Microsatellite analysis of genetic diversity in Czech populations of European beech (Fagus sylvatica L.)

No. of Population	Provenance Name	Average Altitude (m a.s.l.)	Geographic Coordinates		No. of Samples

			latitude	longitude
1	Frýdlant	441	50°52′24.1″N	15°06′36.1″E	20
2	Kladská	755	50°00′11.8″N	12°38′55.5″E	20
3	Litvínov	794	50°36′46.8″N	13°23′14.5″E	20
4	Boubín	916	49°09′05.5″N	13°40′03.2″E	20
5	Nové Hrady	863	48°39′46.6″N	14°40′51.0″E	20
6	Hluboká	538	49°06′24.3″N	14°29′51.6″E	30
7	Jeseník	652	50°11′34.1″N	17°13′55.0″E	30
8	Frýdek Místek	839	49°31′44.7″N	18°28′28.6″E	30
9	Luhačovice	479	49°03′06.0″N	18°04′19.0″E	30
10	Lanškroun	573	49°56′07.4″N	16°30′33.2″E	30

Table 2

Features of microsatellite primers assembled into multiplexes (SSR: simple sequence repeats).

	SSR Locus	Allele Size Range (bp)^*	Primer Sequences 5′ –3′		Repeats	Fluorescent Dye	Source Reference	Primers Volume F + R [μL]^**

			F	R
Multiplex 1	concat14_A_0	170–197	TGAAGAAATTCACAACCCAACA	GGGTTGTTTACGATGGTGGA	(TC)₉	PET	¹	0.6
	EMILY_A_0	142–152	GACCCCAAGGTTACAGTGCT	CGTACAATTGCACCCACATC	(GA)₁₁	PET	¹	0.36
	csolfagus_31	103–130	TCTATTGACACAAGAATAAGAACACC	CTTGGCAAGAAAAGGGGATT	(AG)₁₂	PET	¹	0.45
	mfc11	310–360	ACAGATAAAAACAGAAGCCA	TTTGGTTTTGTTGAGTTTAG	(AG)₁₀	NED	²	0.45
	DE576_A_0	210–240	TCTCCTTAGATCCACAATCACA	AGCTCTTCATTGCTCAGAACG	(CAA)₁₀	NED	¹	0.9
	csolfagus_05	167–180	GGTTTCTAGCAAAATTGGCATT	CCCAAAAGGCCCTACTACAA	(GA)₁₀	NED	¹	0.36
	FS1-03	90–140	CACAGCTTGACACATTCCAAC	TGGTAAAGCACTTTTTCCCACT	(GA)₁₈	NED	³	0.24
	mfc5	270–340	ACTGGGACAAAAAAACAAAA	GAAGGACCAAGGCACATAAA	(AG)₁₀	FAM	²	0.6
	csolfagus_19	150–185	TGCCCATGAGGTTTGTATCA	GCCGAATAACCCAGAAAACA	(TC)₁₃	FAM	¹	0.24
	csolfagus_06	200–225	GTTGTTGCTCACAGCAGTCG	ACGCTTGGTCTTCTTGCACT	(AG)₁₃	FAM	¹	0.24
	sfc0036	90–140	CATGCTTGACTGACTGTAAGTTC	TCCAGGCCTAAAAACATTTATAG	(TC)₂₃	FAM	⁴	0.3
	mfc7	110–104	AAAATACACTGCCCCCAAAA	CAGGTTTTGGTTTCTTACAC	(GA)₉	VIC	²	0.3
	ERHBI_A_0	159–167	TGCAACAACTTAGCACTTTGA	GCGTGTGGCTTATCCAAAAT	(AG)₉	VIC	¹	0.12

