vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/VJ15.086vavilov-488Research ArticleБиоинформатика растенийPlant BioinformaticsИдентификация микросателлитных локусов по данным секвенирования ВАС -клонов и их физическое картирование на хромосому 5B мягкой пшеницыIdentification of microsatellite loci according to BAC sequencing data and their physical mapping to the bread wheat 5B chromosomeНестеровМ. А.NesterovM. A.АфонниковД. А.AfonnikovD. A.СергееваЕ. М.SergeevaE. M.МирошниченкоЛ. А.MiroshnichenkoL. A.БрагинаМ. К.BraginaM. K.БрагинА. О.BraginA. O.ВасильевГ. В.VasilievG. V.СалинаЕ. А.SalinaE. A.salina@bionet.nsc.ruФедеральное государственное бюджетное научное учреждение «Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук», Новосибирск, РоссияРоссияInstitute of Cytology and Genetics SB RA S, Novosibirsk, RussiaRussian FederationФедеральное государственное бюджетное учреждение науки «Институт математики им. С.Л. Соболева Сибирского отделения Российской академии наук», Новосибирск, РоссияРоссияSobolev Institute of Mathematics SB RA S, Novosibirsk, RussiaRussian Federation201504012016196707714Copyright © Нестеров М.А., Афонников Д.А., Сергеева Е.М., Мирошниченко Л.А., Брагина М.К., Брагин А.О., Васильев Г.В., Салина Е.А., 20162016Нестеров М.А., Афонников Д.А., Сергеева Е.М., Мирошниченко Л.А., Брагина М.К., Брагин А.О., Васильев Г.В., Салина Е.А.Nesterov M.A., Afonnikov D.A., Sergeeva E.M., Miroshnichenko L.A., Bragina M.K., Bragin A.O., Vasiliev G.V., Salina E.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/488

Необходимость изучения микросателлитных локусов пшеницы, в первую очередь, обусловлена актуальностью работ по выявлению полиморфных маркеров для участков хромосом, определяющих хозяйственно ценные признаки. В настоящей работе проведено насыщение отдельных районов короткого плеча хромосомы 5B (5BS) мягкой пшеницы SSR-маркерами, разработанными по данным секвенирования BAC -клонов. 130 клонов, отобранных случайным образом из BAC -библиотеки 5BS, были секвенированы на платформе IonTorrent и собраны в контиги с использованием программы MIRA . Характеристики сборки (N50 = 4 136 п. н.) сравнимы с таковыми для сборок генома пшеницы и родственных видов, полученными в последнее время, и приемлемы для решения задачи идентификации микросателлитных локусов. Для выявления последовательностей ДНК с повторяющейся единицей 2–4 п. н. использовался алгоритм, основанный на свойствах сложностных разложений, формирующихся в режиме скользящего окна. По данным анализа 17 770 контигов общей протяженностью 25 879 921 п. н., разработано 113, 79 и 67 маркеров микросателлитных (SSR) локусов c повторяющейся единицей 2, 3 и 4 п. н. соответственно. SSR-маркеры с мотивом 3 п. н. были проверены на нулли-тетрасомных линиях пятой гомеологичной группы хромосом сорта пшеницы Чайниз Спринг (CS). Выявлен 21 маркер, специфичный для хромосомы 5В. Были локализованы 8 маркеров в дистальном районе хромосомы (бин 5BS6) с использованием серии делеционных линий CS по 5ВS. Для 8 и 4 маркеров определена локализация в интерстициальном районе в бинах 5BS5 и 5BS4 соответственно, один маркер был локализован в прицентромерном бине. Сравнительный анализ распределения тринуклеотидных микросателлитов по хромосоме 5Впшеницы и у различных видов злаков указывает на пролиферацию и поддержание количественного содержания повтора (AAG)n в процессе эволюции злаков.

The shortage of polymorphic markers for the regions of wheat chromosomes that encode commercially valuable traits determined the need for studying wheat microsatellite loci. In this work, SSR markers for individual regions in the short arm of bread wheat chromosome 5B (5BS) were designed based on sequencing data for BAC clones, and the regions of the corresponding chromosome were saturated with these markers. Totally, 130 randomly selected BAC clones from the 5BS library were sequenced on the Ion Torrent platform and assembled in contigs using MIRA software. The assembly characteristics (N50 = 4 136 bp) are comparable to the recently obtained data for wheat and relative species and acceptable for identification of microsatellite loci. An algorithm utilizing the properties of complexity decompositions in  he sliding-window mode was used to detect DNA sequences with a repeat unit of 2–4 bp. Analysis of 17 770 contigs with the total length of 25 879 921 bp allowed for designing 113, 79, and 67 microsatellite (SSR) loci with a repeat unit of 2, 3, and 4 bp, respectively. The SSR markers with a motif of 3 bp were tested using nullitetrasomic lines of Chinese Spring wheat homoeologous group 5. Thus, 21 markers specific for chromosome 5B were detected. Eight of these markers were mapped to the distal region of this chromosome (bin 5BS6) using a set of Chinese Spring deletion lines for 5BS. Eight and four markers were mapped to the interstitial region (bins 5BS5 and 5BS4, respectively). One marker was mapped to a pericentromeric bin. A comparative analysis of the distribution of trinucleotide microsatellites over wheat chromosome 5B and in different cereal species suggests that the (AAG)n repeat has proliferated and has been maintained during the evolution of cereals.

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