Construction of a core collection and SNP fingerprinting database for Chinese chive (Allium tuberosum) through Hyper-seq based population genetic analysis
Chinese chive (Allium tuberosum Rottler ex Sprengel), an autotetraploid vegetable cultivated in Asia for over 3,000 years, possesses apomictic characteristics. However, issues like intricate genetic admixture and unclear phylogenetic relationships pose challenges for effective germplasm preservation...
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| Language: | English |
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Frontiers Media S.A.
2025-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2025.1603210/full |
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| author | Huamin Zhang Huamin Zhang Yanlong Li Taotao Li Taotao Li Fangfang Yan Taotao Fu Taotao Fu Chunli Liao Chunli Liao Dongxiao Liu Dongxiao Liu Yutao Zhu Yutao Zhu Mei Zhao Mei Zhao Peifang Ma Lianzhe Wang Lianzhe Wang |
| author_facet | Huamin Zhang Huamin Zhang Yanlong Li Taotao Li Taotao Li Fangfang Yan Taotao Fu Taotao Fu Chunli Liao Chunli Liao Dongxiao Liu Dongxiao Liu Yutao Zhu Yutao Zhu Mei Zhao Mei Zhao Peifang Ma Lianzhe Wang Lianzhe Wang |
| author_sort | Huamin Zhang |
| collection | DOAJ |
| description | Chinese chive (Allium tuberosum Rottler ex Sprengel), an autotetraploid vegetable cultivated in Asia for over 3,000 years, possesses apomictic characteristics. However, issues like intricate genetic admixture and unclear phylogenetic relationships pose challenges for effective germplasm preservation and breeding advancements. In this research, we systematically assessed population structure, constructed a core collection, and developed a DNA fingerprinting system utilizing Hyper-seq sequencing data. Our Hyper-seq-based genotyping revealed 291,547 single nucleotide polymorphisms (SNPs) and 116,223 insertions/deletions (InDels). Population genetic analysis indicated that the 100 A. tuberosum accessions can be categorized into two distinct genetic subgroups. These subgroups partially aligned with previously recognized phenotypic classifications based on dormancy traits, underscoring the complex relationship between genetic divergence and adaptive phenotypic variation. A core collection consisting of 22 accessions (22% of the total) was created, maintaining 90.17% of the original genetic diversity. Additionally, we established a DNA fingerprinting system for all 100 accessions using 14 diagnostic SNP markers. This study marks the first comprehensive integration of SNP and InDel markers in systematic analysis of A. tuberosum genetic diversity, offering valuable resources for germplasm identification and marker-assisted breeding. These findings deepen the understanding of the genetic architecture of A. tuberosum and lay the foundation for molecularly driven breeding strategies. |
| format | Article |
| id | doaj-art-fe26f31f4d2e4200b2d5735be6f60187 |
| institution | DOAJ |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj-art-fe26f31f4d2e4200b2d5735be6f601872025-08-20T02:40:30ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-07-011610.3389/fpls.2025.16032101603210Construction of a core collection and SNP fingerprinting database for Chinese chive (Allium tuberosum) through Hyper-seq based population genetic analysisHuamin Zhang0Huamin Zhang1Yanlong Li2Taotao Li3Taotao Li4Fangfang Yan5Taotao Fu6Taotao Fu7Chunli Liao8Chunli Liao9Dongxiao Liu10Dongxiao Liu11Yutao Zhu12Yutao Zhu13Mei Zhao14Mei Zhao15Peifang Ma16Lianzhe Wang17Lianzhe Wang18College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, ChinaCenter of Healthy Food Engineering and Technology of Henan, Henan University of Urban Construction, Pingdingshan, ChinaHenan Engineering Research Center for Chinese Chive, Pingdingshan Academy of Agricultural Sciences, Pingdingshan, Henan, ChinaCollege of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, ChinaCenter of Healthy Food Engineering and Technology of Henan, Henan University of Urban Construction, Pingdingshan, ChinaHenan Engineering Research Center for Chinese Chive, Pingdingshan Academy of Agricultural Sciences, Pingdingshan, Henan, ChinaCollege of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, ChinaCenter of Healthy Food Engineering and Technology of Henan, Henan University of Urban Construction, Pingdingshan, ChinaCollege of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, ChinaCenter of Healthy Food Engineering and Technology