Two main genetic clusters with high admixture between forest and cultivated chestnut (Castanea sativa Mill.) in France (ICPSR doi:10.15454/E2DFNJ)

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Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Part 5: Other Study-Related Materials
Entire Codebook

Document Description

Citation

Title:

Two main genetic clusters with high admixture between forest and cultivated chestnut (Castanea sativa Mill.) in France

Identification Number:

doi:10.15454/E2DFNJ

Distributor:

Portail Data INRAE

Date of Distribution:

2020-06-30

Version:

1

Bibliographic Citation:

Bouffartigue, Cathy; Sandrine Debille; Ana Maria Ramos Cabrer; Olivier Fabreguettes; Santiago Pereira-Lorenzo; Timothée Flutre; Luc Harvengt, 2020, "Two main genetic clusters with high admixture between forest and cultivated chestnut (Castanea sativa Mill.) in France", https://doi.org/10.15454/E2DFNJ, Portail Data INRAE, V1, UNF:6:0lpmASDvoFi+pHtRkZQiEw== [fileUNF]

Study Description

Citation

Title:

Two main genetic clusters with high admixture between forest and cultivated chestnut (Castanea sativa Mill.) in France

Identification Number:

doi:10.15454/E2DFNJ

Authoring Entity:

Bouffartigue, Cathy (INRA - IAGIR, Université de Toulouse, INRA, INPT, INP-EI PURPAN Castanet Tolosan, France)

Sandrine Debille (Genetics and Biotechnology team, Biotech and Advanced Forestry Department, FCBA tech institute, Campus Recherche Forêt-Bois de Pierroton, 71 route d'Arcachon, 33610 Cestas, France)

Ana Maria Ramos Cabrer (Departamento de Producción Vegetal y Proyectos de Ingeniería, Escola PolitécnicaSuperior, Campus de Lugo, Universidade de Santiago de Compostela, Lugo, Spain.)

Olivier Fabreguettes (INRA - Université de Bordeaux, UMR 1202 BIOGECO Biodiversité, Gènes et Communautés. Centre de recherche Nouvelle-Aquitaine-Bordeaux, Cestas, France. INRA - Bordeaux Sciences Agro, UMR 1065 SAVE Santé et Agroécologie du Vignoble. Centre de recherche de Bordeaux Aquitaine, Villenave D'Ornon, France.)

Santiago Pereira-Lorenzo (Departamento de Producción Vegetal y Proyectos de Ingeniería, Escola PolitécnicaSuperior, Campus de Lugo, Universidade de Santiago de Compostela, Lugo, Spain.)

Timothée Flutre (Departamento de Producción Vegetal y Proyectos de Ingeniería, Escola PolitécnicaSuperior, Campus de Lugo, Universidade de Santiago de Compostela, Lugo, Spain.)

Luc Harvengt (Genetics and Biotechnology team, Biotech and Advanced Forestry Department, FCBA tech institute, Campus Recherche Forêt-Bois de Pierroton, 71 route d'Arcachon, 33610 Cestas, France)

Distributor:

Portail Data INRAE

Access Authority:

Bouffartigue, Cathy

Depositor:

Bouffartigue, Cathy

Date of Deposit:

2019-09-28

Study Scope

Keywords:

Genetic Resource, ; chestnut; genetic diversity; genetic structure; microsatellite markers; landraces

Abstract:

To ensure methodological reproducibility the datasets used in "Two main genetic clusters with high admixture between forest and cultivated chestnut (Castanea sativa Mill.) in France", Rmd and bash files used to perform all analyses used in the article, are stored here. Please start by reading 0_README.html

Kind of Data:

Dataset

Methodology and Processing

Sources Statement

Data Access

Notes:

<img src="https://www.etalab.gouv.fr/wp-content/uploads/2011/10/licence-ouverte-open-licence.gif" alt="Licence Ouverte" height="100"><a href="https://www.etalab.gouv.fr/licence-ouverte-open-licence">Licence Ouverte / Open Licence Version 2.0</a> compatible CC BY

