Structural Variations in the Genome of Potato Varieties of the Ural Selection

Abstract

Potato (Solanum tuberosum L.) is the third most common plant crop in the world. Many studies, such as those using marker-assisted selection (MAS), are devoted to the genomic evaluation of potato. However, the nucleotide composition of some markers has not been described yet, and some regions of the genome remain unknown. Thus, the development of new marker systems for further genetic selection is required. Whole-genome sequencing and the search for structural variants (SVs) should further develop molecular genetic studies of the potato crop. In this paper, we will show the first results of our studies of the three backcrossed varieties Alaska, Argo, and Shah, which were selected for sequencing. Alaska is a patented variety with confirmed resistance to pathogens, while Argo and Shah are new perspective varieties. We sequenced genomes of these varieties using a nanopore platform. As a result, we identified more than 24,000 authentic structural variants with lengths varying from 4 bp to 100 Mbp. Deletion was found to be the most common type of structural variant in the genome and the genes. The majority of SVs are located in non-coding regions, including introns. However, a quarter of the genes of the sequenced varieties have some chromosomal mutations. Some genes responsible for resistance to abiotic stress and pathogens were duplicated, while genes of nucleic acid polymerization and few metabolic proteins were deleted.

Keywords

• potato <i>Solanum tuberosum</i> L.
• structural variants
• potato genome