Analysis of genetic diversity in the coastal and island endangered plant Elaeagnus macrophylla by conserved DNA-derived polymorphism markers
- Published
- Accepted
- Subject Areas
- Conservation Biology, Plant Science
- Keywords
- Elaeagnus macrophylla, CDDP markers, Conservation implications, Genetic variation
- Copyright
- © 2019 Yi et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2019. Analysis of genetic diversity in the coastal and island endangered plant Elaeagnus macrophylla by conserved DNA-derived polymorphism markers. PeerJ Preprints 7:e27850v1 https://doi.org/10.7287/peerj.preprints.27850v1
Abstract
The genetic diversity and genetic structure of five natural populations of the island and coastal endangered plant Elaeagnus macrophylla were analyzed by conserved DNA-derived polymorphism (CDDP) molecular markers. A total of 289 discernible loci were obtained from 102 individuals using fifteen primers, and 100% of the loci were polymorphic. The observed number of alleles (Na) was 1.9654, the effective number of alleles (Ne) was 1.2604, the average of Nei’s genetic diversity index (H) was 0.1724, and Shannon's information index was 0.2869, indicating that E. macrophylla had levels of genetic diversity lower than those reported for continental relatives and other coastal species. The average percentage of polymorphic loci (PPL) was 42.1%, and the maximum and minimum PPL values were 80.97% and 14.88%, belonging to the Nanji Island (NJD) and Liugong Island (LGD) populations, respectively. Populations of E. macrophylla were highly differentiated (Gst=0.3263). The unweighted pair group method with arithmetic mean (UPGMA) clustering results revealed 5 groups: one group comprising the Liugong Island (LGD) and Da Rushan (DRS) populations, one comprising the Lingshan Island (LSD), Laoshan (LS) and Daguan Island (DGD) populations, one comprising the Putuo Island (PTD), and two groups representing the Nanji Island (NJD) samples, which were differentiated into a northwestern group and a southeastern group. There was no cross-clustering among the samples, and the similarity of the relatives was strictly related to geographical location. R software analysis showed no correlation between genetic distance and geographic distance between populations (r = 0.256579, p = 0.8309).
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
A 0-1 matrix of 15 primer-pair amplified 102 samples
0-1 matrix obtained from the results of electropherogram.
Screening of primers ERF2, ERF3, KNOX-1 by 7 samples
It can be seen that the three primer amplification bands are clear and specific and can be used for experiments.
Screening of primers MYB1, MYB2, ERF1 by 7 samples
It can be seen that the MYB1, MYB2, ERF1 amplified bands are clear and specific and can be used for experiments.
Screening of primers WRKY-F1, WRKY-R1, WRKY-R2 by 7 samples
It can be seen that the WRKY-F1, WRKY-R1 amplified bands are clear and specific and can be used for experiments. Although the WRKY-R2 has a strip, the strip is weak and therefore not used.
Screening of primers WRKY-R3, WRKY-R2B, WRKY-R3B by 7 samples
It can be seen that the WRKY-R3 amplified band is clear and specific, and can be used for experiments. WRKY-R2B, WRKY-R3B is not effective, so it is not used.
Screening of primers KNOX-2, KNOX-3, MADS-1 by 7 samples
It can be seen that KNOX-2, KNOX-3, MADS-1 amplified bands are clear and specific and can be used for experiments.
Screening of primers ABP1-1, ABP1-2, ABP1-3 by 7 samples
It can be seen that the ABP1-1, ABP1-3 amplified bands are clear and specific and can be used for experiments. ABP1-2 did not amplify the band and therefore could not be used.
Screening of primers MADS-2, MADS-3, MADS-4 by 7 samples
It can be seen that the MADS-4 amplification band is clear and specific and can be used for experiments. Although the MADS-2 has a band, it is not effective in use, and the MADS-3 does not amplify the band, so it is not used.
LGD1-8,DRS9-20,WRKY-F1
Amplification results of WRKY-F1 on LGD1-8 and DRS9-20.
DRS21-28,NJD1-12
Amplification results of WRKY-F1 on DRS21-28, NJD1-12.
NJD13-NJD32,WRKY-F1
Amplification results of WRKY-F1 on NJD13-NJD32.
NJD 33,LS 1-13,PTD1,LSD1,WRKF-F1
Amplification results of WRKY-F1 on NJD 33, LS 1-13, PTD1, LSD1.
DGD1-13,WRKY-F1
Amplification results of WRKY-F1 on DGD1-13.
DGD14-26,WRKY-F1
Amplification results of WRKY-F1 on DGD14-26.
LGD1-8,DRS9-20,WRKY-R1
Amplification results of WRKY-R1 on LGD1-8 and DRS9-20.
