Identification, evaluation, and application of the genomic-SSR loci in ramie
To provide a theoretical and practical foundation for ramie genetic analysis, simple sequence repeats (SSRs) were identified in the ramie genome and employed in this study. From the 115 369 sequences of a specific-locus amplified fragment library, a type of reduced representation library obtained by...
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| Format: | Article |
| Language: | English |
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Polish Botanical Society
2016-09-01
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| Series: | Acta Societatis Botanicorum Poloniae |
| Subjects: | |
| Online Access: | https://pbsociety.org.pl/journals/index.php/asbp/article/view/6486 |
| _version_ | 1818976282645364736 |
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| author | Ming-Bao Luan Ze-Mao Yang Juan-Juan Zhu Xin Deng Chen-Chen Liu Xiao-Fei Wang Ying Xu Zhi-Min Sun Jian-Hua Chen |
| author_facet | Ming-Bao Luan Ze-Mao Yang Juan-Juan Zhu Xin Deng Chen-Chen Liu Xiao-Fei Wang Ying Xu Zhi-Min Sun Jian-Hua Chen |
| author_sort | Ming-Bao Luan |
| collection | DOAJ |
| description | To provide a theoretical and practical foundation for ramie genetic analysis, simple sequence repeats (SSRs) were identified in the ramie genome and employed in this study. From the 115 369 sequences of a specific-locus amplified fragment library, a type of reduced representation library obtained by high-throughput sequencing, we identified 4774 sequences containing 5064 SSR motifs. SSRs of ramie included repeat motifs with lengths of 1 to 6 nucleotides, and the abundance of each motif type varied greatly. We found that mononucleotide, dinucleotide, and trinucleotide repeat motifs were the most prevalent (95.91%). A total of 98 distinct motif types were detected in the genomic-SSRs of ramie. Of them, The A/T mononucleotide motif was the most abundant, accounting for 41.45% of motifs, followed by AT/TA, accounting for 20.30%. The number of alleles per locus in 31 polymorphic microsatellite loci ranged from 2 to 7, and observed and expected heterozygosities ranged from 0.04 to 1.00 and 0.04 to 0.83, respectively. Furthermore, molecular identity cards (IDs) of the germplasms were constructed employing the ID Analysis 3.0 software. In the current study, the 26 germplasms of ramie can be distinguished by a combination of five SSR primers including Ibg5-5, Ibg3-210, Ibg1-11, Ibg6-468, and Ibg6-481. The allele polymorphisms produced by all SSR primers were used to analyze genetic relationships among the germplasms. The similarity coefficients ranged from 0.41 to 0.88. We found that these 26 germplasms were clustered into five categories using UPGMA, with poor correlation between germplasm and geographical distribution. Our study is the first large-scale SSR identification from ramie genomic sequences. We have further studied the SSR distribution pattern in the ramie genome, and proposed that it is possible to develop SSR loci from genomic data for population genetics studies, linkage mapping, quantitative trait locus mapping, cultivar fingerprinting, and as genetic diversity studies. |
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| id | doaj.art-441daca075ad4f82bdff6b845e2023cd |
| institution | Directory Open Access Journal |
| issn | 2083-9480 |
| language | English |
| last_indexed | 2024-12-20T16:09:22Z |
| publishDate | 2016-09-01 |
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| series | Acta Societatis Botanicorum Poloniae |
| spelling | doaj.art-441daca075ad4f82bdff6b845e2023cd2022-12-21T19:34:02ZengPolish Botanical SocietyActa Societatis Botanicorum Poloniae2083-94802016-09-0185310.5586/asbp.35105698Identification, evaluation, and application of the genomic-SSR loci in ramieMing-Bao Luan0Ze-Mao Yang1Juan-Juan Zhu2Xin Deng3Chen-Chen Liu4Xiao-Fei Wang5Ying Xu6Zhi-Min Sun7Jian-Hua Chen8Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences / Key laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, HunanInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences / Key laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, HunanInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences / Key laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, HunanInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences / Key laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, HunanInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences / Key laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, HunanInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences / Key laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, HunanInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences / Key laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, HunanInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences / Key laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, HunanInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences / Key laboratory of Stem-fiber Biomass and Engineering Microbiology, Ministry of Agriculture, 348 West Xianjiahu Road, Changsha, HunanTo provide a theoretical and practical foundation for ramie genetic analysis, simple sequence repeats (SSRs) were identified in the ramie genome and employed in this study. From the 115 369 sequences of a specific-locus amplified fragment library, a type of reduced representation library obtained by high-throughput sequencing, we identified 4774 sequences containing 5064 SSR motifs. SSRs of ramie included repeat motifs with lengths of 1 to 6 nucleotides, and the abundance of each motif type varied greatly. We found that mononucleotide, dinucleotide, and trinucleotide repeat motifs were the most prevalent (95.91%). A total of 98 distinct motif types were detected in the genomic-SSRs of ramie. Of them, The A/T mononucleotide motif was the most abundant, accounting for 41.45% of motifs, followed by AT/TA, accounting for 20.30%. The number of alleles per locus in 31 polymorphic microsatellite loci ranged from 2 to 7, and observed and expected heterozygosities ranged from 0.04 to 1.00 and 0.04 to 0.83, respectively. Furthermore, molecular identity cards (IDs) of the germplasms were constructed employing the ID Analysis 3.0 software. In the current study, the 26 germplasms of ramie can be distinguished by a combination of five SSR primers including Ibg5-5, Ibg3-210, Ibg1-11, Ibg6-468, and Ibg6-481. The allele polymorphisms produced by all SSR primers were used to analyze genetic relationships among the germplasms. The similarity coefficients ranged from 0.41 to 0.88. We found that these 26 germplasms were clustered into five categories using UPGMA, with poor correlation between germplasm and geographical distribution. Our study is the first large-scale SSR identification from ramie genomic sequences. We have further studied the SSR distribution pattern in the ramie genome, and proposed that it is possible to develop SSR loci from genomic data for population genetics studies, linkage mapping, quantitative trait locus mapping, cultivar fingerprinting, and as genetic diversity studies.https://pbsociety.org.pl/journals/index.php/asbp/article/view/6486ramiegenomic-SSRSLAF |
| spellingShingle | Ming-Bao Luan Ze-Mao Yang Juan-Juan Zhu Xin Deng Chen-Chen Liu Xiao-Fei Wang Ying Xu Zhi-Min Sun Jian-Hua Chen Identification, evaluation, and application of the genomic-SSR loci in ramie Acta Societatis Botanicorum Poloniae ramie genomic-SSR SLAF |
| title | Identification, evaluation, and application of the genomic-SSR loci in ramie |
| title_full | Identification, evaluation, and application of the genomic-SSR loci in ramie |
| title_fullStr | Identification, evaluation, and application of the genomic-SSR loci in ramie |
| title_full_unstemmed | Identification, evaluation, and application of the genomic-SSR loci in ramie |
| title_short | Identification, evaluation, and application of the genomic-SSR loci in ramie |
| title_sort | identification evaluation and application of the genomic ssr loci in ramie |
| topic | ramie genomic-SSR SLAF |
| url | https://pbsociety.org.pl/journals/index.php/asbp/article/view/6486 |
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