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Analysis of transposable element derived polymorphism in Pinus sylvestris gene regions
Leader: Vilnis Šķipars
Start date: 1.12.2020
End date: 30.12.2021

Scots pine (Pinus sylvestris L.) is an important conifer species in Latvia, and germplasm with improved parameters is used for forest renewal. However, potential adaptability of current pine germplasm to changing environmental conditions or pathogens is unknown, and it is important to identify more adaptable plant material for forest restoration to ensure the sustainability of future forests. Transposable element (TE) composition varies between individuals and can influence gene function by disruption of gene functional sequences, influencing transcription, gene splicing and heterochromatin formation, and play a part in functional non-coding RNA formation. In our previous research, the topology of TEs in flanking gene regions was investigated, as well as the distribution of TEs in the non-coding regions of genes. A number of new TEs have been identified that were located in the vicinity of Scots pine (P. sylvestris) exons that contain important gene regulatory motifs. Using a new transcript selection methodology with subsequent massively parallel sequencing developed in our previous studies, a dataset was produced that can be used for further research. The objectives of this proposal are the detailed study of potential P. sylvestris candidate genes with TE-associated structural polymorphisms, verification of TE presence and evaluation of distance from the gene, investigation of diversity of TE-associated polymorphisms in a range of P. sylvestris germplasm.

Keywords: Transposable elements, gene regulation, polymorphism, resistance, adaptation, pine genome


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