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Abstract <p><b>Research objective.</b> Analysis of restriction endonucleases for whole-genome restriction <i>in silico</i> using the GBSX program for further use in genotyping by sequencing. <b>Materials and methods.</b> The study included seven genomes of agricultural crops, such as rye, barley, millet, oats, maize, buckwheat, and soybean. According to the literature data, three single restriction enzymes and 12 combinations of endonucleases that are actively used in global practice were selected. Full-genome restriction was performed <i>in silico</i> using the GBSX program for each plant under study, and fragments of the required length were selected and counted for further high-throughput sequencing. <b>Results.</b> The results of the study showed the possibility of using a wide range of restriction endonucleases for genotyping by sequencing the studied species of agricultural plants, and the most promising enzymes and their combinations were proposed, including MseI, ApekI and the combinations: MseI–HaeIII and BfuCI–NspI. <b>Conclusions.</b> All of the restriction endonucleases studied are available on the Russian market, and all of them, except for the methyl-sensitive endonuclease ApeKI, have domestic analogues. The results of the study can be used to solve problems of genomic selection using the GBS (Genotyping by Sequencing) method.</p>

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Bioinformatic Selection of the Most Optimal Restriction Endonuclease Combinations for Genotyping Major Agricultural Crops Using the GBS Method

  • 期刊论文

  • 发表日期：

    2025年12月1日

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  • T. V. Erofeeva,
  • A. S. Krylova,
  • S. V. Toschakov

摘要

Abstract

Research objective. Analysis of restriction endonucleases for whole-genome restriction in silico using the GBSX program for further use in genotyping by sequencing. Materials and methods. The study included seven genomes of agricultural crops, such as rye, barley, millet, oats, maize, buckwheat, and soybean. According to the literature data, three single restriction enzymes and 12 combinations of endonucleases that are actively used in global practice were selected. Full-genome restriction was performed in silico using the GBSX program for each plant under study, and fragments of the required length were selected and counted for further high-throughput sequencing. Results. The results of the study showed the possibility of using a wide range of restriction endonucleases for genotyping by sequencing the studied species of agricultural plants, and the most promising enzymes and their combinations were proposed, including MseI, ApekI and the combinations: MseI–HaeIII and BfuCI–NspI. Conclusions. All of the restriction endonucleases studied are available on the Russian market, and all of them, except for the methyl-sensitive endonuclease ApeKI, have domestic analogues. The results of the study can be used to solve problems of genomic selection using the GBS (Genotyping by Sequencing) method.