Other Study Description Materials

File Description--f99985

File: avgQmatrix_13_2.tab

  • Number of cases: 1050

  • No. of variables per record: 4

  • Type of File: text/tab-separated-values

Notes:

UNF:6:5Wko+WRSc49qbqVcGP8Y4g==

File Description--f99977

File: avgQmatrix_13_6.tab

  • Number of cases: 1050

  • No. of variables per record: 8

  • Type of File: text/tab-separated-values

Notes:

UNF:6:ce523HRYGim5jMIwuggxOA==

File Description--f99986

File: avgQmatrix_13conEs_2.tab

  • Number of cases: 1060

  • No. of variables per record: 4

  • Type of File: text/tab-separated-values

Notes:

UNF:6:eE+H2lYLWQRcKLTzpuppxA==

File Description--f99978

File: avgQmatrix_13conEs_6.tab

  • Number of cases: 1060

  • No. of variables per record: 8

  • Type of File: text/tab-separated-values

Notes:

UNF:6:gN5u2Sh69pMwKyIJZs09kQ==

File Description--f99979

File: avgQmatrix_13cult_3.tab

  • Number of cases: 312

  • No. of variables per record: 5

  • Type of File: text/tab-separated-values

Notes:

UNF:6:NYtYt5RL3hB/Om2YnuHBfA==

File Description--f99980

File: avgQmatrix_13for_4.tab

  • Number of cases: 717

  • No. of variables per record: 6

  • Type of File: text/tab-separated-values

Notes:

UNF:6:UTksl5JZbg0iI9FPmFpFXg==

File Description--f99981

File: avgQmatrix_24_2.tab

  • Number of cases: 520

  • No. of variables per record: 4

  • Type of File: text/tab-separated-values

Notes:

UNF:6:C05z/jbegned1+9jOiIImQ==

File Description--f99982

File: avgQmatrix_24conEs_2.tab

  • Number of cases: 529

  • No. of variables per record: 4

  • Type of File: text/tab-separated-values

Notes:

UNF:6:jqx8lAOJbKfycuukDrEVDA==

File Description--f99983

File: avgQmatrix_24cult_4.tab

  • Number of cases: 212

  • No. of variables per record: 6

  • Type of File: text/tab-separated-values

Notes:

UNF:6:BBQbnuPTXUtaKsiLL7fPzA==

File Description--f99984

File: avgQmatrix_24for_4.tab

  • Number of cases: 301

  • No. of variables per record: 6

  • Type of File: text/tab-separated-values

Notes:

UNF:6:mT25GFfRP0laTi3OSMVp0w==

Variable Description

List of Variables:

Variables

ind

f99985 Location:

Variable Format: character

Notes: UNF:6:ec49wQtrdjBA4+5t5xEphw==

sampling.region

f99985 Location:

Variable Format: character

Notes: UNF:6:sX8YEcHJn9sYLSwlz6aiSA==

cluster1

f99985 Location:

Summary Statistics: StDev 0.3249994867796225; Mean 0.5834578095238095; Valid 1050.0; Max. 0.9725; Min. 0.0178

Variable Format: numeric

Notes: UNF:6:DpIUhiDwkxpZ155z/JY5Dg==

cluster2

f99985 Location:

Summary Statistics: StDev 0.3249994867796224; Mean 0.4165421904761904; Min. 0.0275; Max. 0.9822; Valid 1050.0

Variable Format: numeric

Notes: UNF:6:ndBlhwtK3AOTbud7OMurew==

ind

f99977 Location:

Variable Format: character

Notes: UNF:6:ec49wQtrdjBA4+5t5xEphw==

sampling.region

f99977 Location:

Variable Format: character

Notes: UNF:6:sX8YEcHJn9sYLSwlz6aiSA==

cluster1

f99977 Location:

