First Report on Development of Genome-Wide Microsatellite Markers for Stock (<i>Matthiola incana</i> L.)
Stock (<i>Matthiola incana</i> (L.) R. Br.) is a famous annual ornamental plant with important ornamental and economic value. The lack of DNA molecular markers has limited genetic analysis, genome evolution, and marker-assisted selective breeding studies of <i>M. incana</i>....
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-02-01
|
| Series: | Plants |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2223-7747/12/4/748 |
| _version_ | 1797618631138344960 |
|---|---|
| author | Chen Tan Haimei Zhang Haidong Chen Miaotian Guan Zhenzhi Zhu Xueying Cao Xianhong Ge Bo Zhu Daozong Chen |
| author_facet | Chen Tan Haimei Zhang Haidong Chen Miaotian Guan Zhenzhi Zhu Xueying Cao Xianhong Ge Bo Zhu Daozong Chen |
| author_sort | Chen Tan |
| collection | DOAJ |
| description | Stock (<i>Matthiola incana</i> (L.) R. Br.) is a famous annual ornamental plant with important ornamental and economic value. The lack of DNA molecular markers has limited genetic analysis, genome evolution, and marker-assisted selective breeding studies of <i>M. incana</i>. Therefore, more DNA markers are needed to support the further elucidation of the biology and genetics of <i>M. incana</i>. In this study, a high-quality genome of <i>M. incana</i> was initially assembled and a set of effective SSR primers was developed at the whole-genome level using genome data. A total of 45,612 loci of SSRs were identified; the di-nucleotide motifs were the most abundant (77.35%). In total, 43,540 primer pairs were designed, of which 300 were randomly selected for PCR validation, and as the success rate for amplification. In addition, 22 polymorphic SSR markers were used to analyze the genetic diversity of 40 stock varieties. Clustering analysis showed that all varieties could be divided into two clusters with a genetic distance of 0.68, which were highly consistent with their flower shape (potted or cut type). Moreover, we have verified that these SSR markers are effective and transferable within the Brassicaceae family. In this study, potential SSR molecular markers were successfully developed for 40 <i>M. incana</i> varieties using whole genome analysis, providing an important genetic tool for theoretical and applied research on <i>M. incana</i>. |
| first_indexed | 2024-03-11T08:15:14Z |
| format | Article |
| id | doaj.art-d5d3475d6d414154a7cea554ab2e843b |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-11T08:15:14Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-d5d3475d6d414154a7cea554ab2e843b2023-11-16T22:46:56ZengMDPI AGPlants2223-77472023-02-0112474810.3390/plants12040748First Report on Development of Genome-Wide Microsatellite Markers for Stock (<i>Matthiola incana</i> L.)Chen Tan0Haimei Zhang1Haidong Chen2Miaotian Guan3Zhenzhi Zhu4Xueying Cao5Xianhong Ge6Bo Zhu7Daozong Chen8College of Life Sciences, Gannan Normal University, Ganzhou 341000, ChinaCollege of Life Sciences, Gannan Normal University, Ganzhou 341000, ChinaCollege of Life Sciences, Gannan Normal University, Ganzhou 341000, ChinaCollege of Life Sciences, Gannan Normal University, Ganzhou 341000, ChinaCollege of Life Sciences, Gannan Normal University, Ganzhou 341000, ChinaCollege of Life Sciences, Gannan Normal University, Ganzhou 341000, ChinaCollege of Plant Science and Technology, Huazhong Agricultural University, Wuhan 431700, ChinaCollege of Life Sciences, Gannan Normal University, Ganzhou 341000, ChinaCollege of Life Sciences, Gannan Normal University, Ganzhou 341000, ChinaStock (<i>Matthiola incana</i> (L.) R. Br.) is a famous annual ornamental plant with important ornamental and economic value. The lack of DNA molecular markers has limited genetic analysis, genome evolution, and marker-assisted selective breeding studies of <i>M. incana</i>. Therefore, more DNA markers are needed to support the further elucidation of the biology and genetics of <i>M. incana</i>. In this study, a high-quality genome of <i>M. incana</i> was initially assembled and a set of effective SSR primers was developed at the whole-genome level using genome data. A total of 45,612 loci of SSRs were identified; the di-nucleotide motifs were the most abundant (77.35%). In total, 43,540 primer pairs were designed, of which 300 were randomly selected for PCR validation, and as the success rate for amplification. In addition, 22 polymorphic SSR markers were used to analyze the genetic diversity of 40 stock varieties. Clustering analysis showed that all varieties could be divided into two clusters with a genetic distance of 0.68, which were highly consistent with their flower shape (potted or cut type). Moreover, we have verified that these SSR markers are effective and transferable within the Brassicaceae family. In this study, potential SSR molecular markers were successfully developed for 40 <i>M. incana</i> varieties using whole genome analysis, providing an important genetic tool for theoretical and applied research on <i>M. incana</i>.https://www.mdpi.com/2223-7747/12/4/748<i>Matthiola incana</i>SSRmolecular makersgenetic diversitygenome sequencing |
| spellingShingle | Chen Tan Haimei Zhang Haidong Chen Miaotian Guan Zhenzhi Zhu Xueying Cao Xianhong Ge Bo Zhu Daozong Chen First Report on Development of Genome-Wide Microsatellite Markers for Stock (<i>Matthiola incana</i> L.) Plants <i>Matthiola incana</i> SSR molecular makers genetic diversity genome sequencing |
| title | First Report on Development of Genome-Wide Microsatellite Markers for Stock (<i>Matthiola incana</i> L.) |
| title_full | First Report on Development of Genome-Wide Microsatellite Markers for Stock (<i>Matthiola incana</i> L.) |
| title_fullStr | First Report on Development of Genome-Wide Microsatellite Markers for Stock (<i>Matthiola incana</i> L.) |
| title_full_unstemmed | First Report on Development of Genome-Wide Microsatellite Markers for Stock (<i>Matthiola incana</i> L.) |
| title_short | First Report on Development of Genome-Wide Microsatellite Markers for Stock (<i>Matthiola incana</i> L.) |
| title_sort | first report on development of genome wide microsatellite markers for stock i matthiola incana i l |
| topic | <i>Matthiola incana</i> SSR molecular makers genetic diversity genome sequencing |
| url | https://www.mdpi.com/2223-7747/12/4/748 |
| work_keys_str_mv | AT chentan firstreportondevelopmentofgenomewidemicrosatellitemarkersforstockimatthiolaincanail AT haimeizhang firstreportondevelopmentofgenomewidemicrosatellitemarkersforstockimatthiolaincanail AT haidongchen firstreportondevelopmentofgenomewidemicrosatellitemarkersforstockimatthiolaincanail AT miaotianguan firstreportondevelopmentofgenomewidemicrosatellitemarkersforstockimatthiolaincanail AT zhenzhizhu firstreportondevelopmentofgenomewidemicrosatellitemarkersforstockimatthiolaincanail AT xueyingcao firstreportondevelopmentofgenomewidemicrosatellitemarkersforstockimatthiolaincanail AT xianhongge firstreportondevelopmentofgenomewidemicrosatellitemarkersforstockimatthiolaincanail AT bozhu firstreportondevelopmentofgenomewidemicrosatellitemarkersforstockimatthiolaincanail AT daozongchen firstreportondevelopmentofgenomewidemicrosatellitemarkersforstockimatthiolaincanail |