Genetic structure analysis and core germplasm construction of Robinia pseudoacacia and its closely related species based on SNP
Abstract Robinia pseudoacacia is a forest biomass energy tree species with substantial potential for development and utilization. However, the lack of research on its genetic structure and the unclear genetic background of its germplasm resources impede the conservation and improvement of R. pseudoa...
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BMC
2025-07-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-025-06872-5 |
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| author | Haoran Wang Yan Ma Ruixue Wang Dekui Zang Xiaoyan Yu Jingtao Li Qichao Wu Fengqi Zang |
| author_facet | Haoran Wang Yan Ma Ruixue Wang Dekui Zang Xiaoyan Yu Jingtao Li Qichao Wu Fengqi Zang |
| author_sort | Haoran Wang |
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| description | Abstract Robinia pseudoacacia is a forest biomass energy tree species with substantial potential for development and utilization. However, the lack of research on its genetic structure and the unclear genetic background of its germplasm resources impede the conservation and improvement of R. pseudoacacia. In this study, Hyper-seq was used to identify the SNP of Robinia spp. (R. pseudoacacia and its closely related species). The genetic diversity and population structure of 105 Robinia spp. germplasm were analyzed, and a core germplasm bank was constructed. A total of 1,298,097 SNPs and 306,188 InDel polymorphic loci were obtained via mapping with the reference genome. Most of the mutations were detected in the intergenic region. For the 101 R. pseudoacacia samples, the polymorphism information content (PIC) was 0.100 and the nucleotide diversity (Pi) was 0.178, indicating a relatively low level of genetic diversity. Population genetics analysis was conducted based on the 1,312 filtered SNP loci. Phylogenetic relationships divided the entire population into three groups. Genetic structure and cross-validation error indicate low genetic divergence among the sampled individuals. Finally, 21 samples were selected as the core germplasms, accounting for 20% of the total samples. This study provided the basis for genetic research, germplasm protection and breeding of Robinia spp. |
| format | Article |
| id | doaj-art-ceac0e53bc0f4a82a78d4e872ff96fdf |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-ceac0e53bc0f4a82a78d4e872ff96fdf2025-08-20T03:37:23ZengBMCBMC Plant Biology1471-22292025-07-0125111110.1186/s12870-025-06872-5Genetic structure analysis and core germplasm construction of Robinia pseudoacacia and its closely related species based on SNPHaoran Wang0Yan Ma1Ruixue Wang2Dekui Zang3Xiaoyan Yu4Jingtao Li5Qichao Wu6Fengqi Zang7College of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural UniversityCollege of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural UniversityShandong Province Forestry Protection and Development Service CenterCollege of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural UniversityShandong Province Forestry Protection and Development Service CenterShandong Province Forestry Protection and Development Service CenterCollege of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural UniversityCollege of Forestry, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural UniversityAbstract Robinia pseudoacacia is a forest biomass energy tree species with substantial potential for development and utilization. However, the lack of research on its genetic structure and the unclear genetic background of its germplasm resources impede the conservation and improvement of R. pseudoacacia. In this study, Hyper-seq was used to identify the SNP of Robinia spp. (R. pseudoacacia and its closely related species). The genetic diversity and population structure of 105 Robinia spp. germplasm were analyzed, and a core germplasm bank was constructed. A total of 1,298,097 SNPs and 306,188 InDel polymorphic loci were obtained via mapping with the reference genome. Most of the mutations were detected in the intergenic region. For the 101 R. pseudoacacia samples, the polymorphism information content (PIC) was 0.100 and the nucleotide diversity (Pi) was 0.178, indicating a relatively low level of genetic diversity. Population genetics analysis was conducted based on the 1,312 filtered SNP loci. Phylogenetic relationships divided the entire population into three groups. Genetic structure and cross-validation error indicate low genetic divergence among the sampled individuals. Finally, 21 samples were selected as the core germplasms, accounting for 20% of the total samples. This study provided the basis for genetic research, germplasm protection and breeding of Robinia spp.https://doi.org/10.1186/s12870-025-06872-5Robinia pseudoacaciaSNPGenetic diversityPopulation structureCore germplasm |
| spellingShingle | Haoran Wang Yan Ma Ruixue Wang Dekui Zang Xiaoyan Yu Jingtao Li Qichao Wu Fengqi Zang Genetic structure analysis and core germplasm construction of Robinia pseudoacacia and its closely related species based on SNP BMC Plant Biology Robinia pseudoacacia SNP Genetic diversity Population structure Core germplasm |
| title | Genetic structure analysis and core germplasm construction of Robinia pseudoacacia and its closely related species based on SNP |
| title_full | Genetic structure analysis and core germplasm construction of Robinia pseudoacacia and its closely related species based on SNP |
| title_fullStr | Genetic structure analysis and core germplasm construction of Robinia pseudoacacia and its closely related species based on SNP |
| title_full_unstemmed | Genetic structure analysis and core germplasm construction of Robinia pseudoacacia and its closely related species based on SNP |
| title_short | Genetic structure analysis and core germplasm construction of Robinia pseudoacacia and its closely related species based on SNP |
| title_sort | genetic structure analysis and core germplasm construction of robinia pseudoacacia and its closely related species based on snp |
| topic | Robinia pseudoacacia SNP Genetic diversity Population structure Core germplasm |
| url | https://doi.org/10.1186/s12870-025-06872-5 |
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