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<article article-type="research-article" dtd-version="1.3" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xml:lang="ru"><front><journal-meta><journal-id journal-id-type="publisher-id">vavilov</journal-id><journal-title-group><journal-title xml:lang="ru">Вавиловский журнал генетики и селекции</journal-title><trans-title-group xml:lang="en"><trans-title>Vavilov Journal of Genetics and Breeding</trans-title></trans-title-group></journal-title-group><issn pub-type="epub">2500-3259</issn><publisher><publisher-name>Institute of Cytology and Genetics of Siberian Branch of the RAS</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="doi">10.18699/VJ17.227</article-id><article-id custom-type="elpub" pub-id-type="custom">vavilov-908</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="ru"><subject>Перспективные направления</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="en"><subject>Promising trends</subject></subj-group></article-categories><title-group><article-title>Достижения и перспективы использования методов высокопроизводительного секвенирования в генетике и селекции картофеля</article-title><trans-title-group xml:lang="en"><trans-title>Achievements and prospects of applying high-throughput sequencing techniques to potato genetics and breeding</trans-title></trans-title-group></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Быкова</surname><given-names>И. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Bykova</surname><given-names>I. V.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Новосибирск</p></bio><bio xml:lang="en"><p>Novosibirsk</p></bio><email xlink:type="simple">bykova@bionet.nsc.ru</email><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Шмаков</surname><given-names>Н. А.</given-names></name><name name-style="western" xml:lang="en"><surname>Shmakov</surname><given-names>N. A.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Новосибирск</p></bio><bio xml:lang="en"><p>Novosibirsk</p></bio><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Афонников</surname><given-names>Д. А.</given-names></name><name name-style="western" xml:lang="en"><surname>Afonnikov</surname><given-names>D. A.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Новосибирск</p></bio><bio xml:lang="en"><p>Novosibirsk</p></bio><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Кочетов</surname><given-names>А. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Kochetov</surname><given-names>A. V.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Новосибирск</p></bio><bio xml:lang="en"><p>Novosibirsk</p></bio><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Хлесткина</surname><given-names>Е. К.</given-names></name><name name-style="western" xml:lang="en"><surname>Khlestkina</surname><given-names>E. K.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Новосибирск</p></bio><bio xml:lang="en"><p>Novosibirsk</p></bio><xref ref-type="aff" rid="aff-2"/></contrib></contrib-group><aff-alternatives id="aff-1"><aff xml:lang="ru">Федеральное государственное бюджетное научное учреждение «Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук»<country>Россия</country></aff><aff xml:lang="en">Institute of Cytology and Genetics SB RAS<country>Russian Federation</country></aff></aff-alternatives><aff-alternatives id="aff-2"><aff xml:lang="ru">Федеральное государственное бюджетное научное учреждение «Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук»;&#13;
Федеральное государственное автономное образовательное учреждение высшего образования «Новосибирский национальный исследовательский государственный университет»<country>Россия</country></aff><aff xml:lang="en">Institute of Cytology and Genetics SB RAS;&#13;
Novosibirsk State University<country>Russian Federation</country></aff></aff-alternatives><pub-date pub-type="collection"><year>2017</year></pub-date><pub-date pub-type="epub"><day>24</day><month>03</month><year>2017</year></pub-date><volume>21</volume><issue>1</issue><fpage>96</fpage><lpage>103</lpage><permissions><copyright-statement>Copyright &amp;#x00A9; Быкова И.В., Шмаков Н.А., Афонников Д.А., Кочетов А.В., Хлесткина Е.К., 2017</copyright-statement><copyright-year>2017</copyright-year><copyright-holder xml:lang="ru">Быкова И.В., Шмаков Н.А., Афонников Д.А., Кочетов А.В., Хлесткина Е.К.</copyright-holder><copyright-holder xml:lang="en">Bykova I.V., Shmakov N.A., Afonnikov D.A., Kochetov A.V., Khlestkina E.K.</copyright-holder><license license-type="creative-commons-attribution" xlink:href="https://creativecommons.org/licenses/by/4.0/" xlink:type="simple"><license-p>This work is licensed under a Creative Commons Attribution 4.0 License.</license-p></license></permissions><self-uri xlink:href="https://vavilov.elpub.ru/jour/article/view/908">https://vavilov.elpub.ru/jour/article/view/908</self-uri><abstract><p>Для повышения эффективности процесса селекции картофеля в последние годы активно используются методы отбора с помощью ДНК-маркеров. Применение маркер-ориентированной селекции, а также геномной селекции и новейших методов создания форм картофеля с заданными свойствами (геномное редактирование) требует широкомасштабного изучения геномов и генов картофеля на основе высокопроизводительных методов секвенирования нового поколения. Цель настоящего обзора – рассмотреть направления исследований в картофелеводстве, основанные на применении данных методов, и систематизировать связанные с этой темой сведения об интернет-ресурсах. Уделяется также внимание особенностям используемых моделей и подходов в генетических исследованиях картофеля ввиду сложной организации его генома и высокого уровня гетерозиготности. В генетических исследованиях