Приоритизация биологических процессов на основе реконструкции и анализа ассоциативных генных сетей, описывающих ответ растений на неблагоприятные факторы внешней среды

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.

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