Summary Statistics: Mean 0.1508540952380952; Valid 1050.0; Min. 0.004; StDev 0.29148706339916064; Max. 0.975

Variable Format: numeric

Notes: UNF:6:pdG7Mv3cK7W8lXjtK5GW2g==

cluster2

f99977 Location:

Summary Statistics: Max. 0.961; StDev 0.28519374208675; Valid 1050.0; Mean 0.19200523809523806; Min. 0.004;

Variable Format: numeric

Notes: UNF:6:wOB+aejOUP+xQa0RztGJKQ==

cluster3

f99977 Location:

Summary Statistics: StDev 0.21022620247952173; Valid 1050.0; Max. 0.9809; Mean 0.08320400000000007; Min. 0.003;

Variable Format: numeric

Notes: UNF:6:H0ZdycPUea8qHaQMLsdvWA==

cluster4

f99977 Location:

Summary Statistics: StDev 0.31034378841623894; Valid 1050.0; Min. 0.003; Mean 0.2164464761904762; Max. 0.9667;

Variable Format: numeric

Notes: UNF:6:6rl3pgnKIUmwtruC4JUUAQ==

cluster5

f99977 Location:

Summary Statistics: Max. 0.9651; StDev 0.30239573696714456; Min. 0.004; Valid 1050.0; Mean 0.19068980952380954

Variable Format: numeric

Notes: UNF:6:1PnmHSdtOM5Yw9k0GOm1Iw==

cluster6

f99977 Location:

Summary Statistics: Valid 1050.0; Max. 0.9609; Mean 0.16680066666666665; StDev 0.2633177160573152; Min. 0.0032

Variable Format: numeric

Notes: UNF:6:vnIH2ld0Oa5rjYOiLjpn2w==

ind

f99986 Location:

Variable Format: character

Notes: UNF:6:yUuQJAKx7aaF75jg8tsJHw==

sampling.region

f99986 Location:

Variable Format: character

Notes: UNF:6:tEO8Pmq4N+UPcUZ9VwVudg==

cluster1

f99986 Location:

Summary Statistics: Mean 0.582280188679245; Min. 0.0195; StDev 0.32496450493168916; Valid 1060.0; Max. 0.9705

Variable Format: numeric

Notes: UNF:6:K0lnW6SVIArCf+ZzFIk7jQ==

cluster2

f99986 Location:

Summary Statistics: StDev 0.3249645049316892; Max. 0.9805; Min. 0.0295; Valid 1060.0; Mean 0.4177198113207549

Variable Format: numeric

Notes: UNF:6:xnpvxwBX9Iw3Ax78jEt3YQ==

ind

f99978 Location:

Variable Format: character

Notes: UNF:6:yUuQJAKx7aaF75jg8tsJHw==

sampling.region

f99978 Location:

Variable Format: character

Notes: UNF:6:tEO8Pmq4N+UPcUZ9VwVudg==

cluster1

f99978 Location:

Summary Statistics: Valid 1060.0; Max. 0.9607; Mean 0.19099716981132078; Min. 0.004; StDev 0.2843965065007472

Variable Format: numeric

Notes: UNF:6:H1pbySkva9+QzIY47kowDA==

cluster2

f99978 Location:

Summary Statistics: Min. 0.003; Mean 0.08334415094339619; Max. 0.98; StDev 0.20925386101820279; Valid 1060.0

Variable Format: numeric

Notes: UNF:6:4Rh9nbktnH8GEwPHIVChHQ==

cluster3

f99978 Location:

Summary Statistics: Min. 0.004; Mean 0.190181037735849; Valid 1060.0; Max. 0.9646; StDev 0.30171654059342856

Variable Format: numeric

Notes: UNF:6:UZ80+iWzKqCct8cSUPSt5Q==

cluster4

f99978 Location:

Summary Statistics: Max. 0.9662; Mean 0.21426424528301885; Min. 0.003; Valid 1060.0; StDev 0.30806950581105347