Multiplex 2	EEU75_A_0	90–115	TTCCAAACCAACCCTTTATCC	GACGGAGATTGAGGAAGAACA	(CT)₁₀	PET	¹	0.3
	Fagsyl_002929	152–210	GCGGCGACTGGAATAATAGC	CAATCACACGCTGCACAAAC	(TTG)_x	NED	⁵	0.3
	Fagsyl_003849	98–128	GCTTCGTTCTTCGGCATCTC	AATAGCACAAATAGCCCGCC	(CT)_x	NED	⁵	0.21
	DZ447_A_0	186–194	GGTGCAATACTTCACTTTAGGACA	ATAGGAGTGGGACGGCTAGG	(TC)₁₀	FAM	¹	0.3
	csolfagus_29	130–150	CACAACCTGCATTCCCTTTC	GTTTGGCACTTTGGCTTGTT	(CT)₁₁	FAM	¹	0.18
	Fagsyl_001018	107–130	AATATCAGGGAGGCAGCACC	CGAGATGGACTTCTAAGTTTTATTTGC	(CA)_x	FAM	⁵	0.21
	DUKCT_A_0	75–95	GCCTCTCGCAGCTCCTATAA	GATCTAATGTGGGTTTGGTTTTG	(AC)₁₄	FAM	¹	0.18
	Fagsyl_003093	150–205	TCATCACCGAGACAAGGGAC	ATGGTGGTGTGGAAGCTAGG	(CA)_x	VIC	⁵	0.18

1 Lefèvre et al., 2012,

2 Tanaka et al., 1999,

3 Pastorelli et al., 2003,

4 Asuka et al., 2004,

5 Pluess & Määttänen, 2013.

* Allele Size Range stands for minimum and maximum lengths of PCR products detected for a locus (in base pairs).

** Final concentration in each primer premix forward + reverse.

Table 3

Locus-specific parameters.

Locus	k	N	H_o	H_e	PIC	HW	F (Null)
concat14_A_0	4	249	0.474	0.494	0.461	NS	0.0229
EMILY_A_0	6	249	0.763	0.770	0.731	NS	0.0009
csolfagus_31	13	249	0.855	0.858	0.842	NS	−0.0005
mfc11	9	249	0.353	0.616	0.594	^***	0.2575
DE576_A_0	7	248	0.710	0.669	0.613	NS	−0.0325
csolfagus_05	8	249	0.675	0.679	0.639	NS	0.0068
FS1-03	14	246	0.528	0.622	0.594	**	0.088
mfc5	22	249	0.669	0.906	0.897	^**	0.1504
csolfagus_19	13	249	0.803	0.844	0.824	NS	0.0262
csolfagus_06	12	248	0.859	0.867	0.851	NS	0.0042
sfc0036	8	248	0.786	0.772	0.744	NS	−0.0114
mfc7	9	249	0.578	0.596	0.559	NS	0.134
ERHBI_A_0	6	249	0.514	0.530	0.491	NS	0.0163

EEU75_A_0	11	245	0.808	0.805	0.777	NS	−0.0040
Fagsyl_002929	11	247	0.765	0.729	0.693	NS	−0.0269
Fagsyl_003849	14	247	0.814	0.808	0.783	NS	−0.0034
DZ447_A_0	4	245	0.592	0.593	0.545	NS	0.0051
csolfagus_29	8	248	0.435	0.436	0.400	NS	−0.001
Fagsyl_001018	9	246	0.390	0.656	0.608	^***	0.2696
DUKCT_A_0	8	246	0.537	0.569	0.449	NS	0.0291
Fagsyl_003093	12	194	0.216	0.571	0.530	^***	0.4491

Mean	9.905	245	0.625	0.685	0.649
SD	4.098	0.183	0.134	0.146
SE	0.894		0.040	0.029	0.032

Number of allele per locus (k), number of individuals genotyped on given locus (N), observed heterozygosity (H_o), expected heterozygosity (H_e), polymorphic information content (PIC), deviation from Hardy-Weinberg equilibrium (HW, level of significance:

*** α = 0.001.

** α = 0.01,

NS – not significant), estimation of null allele frequency (F (Null)), significant estimates are marked bold), standard deviation (SD), standard error (SE).

The discriminatory power of loci expressed by Probability of Identity (PI) for unrelated individuals (orange line) and related individuals (green line).

