LTR retrotransposons and highly informative ISSRs in combination are potential markers for genetic fidelity testing of tissue culture-raised plants in sugarcane
Testing the genetic fidelity of micropropagated clones with DNA markers could curtail the losses caused by somaclonal variation in sugarcane tissue culture industry. Evaluation of 32 inter-retrotransposon amplified polymorphism (IRAP) markers and 100 inter-simple sequence repeats (ISSRs) in 47 sugar...
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| Veröffentlicht in: | Molecular breeding 2019-02, Vol.39 (2), p.1-13, Article 25 |
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| creator | Shingote, Prashant R. Amitha Mithra, S. V. Sharma, Pratima Devanna, Navadagi B. Arora, Kirti Holkar, Somnath K. Khan, Suhail Singh, J. Kumar, Sanjeev Sharma, T. R. Solanke, Amolkumar U. |
| description | Testing the genetic fidelity of micropropagated clones with DNA markers could curtail the losses caused by somaclonal variation in sugarcane tissue culture industry. Evaluation of 32 inter-retrotransposon amplified polymorphism (IRAP) markers and 100 inter-simple sequence repeats (ISSRs) in 47 sugarcane accessions identified 20 (8 IRAPs and 12 ISSRs) polymorphic markers representing 98 loci. IRAP system was superior to ISSR in terms of marker index (2.68 as against 1.76), resolving power (2.85 as against 1.98), and polymorphic loci per assay (6 compared to 4.1), except mean polymorphic information content (0.31 and 0.34). Further evaluation of the 20 polymorphic markers in testing the genetic fidelity of micropropagated sugarcane clones identified a variant clone by three primers of ISSR and one IRAP marker (UBC810, UBC813, UBC840, and LTR6149 + 3′LTR). The unique amplicons from the somaclonal variant were validated by sequencing. Based on the number of bands amplified and proportion of polymorphic loci, a set of six ISSR and four IRAP markers has been recommended to test clonal fidelity for sugarcane tissue culture industry. |
| doi_str_mv | 10.1007/s11032-019-0931-5 |
| format | Article |
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V. ; Sharma, Pratima ; Devanna, Navadagi B. ; Arora, Kirti ; Holkar, Somnath K. ; Khan, Suhail ; Singh, J. ; Kumar, Sanjeev ; Sharma, T. R. ; Solanke, Amolkumar U.</creator><creatorcontrib>Shingote, Prashant R. ; Amitha Mithra, S. V. ; Sharma, Pratima ; Devanna, Navadagi B. ; Arora, Kirti ; Holkar, Somnath K. ; Khan, Suhail ; Singh, J. ; Kumar, Sanjeev ; Sharma, T. R. ; Solanke, Amolkumar U.</creatorcontrib><description>Testing the genetic fidelity of micropropagated clones with DNA markers could curtail the losses caused by somaclonal variation in sugarcane tissue culture industry. Evaluation of 32 inter-retrotransposon amplified polymorphism (IRAP) markers and 100 inter-simple sequence repeats (ISSRs) in 47 sugarcane accessions identified 20 (8 IRAPs and 12 ISSRs) polymorphic markers representing 98 loci. IRAP system was superior to ISSR in terms of marker index (2.68 as against 1.76), resolving power (2.85 as against 1.98), and polymorphic loci per assay (6 compared to 4.1), except mean polymorphic information content (0.31 and 0.34). Further evaluation of the 20 polymorphic markers in testing the genetic fidelity of micropropagated sugarcane clones identified a variant clone by three primers of ISSR and one IRAP marker (UBC810, UBC813, UBC840, and LTR6149 + 3′LTR). The unique amplicons from the somaclonal variant were validated by sequencing. 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V.</creatorcontrib><creatorcontrib>Sharma, Pratima</creatorcontrib><creatorcontrib>Devanna, Navadagi B.