Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.)
Transcriptome analysis is an efficient way to explore molecular markers in plant species, for which genome sequences have not been published. To address the limited number of markers published for the Welsh onion, this study found 6486 loci of genic simple sequence repeats (SSR), which consisted of...
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MDPI AG
2015-11-01
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| Series: | Applied Sciences |
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| Online Access: | http://www.mdpi.com/2076-3417/5/4/1050 |
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| author | Liuyi Yang Changlong Wen Hong Zhao Qianchun Liu Jingjing Yang Lecheng Liu Yongqin Wang |
| author_facet | Liuyi Yang Changlong Wen Hong Zhao Qianchun Liu Jingjing Yang Lecheng Liu Yongqin Wang |
| author_sort | Liuyi Yang |
| collection | DOAJ |
| description | Transcriptome analysis is an efficient way to explore molecular markers in plant species, for which genome sequences have not been published. To address the limited number of markers published for the Welsh onion, this study found 6486 loci of genic simple sequence repeats (SSR), which consisted of 1–5 bp repeat motifs, based on next-generation sequencing (NGS) technology and the RNA-Seq approach. The most abundant motif was mononucleotide (52.33%), followed by trinucleotide (31.96%), and dinucleotide (14.57%). A total of 2525 primer pairs were successfully designed, and 91 out of 311 tested primers were polymorphisms. Overall, 38 genic SSR markers were randomly selected to further validate the degree of genetic diversity, and 22 genic SSR markers (57.89%) showed high levels of polymorphism. The average polymorphism information content (PIC) value and the number of alleles (Na) were 0.63 and 5.27, respectively, and the unweighted pair-group method with arithmetic average (UPGMA) cluster analysis grouped the 22 Allium accessions into three groups with Nei’s similarity coefficients ranging from 0.37 to 0.99. This result suggested that these genic SSR markers could be used to develop a higher resolution genetic map and/or to analyze the phylogenetic relationships among Allium plants in the near future. |
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| institution | Directory Open Access Journal |
| issn | 2076-3417 |
| language | English |
| last_indexed | 2024-12-10T15:31:44Z |
| publishDate | 2015-11-01 |
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| spelling | doaj.art-e8878df1ff9b4a6a8df1766f687852d82022-12-22T01:43:24ZengMDPI AGApplied Sciences2076-34172015-11-01541050106310.3390/app5041050app5041050Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.)Liuyi Yang0Changlong Wen1Hong Zhao2Qianchun Liu3Jingjing Yang4Lecheng Liu5Yongqin Wang6Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, ChinaBeijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, ChinaBeijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, ChinaBeijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, ChinaBeijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, ChinaCollege of Horticulture and Gardening, Yangtze University, Jingzhou 434025, ChinaBeijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, ChinaTranscriptome analysis is an efficient way to explore molecular markers in plant species, for which genome sequences have not been published. To address the limited number of markers published for the Welsh onion, this study found 6486 loci of genic simple sequence repeats (SSR), which consisted of 1–5 bp repeat motifs, based on next-generation sequencing (NGS) technology and the RNA-Seq approach. The most abundant motif was mononucleotide (52.33%), followed by trinucleotide (31.96%), and dinucleotide (14.57%). A total of 2525 primer pairs were successfully designed, and 91 out of 311 tested primers were polymorphisms. Overall, 38 genic SSR markers were randomly selected to further validate the degree of genetic diversity, and 22 genic SSR markers (57.89%) showed high levels of polymorphism. The average polymorphism information content (PIC) value and the number of alleles (Na) were 0.63 and 5.27, respectively, and the unweighted pair-group method with arithmetic average (UPGMA) cluster analysis grouped the 22 Allium accessions into three groups with Nei’s similarity coefficients ranging from 0.37 to 0.99. This result suggested that these genic SSR markers could be used to develop a higher resolution genetic map and/or to analyze the phylogenetic relationships among Allium plants in the near future.http://www.mdpi.com/2076-3417/5/4/1050simple sequence repeats (SSR)genic markertranscriptomegenetic diversityAllium fistulosum L. |
| spellingShingle | Liuyi Yang Changlong Wen Hong Zhao Qianchun Liu Jingjing Yang Lecheng Liu Yongqin Wang Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.) Applied Sciences simple sequence repeats (SSR) genic marker transcriptome genetic diversity Allium fistulosum L. |
| title | Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.) |
| title_full | Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.) |
| title_fullStr | Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.) |
| title_full_unstemmed | Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.) |
| title_short | Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.) |
| title_sort | development of polymorphic genic ssr markers by transcriptome sequencing in the welsh onion allium fistulosum l |
| topic | simple sequence repeats (SSR) genic marker transcriptome genetic diversity Allium fistulosum L. |
| url | http://www.mdpi.com/2076-3417/5/4/1050 |
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