Molecular identification and genetic diversity analysis of sugarcane clones by SSR markers
Sugarcane is one of the important crops with high heterozygosity and phenotypic polymorphism. Varietal identification and characterization is one of the important aspects in any breeding programme. Forty sugarcane clones from Pre -zonal varietal trial (PZVT) conducted at Ugar, North Karnataka were c...
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| Format: | Article |
| Language: | English |
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Society for Sugarcane Research and Development
2021-08-01
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| Series: | Journal of Sugarcane Research |
| Subjects: | |
| Online Access: | https://epubs.icar.org.in/index.php/JSR/article/view/104867 |
| _version_ | 1797794467992829952 |
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| author | Alarmelu Srinivasan Karpagam Elumalai Nagarajan Ranganathan Shanthi Manickavasagam R |
| author_facet | Alarmelu Srinivasan Karpagam Elumalai Nagarajan Ranganathan Shanthi Manickavasagam R |
| author_sort | Alarmelu Srinivasan |
| collection | DOAJ |
| description | Sugarcane is one of the important crops with high heterozygosity and phenotypic polymorphism. Varietal identification and characterization is one of the important aspects in any breeding programme. Forty sugarcane clones from Pre -zonal varietal trial (PZVT) conducted at Ugar, North Karnataka were characterized through Simple sequence repeats (SSR) markers using a set of 15 sugarcane specific primer pairs which amplified a total of 164 alleles with an average of 10.93 alleles per pair. Primer NKS 33 was highly polymorphic and produced more than 15 polymorphic alleles and was unique in all the clones studied. Six primers i.e., NKS 2, NKS 6, NKS 7, NKS 40, NKS 42 and NKS 11 were moderately polymorphic by producing 10 to 13 alleles. Percentage of polymorphic bands ranged from 75.0 % (NKS 3) to 100.0 % (NKS 40 and NKS 42). Primers viz., SMC 1039 GC, mSSCIR 54, NKS 2, NKS 7, NKS 9, NKS 33, NKS 40, NKS 42 and NKS 11 were highly informative and generated above 85.0 % of polymorphic bands. Among the primers used, SMC 1039 GC, NKS 33, NKS 42 and NKS 43 produced the maximum number of unique markers in different clones and hence the combined application of these primers will be useful in unambiguous varietal identification. The cluster analysis based on the genetic similarity matrix grouped the 40 clones into two major clusters CI and CII. The largest cluster CII contained the maximum of 38 clones. Cluster C II was further sub-grouped into IIa, IIb, IIc and IId and each sub-cluster comprised 7, 11, 6 and 14 clones respectively. The unique DNA markers and the genetically diverse combinations identified in the present study will enhance the exploitation of genetic diversity present in the clones in breeding programmes and promising twenty eight entries for yield and quality. |
| first_indexed | 2024-03-13T03:03:16Z |
| format | Article |
| id | doaj.art-02e6ade902ba4011bc6bcd0093411fe5 |
| institution | Directory Open Access Journal |
| issn | 2249-927X 2582-4767 |
| language | English |
| last_indexed | 2024-03-13T03:03:16Z |
| publishDate | 2021-08-01 |
| publisher | Society for Sugarcane Research and Development |
| record_format | Article |
| series | Journal of Sugarcane Research |
| spelling | doaj.art-02e6ade902ba4011bc6bcd0093411fe52023-06-27T09:10:24ZengSociety for Sugarcane Research and DevelopmentJournal of Sugarcane Research2249-927X2582-47672021-08-01102Molecular identification and genetic diversity analysis of sugarcane clones by SSR markersAlarmelu Srinivasan0Karpagam Elumalai1Nagarajan Ranganathan2Shanthi Manickavasagam R3DIVISION OF CROP IMPROVEMENT ICAR -SUGARCANE BREEDING INSTITUTE COIMBATORE INDIADIVISION OF CROP IMPROVEMENT ICAR-SBI COIMBATOREDIVISION OF CROP IMPROVEMENT ICAR-SBI COIMBATOREDIVISION OF CROP IMPROVEMENT, ICAR-SBI, COIMBATORESugarcane is one of the important crops with high heterozygosity and phenotypic polymorphism. Varietal identification and characterization is one of the important aspects in any breeding programme. Forty sugarcane clones from Pre -zonal varietal trial (PZVT) conducted at Ugar, North Karnataka were characterized through Simple sequence repeats (SSR) markers using a set of 15 sugarcane specific primer pairs which amplified a total of 164 alleles with an average of 10.93 alleles per pair. Primer NKS 33 was highly polymorphic and produced more than 15 polymorphic alleles and was unique in all the clones studied. Six primers i.e., NKS 2, NKS 6, NKS 7, NKS 40, NKS 42 and NKS 11 were moderately polymorphic by producing 10 to 13 alleles. Percentage of polymorphic bands ranged from 75.0 % (NKS 3) to 100.0 % (NKS 40 and NKS 42). Primers viz., SMC 1039 GC, mSSCIR 54, NKS 2, NKS 7, NKS 9, NKS 33, NKS 40, NKS 42 and NKS 11 were highly informative and generated above 85.0 % of polymorphic bands. Among the primers used, SMC 1039 GC, NKS 33, NKS 42 and NKS 43 produced the maximum number of unique markers in different clones and hence the combined application of these primers will be useful in unambiguous varietal identification. The cluster analysis based on the genetic similarity matrix grouped the 40 clones into two major clusters CI and CII. The largest cluster CII contained the maximum of 38 clones. Cluster C II was further sub-grouped into IIa, IIb, IIc and IId and each sub-cluster comprised 7, 11, 6 and 14 clones respectively. The unique DNA markers and the genetically diverse combinations identified in the present study will enhance the exploitation of genetic diversity present in the clones in breeding programmes and promising twenty eight entries for yield and quality.https://epubs.icar.org.in/index.php/JSR/article/view/104867SugarcaneMolecular markersSSRClones |
| spellingShingle | Alarmelu Srinivasan Karpagam Elumalai Nagarajan Ranganathan Shanthi Manickavasagam R Molecular identification and genetic diversity analysis of sugarcane clones by SSR markers Journal of Sugarcane Research Sugarcane Molecular markers SSR Clones |
| title | Molecular identification and genetic diversity analysis of sugarcane clones by SSR markers |
| title_full | Molecular identification and genetic diversity analysis of sugarcane clones by SSR markers |
| title_fullStr | Molecular identification and genetic diversity analysis of sugarcane clones by SSR markers |
| title_full_unstemmed | Molecular identification and genetic diversity analysis of sugarcane clones by SSR markers |
| title_short | Molecular identification and genetic diversity analysis of sugarcane clones by SSR markers |
| title_sort | molecular identification and genetic diversity analysis of sugarcane clones by ssr markers |
| topic | Sugarcane Molecular markers SSR Clones |
| url | https://epubs.icar.org.in/index.php/JSR/article/view/104867 |
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