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Research article
Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers
Xiaohua Su
-
Corresponding Author
ORCiD: https://orcid.org/0000-0002-1497-854X
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genetics.
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 (Na) were detected; the expected heterozygosity (He) 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 (Fst) and gene flow (Nm) 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.
Keywords
Populus deltoides, genetic diversity, population structure, simple sequence repeat
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CURRENT STATUS: Published
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On 06 Jan, 2020
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On 19 Dec, 2019
Editor assigned
On 17 Dec, 2019
Submission checks complete
On 16 Dec, 2019
Editor invited
On 16 Dec, 2019
No comments provided
Editorial decision: Minor revision
On 11 Dec, 2019
Review #2 received
Received 15 Sep, 2019
Review #1 received
Received 15 Sep, 2019
Reviewer #2 agreed
On 09 Sep, 2019
Editor assigned
On 06 Sep, 2019
Reviewers invited
Invitations sent on 06 Sep, 2019
Reviewer #1 agreed
On 06 Sep, 2019
Submission checks complete
On 05 Sep, 2019
Editor invited
On 05 Sep, 2019
No comments provided
Editorial decision: Major revision
On 07 Aug, 2019
Review #2 received
Received 29 Jul, 2019
Reviewer #2 agreed
On 24 Jul, 2019
Review #1 received
Received 22 Jul, 2019
Reviewers invited
Invitations sent on 04 Jul, 2019
Reviewer #1 agreed
On 04 Jul, 2019
Submission checks complete
On 19 Jun, 2019
Editor invited
On 19 Jun, 2019
Editor assigned
On 17 Jun, 2019
First submitted
On 10 Jun, 2019
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Subject Areas
Population Genetics
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This preprint is under consideration at BMC Genetics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers
Xiaohua Su
-
Corresponding Author
ORCiD: https://orcid.org/0000-0002-1497-854X
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 3
Posted 19 Dec, 2019
Published
On 06 Jan, 2020
No community comments so far
Editorial decision: Accept
On 19 Dec, 2019
Editor assigned
On 17 Dec, 2019
Submission checks complete
On 16 Dec, 2019
Editor invited
On 16 Dec, 2019
No comments provided
Editorial decision: Minor revision
On 11 Dec, 2019
Review #2 received
Received 15 Sep, 2019
Review #1 received
Received 15 Sep, 2019
Reviewer #2 agreed
On 09 Sep, 2019
Editor assigned
On 06 Sep, 2019
Reviewers invited
Invitations sent on 06 Sep, 2019
Reviewer #1 agreed
On 06 Sep, 2019
Submission checks complete
On 05 Sep, 2019
Editor invited
On 05 Sep, 2019
No comments provided
Editorial decision: Major revision
On 07 Aug, 2019
Review #2 received
Received 29 Jul, 2019
Reviewer #2 agreed
On 24 Jul, 2019
Review #1 received
Received 22 Jul, 2019
Reviewers invited
Invitations sent on 04 Jul, 2019
Reviewer #1 agreed
On 04 Jul, 2019
Submission checks complete
On 19 Jun, 2019
Editor invited
On 19 Jun, 2019
Editor assigned
On 17 Jun, 2019
First submitted
On 10 Jun, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Population Genetics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genetics.
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 (Na) were detected; the expected heterozygosity (He) 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 (Fst) and gene flow (Nm) 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.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7