DRS21-28,NJD1-12,WRKY-R1
Amplification results of WRKY-R1 on DRS21-28, NJD1-12.
NJD13-32,WRKY-R1
Amplification results of WRKY-R1 on NJD13-32.
NJD 33,LS1-13,PTD1,LSD1,WRKY-R1
Amplification results of WRKY-R1 on NJD 33, LS1-13, PTD1, LSD1.
DGD1-20,WRKY-R1
Amplification results of WRKY-R1 on DGD1-20.
DGD21-26,WRKY-R1
Amplification results of WRKY-R1 on DGD21-26.
LGD1-8,DRS9-20,WRKY-R3
Amplification results of WRKY-R3 on LGD1-8, DRS9-20 samples.
DRS21-28,NJD1-12,WRKY-R3
Amplification results of WRKY-R3 on DRS21-28, NJD1-12 samples.
NJD13-32,WRKY-R3
Amplification results of WRKY-R3 on DRS21-28, NJD13-32 samples.
NJD33,LS1-13,PTD1,LSD1,WRKY-R3
Amplification results of WRKY-R3 on NJD33, LS1-13, PTD1, LSD1 samples.
DGD1-20,WRKY-R3
Amplification results of WRKY-R3 on DGD1-20 samples.
DGD21-26,WRKY-R3
Amplification results of WRKY-R3 on DGD21-26 samples.
LGD1-8,DRS9-20,MYB1
Amplification results of MYB1 on LGD1-8, DRS9-20 samples.
DRS21-28,NJD1-12,MYB1
Amplification results of MYB1 on DRS21-28, NJD1-12 samples.
NJD13-33,MYB1
Amplification results of MYB1 on NJD13-33 samples.
NJD33,LS1-13,PTD1,LSD1,MYB1
Amplification results of MYB1 on NJD33, LS1-13, PTD1, LSD1 samples.
DGD1-20,MYB1
Amplification results of MYB1 on DGD1-20 samples.
DGD21-26,MYB1
Amplification results of MYB1 on DGD21-26 samples.
LGD1-8,DRS9-20,MYB2
Amplification results of MYB2 on LGD1-8, DRS9-20 samples.
DRS21-28,NJD1-12,MYB2
Amplification results of MYB2 on DRS21-28, NJD1-12 samples.
NJD13-32,MYB2
Amplification results of MYB2 on NJD13-32 samples.
NJD33,LS1-13,PUD1,LSD1,MYB2
Amplification results of MYB2 on NJD33, LS1-13, PUD1, LSD1 samples.
DGD1-20,MYB2
Amplification results of MYB2 on DGD1-20 samples.
DGD21-26,MYB2
Amplification results of MYB2 on DGD21-26 samples.
LGD1-8,DRS9-20,ERF1
Amplification results of ERF1 on LGD1-8, DRS9-20 samples.
DRS21-28,NJD1-12,ERF1
Amplification results of ERF1 on DRS21-28, NJD1-12 samples.
NJD13-32,ERF1
Amplification results of ERF1 on NJD13-32 samples.
NJD33,LS1-13,PTD1,LSD1,ERF1
Amplification results of ERF1 on NJD33, LS1-13, PTD1, LSD1 samples.
DGD1-20,ERF1
Amplification results of ERF1 on DGD1-20 samples.
LS1-6,DGD21-26,ERF1
Amplification results of ERF1 on LS1-6, DGD21-26 samples.
LGD1-8,DRS9-20,ERF2
Amplification results of ERF2 on LGD1-8, DRS9-20 samples.
DRS21-28,NJD1-12,ERF2
Amplification results of ERF2 on DRS21-28, NJD1-12 samples.
NJD13-32,ERF2
Amplification results of ERF2 on NJD13-32 samples.
NJD33,LS1-13,PTD1,LSD1,ERF2
Amplification results of ERF2 on NJD33, LS1-13, PTD1, and LSD1 samples.
DGD1-20,ERF2
Amplification results of ERF2 on DGD1-20 samples.
DGD21-26,ERF2
Amplification results of ERF2 on DGD21-26 samples.
LGD1-8,DRS9-20,ERF3
Amplification results of ERF3 on LGD1-8, DRS9-20 samples.
DRS21-28,NJD1-12,ERF3
Amplification results of ERF3 on DRS21-28, NJD1-12 samples.
NJD13-32,ERF3
Amplification results of ERF3 on NJD13-32 samples.
NJD33,LS1-13,PTU1,LSD1,DGD24-26,ERF3
Amplification results of ERF3 on NJD33, LS1-13, PTU1, LSD1, and DGD24-26 samples.
DGD1-23,ERF3
Amplification results of ERF3 on DGD1-23 samples.
