum vulgare L.)Genome-wide association study for identification of SNP markers associated with barley spike productivity (Hordeum vulgare L.)https://orcid.org/0000-0001-5477-8684ЛукинаК. А.LukinaK. A.

Ксения Андреевна Лукина, аспирант, младший научный сотрудник, ВИР

190000 Россия, Санкт-Петербург, ул. Б. Морская, 42, 44

Kseniia A. Lukina, Postgraduate Student, Associate Researcher, VIR

42, 44 Bolshaya Morskaya Street, St. Petersburg 190000, Russia

k.lukina@vir.nw.ruhttps://orcid.org/0000-0003-4341-0766РозановаИ. В.RozanovaI. V.

Ирина Вениаминовна Розанова, кандидат биологических наук, старший научный сотрудник, Научно-технологический университет «Сириус», Научный центр генетики и наук о жизни

354340 Россия, Краснодарский край, федеральная территория «Сириус», пгт. Сириус, Олимпийский пр., 1

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

rozanova.iv@talantiuspeh.ruhttps://orcid.org/0000-0002-3990-6526КовалеваО. Н.KovalevaO. N.

Ольга Николаевна Ковалева, кандидат биологических наук, ведущий научный сотрудник, ВИР

190000 Россия, Санкт-Петербург, ул. Б. Морская, 42, 44

Olga N. Kovaleva, Cand. Sci. (Biology), Leading Researcher,  VIR

42, 44 Bolshaya Morskaya Street, St. Petersburg 190000, Russia

o.kovaleva@vir.nw.ruhttps://orcid.org/0000-0002-1958-5008ШвачкоН. А.ShvachkoN. A.

Наталия Альбертовна Швачко, кандидат биологических наук, ведущий научный сотрудник, ВИР

190000 Россия, Санкт-Петербург, ул. Б. Морская, 42, 44

Nataliya A. Shvachko, Cand. Sci. (Biology), Leading Researcher, VIR

42, 44 Bolshaya Morskaya Street, St. Petersburg 190000, Russia

n.shvachko@vir.nw.ruhttps://orcid.org/0000-0002-9250-7225ЛоскутовИ. Г.LoskutovI. G.

Игорь Градиславович Лоскутов, доктор биологических наук, главный научный сотрудник, заведующий отделом, ВИР

190000 Россия, Санкт-Петербург, ул. Б. Морская, 42, 44

Igor G. Loskutov, Dr. Sci. (Biology), Chief Researcher, Head of a Department, VIR

42, 44 Bolshaya Morskaya Street, St. Petersburg 190000, Russia

i.loskutov@vir.nw.ruФедеральный исследовательский центр Всероссийский институт генетических ресурсов растений имени Н.И. ВавиловаРоссияN.I. Vavilov All-Russian Institute of Plant Genetic ResourcesRussian FederationНаучно-технологический университет «Сириус», Центр генетики и наук о жизниРоссияSirius University of Science and Technology, Research Center of Genetics and Life SciencesRussian Federation2025271220251864182194Copyright © Лукина К.А., Розанова И.В., Ковалева О.Н., Швачко Н.А., Лоскутов И.Г., 20252025Лукина К.А., Розанова И.В., Ковалева О.Н., Швачко Н.А., Лоскутов И.Г.Lukina K.A., Rozanova I.V., Kovaleva O.N., Shvachko N.A., Loskutov I.G.This work is licensed under a Creative Commons Attribution 4.0 License.https://elpub.vir.nw.ru/jour/article/view/2374Актуальность

Актуальность. Ячмень (Hordeum vulgare L.) является важной зерновой культурой широкого использования. Урожайность ячменя – это комплексный признак, на который влияют основные элементы структуры урожая. Идентификация молекулярных маркеров, сцепленных с морфологией колоса, очень важна для селекционного улучшения ячменя. Целью исследования является выявление геномных локусов, ассоциированных с архитектурой колоса ячменя, с использованием полногеномного анализа ассоциаций (GWAS).

Материал и методы

Материал и методы. Изучен набор из 199 образцов преимущественно голозерного ярового ячменя коллекции ВИР разного селекционного уровня, включая 103 образца шестирядного и 96 образцов двурядного ячменя разного происхождения. Фенотипирование по колосовым признакам выполнено в 2021–2023 гг. на экспериментальном поле научно-производственной базы «Пушкинские и Павловские лаборатории ВИР». Генотипирование проведено с использованием чипа Barley 50K Illumina Infinium iSELECT. GWAS выполнен в R с использованием смешанной линейной модели с учетом матрицы родства (MLM).

Результаты

Результаты. Показано широкое разнообразие признаков структуры урожая: длина колоса (SL), число колосков в колосе (SN), число зерен в колосе (GN), масса зерна с колоса (GW), масса 1000 зерен (TGW) в зависимости от рядности колоса и влияния окружающей среды. В результате GWAS выявлены 129 маркеров для всех признаков, включая 12 для SL, 73 для SN, 19 для GN, 9 для GW, 16 для TGW. Выделенные значимые маркеры сопоставлены с геномными районами на всех хромосомах ячменя. Часть выделенных маркеров ассоциирована с уже известными генами Vrs на первых пяти хромосомах. Анализ белок-белковых взаимодействий выделил 3 функциональных кластера, включающие 19 SNP, сцепленных с генами-ортологами развития колоса.

Заключение

Заключение. Выделенные маркеры, локусы и белковые взаимосвязи представляют интерес для дальнейшего изучения архитектуры колоса и количественных признаков, вносящих значительный вклад в урожайность ячменя.

Background

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

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

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

Conclusion. The identified markers, loci, and protein interactions are interesting for further studies of the spike architecture and quantitative traits contributing to barley yield.

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The authors declare that there are no conflicts of interest present.