Development of SSR Markers Based on Transcriptome Sequencing and Verification of Their Conservation across Species of Ornamental <i>Pennisetum</i> Rich. (Poaceae)
<i>Pennisetum</i> species have importance in foraging, agriculture, energy-production, the environment, and landscaping. To promote the preservation and utilization of ornamental <i>Pennisetum</i> resources, we developed simple sequence repeat (SSR) markers from the <i>...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-07-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/12/7/1683 |
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| author | Yidi Guo Lingyun Liu Yuesen Yue Xifeng Fan Wenjun Teng Hui Zhang Kang Gao Jin Guan Zhihui Chang Ke Teng |
| author_facet | Yidi Guo Lingyun Liu Yuesen Yue Xifeng Fan Wenjun Teng Hui Zhang Kang Gao Jin Guan Zhihui Chang Ke Teng |
| author_sort | Yidi Guo |
| collection | DOAJ |
| description | <i>Pennisetum</i> species have importance in foraging, agriculture, energy-production, the environment, and landscaping. To promote the preservation and utilization of ornamental <i>Pennisetum</i> resources, we developed simple sequence repeat (SSR) markers from the <i>Pennisetum setaceum</i> cv. ‘Rubrum’ transcriptome and verified their conservation in 38 sources. Our transcriptome sequencing efforts generated 58.91 Gb of clean data containing 55,627 unigenes. We functionally annotated 30,930 unigenes, with functions enriched in translation and ribosomal structure and biogenesis. Database comparisons indicated that the closest relative of <i>P. setaceum</i> cv. ‘Rubrum’ is <i>Setaria italica</i>. Over five thousand SSR markers were detected in the transcriptomic data. We selected 38 pairs of highly polymorphic SSR markers from 50 randomly selected SSR markers. Based on genetic diversity analysis of 38 ornamental <i>Pennisetum</i> sources, we obtained 312 polymorphic bands, with an average of 8.21 alleles per primer. Principal coordinate analyses and generation of a, which proved that <i>Pennisetum</i> has moderate genetic diversity. In addition, fingerprint maps were constructed to improve <i>Pennisetum</i> identification. The transcriptome data generated by our study enhances the transcriptional information available for <i>P. setaceum</i>. This study lays the foundation for the collection and utilization of ornamental <i>Pennisetum</i> resources and provides a basis for future breeding projects using this species. |
| first_indexed | 2024-03-09T12:22:25Z |
| format | Article |
| id | doaj.art-0b2443cf20d94147b11dcfc8fc772463 |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-09T12:22:25Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-0b2443cf20d94147b11dcfc8fc7724632023-11-30T22:39:10ZengMDPI AGAgronomy2073-43952022-07-01127168310.3390/agronomy12071683Development of SSR Markers Based on Transcriptome Sequencing and Verification of Their Conservation across Species of Ornamental <i>Pennisetum</i> Rich. (Poaceae)Yidi Guo0Lingyun Liu1Yuesen Yue2Xifeng Fan3Wenjun Teng4Hui Zhang5Kang Gao6Jin Guan7Zhihui Chang8Ke Teng9College of Grassland Science, Beijing Forestry University, Beijing 100083, ChinaCollege of Grassland Science, Beijing Forestry University, Beijing 100083, ChinaInstitute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, ChinaInstitute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, ChinaInstitute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, ChinaInstitute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, ChinaInstitute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, ChinaCollege of Grassland Science, Beijing Forestry University, Beijing 100083, ChinaCollege of Grassland Science, Beijing Forestry University, Beijing 100083, ChinaInstitute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China<i>Pennisetum</i> species have importance in foraging, agriculture, energy-production, the environment, and landscaping. To promote the preservation and utilization of ornamental <i>Pennisetum</i> resources, we developed simple sequence repeat (SSR) markers from the <i>Pennisetum setaceum</i> cv. ‘Rubrum’ transcriptome and verified their conservation in 38 sources. Our transcriptome sequencing efforts generated 58.91 Gb of clean data containing 55,627 unigenes. We functionally annotated 30,930 unigenes, with functions enriched in translation and ribosomal structure and biogenesis. Database comparisons indicated that the closest relative of <i>P. setaceum</i> cv. ‘Rubrum’ is <i>Setaria italica</i>. Over five thousand SSR markers were detected in the transcriptomic data. We selected 38 pairs of highly polymorphic SSR markers from 50 randomly selected SSR markers. Based on genetic diversity analysis of 38 ornamental <i>Pennisetum</i> sources, we obtained 312 polymorphic bands, with an average of 8.21 alleles per primer. Principal coordinate analyses and generation of a, which proved that <i>Pennisetum</i> has moderate genetic diversity. In addition, fingerprint maps were constructed to improve <i>Pennisetum</i> identification. The transcriptome data generated by our study enhances the transcriptional information available for <i>P. setaceum</i>. This study lays the foundation for the collection and utilization of ornamental <i>Pennisetum</i> resources and provides a basis for future breeding projects using this species.https://www.mdpi.com/2073-4395/12/7/1683<i>Pennisetum</i>illumina sequencinggenetic diversitySSR molecular markertranscriptome |
| spellingShingle | Yidi Guo Lingyun Liu Yuesen Yue Xifeng Fan Wenjun Teng Hui Zhang Kang Gao Jin Guan Zhihui Chang Ke Teng Development of SSR Markers Based on Transcriptome Sequencing and Verification of Their Conservation across Species of Ornamental <i>Pennisetum</i> Rich. (Poaceae) Agronomy <i>Pennisetum</i> illumina sequencing genetic diversity SSR molecular marker transcriptome |
| title | Development of SSR Markers Based on Transcriptome Sequencing and Verification of Their Conservation across Species of Ornamental <i>Pennisetum</i> Rich. (Poaceae) |
| title_full | Development of SSR Markers Based on Transcriptome Sequencing and Verification of Their Conservation across Species of Ornamental <i>Pennisetum</i> Rich. (Poaceae) |
| title_fullStr | Development of SSR Markers Based on Transcriptome Sequencing and Verification of Their Conservation across Species of Ornamental <i>Pennisetum</i> Rich. (Poaceae) |
| title_full_unstemmed | Development of SSR Markers Based on Transcriptome Sequencing and Verification of Their Conservation across Species of Ornamental <i>Pennisetum</i> Rich. (Poaceae) |
| title_short | Development of SSR Markers Based on Transcriptome Sequencing and Verification of Their Conservation across Species of Ornamental <i>Pennisetum</i> Rich. (Poaceae) |
| title_sort | development of ssr markers based on transcriptome sequencing and verification of their conservation across species of ornamental i pennisetum i rich poaceae |
| topic | <i>Pennisetum</i> illumina sequencing genetic diversity SSR molecular marker transcriptome |
| url | https://www.mdpi.com/2073-4395/12/7/1683 |
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