Developing seed is a unique stage of plant development with highly dynamic changes in transcriptome. Here, we aimed to detect the novel previously unannotated, genes of the triticale (x Triticosecale Wittmack, AABBRR genome constitution) genome that are expressed during different stages and at different parts of the developing seed. For this, we carried out the Oxford Nanopore sequencing of cDNA obtained for middle (15 days post-anthesis, dpa) and late (20 dpa) stages of seed development. The obtained data together with our previous direct RNA sequencing of early stage (10 dpa) of seed development revealed 39,914 expressed genes including 7128 (17.6%) genes that were not previously annotated in A, B, and R genomes. The bioinformatic analysis showed that the identified genes belonged to long non-coding RNAs (lncRNAs), protein-coding RNAs, and TE-derived RNAs. The gene set analysis revealed the transcriptome dynamics during seed development with distinct patterns of over-represented gene functions in early and middle/late stages. We performed analysis of the lncRNA genes polymorphism and showed that the genes of some of the tested lncRNAs are indeed polymorphic in the triticale collection. Altogether, our results provide information on thousands of novel loci expressed during seed development that can be used as new targets for GWAS analysis, the marker-assisted breeding of triticale, and functional elucidation.

Genetic variation in high molecular weight glutenin (HMW-GS) genes is tightly linked with the breadmaking quality of wheat. Hundreds of different alleles have been identified in HMW-GS genes worldwide. Such huge variability makes it difficult to distinguish them using conventional genotyping methods (for example, SDS-PAGE, SNP detection, etc.). Here, we exploited the nanopore amplicon sequencing technique (Amplicon-Seq) to uncover genetic variants distributed along the full-length sequence of six HMW-GSs, including the promoter and protein-coding regions. We analyzed 23 wheat accessions for allelic variants of HMW-GSs using the Amplicon-Seq and SDS-PAGE methods. We obtained sufficient (>50×) target gene coverage by ONT reads in just one hour. Using the obtained data, we identified numerous single nucleotide polymorphisms and InDels in the protein coding and promoter regions. Moreover, Amplicon-Seq allowed for the identification of new alleles (Glu-A1x1-T) of the Glu-1Ax gene that could not be recognized by SDS-PAGE. Collectively, our results showed that Amplicon-Seq is a rapid, multiplexed, and efficient method for high-throughput genotyping of full-length genes in large and complex genomes. This opens new avenues for the assessment of target gene variation to select novel alleles and create unique combinations of desirable traits in plant breeding programs.

Mobile elements, particularly long terminal repeat retrotransposons (LTR-RTEs), are abundant and dynamic components of plant genomes. Although viral infections are known to transcriptionally activate retrotransposons, it remains unclear whether such virus-induced activation leads to their mobilization. To address this question, we examined LTR-RTE activation in Arabidopsis thaliana, Brassica napus, and Nicotiana benthamiana following infection with the RNA viruses Tobacco rattle virus (TRV), Potato virus X (PVX), and Tobacco ringspot virus (TRSV). Nanopore cDNA sequencing revealed virus-specific transcriptional responses, with PVX uniquely triggering a strong transcriptional burst of diverse LTR-RTE families in N. benthamiana. To test the role of viral suppressors of RNA silencing (VSRs) in this process, we analyzed extrachromosomal circular DNA (eccDNA) from plants infected with TRV expressing the VSR P19. This analysis identified eccDNA derived from Ty3/Gypsy Galadriel elements, demonstrating that viral infection can promote not only retrotransposon transcription but also eccDNA production, which may indicate the ability of LTR-RTEs to transpose. These findings clearly illustrate that plant–virus interactions can induce not only changes in gene transcription, but also the activation of multiple retrotransposons, highlighting a potential evolutionary interface linking antiviral defense and transposon regulation.

Достижения в технологии секвенирования следующего поколения привели к аккумулированию большого объема геномных данных, открыв новые перспективы для поиска функциональных генов. Для установления и изучения функций генов могут быть использованы методы обратной генетики, например с помощью сайленсинга их экспрессии. Вирус-индуцированнный сайленсинг генов (англ. Virus-Induced Gene Silencing, VIGS) – это метод, основанный на пост-транскрипционном подавлении генов (англ. - Post-Transcriptional Gene Silencing, PTGS), реализуемый с применением естественного механизма РНК-интерференции, используемого растениями для борьбы с вирусными инфекциями.

Хлебопекарные качества зерна определяются запасными белками эндосперма. Значительная часть проламинов представлена глютенинами, которые наиболее интенсивно экспрессируются начиная с 10-го дня после цветения [1]. The baking qualities of grain are determined by endosperm storage proteins. A significant part of the prolamins is represented by glutenins, which are most intensively expressed starting from the 10th day after flowering [1].

Тритикале (×Triticosecale Wittm.) в основном является кормовой культурой, однако она обладает не только высокими потенциальными возможностями урожайности, но и повышенной устойчивостью к биотическим и абиотическим факторам окружающей среды [1]. Поэтому изучение принципов и закономерностей регуляции биологических процессов тритикале имеет высокий потенциал для производства и селекции растений. Тритикале имеет огромный геном (24 Gb), большая часть которого состоит из неизвестных генов, таких как, например, некодирующие РНК (нРНК). Известно, что у растений длинные некодирующие РНК (днРНК) регулируют важные процессы в развитии и реакции растений на стресс [2-3]. К настоящему моменту днРНК малоизучены изучены в отношении тритикале. Triticale (×Triticosecale Wittm.) is mainly a fodder crop, but it has not only high yield potential, but also increased resistance to biotic and abiotic environmental factors [1]. Therefore, the study of the principles and regularities of the regulation of biological processes of triticale has a high potential for the production and breeding of plants. Triticale has a huge genome (24 Gb), most of which consists of unknown genes, such as, for example, non-coding RNA (nRNA). In plants, long noncoding RNAs (lncRNAs) are known to regulate important processes in the development and response of plants to stress [2–3]. To date, lncRNAs have been little studied in relation to triticale.