Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources
Jujube (<i>Ziziphus jujuba</i> Mill.) is a commercially important tree native to China, known for its high nutritional value and widespread distribution, as well as its diverse germplasm resources. Being resilient to harsh climatic conditions, the cultivation of jujube could provide a so...
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| Format: | Article |
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MDPI AG
2023-08-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/15/2885 |
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| author | Bin Li Noor Muhammad Shufeng Zhang Yunxin Lan Yihan Yang Shoukun Han Mengjun Liu Meng Yang |
| author_facet | Bin Li Noor Muhammad Shufeng Zhang Yunxin Lan Yihan Yang Shoukun Han Mengjun Liu Meng Yang |
| author_sort | Bin Li |
| collection | DOAJ |
| description | Jujube (<i>Ziziphus jujuba</i> Mill.) is a commercially important tree native to China, known for its high nutritional value and widespread distribution, as well as its diverse germplasm resources. Being resilient to harsh climatic conditions, the cultivation of jujube could provide a solution to food insecurity and income for people of arid and semi-arid regions in and outside of China. The evaluation of germplasm resources and genetic diversity in jujube necessitates the use of Simple Sequence Repeat (SSR) markers. SSR markers are highly polymorphic and can be used to evaluate the genetic diversity within and between cultivars of Chinese jujube, and are important for conservation biology, breeding programs, and the discovery of important traits for Chinese jujube improvement in China and abroad. However, traditional methods of SSR development are time-consuming and inadequate to meet the growing research demands. To address this issue, we developed a novel approach called Multiple-Genome-Based SSR identification (MGB-SSR), which utilizes the genomes of three jujube cultivars to rapidly screen for polymorphic SSRs in the jujube genome. Through the screening process, we identified 12 pairs of SSR primers, which were then used to successfully classify 249 jujube genotypes. Based on the genotyping results, a digital ID card was established, enabling the complete identification of all 249 jujube plants. The MGB-SSR approach proved efficient in rapidly detecting polymorphic SSRs within the jujube genome. Notably, this study represents the first successful differentiation of jujube germplasm resources using 12 SSR markers, with 4 markers successfully identifying triploid jujube genotypes. These findings offer valuable information for the classification of Chinese jujube germplasm, thereby providing significant assistance to jujube researchers and breeders in identifying unknown jujube germplasm. |
| first_indexed | 2024-03-11T00:18:02Z |
| format | Article |
| id | doaj.art-07ea68aaccde4520bd3e243fda76c8bd |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-11T00:18:02Z |
| publishDate | 2023-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-07ea68aaccde4520bd3e243fda76c8bd2023-11-18T23:27:12ZengMDPI AGPlants2223-77472023-08-011215288510.3390/plants12152885Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm ResourcesBin Li0Noor Muhammad1Shufeng Zhang2Yunxin Lan3Yihan Yang4Shoukun Han5Mengjun Liu6Meng Yang7College of Horticulture, Hebei Agricultural University, Baoding 071000, ChinaCollege of Horticulture, Hebei Agricultural University, Baoding 071000, ChinaCollege of Horticulture, Hebei Agricultural University, Baoding 071000, ChinaCollege of Horticulture, Hebei Agricultural University, Baoding 071000, ChinaCollege of Horticulture, Hebei Agricultural University, Baoding 071000, ChinaCollege of Horticulture, Hebei Agricultural University, Baoding 071000, ChinaCollege of Horticulture, Hebei Agricultural University, Baoding 071000, ChinaCollege of Horticulture, Hebei Agricultural University, Baoding 071000, ChinaJujube (<i>Ziziphus jujuba</i> Mill.) is a commercially important tree native to China, known for its high nutritional value and widespread distribution, as well as its diverse germplasm resources. Being resilient to harsh climatic conditions, the cultivation of jujube could provide a solution to food insecurity and income for people of arid and semi-arid regions in and outside of China. The evaluation of germplasm resources and genetic diversity in jujube necessitates the use of Simple Sequence Repeat (SSR) markers. SSR markers are highly polymorphic and can be used to evaluate the genetic diversity within and between cultivars of Chinese jujube, and are important for conservation biology, breeding programs, and the discovery of important traits for Chinese jujube improvement in China and abroad. However, traditional methods of SSR development are time-consuming and inadequate to meet the growing research demands. To address this issue, we developed a novel approach called Multiple-Genome-Based SSR identification (MGB-SSR), which utilizes the genomes of three jujube cultivars to rapidly screen for polymorphic SSRs in the jujube genome. Through the screening process, we identified 12 pairs of SSR primers, which were then used to successfully classify 249 jujube genotypes. Based on the genotyping results, a digital ID card was established, enabling the complete identification of all 249 jujube plants. The MGB-SSR approach proved efficient in rapidly detecting polymorphic SSRs within the jujube genome. Notably, this study represents the first successful differentiation of jujube germplasm resources using 12 SSR markers, with 4 markers successfully identifying triploid jujube genotypes. These findings offer valuable information for the classification of Chinese jujube germplasm, thereby providing significant assistance to jujube researchers and breeders in identifying unknown jujube germplasm.https://www.mdpi.com/2223-7747/12/15/2885jujubeSimple Sequence Repeat (SSR)multiple-genome-based SSR (MGB-SSR)genetic diversitydigital ID card |
| spellingShingle | Bin Li Noor Muhammad Shufeng Zhang Yunxin Lan Yihan Yang Shoukun Han Mengjun Liu Meng Yang Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources Plants jujube Simple Sequence Repeat (SSR) multiple-genome-based SSR (MGB-SSR) genetic diversity digital ID card |
| title | Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources |
| title_full | Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources |
| title_fullStr | Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources |
| title_full_unstemmed | Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources |
| title_short | Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources |
| title_sort | multiple genome based simple sequence repeat is an efficient and successful method in genotyping and classifying different jujube germplasm resources |
| topic | jujube Simple Sequence Repeat (SSR) multiple-genome-based SSR (MGB-SSR) genetic diversity digital ID card |
| url | https://www.mdpi.com/2223-7747/12/15/2885 |
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