6. Sow the seeds or transfer the seedlings of all experimental
genotypes, if possible, in a single day. This will be the starting
date for phenological characterization. Cover the pots with a
wire mesh. Place several climate sensors in the experiment and
switch them on (see Notes 8–10, 16, 18–21).
Table 1
Software and internet resources for the analysis of nucleotide and environmental diversity
Resource
Internet address
Reference
Nucleotide diversity
1001 Arabidopsis Genomes Project https://1001genomes.org/
[22]
1001 Epigenomes and
Transcriptomes
http://signal.salk.edu/1001.php
[42]
AraGWAS
https://aragwas.1001genomes.org
[43]
GWAPP/easyGWAS
https://easygwas.ethz.ch/
[44, 45]
AraPheno
https://arapheno.1001genomes.org/
[46]
TASSEL
https://www.maizegenetics.net/tassel
[47]
DnaSP
http://www.ub.edu/dnasp/
[48]
MEGA
https://www.megasoftware.net/
[49]
Network
http://www.fluxus-engineering.com/
POP ART
http://popart.otago.ac.nz/
[50]
Phytozome
https://phytozome.jgi.doe.gov
[51]
Clustal Omega
https://www.ebi.ac.uk/Tools/msa/clustalo/
[52]
Genedoc
https://genedoc.software.informer.com/
[53]
SNPtools
https://sourceforge.net/p/snptools/
[54]
VCFtools
http://vcftools.sourceforge.net/
[55]
Environmental analyses
WorldClim database
http://worldclim.org/
Soil geographical database of
Eurasia
http://eusoils.jrc.ec.europa.eu
Corine land cover database
http://www.eea.europa.eu/publications/COR0landcover
Arabidopsis CLIMtools
https://github.com/CLIMtools/
[56]
LFMM
http://membres-timc.imag.fr/Olivier.Francois/
lfmm/
[57]
BAYENV2
https://gcbias.org/bayenv/
[58]
SAM
https://ecoevol.ufg.br/sam/
[59]
96
Carlos Alonso-Blanco et al.