Characterization of new microsatellite markers from sugarcane (Saccharum officinarum) transcriptome
Microsatellites, or simple sequence repeats (SSR), developed by expressed sequence tag (EST) databases is an economical and efficient tools that can be used to perform genetic investigations at a functional level. Here, a new sugarcane database of transcriptome from our variety, GT35, was examined f...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Indian Council of Agricultural Research
2020-09-01
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| Series: | The Indian Journal of Agricultural Sciences |
| Subjects: | |
| Online Access: | https://epubs.icar.org.in/index.php/IJAgS/article/view/104330 |
| _version_ | 1811164706000338944 |
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| author | Yijing Gao Hui Zhou Junxian Liu Jingchao Lei Weixing Duan Cuifang Yang Shan Zhou Xiang Li Gemin Zhang Baoqing Zhang Hongwei Tan Zeping Wang Yangrui Li |
| author_facet | Yijing Gao Hui Zhou Junxian Liu Jingchao Lei Weixing Duan Cuifang Yang Shan Zhou Xiang Li Gemin Zhang Baoqing Zhang Hongwei Tan Zeping Wang Yangrui Li |
| author_sort | Yijing Gao |
| collection | DOAJ |
| description | Microsatellites, or simple sequence repeats (SSR), developed by expressed sequence tag (EST) databases is an economical and efficient tools that can be used to perform genetic investigations at a functional level. Here, a new sugarcane database of transcriptome from our variety, GT35, was examined for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 51 new EST-SSRs were identified for possible use as potential genetic markers from no redundant SSR-positive ESTs, which were unmapped with the sequences available in the NCBI’EST database of sugarcane by BLASTN. Polymorphisms of the identified 51 EST-SSR markers were evaluated in 21 sugarcane genotypes, planted and collected in 2013 at Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences (SRI-GXAAS) in China. High polymorphisms were detected in terms of number of alleles ranging from 5-36 with an average of 16.8 per locus and polymorphism information content values ranging from 0.74 to 0.95 with a mean of 0.92. Average transferability to Erianthus arundinaceus and Narenga porphyrocoma was 23.9% and 34.4%, respectively. The ability to establish genetic relationship was analyzed by cluster analysis, the result of which revealed that the major grouping was in accordance with taxonomical classification. The development of new EST-SSR markers presented in this work will have important implications for genetic analysis and breeding. |
| first_indexed | 2024-04-10T15:25:48Z |
| format | Article |
| id | doaj.art-5f440c53cf264f6ebc799e1954fbdbfc |
| institution | Directory Open Access Journal |
| issn | 0019-5022 2394-3319 |
| language | English |
| last_indexed | 2024-04-10T15:25:48Z |
| publishDate | 2020-09-01 |
| publisher | Indian Council of Agricultural Research |
| record_format | Article |
| series | The Indian Journal of Agricultural Sciences |
| spelling | doaj.art-5f440c53cf264f6ebc799e1954fbdbfc2023-02-14T09:09:50ZengIndian Council of Agricultural ResearchThe Indian Journal of Agricultural Sciences0019-50222394-33192020-09-0190510.56093/ijas.v90i5.104330Characterization of new microsatellite markers from sugarcane (Saccharum officinarum) transcriptomeYijing Gao0Hui Zhou1Junxian Liu2Jingchao Lei3Weixing Duan4Cuifang Yang5Shan Zhou6Xiang Li7Gemin Zhang8Baoqing Zhang9Hongwei Tan10Zeping Wang11Yangrui Li12Guangxi Academy of Agricultural Sciences, Nanning 530 007, ChinaGuangxi Academy of Agricultural Sciences, Nanning 530 007, ChinaGuangxi Academy of Agricultural Sciences, Nanning 530 007, ChinaGuangxi Academy of Agricultural Sciences, Nanning 530 007, ChinaGuangxi Academy of Agricultural Sciences, Nanning 530 007, ChinaGuangxi Academy of Agricultural Sciences, Nanning 530 007, ChinaGuangxi Academy of Agricultural Sciences, Nanning 530 007, ChinaGuangxi Academy of Agricultural Sciences, Nanning 530 007, ChinaGuangxi Academy of Agricultural Sciences, Nanning 530 007, ChinaGuangxi Academy of Agricultural Sciences, Nanning 530 007, ChinaGuangxi Academy of Agricultural Sciences, Nanning 530 007, ChinaGuangxi Academy of Agricultural Sciences, Nanning 530 007, ChinaGuangxi Academy of Agricultural Sciences, Nanning 530 007, ChinaMicrosatellites, or simple sequence repeats (SSR), developed by expressed sequence tag (EST) databases is an economical and efficient tools that can be used to perform genetic investigations at a functional level. Here, a new sugarcane database of transcriptome from our variety, GT35, was examined for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 51 new EST-SSRs were identified for possible use as potential genetic markers from no redundant SSR-positive ESTs, which were unmapped with the sequences available in the NCBI’EST database of sugarcane by BLASTN. Polymorphisms of the identified 51 EST-SSR markers were evaluated in 21 sugarcane genotypes, planted and collected in 2013 at Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences (SRI-GXAAS) in China. High polymorphisms were detected in terms of number of alleles ranging from 5-36 with an average of 16.8 per locus and polymorphism information content values ranging from 0.74 to 0.95 with a mean of 0.92. Average transferability to Erianthus arundinaceus and Narenga porphyrocoma was 23.9% and 34.4%, respectively. The ability to establish genetic relationship was analyzed by cluster analysis, the result of which revealed that the major grouping was in accordance with taxonomical classification. The development of new EST-SSR markers presented in this work will have important implications for genetic analysis and breeding.https://epubs.icar.org.in/index.php/IJAgS/article/view/104330ESTMicrosatellitesSugarcaneTranscriptome |
| spellingShingle | Yijing Gao Hui Zhou Junxian Liu Jingchao Lei Weixing Duan Cuifang Yang Shan Zhou Xiang Li Gemin Zhang Baoqing Zhang Hongwei Tan Zeping Wang Yangrui Li Characterization of new microsatellite markers from sugarcane (Saccharum officinarum) transcriptome The Indian Journal of Agricultural Sciences EST Microsatellites Sugarcane Transcriptome |
| title | Characterization of new microsatellite markers from sugarcane (Saccharum officinarum) transcriptome |
| title_full | Characterization of new microsatellite markers from sugarcane (Saccharum officinarum) transcriptome |
| title_fullStr | Characterization of new microsatellite markers from sugarcane (Saccharum officinarum) transcriptome |
| title_full_unstemmed | Characterization of new microsatellite markers from sugarcane (Saccharum officinarum) transcriptome |
| title_short | Characterization of new microsatellite markers from sugarcane (Saccharum officinarum) transcriptome |
| title_sort | characterization of new microsatellite markers from sugarcane saccharum officinarum transcriptome |
| topic | EST Microsatellites Sugarcane Transcriptome |
| url | https://epubs.icar.org.in/index.php/IJAgS/article/view/104330 |
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