of Henan, Henan University of Urban Construction, Pingdingshan, ChinaCollege of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, ChinaCenter of Healthy Food Engineering and Technology of Henan, Henan University of Urban Construction, Pingdingshan, ChinaCollege of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, ChinaCenter of Healthy Food Engineering and Technology of Henan, Henan University of Urban Construction, Pingdingshan, ChinaCollege of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, ChinaCenter of Healthy Food Engineering and Technology of Henan, Henan University of Urban Construction, Pingdingshan, ChinaHenan Engineering Research Center for Chinese Chive, Pingdingshan Academy of Agricultural Sciences, Pingdingshan, Henan, ChinaCollege of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan, ChinaCenter of Healthy Food Engineering and Technology of Henan, Henan University of Urban Construction, Pingdingshan, ChinaChinese chive (Allium tuberosum Rottler ex Sprengel), an autotetraploid vegetable cultivated in Asia for over 3,000 years, possesses apomictic characteristics. However, issues like intricate genetic admixture and unclear phylogenetic relationships pose challenges for effective germplasm preservation and breeding advancements. In this research, we systematically assessed population structure, constructed a core collection, and developed a DNA fingerprinting system utilizing Hyper-seq sequencing data. Our Hyper-seq-based genotyping revealed 291,547 single nucleotide polymorphisms (SNPs) and 116,223 insertions/deletions (InDels). Population genetic analysis indicated that the 100 A. tuberosum accessions can be categorized into two distinct genetic subgroups. These subgroups partially aligned with previously recognized phenotypic classifications based on dormancy traits, underscoring the complex relationship between genetic divergence and adaptive phenotypic variation. A core collection consisting of 22 accessions (22% of the total) was created, maintaining 90.17% of the original genetic diversity. Additionally, we established a DNA fingerprinting system for all 100 accessions using 14 diagnostic SNP markers. This study marks the first comprehensive integration of SNP and InDel markers in systematic analysis of A. tuberosum genetic diversity, offering valuable resources for germplasm identification and marker-assisted breeding. These findings deepen the understanding of the genetic architecture of A. tuberosum and lay the foundation for molecularly driven breeding strategies.https://www.frontiersin.org/articles/10.3389/fpls.2025.1603210/fullChinese chivegenetic diversitypopulation structurecore collectionDNA fingerprinting |
| spellingShingle | Huamin Zhang Huamin Zhang Yanlong Li Taotao Li Taotao Li Fangfang Yan Taotao Fu Taotao Fu Chunli Liao Chunli Liao Dongxiao Liu Dongxiao Liu Yutao Zhu Yutao Zhu Mei Zhao Mei Zhao Peifang Ma Lianzhe Wang Lianzhe Wang Construction of a core collection and SNP fingerprinting database for Chinese chive (Allium tuberosum) through Hyper-seq based population genetic analysis Frontiers in Plant Science Chinese chive genetic diversity population structure core collection DNA fingerprinting |
| title | Construction of a core collection and SNP fingerprinting database for Chinese chive (Allium tuberosum) through Hyper-seq based population genetic analysis |
| title_full | Construction of a core collection and SNP fingerprinting database for Chinese chive (Allium tuberosum) through Hyper-seq based population genetic analysis |
| title_fullStr | Construction of a core collection and SNP fingerprinting database for Chinese chive (Allium tuberosum) through Hyper-seq based population genetic analysis |
| title_full_unstemmed | Construction of a core collection and SNP fingerprinting database for Chinese chive (Allium tuberosum) through Hyper-seq based population genetic analysis |
| title_short | Construction of a core collection and SNP fingerprinting database for Chinese chive (Allium tuberosum) through Hyper-seq based population genetic analysis |
| title_sort | construction of a core collection and snp fingerprinting database for chinese chive allium tuberosum through hyper seq based population genetic analysis |
| topic | Chinese chive genetic diversity population structure core collection DNA fingerprinting |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2025.1603210/full |
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