Bioinformatic analysis of nucleotide sequences of the acetolactate synthase (als) gene of different members of the Poaceae family

Abstract

Purpose. Provide bioinformatic analysis and comparison of target regions of the acetolactate synthase (als) gene in several members of the Poaceae family and, on the basis of the obtained data, explore the possibility of creating a unified genetic construct for als gene editing using the CRISPR-Cas9 system.

Methods. The als gene sequences of various members of the Poaceae family were obtained from the NCBI: Nucleotide database. For comparison, a fragment of the imi-2 gene of wheat of the soft line ‘TealIMI11A’ was used in two regions of the 367–390 and 1729–1749 nucleotide sequences. The Sequence Viewer 3.37.0 tool was used to assess the presence of nucleotide substitutions in the working sequence of the imi-2 gene. The dendrogram was built using the “Blast Tree” tool from the NCBI: Blast: Nucleotide resource. Results. A comparative analysis of the nucleotide sequences of seven different species was carried out: soft wheat (Triticum aestivum L.), common wild oat (Avena fatua L.), barley (Hordeum vulgare L.), Asian rice (Oryza sativa L.), maize (Zea mays L.), aleppo grass (Sorghum halepense Pers.) and Tausch’s goatgrass (Aegilops tauschii Coss.). The dendrogram is based on the gene sequence als, showed that all studied genotypes can be divided into two blocks: the first block included maize and aleppo grass, and the second block, a separate branch includes Asian rice and common wild oat, barley, soft wheat and Tausch’s goatgrass. 367–390 nucleotide sequences of soft wheat showed the highest 100% homology to Asian rice, Tausch’s goatgrass and common wild oat. The lowest homo­logy was for maize and aleppo grass at 83.3%. Evaluation of the nucleotide sequence 1729–1749 showed no complete homology at the 100% level. It was the highest for barley and Tausch’s goatgrass – 95.2%, and the lowest for rice, maize and aleppo grass – 80.9% each.

Conclusions. The analysis confirms a significant degree of homology of the als gene sequence for various species of the Poaceae family, which allows us to create a universal genetic vector. However, taking into account the high degree of sequence homology for species such as soft wheat, Tausch’s goatgrass, barley, Asian rice and common wild oat, it can be assumed that the corresponding genetic vector can be used with the greatest efficiency to alter the als gene of these genotypes.