Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers
Abstract Background Black cottonwood (Populus deltoides) is one of the keystone forest tree species, and has become the main breeding parents in poplar hybrid breeding. However, the genetic diversity and population structure of the introduced resources are not fully understood. Results In the presen...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-01-01
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| Series: | BMC Genetics |
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| Online Access: | https://doi.org/10.1186/s12863-019-0805-1 |
| _version_ | 1818006448612835328 |
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| author | Cun Chen Yanguang Chu Changjun Ding Xiaohua Su Qinjun Huang |
| author_facet | Cun Chen Yanguang Chu Changjun Ding Xiaohua Su Qinjun Huang |
| author_sort | Cun Chen |
| collection | DOAJ |
| description | Abstract Background Black cottonwood (Populus deltoides) is one of the keystone forest tree species, and has become the main breeding parents in poplar hybrid breeding. However, the genetic diversity and population structure of the introduced resources are not fully understood. Results In the present study, five loci containing null alleles were excluded and 15 pairs of SSR (simple sequence repeat) primers were used to analyze the genetic diversity and population structure of 384 individuals from six provenances (Missouri, Iowa, Washington, Louisiana, and Tennessee (USA), and Quebec in Canada) of P. deltoides. Ultimately, 108 alleles (N a ) were detected; the expected heterozygosity (H e ) per locus ranged from 0.070 to 0.905, and the average polymorphic information content (PIC) was 0.535. The provenance ‘Was’ had a relatively low genetic diversity, while ‘Que’, ‘Lou’, and ‘Ten’ provenances had high genetic diversity, with Shannon’s information index (I) above 1.0. The mean coefficient of genetic differentiation (F st ) and gene flow (N m ) were 0.129 and 1.931, respectively. Analysis of molecular variance (AMOVA) showed that 84.88% of the genetic variation originated from individuals. Based on principal coordinate analysis (PCoA) and STRUCTURE cluster analysis, individuals distributed in the Mississippi River Basin were roughly classified as one group, while those distributed in the St. Lawrence River Basin and Columbia River Basin were classified as another group. The cluster analysis based on the population level showed that provenance ‘Iow’ had a small gene flow and high degree of genetic differentiation compared with the other provenances, and was classified into one group. There was a significant relationship between genetic distance and geographical distance. Conclusions P. deltoides resources have high genetic diversity and there is a moderate level of genetic differentiation among provenances. Geographical isolation and natural conditions may be the main factors causing genetic differences among individuals. Individuals reflecting population genetic information can be selected to build a core germplasm bank. Meanwhile, the results could provide theoretical support for the scientific management and efficient utilization of P. deltoides genetic resources, and promote the development of molecular marker-assisted breeding of poplar. |
| first_indexed | 2024-04-14T05:01:15Z |
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| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-04-14T05:01:15Z |
| publishDate | 2020-01-01 |
| publisher | BMC |
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| series | BMC Genetics |
| spelling | doaj.art-f98475aa667f44db946332f9f6298be82022-12-22T02:10:55ZengBMCBMC Genetics1471-21562020-01-0121111210.1186/s12863-019-0805-1Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markersCun Chen0Yanguang Chu1Changjun Ding2Xiaohua Su3Qinjun Huang4State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of ForestryState Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of ForestryState Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of ForestryState Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of ForestryState Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of ForestryAbstract Background Black cottonwood (Populus deltoides) is one of the keystone forest tree species, and has become the main breeding parents in poplar hybrid breeding. However, the genetic diversity and population structure of the introduced resources are not fully understood. Results In the present study, five loci containing null alleles were excluded and 15 pairs of SSR (simple sequence repeat) primers were used to analyze the genetic diversity and population structure of 384 individuals from six provenances (Missouri, Iowa, Washington, Louisiana, and Tennessee (USA), and Quebec in Canada) of P. deltoides. Ultimately, 108 alleles (N a ) were detected; the expected heterozygosity (H e ) per locus ranged from 0.070 to 0.905, and the average polymorphic information content (PIC) was 0.535. The provenance ‘Was’ had a relatively low genetic diversity, while ‘Que’, ‘Lou’, and ‘Ten’ provenances had high genetic diversity, with Shannon’s information index (I) above 1.0. The mean coefficient of genetic differentiation (F st ) and gene flow (N m ) were 0.129 and 1.931, respectively. Analysis of molecular variance (AMOVA) showed that 84.88% of the genetic variation originated from individuals. Based on principal coordinate analysis (PCoA) and STRUCTURE cluster analysis, individuals distributed in the Mississippi River Basin were roughly classified as one group, while those distributed in the St. Lawrence River Basin and Columbia River Basin were classified as another group. The cluster analysis based on the population level showed that provenance ‘Iow’ had a small gene flow and high degree of genetic differentiation compared with the other provenances, and was classified into one group. There was a significant relationship between genetic distance and geographical distance. Conclusions P. deltoides resources have high genetic diversity and there is a moderate level of genetic differentiation among provenances. Geographical isolation and natural conditions may be the main factors causing genetic differences among individuals. Individuals reflecting population genetic information can be selected to build a core germplasm bank. Meanwhile, the results could provide theoretical support for the scientific management and efficient utilization of P. deltoides genetic resources, and promote the development of molecular marker-assisted breeding of poplar.https://doi.org/10.1186/s12863-019-0805-1Populus deltoidesGenetic diversityPopulation structureSimple sequence repeat |
| spellingShingle | Cun Chen Yanguang Chu Changjun Ding Xiaohua Su Qinjun Huang Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers BMC Genetics Populus deltoides Genetic diversity Population structure Simple sequence repeat |
| title | Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers |
| title_full | Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers |
| title_fullStr | Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers |
| title_full_unstemmed | Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers |
| title_short | Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers |
| title_sort | genetic diversity and population structure of black cottonwood populus deltoides revealed using simple sequence repeat markers |
| topic | Populus deltoides Genetic diversity Population structure Simple sequence repeat |
| url | https://doi.org/10.1186/s12863-019-0805-1 |
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