vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJ21.065vavilov-3116Research ArticleБИОИНФОРМАТИКА И СИСТЕМНАЯ КОМПЬЮТЕРНАЯ БИОЛОГИЯBIOINFORMATICS AND COMPUTATIONAL SYSTEMS BIOLOGYПриоритизация биологических процессов на основе реконструкции и анализа ассоциативных генных сетей, описывающих ответ растений на неблагоприятные факторы внешней средыPrioritization of biological processes based on the reconstruction and analysis of associative gene networks describing the response of plants to adverse environmental factorshttps://orcid.org/0000-0001-9433-8341ДеменковП. С.DemenkovP. S.

Новосибирск

Novosibirsk

ОщепковаЕ. А.OshchepkovaE. A.

Новосибирск

Novosibirsk

ИванисенкоТ. В.IvanisenkoT. V.

Новосибирск

Novosibirsk

ИванисенкоВ. А.IvanisenkoV. A.

Новосибирск

Novosibirsk

salix@bionet.nsc.ruФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университетРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State UniversityRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesRussian FederationНовосибирский национальный исследовательский государственный университет; Курчатовский геномный центр ИЦиГ СО РАНРоссияNovosibirsk State University; Kurchatov Genomic Center of ICG SB RASRussian Federation202110092021255580592Copyright © Деменков П.С., Ощепкова Е.А., Иванисенко Т.В., Иванисенко В.А., 20212021Деменков П.С., Ощепкова Е.А., Иванисенко Т.В., Иванисенко В.А.Demenkov P.S., Oshchepkova E.A., Ivanisenko T.V., Ivanisenko V.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/3116

Методы приоритизации или ранжирование кандидатных генов по их важности в соответствии с заданными критериями, основанными на анализе генных сетей, широко применяются в биомедицине для поиска ассоциаций генов с заболеваниями, предсказания биомаркеров, фармакологических мишеней и т. д. При этом наблюдается тенденция их использования и в других областях знаний, в частности в растениеводстве. В значительной степени это обусловлено развитием технологий для решения задач маркер-ориентированной и геномной селекции, требующих знаний о молекулярно-генетических механизмах, лежащих в основе формирования хозяйственно ценных признаков. Новым направлением для изучения молекулярно-генетических механизмов является приоритизация биологических процессов с применением анализа ассоциативных генных сетей. Ассоциативная генная сеть – это гетерогенная сеть, в качестве вершин которой наряду с молекулярно-генетическими объектами (гены, белки, метаболиты и т. д.) могут быть представлены сущности более высокого уровня (биологические процессы, заболевания, факторы внешней среды и т. д.), связанные между собой регуляторными, физико-химическими или ассоциативными взаимодействиями. С использованием разработанного нами ранее метода осуществлена приоритизация биологических процессов по степени их связи с генными сетями, представленными в базе знаний SOLANUM TUBEROSUM и описывающими ответ растений на повышенное содержание кадмия, солевой стресс и условия засухи. Результаты приоритизации свидетельствуют о том, что фундаментальные процессы, такие как экспрессия генов, посттрансляционная модификация, деградация белков, программируемая клеточная смерть, фотосинтез, передача сигналов, ответ на стресс, играют важную роль в общих молекулярно-генетических механизмах ответа растений на различные неблагоприятные факторы. С другой стороны, среди специфичных для устойчивости к засухе была выявлена группа процессов, связанных с развитием семян (seeding development). Процессы, связанные с ионным транспортом (ion transport), вошли в список специфичных для ответа на солевой стресс, а связанные с метаболизмом липидов (phospholipid degradation – деградация фосфолипидов) – для ответа на кадмий.

Methods for prioritizing or ranking candidate genes according to their importance based on specific criteria via the analysis of gene networks are widely used in biomedicine to search for genes associated with diseases and to predict biomarkers, pharmacological targets and other clinically relevant molecules. These methods have also been used in other fields, particularly in crop production. This is largely due to the development of technologies to solve problems in marker-oriented and genomic selection, which requires knowledge of the molecular genetic mechanisms underlying the formation of agriculturally valuable traits. A new direction for the study of molecular genetic mechanisms is the prioritization of biological processes based on the analysis of associative gene networks. Associative gene networks are heterogeneous networks whose vertices can depict both molecular genetic objects (genes, proteins, me tabolites, etc.) and the higher-level factors (biological processes, diseases, external environmental factors, etc.) related to regulatory, physicochemical or associative interactions. Using a previously developed method, biological processes involved in plant responses to increased cadmium content, saline stress and drought conditions were prioritized according to their degree of connection with the gene networks in the SOLANUM TUBEROSUM knowledge base. The prioritization results indicate that fundamental processes, such as gene expression, post-translational modifications, protein degradation, programmed cell death, photosynthesis, signal transmission and stress response play important roles in the common molecular genetic mechanisms for plant response to various adverse factors. On the other hand, a group of processes related to the development of seeds (“seeding development”) was revealed to be drought specific, while processes associated with ion transport (“ion transport”) were included in the list of responses specific to salt stress and processes associated with the metabolism of lipids were found to be involved specifically in the response to cadmium.

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