An initial exploration of core collection construction and DNA fingerprinting in Elymus sibiricus L. using SNP markers
Elymus sibiricus L., an excellent forage and ecological restoration grass, plays a key role in grassland ecological construction and the sustainable development of animal husbandry. In China, the wild germplasm resources of E. sibiricus are abundant, and they are shaped by similar and contrasting cl...
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| Format: | Article |
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Frontiers Media S.A.
2025-02-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2025.1534085/full |
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| author | Xinrui Li Xinrui Li Xinrui Li Daping Song Mingfeng Li Daxu Li Minghong You Yan Peng Jiajun Yan Shiqie Bai |
| author_facet | Xinrui Li Xinrui Li Xinrui Li Daping Song Mingfeng Li Daxu Li Minghong You Yan Peng Jiajun Yan Shiqie Bai |
| author_sort | Xinrui Li |
| collection | DOAJ |
| description | Elymus sibiricus L., an excellent forage and ecological restoration grass, plays a key role in grassland ecological construction and the sustainable development of animal husbandry. In China, the wild germplasm resources of E. sibiricus are abundant, and they are shaped by similar and contrasting climatic conditions to form distinct populations, which enrich the genetic diversity of E. sibiricus. To more comprehensively aggregate E. sibiricus germplasm resources at a lower cost and to more accurately utilize its genetic variation, this study conducted a preliminary exploration of core germplasm collections and fingerprinting of E. sibiricus using single nucleotide polymorphism (SNP) markers. By combining multiple evaluation measures with weighted processing, we successfully identified 36 materials from 90 wild E. sibiricus samples to serve as a core collection. Genetic diversity assessments, allele evaluations, and principal component analyses of the 36 core germplasm samples all indicate that these 36 samples accurately and comprehensively represent the genetic diversity of all 90 E. sibiricus germplasm accessions. Additionally, we identified 290 SNP loci from among the high-quality SNP loci generated by whole-genome sequencing of the 90 E. sibiricus samples as candidate markers. Of these, 52 SNP loci were selected as core markers for DNA fingerprinting of E. sibiricus. Using kompetitive allele-specific PCR (KASP) technology, we also performed population origin identification for 60 wild E. sibiricus germplasm accessions based on these core markers. The core SNP markers screened in this study were able to accurately distinguish between E. sibiricus germplasms from the Qinghai–Tibet Plateau and those from elsewhere. This study not only provides a reference for the continued collection and identification of E. sibiricus germplasm resources but also offers a scientific basis for their conservation and utilization. |
| format | Article |
| id | doaj-art-ff2eb2326c0f4387865a379df34cdce5 |
| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj-art-ff2eb2326c0f4387865a379df34cdce52025-02-07T20:20:59ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-02-011610.3389/fpls.2025.15340851534085An initial exploration of core collection construction and DNA fingerprinting in Elymus sibiricus L. using SNP markersXinrui Li0Xinrui Li1Xinrui Li2Daping Song3Mingfeng Li4Daxu Li5Minghong You6Yan Peng7Jiajun Yan8Shiqie Bai9School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, ChinaCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaInstitute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, ChinaSchool of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, ChinaInstitute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, ChinaInstitute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, ChinaInstitute of Herbaceous Plants, Sichuan Academy of Grassland Science, Chengdu, ChinaCollege of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, ChinaSchool of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, ChinaSchool of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, ChinaElymus sibiricus L., an excellent forage and ecological restoration grass, plays a key role in grassland ecological construction and the sustainable development of animal husbandry. In China, the wild germplasm resources of E. sibiricus are abundant, and they are shaped by similar and contrasting climatic conditions to form distinct populations, which enrich the genetic diversity of E. sibiricus. To more comprehensively aggregate E. sibiricus germplasm resources at a lower cost and to more accurately utilize its genetic variation, this study conducted a preliminary exploration of core germplasm collections and fingerprinting of E. sibiricus using single nucleotide polymorphism (SNP) markers. By combining multiple evaluation measures with weighted processing, we successfully identified 36 materials from 90 wild E. sibiricus samples to serve as a core collection. Genetic diversity assessments, allele evaluations, and principal component analyses of the 36 core germplasm samples all indicate that these 36 samples accurately and comprehensively represent the genetic diversity of all 90 E. sibiricus germplasm accessions. Additionally, we identified 290 SNP loci from among the high-quality SNP loci generated by whole-genome sequencing of the 90 E. sibiricus samples as candidate markers. Of these, 52 SNP loci were selected as core markers for DNA fingerprinting of E. sibiricus. Using kompetitive allele-specific PCR (KASP) technology, we also performed population origin identification for 60 wild E. sibiricus germplasm accessions based on these core markers. The core SNP markers screened in this study were able to accurately distinguish between E. sibiricus germplasms from the Qinghai–Tibet Plateau and those from elsewhere. This study not only provides a reference for the continued collection and identification of E. sibiricus germplasm resources but also offers a scientific basis for their conservation and utilization.https://www.frontiersin.org/articles/10.3389/fpls.2025.1534085/fullElymus sibiricus L.SNPcore collectionDNA fingerprintingKASPpopulation identification |
| spellingShingle | Xinrui Li Xinrui Li Xinrui Li Daping Song Mingfeng Li Daxu Li Minghong You Yan Peng Jiajun Yan Shiqie Bai An initial exploration of core collection construction and DNA fingerprinting in Elymus sibiricus L. using SNP markers Frontiers in Plant Science Elymus sibiricus L. SNP core collection DNA fingerprinting KASP population identification |
| title | An initial exploration of core collection construction and DNA fingerprinting in Elymus sibiricus L. using SNP markers |
| title_full | An initial exploration of core collection construction and DNA fingerprinting in Elymus sibiricus L. using SNP markers |
| title_fullStr | An initial exploration of core collection construction and DNA fingerprinting in Elymus sibiricus L. using SNP markers |
| title_full_unstemmed | An initial exploration of core collection construction and DNA fingerprinting in Elymus sibiricus L. using SNP markers |
| title_short | An initial exploration of core collection construction and DNA fingerprinting in Elymus sibiricus L. using SNP markers |
| title_sort | initial exploration of core collection construction and dna fingerprinting in elymus sibiricus l using snp markers |
| topic | Elymus sibiricus L. SNP core collection DNA fingerprinting KASP population identification |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2025.1534085/full |
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