Variable Format: numeric

Notes: UNF:6:KJt4FsBJnhVifvOFmGSpEA==

cluster5

f99978 Location:

Summary Statistics: Min. 0.004; Valid 1060.0; Max. 0.9749; StDev 0.2913188886994171; Mean 0.15272707547169811;

Variable Format: numeric

Notes: UNF:6:M8/dkH0izrh4sV8xUCUQOA==

cluster6

f99978 Location:

Summary Statistics: Valid 1060.0; Min. 0.0035; Mean 0.16848594339622638; Max. 0.9598; StDev 0.2637256674069682

Variable Format: numeric

Notes: UNF:6:RoEXAaw1oQSRSbQJTH2eUg==

ind

f99979 Location:

Variable Format: character

Notes: UNF:6:r6me4RlKJQD8sWePELCJ1A==

sampling.region

f99979 Location:

Variable Format: character

Notes: UNF:6:qEAbvxusG4sH71ePtb6qAw==

cluster1

f99979 Location:

Summary Statistics: Min. 0.0103; Mean 0.3436939102564103; Valid 312.0; StDev 0.3581266745764433; Max. 0.9711

Variable Format: numeric

Notes: UNF:6:KOn5bdYujTfbI26K/N2SXA==

cluster2

f99979 Location:

Summary Statistics: Valid 312.0; StDev 0.3610421834390576; Min. 0.0103; Mean 0.3019897435897436; Max. 0.9783;

Variable Format: numeric

Notes: UNF:6:zpj0EFI8qUn4dila5oCIQA==

cluster3

f99979 Location:

Summary Statistics: StDev 0.36835231404771246; Mean 0.35431506410256414; Valid 312.0; Min. 0.0099; Max. 0.9745;

Variable Format: numeric

Notes: UNF:6:whH7FotvwKh2rnvq3TfeEg==

ind

f99980 Location:

Variable Format: character

Notes: UNF:6:Za0D4ECSKxqlCw37flQs+A==

sampling.region

f99980 Location:

Variable Format: character

Notes: UNF:6:PrDymBTY5DQrgFB+LqMcUw==

cluster1

f99980 Location:

Summary Statistics: StDev 0.37265886971187145; Max. 0.98; Min. 0.0042; Valid 717.0; Mean 0.2786697350069735

Variable Format: numeric

Notes: UNF:6:/R0vB6wfvJNVL5EAjnKtCA==

cluster2

f99980 Location:

Summary Statistics: Max. 0.9798; Min. 0.004; StDev 0.3805168473346671; Valid 717.0; Mean 0.31121046025104604

Variable Format: numeric

Notes: UNF:6:08ZsbxnRGafNKHO4EG8Giw==

cluster3

f99980 Location:

Summary Statistics: Mean 0.1802195258019527; Min. 0.005; Valid 717.0; Max. 0.9868; StDev 0.3270022631314207

Variable Format: numeric

Notes: UNF:6:cADG2T9hRjWgp2JO4/rwCQ==

cluster4

f99980 Location:

Summary Statistics: Mean 0.22989818688981875; Valid 717.0; StDev 0.3399886246200151; Min. 0.004; Max. 0.984;

Variable Format: numeric

Notes: UNF:6:6cDh4piAygGN01CgKBW5hw==

ind

f99981 Location:

Variable Format: character

Notes: UNF:6:NXagC6hAFnJvD3VEhHhPrg==

sampling.region

f99981 Location:

Variable Format: character

Notes: UNF:6:QPLZDG2Nh5DQY5uuKjDV6g==

cluster1

f99981 Location:

Summary Statistics: StDev 0.3941375933024861; Mean 0.6469734615384616; Min. 0.009; Valid 520.0; Max. 0.991

Variable Format: numeric

Notes: UNF:6:rM4Tzmy8zQ56V8fWNvUuPw==

cluster2

f99981 Location:

Summary Statistics: Valid 520.0; Max. 0.991; Mean 0.3530265384615385; StDev 0.3941375933024861; Min. 0.009;