DGD24-26,ERF3
Amplification results of ERF3 on DGD24-26 samples.
LGD1-8,DRS9-20,KNOX-1
KNOX-1 amplification results for LGD1-8, DRS9-20 samples.
DRS21-28,NJD1-12,KNOX-1
KNOX-1 amplification results for DRS21-28, NJD1-12 samples.
NJD13-32,KNOX-1
KNOX-1 amplification results for NJD13-32 samples.
NJD33,LS1-13,PUD1,LSD1,KNOX-1
KNOX-1 amplification results for NJD33, LS1-13, PUD1, LSD1 samples.
DGD1-20,KNOX-1
KNOX-1 amplification results for DGD1-20 samples.
DGD21-26,KNOX-1
KNOX-1 amplification results for DGD21-26 samples.
LGD1-8,DRS9-23,KNOX-2
KNOX-2 amplification results for LGD1-8, DRS9-23 samples.
DRS24-28,NJD1-18,KNOX-2
KNOX-2 amplification results for DRS24-28, NJD1-18 samples.
NJD19-33,LS1-6,KNOX-2
KNOX-2 amplification results for NJD19-33, LS1-6 samples.
LS7-13,PTD1,LSD1,DGD1-13,KNOX-2
KNOX-2 amplification results for LS7-13, PTD1, LSD1and DGD1-13 samples.
DGD14-26,KNOX-2
KNOX-2 amplification results for DGD14-26 samples.
LGD1-8,DRS9-23,KNOX-3
KNOX-3 amplification results for LGD1-8, DRS9-23 samples.
DRS24-28,NJD1-18,KNOX-3
KNOX-3 amplification results for DRS24-28, NJD1-18 samples.
NJD19-33,PTD1,LSD1,LS1-4,KNOX-3
KNOX-3 amplification results for NJD19-33, PTD1, LSD1, LS1-4 samples.
LS5-13,DGD1-13,KNOX-3
KNOX-3 amplification results for LS5-13, DGD1-13 samples.
DGD14-26,KNOX-3
KNOX-3 amplification results for DGD14-26 samples.
LGD1-8,DRS9-23,MADS-1
Amplification results of MADS-1 on LGD1-8, DRS9-23 samples.
DRS24-28,NJD1-18,MADS-1
Amplification results of MADS-1 on DRS24-28, NJD1-18 samples.
NJD19-NJD33,PTD1,LSD1,LS1-4,MADS-1
Amplification results of MADS-1 on NJD19-NJD33, PTD1, LSD1, LS1-4 samples.
LS5-13,DGD1-13,MADS-1
Amplification results of MADS-1 on LS5-13, DGD1-13 samples.
DGD14-26,MADS-1
Amplification results of MADS-1 on DGD14-26 samples.
LGD1-8,DRS9-23,MADS-4
Amplification results of MADS-4 on LGD1-8 and DRS9-23 samples.
DRS24-28,NJD1-18,MADS-4
Amplification results of MADS-4 on DRS24-28, NJD1-18 samples.
NJD19-33,PUD1,LSD1,LS1-4,MADS-4
Amplification results of MADS-4 on NJD19-33, PUD1, LSD1, LS1-4 samples.
LS5-13,DGD1-13,MADS-4
Amplification results of MADS-4 on LS5-13, DGD1-13 samples.
DGD14-26,MADS-4
Amplification results of MADS-4 on DGD14-26 samples.
LGD1-8,DRS9-23,ABP1-1
ABP1-1 amplification results for LGD1-8, DRS9-23 samples.
DRS24-28,NJD1-18,ABP1-1
ABP1-1 amplification results for DRS24-28, NJD1-18 samples.
NJD19-33,LS1-4,ABP1-1
ABP1-1 amplification results for NJD19-33, LS1-4 samples.
LS5-13,DGD1-13,ABP1-1
ABP1-1 amplification results for LS5-13, DGD1-13 samples.
DGD14-26,ABP1-1
ABP1-1 amplification results for DGD14-26 samples.
LGD1-8,DRS9-23,ABP1-3
ABP1-3 amplification results for LGD1-8, DRS9-23 samples.
DRS24-28,NJD1-18,ABP1-3
ABP1-3 amplification results of DRS24-28, NJD1-18 samples.
NJD19-33,PTD1,LSD1,LS1-4,ABP1-3
ABP1-3 amplification results for NJD19-33, PTD1, LSD1, LS1-4 samples.
LS5-13,DGD1-13,ABP1-3
ABP1-3 amplification results for LS5-13, DGD1-13 samples.
DGD14-26,ABP1-3
ABP1-3 amplification results for DGD14-26 samples.
