Este archivo ha sido creado el 05-04-2022 por Francisco Javier Jiménez López

 
GENERAL INFORMATION
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1. Dataset title: Dataset of Open Array Loci for genotyping Abies nebrodensis


2. Authorship:

	Name:Montserrat Arista Palmero

	Institution: Universidad de Sevilla

	Email: marista@us.es

	ORCID: 0000-0003-0914-9525  

	
	Name:Francisco Javier Balao Robles

	Institution: Universidad de Sevilla

	Email: fbalao@us.es

	ORCID: 0000-0003-2104-3846


	Name:Pedro Luis Ortiz Ballesteros

	Institution: Universidad de Sevilla

	Email: plortiz@us.es

	ORCID: 0000-0002-4150-565X


	Name:Anass Terrab Benjelloun

	Institution: Universidad de Sevilla

	Email: anass@us.es

	ORCID: 0000-0002-7979-3669


	Name:Jose Carlos del Valle García

	Institution: Universidad de Sevilla

	Email: jvgarcia@us.es

	ORCID: 0000-0001-6023-6208


	Name:Francisco Javier Jiménez López

	Institution: Universidad de Sevilla

	Email: fjimenez16@us.es

	ORCID: 0000-0001-9905-6482



DESCRIPTION
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1. Dataset language: English

2. Abstract: This is a list with the sequence of the 124 SNPS specifically designed for Abies nebrodensis.

3. Keywords: Abies nebrodensis, snps, sequences

4. Date of data collection: 30-09-2021

5. Publication Date: 06-04-2022

6. Grant information:

	Grant Agency:Programa LIFE de la UNION EUROPEA.
	Grant Number:LIFE18 NAT/IT/000164

7. Geographical location/s of data collection: 37°51'N 14°00'E, Polizzi Generosa, Sicily, Italy.



ACCESS INFORMATION
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1. Creative Commons License of the dataset: CC-BY

2. Dataset DOI:

3. Related publication:

4. Link to related datasets:
	DOI/URL: http://www.life4fir.com/es/



VERSIONING AND PROVENANCE
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1. Last modification date: 30/09/2021

2. Were data derived from another source?: No



METHODOLOGICAL INFORMATION
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1. Description of the methods used to collect and generate the data:
In November 2019, we collected leaves from all the mature trees (n=30) and young individuals over 5-year-old resulted from regenerations (n=118) from the natural population of A. nebrodensis. Additionally, we collected leaves from 2062 seedlings (belonging to eight maternal families) randomly selected from the local nursery 'Vivaio Piano Noce’. Samples were preserved in silica gel until the subsequent DNA extractions.

2. Data processing methods:
DNA was isolated using the NucleoMag Plant kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s protocol but with some modifications. Extracted DNA was stored at −20ºC. Total DNA was used to genotype A. nebrodensis individuals using the PCR-based OpenArrays technology following manufacter’s protocol (Thermofisher Inc., United States) at the Universitat Autònoma de Barcelona (Department of Animal and Food Science). Based on previous genomic data (Balao et al. 2020), we designed an OpenArray assay with 120 single nucleotide polymorphisms (SNPs) composed by information-rich SNPs in samples of A. nebrodensis, A. alba and A. cephalonica. 
* Balao, F., Lorenzo, M.T., Sánchez-Robles, J.M., ...García-Castaño, J.L., Terrab, A. 2020. Early diversification and permeable species boundaries in the Mediterranean firs. Annals of Botany, 125(3), pp. 495–507.

3. Software or instruments needed to interpret the data:
All data was analyzed using R (R Core Team 2021).
* R Core Team. R: a language and environment for statistical computing. 2021. http://www.r-project.org.

4. Quality-assurance procedures performed on the data:
Concentration of DNA was measured with Qubit 3.0 (Thermo-Fisher, Waltham, MA) and purity of DNA extracted was assessed by measuring the 260/280 and 260/230 ratios with a NanoDrop DS-11 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, USA). 
A subset of 160 samples were genotyped in two independent runs (replicates) to evaluate the confidence of the results obtained. Replicability was higher than 99%, ensuring the validity of the genotyping data obtained. 


FILE OVERVIEW 
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1. File list:
	File name: nebrodi_124snps_flanks
	Description: Text file with list of sequences corresponding to SNPS developed for Abie nebrodensis 

2. Relationship between files: only one file

3. File format: .txt