нередко прибегают к использованию диплоидных форм, к которым относятся диплоидные виды картофеля, искусственно полученные гетерозиготные дигаплоиды и гомозиготные удвоенные моноплоиды. Наличие искусственно созданных диплоидных форм сыграло важную роль в успешном секвенировании генома картофеля, завершенном в 2011 г. Работа Международного консорциума по секвенированию генома картофеля включала не только конструирование геномных библиотек, секвенирование, сборку и аннотирование генома, но и фундаментальные исследования на основе полученной последовательности, направленные на выявление особенностей эволюции генома картофеля, идентификацию SNP (single nucleotide polymorphism – однонуклеотидный полиморфизм), анализ генов и генных сетей, контролирующих устойчивость к фитопатогенам и технологические свойства. Важным следствием секвенирования генома стала идентификация более 8 тыс. SNP и апробация метода GBS (genotyping-bysequencing – генотипирование путем секвенирования) на картофеле, что является основой для геномной селекции этой культуры и выявления новых хозяйственно ценных генов картофеля методом полногеномного анализа ассоциаций (genome-wide association studies – GWAS). Ведется работа по оптимизации существующих биоинформатических методов анализа для осуществления работ в этом направлении, учитывающая особенности организации генома картофеля. В обзоре приведен анализ доступных электронных баз данных, содержащих результаты работ по секвенированию генома и транскриптома картофеля, а также сопутствующих ресурсов. Эта информация будет полезна для планирования работ по сравнительному анализу транскриптома картофеля и исследований с использованием геномных ДНК-маркеров. Результаты секвенирования генома, а также сравнительных иссле- дований, базирующихся на анализе транскриптома и микроРНК образцов культивируемого картофеля и его дикорастущих сородичей, с одной стороны, представляют фундаментальный интерес, способствуя выявлению особенностей эволюции генома, онтогенетического развития растений картофеля и механизмов ответа на различные стимулы окружающей среды, а с другой – позволяют осуществлять широкий спектр прикладных работ, направленных на разработку эффективных геномных и ген-специфичных маркеров и получения с их помощью новых сортов картофеля с заданными свойствами.</p></abstract><trans-abstract xml:lang="en"><p>In recent years, marker-assisted selection (MAS) has been intensively used to increase potato breeding efficiency. Large-scale studies of the potato genome and genes exploiting next-generation sequence (NGS) approaches are required for broad application of MAS, genomic selection as well as genomic editing (the newest approach for creating potato with desired properties). In this review, trends in potato NGS-based research are overviewed, and related Internet resources are systematized. Special attention is given to peculiarities of the models and the approaches used in potato genetic studies, taking into account the complex organization of its genome and a high level of heterozygosity. In genetic studies diploids are used often, including diploid potato species, artificially obtained heterozygous dihaploids and homozygous double monoploids. The availability of artificially created diploid forms played an essential role in potato genome sequencing, which was completed in 2011. The Potato Genome Sequencing Consortium activities included not only constructing genome libraries, sequencing, assembling and annotation of the genome, but also genome sequence-based investigations uncovering features of potato genome evolution, SNP identification, analysis of genes and gene networks regulating resistance to phytopathogens and technological characteristics. An important outcome of the genome sequencing was further identification of more than 8 thousand SNPs and approbation of the Genotyping-by-sequencing (GBS) method on potato, which is the basis for potato genomic selection and for discovery of economically important genes using genome wide association studies (GWAS). Optimization of existing bioinformatic tools to support these studies, taking into account potato genome organization peculiarities, are carried out. This review gives analysis of databases containing potato genome and transcriptome sequencing results, as well as accompanying resources. This information should prove useful while planning comparative assays of potato transcriptome or application of DNA-markers. Sequencing of the genome as well as transcriptomes and microRNomes of cultivated potato and its wild relatives, on one hand, is of fundamental interest, assisting in detecting features of genome evolution, ontogenetic development and mechanisms of various environmental stresses responses. On the other hand, it is the basis for a wide range of practical applications for developing effective genomic and gene-specific markers and marker-assisted breeding of new potato cultivars with desired properties.</p></trans-abstract><kwd-group xml:lang="ru"><kwd>RNAseq</kwd><kwd>Solanum tuberosum</kwd><kwd>картофель</kwd><kwd>геном</kwd><kwd>транскриптом</kwd><kwd>секвенирование</kwd><kwd>гены</kwd><kwd>маркеры</kwd><kwd>базы данных</kwd></kwd-group><kwd-group xml:lang="en"><kwd>databases</kwd><kwd>genes</kwd><kwd>genome</kwd><kwd>markers</kwd><kwd>potato</kwd><kwd>RNAseq</kwd><kwd>Solanum tuberosum</kwd><kwd>sequencing</kwd><kwd>transcriptome</kwd></kwd-group></article-meta></front><back><ref-list><title>References</title><ref id="cit1"><label>1</label><citation-alternatives><mixed-citation xml:lang="ru">Ali A., Alexandersson E., Sandin M., Resjö S., Lenman M., Hedley P., Levander F., Andreasson E. 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