Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers
Random Amplified Polymorphic DNA (RAPD) analysis was performed to assess the genetic variability in sixteen selected germplasms of rice, Oryza sativa L. using eight decamer RAPD primers. The data obtained from this investigation reveals a high level of polymorphism between cultivars. The primers pro...
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| Format: | Article |
| Language: | English |
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Elsevier
2020-08-01
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| Series: | Heliyon |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844020311774 |
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| author | Sonia Rani Mazumder Hammadul Hoque Beethi Sinha Woasifur Rahman Chowdhury Md Nazmul Hasan Shamsul H. Prodhan |
| author_facet | Sonia Rani Mazumder Hammadul Hoque Beethi Sinha Woasifur Rahman Chowdhury Md Nazmul Hasan Shamsul H. Prodhan |
| author_sort | Sonia Rani Mazumder |
| collection | DOAJ |
| description | Random Amplified Polymorphic DNA (RAPD) analysis was performed to assess the genetic variability in sixteen selected germplasms of rice, Oryza sativa L. using eight decamer RAPD primers. The data obtained from this investigation reveals a high level of polymorphism between cultivars. The primers produced a total of 255 bands of which all 255 bands were polymorphic indicating 100% polymorphism. The size of the amplified bands ranged from 220 bp to 2290 bp. The number of polymorphic fragments ranged from 24 to 49 with an average of 32 polymorphic fragments for each primer. The primer OPX04 produced the maximum number (49) of polymorphic bands while the OPB04 and OPB17 produced the minimum number (24) of polymorphic bands. The polymorphic information content (PIC) values ranged from 0.6616 to 0.8845 with an average of 0.832. The highest PIC value (0.8845) was obtained for primer OPL03. The RAPD data was analyzed to determine the pair-wise genetic similarity coefficients which ranged from 0.00 to 0.83. The BRRIdhan 23 and the BRRIdhan 41 varieties were the closest genotypes with the highest similarity index of 83%. This was followed by 77% similarity between a pair of cultivars Kalamona and Horkuch. On the other hand, 100% dissimilarity was seen between BRRIdhan 53, BRRIdhan 50, BRRIdhan 10, BRRIdhan 70, BRRIdhan 54, BRRIdhan 40, BRRIdhan 23, BRRIdhan 47, BRRIdhan 41 and Dadsail respectively and between BRRIdhan 53 and Horkuch; indicating a high level of variability between paired genotypes. Cluster analysis was performed using Unweighted Paired Group of Arithmetic Means (UPGMA). The UPGMA dendrogram resolved the selected rice cultivars into four clusters. |
| first_indexed | 2024-12-11T13:38:33Z |
| format | Article |
| id | doaj.art-26d05d915145410aa0ec99a23b9e9dd2 |
| institution | Directory Open Access Journal |
| issn | 2405-8440 |
| language | English |
| last_indexed | 2024-12-11T13:38:33Z |
| publishDate | 2020-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj.art-26d05d915145410aa0ec99a23b9e9dd22022-12-22T01:04:54ZengElsevierHeliyon2405-84402020-08-0168e04333Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markersSonia Rani Mazumder0Hammadul Hoque1Beethi Sinha2Woasifur Rahman Chowdhury3Md Nazmul Hasan4Shamsul H. Prodhan5Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, BangladeshDepartment of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, BangladeshDepartment of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, BangladeshDepartment of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, BangladeshDepartment of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, BangladeshDepartment of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh; Corresponding author.Random Amplified Polymorphic DNA (RAPD) analysis was performed to assess the genetic variability in sixteen selected germplasms of rice, Oryza sativa L. using eight decamer RAPD primers. The data obtained from this investigation reveals a high level of polymorphism between cultivars. The primers produced a total of 255 bands of which all 255 bands were polymorphic indicating 100% polymorphism. The size of the amplified bands ranged from 220 bp to 2290 bp. The number of polymorphic fragments ranged from 24 to 49 with an average of 32 polymorphic fragments for each primer. The primer OPX04 produced the maximum number (49) of polymorphic bands while the OPB04 and OPB17 produced the minimum number (24) of polymorphic bands. The polymorphic information content (PIC) values ranged from 0.6616 to 0.8845 with an average of 0.832. The highest PIC value (0.8845) was obtained for primer OPL03. The RAPD data was analyzed to determine the pair-wise genetic similarity coefficients which ranged from 0.00 to 0.83. The BRRIdhan 23 and the BRRIdhan 41 varieties were the closest genotypes with the highest similarity index of 83%. This was followed by 77% similarity between a pair of cultivars Kalamona and Horkuch. On the other hand, 100% dissimilarity was seen between BRRIdhan 53, BRRIdhan 50, BRRIdhan 10, BRRIdhan 70, BRRIdhan 54, BRRIdhan 40, BRRIdhan 23, BRRIdhan 47, BRRIdhan 41 and Dadsail respectively and between BRRIdhan 53 and Horkuch; indicating a high level of variability between paired genotypes. Cluster analysis was performed using Unweighted Paired Group of Arithmetic Means (UPGMA). The UPGMA dendrogram resolved the selected rice cultivars into four clusters.http://www.sciencedirect.com/science/article/pii/S2405844020311774AgricultureBiochemistryGeneticsMolecular biologyVariabilityIndica rice |
| spellingShingle | Sonia Rani Mazumder Hammadul Hoque Beethi Sinha Woasifur Rahman Chowdhury Md Nazmul Hasan Shamsul H. Prodhan Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers Heliyon Agriculture Biochemistry Genetics Molecular biology Variability Indica rice |
| title | Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers |
| title_full | Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers |
| title_fullStr | Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers |
| title_full_unstemmed | Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers |
| title_short | Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers |
| title_sort | genetic variability analysis of partially salt tolerant local and inbred rice oryza sativa l through molecular markers |
| topic | Agriculture Biochemistry Genetics Molecular biology Variability Indica rice |
| url | http://www.sciencedirect.com/science/article/pii/S2405844020311774 |
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