Principal Coordinate Analysis (PCoA) of the populations 1–10 (further described in Table 1).

Populations 1–10 divided into three regions by PCoA (populations further described in Table 1).

Table 4

Estimations of population parameters.

Population		N	N_a	N_e	I	H_o	H_e	F
1	Mean	19.524	6.905	3.925	1.447	0.635	0.674	0.074
1	SE	0.290	0.581	0.522	0.102	0.046	0.030	0.042
2	Mean	19.571	6.476	3.583	1.414	0.629	0.662	0.072
2	SE	0.335	0.550	0.339	0.093	0.057	0.034	0.063
3	Mean	19.381	6.238	3.427	1.363	0.595	0.650	0.089
3	SE	0.288	0.530	0.335	0.095	0.047	0.033	0.054
4	Mean	19.667	6.571	3.627	1.410	0.623	0.667	0.069
4	SE	0.159	0.500	0.364	0.091	0.049	0.032	0.054
5	Mean	19.810	6.667	3.625	1.416	0.632	0.664	0.045
5	SE	0.190	0.618	0.383	0.095	0.048	0.032	0.054
6	Mean	29.381	6.905	3.549	1.393	0.607	0.651	0.082
6	SE	0.288	0.589	0.417	0.098	0.044	0.032	0.042
7	Mean	29.857	7.238	3.792	1.439	0.623	0.667	0.064
7	SE	0.143	0.617	0.419	0.104	0.044	0.035	0.046
8	Mean	29.667	7.381	3.879	1.484	0.630	0.678	0.064
8	SE	0.333	0.674	0.502	0.099	0.039	0.030	0.046
9	Mean	29.190	6.905	3.501	1.415	0.654	0.670	0.041
9	SE	0.190	0.625	0.290	0.088	0.043	0.028	0.038
10	Mean	29.143	6.905	3.648	1.419	0.619	0.662	0.062
10	SE	0.469	0.625	0.419	0.098	0.042	0.032	0.046

Total	Mean	24.519	6.819	3.655	1.420	0.625	0.664	0.066
Total	SE	0.352	0.185	0.126	0.030	0.014	0.010	0.015

[i] Sample size (N), mean number of alleles per locus (N_a), effective number of alleles (N_e), mean Shannon's information index (I), observed heterozygosity (H_o), expected heterozygosity (H_e), mean fixation index (F).

Table 5

Nei's genetic distances between the provenances (Nei, 1972, 1987)

1	2	3	4	5	6	7	8	9	10
0.000										1
0.067	0.000									2
0.071	0.078	0.000								3
0.064	0.061	0.069	0.000							4
0.078	0.061	0.064	0.049	0.000						5
0.062	0.070	0.076	0.061	0.077	0.000					6
0.064	0.059	0.053	0.051	0.062	0.067	0.000				7
0.082	0.062	0.064	0.062	0.067	0.056	0.049	0.000			8
0.079	0.075	0.088	0.081	0.091	0.056	0.074	0.057	0.000		9
0.055	0.065	0.074	0.065	0.072	0.079	0.060	0.061	0.087	0.000	10

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DOI: https://doi.org/10.2478/fsmu-2020-0015 | Journal eISSN: 1736-8723 | Journal ISSN: 1406-9954

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Language: English, Estonian

Page range: 64 - 76

Submitted on: Jun 26, 2020

Accepted on: Nov 23, 2020

Published on: Mar 11, 2021

Published by: Estonian University of Life Sciences

In partnership with: Paradigm Publishing Services

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© 2021 Dagmar Zádrapová, Jiří Korecký, Jakub Dvořák, Zuzana Faltinová, Jan Bílý, published by Estonian University of Life Sciences
This work is licensed under the Creative Commons Attribution 4.0 License.

Volume 73 (2020): Issue 1 (December 2020)

Microsatellite analysis of genetic diversity in Czech populations of European beech (Fagus sylvatica L.)

Figures & Tables

Table 1

Table 2

Table 3

Figure 1

Figure 2

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Table 4

Table 5

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