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Data of microsatellites of 29 Castanea sativa populations

Citation

Fernández-López, Josefa; Fernández-Cruz, Javier; Míguez-Soto, Beatriz (2021), Data of microsatellites of 29 Castanea sativa populations, Dryad, Dataset, https://doi.org/10.5061/dryad.b8gtht7bj

Abstract

We present microsatellite data of 29 Castanea sativa populations to be analized through systematic Bayesian clustering using modifications of a previously analyzed model to detect the existence of hidden population structures that have not previously been identified. The results will be used to establish plausible scenarios to interpret the natural evolutionary history of this species in southwestern Europe and ascertain the origin of some possible germplasm translocations using approximate Bayesian computation (ABC).

Data are 715 samples genotyped with eight microsatellites.

Samples were collected in 25 stands in the Iberian Peninsula, two stands in Italy and other two in Greece. The stands are wild populations, not grafted domesticated stands.

Methods

Plant materials (data collection)

Twenty-nine wild stands were sampled: 25 representing the most important areas of the C. sativa Iberian distribution; two stands in Italy and two in Greece (Figure). In the northwest Iberian Peninsula, the majority of sampling was conducted close to the sea shore, an area in which the influence of domestication is less important.

In the northwest and north, 14 stands were sampled between Galicia and Navarra: five stands (stands 1 to 5) in the Atlantic area and nine (stands 6 to 14) from the northwestern corner of Galicia to the Basque Country. In inland Galicia and León six stands were sampled (stands 15 to 20), which exhibited different evidence of management for wood or nuts. In the Central and Toledo Mountains range, four stands were sampled (stands 21 to 24). Smaller patches of chestnut are present in the south (Andalucía), where only one stand (25) was sampled. Italian stands (26 and 27) were in Piedmont and Sicily, and the Greek stands (28 and 29) were in Macedonia.

The total number of trees was 715, with 16 to 29 (mean 24.65) trees per stand. The names of stands, their geographic information, silviculture and number of trees per stand are summarized in the Table.

Table. The geographic position, type of management, sample size, and assignment to a genetic cluster and degree of unbalance of sampling for the Castanea sativa stands sampled in the present study. * 1: close to orchards; 2: mixed with orchards; **previous assignation to a population according to Fernández-Cruz and Fernández-López (2016); mixed W-E m3: hybrid ancestry between the western and Eastern Mediterranean population. In 11 cases, stands were high forest without apparent influence of domesticated varieties (stands 1 to 6, 8, 12, 13, 21 and 25) and two stands were old coppices (stands 20 and 24). Other stands contained mixtures of grafted and wild trees resulting from abandonment of orchards and natural regeneration of free spaces (stands 9, 10, 11, 14 and 15). A mixture of grafted trees and seedlings is the traditional way of cultivation in some areas (stands 17, 18 and 19). In most situations, stands are not far from old grafted orchards. The exceptions are most stands by the sea, in areas where there are no grafted orchards, and in consequence there is no evidence of an influence of domesticated varieties through naturalization (stands 16, 8, 12, 13). Trees in coppices reproduce from shoot stumps and coppices with standards (stands 22 and 23) are a mixture of trees that reproduced from shoot stumps and seedlings.

Geographic zone

Stand

Site name

Province

Longitude

Latitude

Altitude

Management type*

Nº trees

Population **

 

Atlantic

 

 

1

San Cibrán

Pontevedra

8º40'56"W

42º11'17"N

225

high forest

21

Atlantic

2

Mogor

Pontevedra

8°43'12"W

42°22'56"N

35

high forest

29

Atlantic

3

Mondariz

Pontevedra

8°27'56"W

42°13'37"N

65

high forest

28

Atlantic

4

Ai

Pontevedra

8°40'03"W

42°32'17"N

98

high forest

18

Atlantic

5

Serra de Outes

Coruña

8°55'35"W

42°53'44"N

172

high forest

26

Atlantic

 

Cantabric

 

 

 

 

 

 

6

Anllóns

Coruña

8°53'22"W

43°13'47"N

160

high forest

26

Cantabric

7

Sigrás

A Coruña

8º21'47"W

43º17'07"N

100

high forest1

21

Cantabric

8

Maniños

A Coruña

8º11'41"W

43º26'39"N

90

high forest

26

Cantabric

9

Fragas do Eume

A Coruña

8º02'16"W

43º24'17"N

214

high forest 2

23

Cantabric

10

Mondoñedo

Lugo

7°21'46"W

43°25'41"N

270

high forest 2

26

Cantabric

11

Nandiello

Asturias

5º45'05"W

43º13'04"N

400

high forest 2

24

Cantabric

12

Urdaibai

Vizcaya

2°39'43"W

43°20'14"N

210

high forest

20

Cantabric

13

Etxaguen

Álava

2º43'30"W

42º59'30"N

680

high forest

27

Cantabric

14

Antoñana

Álava

2º24'28"W

42º41'48"N

735

high forest 2

25

Cantabric

 

