vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJ20.638vavilov-2708Research ArticleГЕНЕТИЧЕСКИЕ РЕСУРСЫ И БИОКОЛЛЕКЦИИPLANT GENETICSГеномные районы Solanum tuberosum L., ассоциированные с глубиной залегания глазков клубнейGenomic regions of Solanum tuberosum L. associated with the tuber eye depthhttps://orcid.org/0000-0001-5565-9097ТоцкийИ. В.TotskyI. V.totsky@bionet.nsc.ruРозановаИ. В.RozanovaI. V.СафоноваА. Д.SafonovaA. D.БатовА. С.BatovA. S.ГурееваЮ. А.GureevaYu. A.https://orcid.org/0000-0003-3151-5181КочетовА. В.KochetovA. V.https://orcid.org/0000-0002-8470-8254ХлесткинаЕ. К.KhlestkinaE. K.

Novosibirsk, St. Petersburg

Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Сибирский научно-исследовательский Институт растениеводства и селекции – филиал Федерального исследовательского центра Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Siberian Research Institute of Plant Production and Breeding – Branch of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Федеральный исследовательский центр Всероссийский институт генетических ресурсов растений им. Н.И. Вавилова (ВИР)РоссияInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences; Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)Russian FederationСибирский научно-исследовательский Институт растениеводства и селекции – филиал Федерального исследовательского центра Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияSiberian Research Institute of Plant Production and Breeding – Branch of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesRussian Federation202027082020245465473Copyright © Тоцкий И.В., Розанова И.В., Сафонова А.Д., Батов А.С., Гуреева Ю.А., Кочетов А.В., Хлесткина Е.К., 20202020Тоцкий И.В., Розанова И.В., Сафонова А.Д., Батов А.С., Гуреева Ю.А., Кочетов А.В., Хлесткина Е.К.Totsky I.V., Rozanova I.V., Safonova A.D., Batov A.S., Gureeva Y.A., Kochetov A.V., Khlestkina E.K.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/2708

Картофель (Solanum tuberosum L.) – одна из важнейших в мире продовольственных культур. Геном вида автотетраплоидный, отличается высоким уровнем гетерозиготности, этот вид является также перекрестноопыляемым. Все это затрудняет генетический анализ и селекционный процесс. Глубина залегания глазков клубня картофеля продовольственного назначения – важный признак, влияющий на пригодность сортов картофеля для переработки. Селекция по этому признаку ведется на основе фенотипической оценки. Идентификация локусов, контролирующих данный признак, позволила бы проводить маркер-контролируемый отбор гибридов, отбраковывая формы с глубоким залеганием глазков на ранних этапах селекции. Целью настоящего исследования было выявление геномных районов, ассоциированных с глубиной залегания глазков, путем анализа сортообразцов картофеля S. tuberosum L. из коллекции ГенАгро Института цитологии и генетики СО РАН. При использовании 15214 SNP-маркеров, генотипированных с помощью чипа Illumina 22K SNP potato array, и обобщенной линейной модели (General Linear Model, GLM) с учетом популяционной структуры найдены 24 значимых маркера, ассоциированных с признаком «глубина залегания глазков». Полученные данные показали наличие SNP в четырех геномных районах: в хромосомах 4 (1 маркер в районе 3.92 Mб), 5 (1 маркер в районе 4.67 Mб) и 10 (1 маркер, относящийся к району 4.87 Mб, и 21 маркер в районе 48.1–48.9 Mб). Сопоставление выявленных геномных районов в нашем исследовании с более ранними работами подтвердило, что локус между 48.1–48.9 Mб был известен ранее, остальные три района обнаружены впервые. Участки ДНК, содержащие SNP, сцепленные с глубиной залегания глазков, были изучены в сборке генома картофеля SolTub_3.0 (https://plants.ensembl.org/), и на основе полученных данных были разработаны КASP-маркеры, при применении которых можно будет более эффективно вести скрининг селекционного материала и селекцию сортов с мелким залеганием глазков.

Potato (Solanum tuberosum L.) is one of the most important food crops in the world. The genome of this potato species is autotetraploid and has a high level of heterozygosity, also this potato species is a cross-pollinated plant. These characteristics complicate the genetic analysis and breeding process. The tuber’s eye depth is an important trait that affects the suitability of potato varieties for processing. Potato breeding for this trait is based on phenotypic assessment. Identification of the loci that control tuber eye depth would allow diagnostic markers for the marker-assisted selection to be created. The aim of this study is to search for loci associated with the eye depth by analyzing Solanum tuberosum varieties from the GenAgro collection of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, genotyped using the Illumina 22K SNP potato array DNA chip. The 24 significant markers associated with the “eye depth” trait were identified using 15,214 SNP markers genotyped with the Illumina 22K SNP potato array chip and the general linear model (GLM) taking into account the population structure. Data obtained showed the presence of SNPs in four genomic regions: on chromosome 4 (1 marker in the 3.92 Mb area), 5 (1 marker in the 4.67 Mb area) and 10 (1 marker in the 4.87 Mb area and 21 markers in the region between 48.1–48.9 Mb). The results of localization in the region 48.1–48.9 Mb of chromosome 10 correspond to previously published studies, the remaining three regions were detected for the first time. DNA sections containing SNPs linked to the tuber’s eye depth were studied in the SolTub_3.0 potato genome assembly (https:// plants.ensembl.org/). KASP markers were developed based on the data obtained. It will be possible to screen the breeding material and to breed the varieties more effectively using current markers associated with a shallow tuber’s eye depth.

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