Genetic Diversity and Population Structure of Jujube Cultivars in the United States Revealed by Single Nucleotide Polymorphism Markers
The nutritional and medicinal significance of jujube (Ziziphus jujuba) has led to persistent efforts in genomics to accelerate the utilization of its germplasm resources. However, the absence of accurate genetic identity of existing germplasm limits these studies. In the United States, different nam...
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American Society for Horticultural Science (ASHS)
2024-03-01
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| Series: | Journal of the American Society for Horticultural Science |
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| Online Access: | https://journals.ashs.org/jashs/view/journals/jashs/149/2/article-p107.xml |
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| author | Dikshya Sapkota Dapeng Zhang Sunchung Park Lyndel W. Meinhardt Dennis N. Lozada Robert Steiner Shengrui Yao |
| author_facet | Dikshya Sapkota Dapeng Zhang Sunchung Park Lyndel W. Meinhardt Dennis N. Lozada Robert Steiner Shengrui Yao |
| author_sort | Dikshya Sapkota |
| collection | DOAJ |
| description | The nutritional and medicinal significance of jujube (Ziziphus jujuba) has led to persistent efforts in genomics to accelerate the utilization of its germplasm resources. However, the absence of accurate genetic identity of existing germplasm limits these studies. In the United States, different names were frequently given to the same jujube cultivars because the pedigrees of the imported germplasm are unclear. The present study selected a panel of 147 single nucleotide polymorphism (SNP) markers distributed across the jujube genome to examine genetic identity, genetic diversity, and population structure in 177 jujube cultivars sampled from different locations in the United States. SNP profile multilocus matching reported a total of 23 synonymous groups including 116 samples that were identical to at least one other sample. This led to the detection of 74 unique genotypes for subsequent diversity analysis. Model-based genetic structure analysis divided the distinctive genotypes into three major groups, with some admixtures among the groups. The genetic differentiation among these groups was further validated by analysis of molecular variance (Fst = 0.199, P value < 0.001), principal coordinate analysis, and clustering analysis. Morphological traits were studied in some of the genetically identical commercial cultivar groups, (i.e., Li, Lang, and Jinsi). Results demonstrated significant morphological differences within genetically identical cultivars in the Jinsi group, indicating phenotypic variation resulting from mutations in these clones. |
| first_indexed | 2024-04-24T22:32:37Z |
| format | Article |
| id | doaj.art-5c60b2e78dde44edbc48874f09abd923 |
| institution | Directory Open Access Journal |
| issn | 2327-9788 |
| language | English |
| last_indexed | 2024-04-24T22:32:37Z |
| publishDate | 2024-03-01 |
| publisher | American Society for Horticultural Science (ASHS) |
| record_format | Article |
| series | Journal of the American Society for Horticultural Science |
| spelling | doaj.art-5c60b2e78dde44edbc48874f09abd9232024-03-19T16:20:50ZengAmerican Society for Horticultural Science (ASHS)Journal of the American Society for Horticultural Science2327-97882024-03-011492https://doi.org/10.21273/JASHS05370-23Genetic Diversity and Population Structure of Jujube Cultivars in the United States Revealed by Single Nucleotide Polymorphism MarkersDikshya Sapkota0Dapeng Zhang1Sunchung Park2Lyndel W. Meinhardt3Dennis N. Lozada4Robert Steiner5Shengrui Yao6Department of Plant and Environmental Sciences, New Mexico State UniversitySustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research CenterSustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research CenterSustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research CenterDepartment of Plant and Environmental Sciences, New Mexico State UniversityDepartment of Economics and International Business, New Mexico State UniversityDepartment of Plant and Environmental Sciences, New Mexico State UniversityThe nutritional and medicinal significance of jujube (Ziziphus jujuba) has led to persistent efforts in genomics to accelerate the utilization of its germplasm resources. However, the absence of accurate genetic identity of existing germplasm limits these studies. In the United States, different names were frequently given to the same jujube cultivars because the pedigrees of the imported germplasm are unclear. The present study selected a panel of 147 single nucleotide polymorphism (SNP) markers distributed across the jujube genome to examine genetic identity, genetic diversity, and population structure in 177 jujube cultivars sampled from different locations in the United States. SNP profile multilocus matching reported a total of 23 synonymous groups including 116 samples that were identical to at least one other sample. This led to the detection of 74 unique genotypes for subsequent diversity analysis. Model-based genetic structure analysis divided the distinctive genotypes into three major groups, with some admixtures among the groups. The genetic differentiation among these groups was further validated by analysis of molecular variance (Fst = 0.199, P value < 0.001), principal coordinate analysis, and clustering analysis. Morphological traits were studied in some of the genetically identical commercial cultivar groups, (i.e., Li, Lang, and Jinsi). Results demonstrated significant morphological differences within genetically identical cultivars in the Jinsi group, indicating phenotypic variation resulting from mutations in these clones.https://journals.ashs.org/jashs/view/journals/jashs/149/2/article-p107.xmlcultivar identificationdna genotypingprincipal coordinate analysissnp markerssynonymous cultivarsziziphus jujuba |
| spellingShingle | Dikshya Sapkota Dapeng Zhang Sunchung Park Lyndel W. Meinhardt Dennis N. Lozada Robert Steiner Shengrui Yao Genetic Diversity and Population Structure of Jujube Cultivars in the United States Revealed by Single Nucleotide Polymorphism Markers Journal of the American Society for Horticultural Science cultivar identification dna genotyping principal coordinate analysis snp markers synonymous cultivars ziziphus jujuba |
| title | Genetic Diversity and Population Structure of Jujube Cultivars in the United States Revealed by Single Nucleotide Polymorphism Markers |
| title_full | Genetic Diversity and Population Structure of Jujube Cultivars in the United States Revealed by Single Nucleotide Polymorphism Markers |
| title_fullStr | Genetic Diversity and Population Structure of Jujube Cultivars in the United States Revealed by Single Nucleotide Polymorphism Markers |
| title_full_unstemmed | Genetic Diversity and Population Structure of Jujube Cultivars in the United States Revealed by Single Nucleotide Polymorphism Markers |
| title_short | Genetic Diversity and Population Structure of Jujube Cultivars in the United States Revealed by Single Nucleotide Polymorphism Markers |
| title_sort | genetic diversity and population structure of jujube cultivars in the united states revealed by single nucleotide polymorphism markers |
| topic | cultivar identification dna genotyping principal coordinate analysis snp markers synonymous cultivars ziziphus jujuba |
| url | https://journals.ashs.org/jashs/view/journals/jashs/149/2/article-p107.xml |
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