In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family Euphorbiaceae
(1) Background: To assess the genetic makeup among the agro-economically important members of Euphorbiaceae, the present study was conducted to identify and characterize high-quality single-nucleotide polymorphism (SNP) markers and their comparative distribution in exonic and intronic regions from t...
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MDPI AG
2023-01-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/2/332 |
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| author | Surojit Sen Sunayana Rathi Jagajjit Sahu Subhash C. Mandal Supratim Ray Petr Slama Shubhadeep Roychoudhury |
| author_facet | Surojit Sen Sunayana Rathi Jagajjit Sahu Subhash C. Mandal Supratim Ray Petr Slama Shubhadeep Roychoudhury |
| author_sort | Surojit Sen |
| collection | DOAJ |
| description | (1) Background: To assess the genetic makeup among the agro-economically important members of Euphorbiaceae, the present study was conducted to identify and characterize high-quality single-nucleotide polymorphism (SNP) markers and their comparative distribution in exonic and intronic regions from the publicly available expressed sequence tags (ESTs). (2) Methods: Quality sequences obtained after pre-processing by an EG assembler were assembled into contigs using the CAP3 program at 95% identity; the mining of SNP was performed by QualitySNP; GENSCAN (standalone) was used for detecting the distribution of SNPs in the exonic and intronic regions. (3) Results: A total of 25,432 potential SNPs (pSNP) and 14,351 high-quality SNPs (qSNP), including 2276 indels, were detected from 260,479 EST sequences. The ratio of quality SNP to potential SNP ranged from 0.22 to 0.75. A higher frequency of transitions and transversions was observed more in the exonic than the intronic region, while indels were present more in the intronic region. C↔T (transition) was the most dominant nucleotide substitution, while in transversion, A↔T was the dominant nucleotide substitution, and in indel, A/- was dominant. (4) Conclusions: Detected SNP markers may be useful for linkage mapping; marker-assisted breeding; studying genetic diversity; mapping important phenotypic traits, such as adaptation or oil production; or disease resistance by targeting and screening mutations in important genes. |
| first_indexed | 2024-03-11T08:46:45Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T08:46:45Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-478cb40e60434052b3ea816eae8f09a92023-11-16T20:41:30ZengMDPI AGGenes2073-44252023-01-0114233210.3390/genes14020332In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family EuphorbiaceaeSurojit Sen0Sunayana Rathi1Jagajjit Sahu2Subhash C. Mandal3Supratim Ray4Petr Slama5Shubhadeep Roychoudhury6Department of Zoology, Mariani College, Mariani 785634, IndiaDepartment of Biochemistry and Agricultural Chemistry, Assam Agricultural University, Jorhat 785013, IndiaGyanArras Academy, Gothapatna, Malipada, Bhubaneswar 751003, IndiaDepartment of Pharmaceutical Technology, Division of Pharmacognosy, Jadavpur University, Kolkata 700032, IndiaDepartment of Pharmaceutical Sciences, Assam University, Silchar 788011, IndiaLaboratory of Animal Immunology and Biotechnology, Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, 61300 Brno, Czech RepublicDepartment of Life Science and Bioinformatics, Assam University, Silchar 788011, India(1) Background: To assess the genetic makeup among the agro-economically important members of Euphorbiaceae, the present study was conducted to identify and characterize high-quality single-nucleotide polymorphism (SNP) markers and their comparative distribution in exonic and intronic regions from the publicly available expressed sequence tags (ESTs). (2) Methods: Quality sequences obtained after pre-processing by an EG assembler were assembled into contigs using the CAP3 program at 95% identity; the mining of SNP was performed by QualitySNP; GENSCAN (standalone) was used for detecting the distribution of SNPs in the exonic and intronic regions. (3) Results: A total of 25,432 potential SNPs (pSNP) and 14,351 high-quality SNPs (qSNP), including 2276 indels, were detected from 260,479 EST sequences. The ratio of quality SNP to potential SNP ranged from 0.22 to 0.75. A higher frequency of transitions and transversions was observed more in the exonic than the intronic region, while indels were present more in the intronic region. C↔T (transition) was the most dominant nucleotide substitution, while in transversion, A↔T was the dominant nucleotide substitution, and in indel, A/- was dominant. (4) Conclusions: Detected SNP markers may be useful for linkage mapping; marker-assisted breeding; studying genetic diversity; mapping important phenotypic traits, such as adaptation or oil production; or disease resistance by targeting and screening mutations in important genes.https://www.mdpi.com/2073-4425/14/2/332ESTpotential SNPnucleotide substitutionC↔T transitionA↔T transversionindel |
| spellingShingle | Surojit Sen Sunayana Rathi Jagajjit Sahu Subhash C. Mandal Supratim Ray Petr Slama Shubhadeep Roychoudhury In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family Euphorbiaceae Genes EST potential SNP nucleotide substitution C↔T transition A↔T transversion indel |
| title | In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family Euphorbiaceae |
| title_full | In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family Euphorbiaceae |
| title_fullStr | In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family Euphorbiaceae |
| title_full_unstemmed | In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family Euphorbiaceae |
| title_short | In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family Euphorbiaceae |
| title_sort | in silico mining and characterization of high quality snp indels in some agro economically important species belonging to the family euphorbiaceae |
| topic | EST potential SNP nucleotide substitution C↔T transition A↔T transversion indel |
| url | https://www.mdpi.com/2073-4425/14/2/332 |
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