vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/vjgb-25-131vavilov-4934Research ArticleСТРУКТУРА И ЭВОЛЮЦИЯ ГЕНОМА РАСТЕНИЙPLANT GENOME STRUCTURE AND EVOLUTIONТранспозоны льна: роль в генетическом разнообразии, окультуривании и детерминации хозяйственно ценных признаковFlax transposons: unraveling their impact on domestication and agronomic trait variationhttps://orcid.org/0000-0003-4634-5656ДукМ. А.DukM. A.

 Санкт-Петербург

St. Petersburg

СтанинВ. А.StaninV. A.

 Санкт-Петербург

St. Petersburg

https://orcid.org/0000-0001-9802-5297КанапинА. А.KanapinA. A.

 Санкт-Петербург

St. Petersburg

https://orcid.org/0000-0002-9353-9173СамсоноваА. А.SamsonovaA. A.

 Санкт-Петербург

St. Petersburg

РожминаТ. А.RozhminaT. A.

Торжок

Torzhok

https://orcid.org/0000-0003-2530-0395СамсоноваМ. Г.SamsonovaM. G.

 Санкт-Петербург

St. Petersburg

m.g.samsonova@gmail.comФизико-технический институт им. А.Ф. Иоффе Российской академии наукРоссияIoffe Institute of the Russian Academy of Sciences,Russian FederationСанкт-Петербургский политехнический университет Петра ВеликогоРоссияPeter the Great St. Petersburg Polytechnic UniversityRussian FederationФедеральный научный центр лубяных культурРоссияFederal Research Center for Bast Fiber CropsRussian Federation20251101202629812671276Copyright © Дук М.А., Станин В.А., Канапин А.А., Самсонова А.А., Рожмина Т.А., Самсонова М.Г., 20262026Дук М.А., Станин В.А., Канапин А.А., Самсонова А.А., Рожмина Т.А., Самсонова М.Г.Duk M.A., Stanin V.A., Kanapin A.A., Samsonova A.A., Rozhmina T.A., Samsonova M.G.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/4934

Лен – важная сельскохозяйственная культура многофункционального использования. Pазно направленная селекция на содержание масла в семенах и волокна в стеблях привела к возникновению двух морфотипов – льна-долгунца и льна масличного. Ранее, используя однонуклеотидные полиморфизмы, мы охарактеризовали генетическое разнообразие у 306 образцов льна из коллекции российского Федерального научного центра лубяных культур. Вместе с тем более крупные структурные вариации также играют существенную роль в формировании агрономически важных признаков растений и могут быть применены для дальнейшего улучшения льна. Здесь мы задействовали ту же коллекцию льна, чтобы предсказать сайты новых инсерций транспозонов и оценить роль таких инсерций в формировании агрономически важных признаков, а также в процессе окультуривания льна. Мы обнаружили 588 480 новых сайтов инсерций транспозонов, не содержащихся в референсном геноме льна (сборка NCBI ASM22429v2), из которых большая часть приходилась на ретротранспозоны суперсемейств Copia и Gypsy, а среди ДНК транспозонов чаще всего встречались сайты инсерции суперсемейств MULE-MuDR, hAT и CMC-EnSpm. В отличие от однонуклеотидных полиморфизмов, которых было значительно больше у льна масличного, чем у долгунцов, мы не обнаружили столь существенной разницы в числе инсерций разных семейств транспозонов на одно растение у образцов разного морфотипа. Aнализ геномных областей, затронутых недавними селекционными усилиями, выявил в общей сложности 61 район-кандидат, из которых 18 районов пересекались с QTL, ассоциированными с важными агрономическими признаками. Интересно, что пять участков уменьшения генетического разнообразия у культурных сортов и кряжей при сравнении их со староместными сортами также были идентифицированы как участки уменьшения разнообразия при использовании в качестве маркеров однонуклеотидных полиморфизмов. При полногеномном поиске ассоциаций найдено 50 инсерций ТЕ, ассоциированных с разными фенотипическими признаками, причем многие ассоциации подтверждаются несколькими моделями или обнаруживаются в данных по нескольким годам. Таким образом, сайты инсерции транспозонов – важный источник генетического разнообразия у льна наряду с однонуклеотидными полиморфизмами, что позволяет использовать их для дальнейшего улучшения культуры при селекции. 

Flax is an important agricultural crop with multifunctional uses. Diversified breeding for oil content in seeds and fiber in stems has led to the emergence of two morphotypes – fiber flax and oilseed flax. Previously, using single nucleotide polymorphisms (SNPs), we characterized the genetic diversity of 306 flax samples from the collection of the Russian Federal Research Center for Bast Crops. However, larger structural variations, such as mobile genetic elements, also play a significant role in shaping agronomically important plant traits and can be used for further flax improvement. Here, we used the same flax collection to predict sites of new transposon insertions and to assess the role of such insertions in the formation of agronomically important traits, as well as in the process of flax domestication. We discovered 588,480 new transposon insertion sites not present in the reference flax genome (NCBI assembly ASM22429v2), the majority of which were attributed to retrotransposons of the Copia and Gypsy superfamilies, while among DNA transposons, insertion sites of the MULE-MuDR, hAT, and CMC-EnSpm superfamilies were most common. Unlike SNPs, which were significantly more numerous in oilseed flax than in fiber flax, we did not find such a substantial difference in the number of insertions of different transposon families per plant among samples of different morphotypes. Analysis of genomic regions affected by recent breeding efforts revealed a total of 61 candidate regions, of which 18 regions overlapped with QTLs associated with important agronomic traits. Interestingly, 5 regions of reduced genetic diversity in kryazhs and cultivars compared to landraces were also identified as regions of reduced diversity when using single nucleotide polymorphisms as markers. A genomewide association study (GWAS) identified 50 TE insertions associated with different phenotypic traits, with many associations confirmed by multiple models or detected in data from multiple years. Thus, transposon insertion sites are an important source of genetic diversity in flax, alongside single nucleotide polymorphisms, making them suitable for further crop improvement in breeding.

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