Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum
Sugarcane has a large, complex, polyploid genome that has hindered the progress of genomic research and molecular marker-assisted selection. The user-friendly SSR markers have attracted considerable attention owing to their ideal genetic attributes. However, these markers were not characterized and...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311922002076 |
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| author | Lei LIU Heng-bo WANG Yi-han LI Shu-qi CHEN Ming-xing WU Mei-jie DOU Yi-yin QI Jing-ping FANG Ji-sen ZHANG |
| author_facet | Lei LIU Heng-bo WANG Yi-han LI Shu-qi CHEN Ming-xing WU Mei-jie DOU Yi-yin QI Jing-ping FANG Ji-sen ZHANG |
| author_sort | Lei LIU |
| collection | DOAJ |
| description | Sugarcane has a large, complex, polyploid genome that has hindered the progress of genomic research and molecular marker-assisted selection. The user-friendly SSR markers have attracted considerable attention owing to their ideal genetic attributes. However, these markers were not characterized and developed at the genome-wide scale due to the previously lacking high-quality chromosome-level assembled sugarcane genomes. In this present study, 744305 and 361638 candidate SSRs were identified from the genomes of S. officinarum and S. spontaneum, respectively. We verified the reliability of the predicted SSRs by using 1200 interspecific SSR primer pairs to detect polymorphisms among 11 representative accessions of Saccharum, including S. spontaneum, S. officinarum, S. robustum, and modern sugarcane hybrid. The results showed that 660 SSR markers displayed interspecific polymorphisms among these accessions. Furthermore, 100 SSRs were randomly selected to detect the genetic diversity for 39 representative Saccharum accessions. A total of 320 alleles were generated using 100 polymorphic primers, with each marker ranging from two to seven alleles. The genetic diversity analysis revealed that these accessions were distributed in four main groups, including group I (14 S. spontaneum accessions), group II (two S. officinarum accessions), group III (18 modern sugarcane hybrid accessions), and group IV (five S. robustum accessions). Experimental verification supported the reliability of the SSR markers based on genome-wide predictions. The development of a large number of SSR markers based on wet experiments is valuable for genetic studies, including genetic linkage maps, comparative genome analysis, genome-wide association studies, and marker-assisted selection in Saccharum. |
| first_indexed | 2024-04-13T14:47:57Z |
| format | Article |
| id | doaj.art-58e045ef5ed64f4a906e91ef2b62ec66 |
| institution | Directory Open Access Journal |
| issn | 2095-3119 |
| language | English |
| last_indexed | 2024-04-13T14:47:57Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj.art-58e045ef5ed64f4a906e91ef2b62ec662022-12-22T02:42:42ZengElsevierJournal of Integrative Agriculture2095-31192022-01-01211132303244Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneumLei LIU0Heng-bo WANG1Yi-han LI2Shu-qi CHEN3Ming-xing WU4Mei-jie DOU5Yi-yin QI6Jing-ping FANG7Ji-sen ZHANG8Center for Genomics and Biotechnology/Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology/Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, P.R. ChinaCenter for Genomics and Biotechnology/Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology/Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, P.R. ChinaCenter for Genomics and Biotechnology/Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology/Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, P.R. China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. ChinaCenter for Genomics and Biotechnology/Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology/Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, P.R. ChinaCenter for Genomics and Biotechnology/Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology/Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, P.R. ChinaCenter for Genomics and Biotechnology/Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology/Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, P.R. ChinaCenter for Genomics and Biotechnology/Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology/Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, P.R. ChinaCollege of Life Sciences, Fujian Normal University, Fuzhou 350007, P.R. China; Correspondence FANG Jing-pingCenter for Genomics and Biotechnology/Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology/Key Laboratory of Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, P.R. China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Biological Resources & Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China; Correspondence ZHANG Ji-senSugarcane has a large, complex, polyploid genome that has hindered the progress of genomic research and molecular marker-assisted selection. The user-friendly SSR markers have attracted considerable attention owing to their ideal genetic attributes. However, these markers were not characterized and developed at the genome-wide scale due to the previously lacking high-quality chromosome-level assembled sugarcane genomes. In this present study, 744305 and 361638 candidate SSRs were identified from the genomes of S. officinarum and S. spontaneum, respectively. We verified the reliability of the predicted SSRs by using 1200 interspecific SSR primer pairs to detect polymorphisms among 11 representative accessions of Saccharum, including S. spontaneum, S. officinarum, S. robustum, and modern sugarcane hybrid. The results showed that 660 SSR markers displayed interspecific polymorphisms among these accessions. Furthermore, 100 SSRs were randomly selected to detect the genetic diversity for 39 representative Saccharum accessions. A total of 320 alleles were generated using 100 polymorphic primers, with each marker ranging from two to seven alleles. The genetic diversity analysis revealed that these accessions were distributed in four main groups, including group I (14 S. spontaneum accessions), group II (two S. officinarum accessions), group III (18 modern sugarcane hybrid accessions), and group IV (five S. robustum accessions). Experimental verification supported the reliability of the SSR markers based on genome-wide predictions. The development of a large number of SSR markers based on wet experiments is valuable for genetic studies, including genetic linkage maps, comparative genome analysis, genome-wide association studies, and marker-assisted selection in Saccharum.http://www.sciencedirect.com/science/article/pii/S2095311922002076Saccharumgenome-widesimple repeat sequences (SSR)microsatellitemolecular markers |
| spellingShingle | Lei LIU Heng-bo WANG Yi-han LI Shu-qi CHEN Ming-xing WU Mei-jie DOU Yi-yin QI Jing-ping FANG Ji-sen ZHANG Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum Journal of Integrative Agriculture Saccharum genome-wide simple repeat sequences (SSR) microsatellite molecular markers |
| title | Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum |
| title_full | Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum |
| title_fullStr | Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum |
| title_full_unstemmed | Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum |
| title_short | Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum |
| title_sort | genome wide development of interspecific microsatellite markers for saccharum officinarum and saccharum spontaneum |
| topic | Saccharum genome-wide simple repeat sequences (SSR) microsatellite molecular markers |
| url | http://www.sciencedirect.com/science/article/pii/S2095311922002076 |
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