Variable Format: numeric

Notes: UNF:6:GMOtJINpJy2gKjc1ctC1lw==

ind

f99982 Location:

Variable Format: character

Notes: UNF:6:ee8AxMxu/sF7yQt3eu+RTA==

sampling.region

f99982 Location:

Variable Format: character

Notes: UNF:6:U3pabnW6oNpR1u7IltxU/Q==

cluster1

f99982 Location:

Summary Statistics: Min. 0.0108; Max. 0.99; Mean 0.3613102079395084; Valid 529.0; StDev 0.38851293435451056

Variable Format: numeric

Notes: UNF:6:CTuo0+C1snlj7bU/8fiF4Q==

cluster2

f99982 Location:

Summary Statistics: Max. 0.9892; Valid 529.0; StDev 0.3885129343545105; Mean 0.6386897920604916; Min. 0.01;

Variable Format: numeric

Notes: UNF:6:vyyN7Ysod3uJaq0W7eLRqA==

ind

f99983 Location:

Variable Format: character

Notes: UNF:6:3xyKOYIcMVXKgOIcMBvhFg==

sampling.region

f99983 Location:

Variable Format: character

Notes: UNF:6:n1Ka6Kus3sq7LxmPkUQ2sQ==

cluster1

f99983 Location:

Summary Statistics: Min. 0.004; StDev 0.3588134485510939; Max. 0.986; Valid 212.0; Mean 0.2260849056603774

Variable Format: numeric

Notes: UNF:6:rmbMX6AwPQk2Ff2aHBkbjw==

cluster2

f99983 Location:

Summary Statistics: Mean 0.3574702830188679; StDev 0.4164276278148489; Min. 0.005; Valid 212.0; Max. 0.9819

Variable Format: numeric

Notes: UNF:6:aME+K2voY4UiJayfyf5EiQ==

cluster3

f99983 Location:

Summary Statistics: Max. 0.9858; StDev 0.34551019579639997; Mean 0.21194811320754708; Valid 212.0; Min. 0.003;

Variable Format: numeric

Notes: UNF:6:KLna1YFZXZfGJw1gXLDjsA==

cluster4

f99983 Location:

Summary Statistics: Valid 212.0; StDev 0.34715489542598144; Max. 0.9849; Min. 0.003; Mean 0.20449811320754716

Variable Format: numeric

Notes: UNF:6:Wm7HJUo4ps40uXOzpxt65Q==

ind

f99984 Location:

Variable Format: character

Notes: UNF:6:pFM1S3zkBS/KUxM/azLmPA==

sampling.region

f99984 Location:

Variable Format: character

Notes: UNF:6:7wkwxXQBYNpHMrdlrhJhzg==

cluster1

f99984 Location:

Summary Statistics: Max. 0.9804; StDev 0.33540815097228777; Min. 0.003; Mean 0.25703986710963456; Valid 301.0

Variable Format: numeric

Notes: UNF:6:zb9wKuFcnQFJ1aTQ4s/TNQ==

cluster2

f99984 Location:

Summary Statistics: Mean 0.32151561461794026; StDev 0.39423153221007645; Min. 0.0031; Valid 301.0; Max. 0.9845

Variable Format: numeric

Notes: UNF:6:iGNFTHFGaLk5nZg775SjYg==

cluster3

f99984 Location:

Summary Statistics: StDev 0.18065958449400343; Min. 0.0035; Mean 0.12272225913621267; Max. 0.5933; Valid 301.0

Variable Format: numeric

Notes: UNF:6:87th6GUyRpJNB05OZ2bfAQ==

cluster4

f99984 Location:

Summary Statistics: StDev 0.38226020680520134; Max. 0.9893; Min. 0.0035; Valid 301.0; Mean 0.29872691029900333;

Variable Format: numeric

Notes: UNF:6:maMvu39xlxDV3df4/fJ0Bw==

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