</creatorcontrib><creatorcontrib>Arora, Kirti</creatorcontrib><creatorcontrib>Holkar, Somnath K.</creatorcontrib><creatorcontrib>Khan, Suhail</creatorcontrib><creatorcontrib>Singh, J.</creatorcontrib><creatorcontrib>Kumar, Sanjeev</creatorcontrib><creatorcontrib>Sharma, T. R.</creatorcontrib><creatorcontrib>Solanke, Amolkumar U.</creatorcontrib><title>LTR retrotransposons and highly informative ISSRs in combination are potential markers for genetic fidelity testing of tissue culture-raised plants in sugarcane</title><title>Molecular breeding</title><addtitle>Mol Breeding</addtitle><description>Testing the genetic fidelity of micropropagated clones with DNA markers could curtail the losses caused by somaclonal variation in sugarcane tissue culture industry. Evaluation of 32 inter-retrotransposon amplified polymorphism (IRAP) markers and 100 inter-simple sequence repeats (ISSRs) in 47 sugarcane accessions identified 20 (8 IRAPs and 12 ISSRs) polymorphic markers representing 98 loci. IRAP system was superior to ISSR in terms of marker index (2.68 as against 1.76), resolving power (2.85 as against 1.98), and polymorphic loci per assay (6 compared to 4.1), except mean polymorphic information content (0.31 and 0.34). Further evaluation of the 20 polymorphic markers in testing the genetic fidelity of micropropagated sugarcane clones identified a variant clone by three primers of ISSR and one IRAP marker (UBC810, UBC813, UBC840, and LTR6149 + 3′LTR). The unique amplicons from the somaclonal variant were validated by sequencing. Based on the number of bands amplified and proportion of polymorphic loci, a set of six ISSR and four IRAP markers has been recommended to test clonal fidelity for sugarcane tissue culture industry.</description><subject>Amplification</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Cloning</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Fidelity</subject><subject>Life Sciences</subject><subject>Loci</subject><subject>Markers</subject><subject>Molecular biology</subject><subject>Plant biology</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Pathology</subject><subject>Plant Physiology</subject><subject>Plant Sciences</subject><subject>Polymorphism</subject><subject>Primers</subject><subject>Resolution</subject><subject>Sequences</subject><subject>Simple sequence repeats</subject><subject>Somaclonal variation</subject><subject>Sugarcane</subject><subject>Tissue culture</subject><issn>1380-3743</issn><issn>1572-9788</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><recordid>eNp1kc1q3TAQhU1pIGnSB8hOkLVa_dmylyE0TeBCID9rIctjR6mv5GrkwH2bPGp1ewNZZTXDcL4zM5yqOufsB2dM_0TOmRSU8Y6yTnJaf6lOeK0F7XTbfi29bBmVWsnj6hviCytM1zQn1dvm8Z4kyCnmZAMuEWNAYsNAnv30PO-ID2NMW5v9K5Dbh4d7LBPi4rb3oQxjIDYBWWKGkL2dydamP5CQFIhMECB7R0Y_wOzzjmTA7MNE4kiyR1yBuHXOawKarEcYyDLbkP9vwHWyydkAZ9XRaGeE7-_1tHq6_vV4dUM3d79vry431EneZApKsJ7zXvd92wMXWtVNI5jrmZbKctW2dcMVk2xQbWdrULLpBjeKmrmOi6GVp9XFwXdJ8e9aDjUvcU2hrDSCa60VU6IuKn5QuRQRE4xmSb78vDOcmX0Q5hCEKUGYfRBmz4gDg0UbJkgfzp9D_wA1k44E</recordid><startdate>20190201</startdate><enddate>20190201</enddate><creator>Shingote, Prashant R.</creator><creator>Amitha Mithra, S. V.</creator><creator>Sharma, Pratima</creator><creator>Devanna, Navadagi B.</creator><creator>Arora, Kirti</creator><creator>Holkar, Somnath K.</creator><creator>Khan, Suhail</creator><creator>Singh, J.</creator><creator>Kumar, Sanjeev</creator><creator>Sharma, T. R.</creator><creator>Solanke, Amolkumar U.