Inland NW

Galicia and León

15

Folgoso

Pontevedra

8°21'26"W

42°32'41"N

494

high forest 2

26

Mixed

16

Fraga Catasós

Pontevedra

8º05'32"W

42º38'12"N

580

high forest 2

24

Mixed

17

Chantada

Lugo

7º51'60"W

42º36'32"N

680

high forest 2

22

Mixed

18

O Caurel A

Lugo

7º10'16"W

42º37'51"N

800

high forest 2

27

W. mediterranean

19

O Caurel B

Lugo

7º09’05”W

42º38’18”N

650

high forest 2

23

W. mediterranean

20

Las Médulas

León

6º46'10''W

42º27'25''N

850

coppice1

25

Mixed

Center and south Spain

21

El Tiemblo

Ávila

4º31'57"W

40º20'43"N

1275

high forest

26

W. mediterranean

22

Hervás A

Cáceres

5º51'52"W

40º15'13"N

945

coppice with standards1

29

W. mediterranean

23

Hervás B

Cáceres

5º52'31"W

40º15'21"N

850

coppice with standards1

27

W. mediterranean

24

Guadalupe

Cáceres

5º20'00"W

39º28'00"N

950

coppice

25

Mixed

25

Gaucín

Málaga

5º18'04"W

36º32'14"N

700

high forest

33

Mixed W-E mediter3

 

Italy

26

Pellice

Piemonte

07º09'00"E

44º49'00"N

775

high forest

24

Mixed W-E mediter3

27

Petralia

Sicily

14º05'18"E

37º54'34"N

925

high forest

16

Mixed W-E mediter3

Greece

28

Paiko

N. Macedonia

22º22'18"E

40º57'42"N

650

high forest

24

E. mediterranean

29

Hortiatis

C. Macedonia

23º09´18"E

40º22'45"N

490

high forest

24

E. mediterranean

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Microsatellites

The eight multilocus genotypes of 715 trees collected in the 29 chestnut stands are in the excel “Data of SSRs of 29 Castanea sativa populations” were previously used for population-genetic description of the same samples (Fernández-Cruz & Fernández-López, 2016). There were no missing values in the present selected set. The microsatellites and their linkage groups in parentheses (Barreneche et al., 2004) were: CsCAT14 (2); CsCAT16 (6); CsCAT41 (8) (Marinoni et al., 2003); EMCs2 (6); EMCs14 (5); EMCs15 (9) (Buck et al., 2003); QpZAG36 (2) and QpZAG110 (8) (Steinkellner et al., 1997). The microsatellite CsCAT41 possesses two loci, CsCAT41a and CsCAT41b. The former was removed from the analysis because of null alleles. DNA extraction methods, PCR amplification conditions and capillary electrophoresis were described in Fernández-Cruz & Fernández-López (2012).

References

Barreneche T, Casasoli M, Russell K, Akkak A, Meddour H, Plomion C, Villani F, Kremer A. 2004. Comparative mapping between Quercus and Castanea using simple-sequence repeats (SSRs). Theoretical and Applied Genetics 108: 558–566.

Buck EJ, Hadonou M, James CJ, Blakesley D, Russell K. 2003. Isolation and characterization of polymorphic microsatellites in European chestnut (Castanea sativaMill.). Molecular Ecology Notes 3: 2137–2153.

Fernández-Cruz J, Fernández-López J. 2012. Morphological, molecular and statistical tools to identify Castanea species and their hybrids. Conservation Genetics 13: 1589–1600.

Fernández-Cruz J, Fernández-López J. 2016. Genetic structure of wild sweet chestnut (Castanea sativa Mill.) populations in northwest of Spain and their differences with other European stands. Conservation Genetics 17: 949–967.

Marinoni D, Akkak A, Bounous G Edwards KJ, Botta R. 2003. Development and characterization of microsatellite markers in Castanea sativa (Mill.). Molecular Breeding 11: 127–136.

Steinkellner H, Fluch S, Turetschek E et al. 1997. Identification and characterization of (GA/CT)(n)-microsatellite loci from Quercus petraea. Plant Molecular Biology 33: 1093–1096.

Usage Notes

There are no missing values

Funding

Interreg, Award: Castaneareg

INCITE, Award: The evolutive origin of the European chestnut in the Atlantic Galicia

Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Award: Genetic structure of Castanea sativa populations

INCITE, Award: The evolutive origin of the European chestnut in the Atlantic Galicia