Bioinformatic analysis of maize gene encoding starch branching enzyme SBEIIb.
Purpose. Investigation of maize ae1 gene polymorphism by bioinformatic methods. Methods. Global and local alignment of the nucleotide and amino acid sequences, in silico translation and transcription, translates modeling, primers design, phylogenetic analysis. Results. 255 nucleotide sequences of...
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Ukrainian Institute for Plant Variety Examination
2016-07-01
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| Series: | Plant Varieties Studying and Protection |
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| Online Access: | http://journal.sops.gov.ua/article/view/75972 |
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| author | Г. І. Сліщук Т. Ю. Жернаков Н. Е. Волкова |
| author_facet | Г. І. Сліщук Т. Ю. Жернаков Н. Е. Волкова |
| author_sort | Г. І. Сліщук |
| collection | DOAJ |
| description | Purpose. Investigation of maize ae1 gene polymorphism by bioinformatic methods.
Methods. Global and local alignment of the nucleotide and amino acid sequences, in silico translation and transcription, translates modeling, primers design, phylogenetic analysis.
Results. 255 nucleotide sequences of maize аe1 gene, 500 amino acid sequences of homology translates of maize ae1 gene (SBEIIb enzyme homologs) and 100 mRNA expressed from the maize ae1 gene were analyzed to establish phylogenetic relationships. Polymorphism of maize ae1 gene different regions was investigated by bioinformatic methods. Modeling of the maize enzyme SBEIIb was performed.
Conclusions. According to the results of amino acid sequences of SBEIIb enzyme homologs alignment, it was found that ae1 gene orthologs are present only in monocots, paralogs – in monocots, dicots, and other taxa, including algae and animals. Based on the results of alignment of plants mRNA from which enzyme SBEIIb is translated, maize ae1 gene orthologs and the nearest paralogs encoding starch branching enzymes with chloroplast localization were defined; this suggests a possible origin of ae1 gene due to duplication of the gene encoding the 1,4-alpha-glucan-branching enzyme 2 with chloroplast or amyloplast localization. In the maize ae1 gene structure, regions were found that include polymorphic sites not defined previously. For the polymorphic sites design primers were developed that allowed to differentiate the maize lines. It was determined that the detection of polymorphism in theory can influence the enzyme function and, as a result, change the concentration of amylopectin in maize grain. |
| format | Article |
| id | doaj-art-fee2afd99c0a444a81775a1eca2a67c8 |
| institution | OA Journals |
| issn | 2518-1017 2518-7457 |
| language | English |
| publishDate | 2016-07-01 |
| publisher | Ukrainian Institute for Plant Variety Examination |
| record_format | Article |
| series | Plant Varieties Studying and Protection |
| spelling | doaj-art-fee2afd99c0a444a81775a1eca2a67c82025-08-20T01:48:02ZengUkrainian Institute for Plant Variety ExaminationPlant Varieties Studying and Protection2518-10172518-74572016-07-0103(32)131810.21498/2518-1017.3(32).2016.7597275972Bioinformatic analysis of maize gene encoding starch branching enzyme SBEIIb.Г. І. Сліщук0Т. Ю. Жернаков1Н. Е. Волкова2Plant Breeding and Genetics Institute – National center of Seed and Cultivar InvestigationPlant Breeding and Genetics Institute – National center of Seed and Cultivar InvestigationPlant Breeding and Genetics Institute – National Center of Seed and Cultivar InvestigationPurpose. Investigation of maize ae1 gene polymorphism by bioinformatic methods. Methods. Global and local alignment of the nucleotide and amino acid sequences, in silico translation and transcription, translates modeling, primers design, phylogenetic analysis. Results. 255 nucleotide sequences of maize аe1 gene, 500 amino acid sequences of homology translates of maize ae1 gene (SBEIIb enzyme homologs) and 100 mRNA expressed from the maize ae1 gene were analyzed to establish phylogenetic relationships. Polymorphism of maize ae1 gene different regions was investigated by bioinformatic methods. Modeling of the maize enzyme SBEIIb was performed. Conclusions. According to the results of amino acid sequences of SBEIIb enzyme homologs alignment, it was found that ae1 gene orthologs are present only in monocots, paralogs – in monocots, dicots, and other taxa, including algae and animals. Based on the results of alignment of plants mRNA from which enzyme SBEIIb is translated, maize ae1 gene orthologs and the nearest paralogs encoding starch branching enzymes with chloroplast localization were defined; this suggests a possible origin of ae1 gene due to duplication of the gene encoding the 1,4-alpha-glucan-branching enzyme 2 with chloroplast or amyloplast localization. In the maize ae1 gene structure, regions were found that include polymorphic sites not defined previously. For the polymorphic sites design primers were developed that allowed to differentiate the maize lines. It was determined that the detection of polymorphism in theory can influence the enzyme function and, as a result, change the concentration of amylopectin in maize grain.http://journal.sops.gov.ua/article/view/75972ae1 genestarch branching enzyme SBEIIbmaizebioinformatic |
| spellingShingle | Г. І. Сліщук Т. Ю. Жернаков Н. Е. Волкова Bioinformatic analysis of maize gene encoding starch branching enzyme SBEIIb. Plant Varieties Studying and Protection ae1 gene starch branching enzyme SBEIIb maize bioinformatic |
| title | Bioinformatic analysis of maize gene encoding starch branching enzyme SBEIIb. |
| title_full | Bioinformatic analysis of maize gene encoding starch branching enzyme SBEIIb. |
| title_fullStr | Bioinformatic analysis of maize gene encoding starch branching enzyme SBEIIb. |
| title_full_unstemmed | Bioinformatic analysis of maize gene encoding starch branching enzyme SBEIIb. |
| title_short | Bioinformatic analysis of maize gene encoding starch branching enzyme SBEIIb. |
| title_sort | bioinformatic analysis of maize gene encoding starch branching enzyme sbeiib |
| topic | ae1 gene starch branching enzyme SBEIIb maize bioinformatic |
| url | http://journal.sops.gov.ua/article/view/75972 |
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