</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><orcidid>https://orcid.org/0000-0003-1773-3959</orcidid></search><sort><creationdate>20190201</creationdate><title>LTR retrotransposons and highly informative ISSRs in combination are potential markers for genetic fidelity testing of tissue culture-raised plants in sugarcane</title><author>Shingote, Prashant R. ; Amitha Mithra, S. V. ; Sharma, Pratima ; Devanna, Navadagi B. ; Arora, Kirti ; Holkar, Somnath K. ; Khan, Suhail ; Singh, J. ; Kumar, Sanjeev ; Sharma, T. 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V.</creatorcontrib><creatorcontrib>Sharma, Pratima</creatorcontrib><creatorcontrib>Devanna, Navadagi B.</creatorcontrib><creatorcontrib>Arora, Kirti</creatorcontrib><creatorcontrib>Holkar, Somnath K.</creatorcontrib><creatorcontrib>Khan, Suhail</creatorcontrib><creatorcontrib>Singh, J.</creatorcontrib><creatorcontrib>Kumar, Sanjeev</creatorcontrib><creatorcontrib>Sharma, T. R.</creatorcontrib><creatorcontrib>Solanke, Amolkumar U.</creatorcontrib><collection>CrossRef</collection><jtitle>Molecular breeding</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shingote, Prashant R.</au><au>Amitha Mithra, S. V.</au><au>Sharma, Pratima</au><au>Devanna, Navadagi B.</au><au>Arora, Kirti</au><au>Holkar, Somnath K.</au><au>Khan, Suhail</au><au>Singh, J.</au><au>Kumar, Sanjeev</au><au>Sharma, T. R.</au><au>Solanke, Amolkumar U.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>LTR retrotransposons and highly informative ISSRs in combination are potential markers for genetic fidelity testing of tissue culture-raised plants in sugarcane</atitle><jtitle>Molecular breeding</jtitle><stitle>Mol Breeding</stitle><date>2019-02-01</date><risdate>2019</risdate><volume>39</volume><issue>2</issue><spage>1</spage><epage>13</epage><pages>1-13</pages><artnum>25</artnum><issn>1380-3743</issn><eissn>1572-9788</eissn><abstract>Testing the genetic fidelity of micropropagated clones with DNA markers could curtail the losses caused by somaclonal variation in sugarcane tissue culture industry. Evaluation of 32 inter-retrotransposon amplified polymorphism (IRAP) markers and 100 inter-simple sequence repeats (ISSRs) in 47 sugarcane accessions identified 20 (8 IRAPs and 12 ISSRs) polymorphic markers representing 98 loci. IRAP system was superior to ISSR in terms of marker index (2.68 as against 1.76), resolving power (2.85 as against 1.98), and polymorphic loci per assay (6 compared to 4.1), except mean polymorphic information content (0.31 and 0.34). Further evaluation of the 20 polymorphic markers in testing the genetic fidelity of micropropagated sugarcane clones identified a variant clone by three primers of ISSR and one IRAP marker (UBC810, UBC813, UBC840, and LTR6149 + 3′LTR). The unique amplicons from the somaclonal variant were validated by sequencing. Based on the number of bands amplified and proportion of polymorphic loci, a set of six ISSR and four IRAP markers has been recommended to test clonal fidelity for sugarcane tissue culture industry.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s11032-019-0931-5</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0003-1773-3959</orcidid></addata></record> |
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| subjects | Amplification Biomedical and Life Sciences Biotechnology Cloning Deoxyribonucleic acid DNA Fidelity Life Sciences Loci Markers Molecular biology Plant biology Plant Genetics and Genomics Plant Pathology Plant Physiology Plant Sciences Polymorphism Primers Resolution Sequences Simple sequence repeats Somaclonal variation Sugarcane Tissue culture |
| title | LTR retrotransposons and highly informative ISSRs in combination are potential markers for genetic fidelity testing of tissue culture-raised plants in sugarcane |
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