8, 16, and 23). Fecundity can be measured by counting the
number of fruits, or weighting the number of seeds per plant
or pot. When the number of samples is rather large, dry plants
can be collected in paper bags and stored in the laboratory for
later scoring. The total number of seeds produced per plant can
be estimated using equations relating the number of fruits per
plant or the fruit size, with the number of seeds per fruit
[27, 39].
28. Fitness might also be scored by quantifying or phenotyping
offspring survival in the next generation(s), but this will involve
leaving plants to set seeds until next year(s). Such design might
require controls for seed contamination among pots (e.g.,
genotyping during next generation) and should comply with
local legislation (see Note 11).
29. The weather during growth and fruiting of plants will strongly
determine phenology, survival, fitness, and the overall plant
phenotypes in the field experiment [33, 39, 69]. Given the
large effect of the sowing date and the weather across the life
cycle on field plant phenotypes (see Note 9), it is advisable to
repeat field experiments with different sowing dates, either in
different seasons of the same year, or in the same season in
different years. This will enable estimations of phenotypic
repeatability, genotype by environment interactions, and temporal variation of fitness and natural selection.
30. Aligned gene sequences available at the 1001 Arabidopsis genomes database are extracted from pseudogenomes that were
generated by alignment with Col reference strain. They include
SNPs and small indels identified in 1135 genome sequences
[22]. The complete gene sequence, or only the set of segregating SNPs within the gene, can be downloaded. Sequences can
be extracted for all worldwide accessions available, or for specific geographic regions. Complete gene sequences allow estimates of overall gene diversity including monomorphic sites.
Filtered files with only non-singleton (informative) polymorphic sites might be easier to handle for some nucleotide diversity analyses.
31. Gene sequences can be downloaded without alignment, and
they can be subsequently aligned with Clustal Omega. In this
case, alignments should be carefully inspected and corrected by
hand using free software packages such as GeneDoc or other
commercial packages (see Table 1).
32. It is necessary to inspect the file with the aligned nucleotide
sequences or polymorphisms to remove the accessions with
bad quality sequences (an excess of Ns—missing data—)
because they will strongly limit the gene regions to be included
Analyses of Natural Variation
105
number of fruits, or weighting the number of seeds per plant
or pot. When the number of samples is rather large, dry plants
can be collected in paper bags and stored in the laboratory for
later scoring. The total number of seeds produced per plant can
be estimated using equations relating the number of fruits per
plant or the fruit size, with the number of seeds per fruit
[27, 39].
28. Fitness might also be scored by quantifying or phenotyping
offspring survival in the next generation(s), but this will involve
leaving plants to set seeds until next year(s). Such design might
require controls for seed contamination among pots (e.g.,
genotyping during next generation) and should comply with
local legislation (see Note 11).
29. The weather during growth and fruiting of plants will strongly
determine phenology, survival, fitness, and the overall plant
phenotypes in the field experiment [33, 39, 69]. Given the
large effect of the sowing date and the weather across the life
cycle on field plant phenotypes (see Note 9), it is advisable to
repeat field experiments with different sowing dates, either in
different seasons of the same year, or in the same season in
different years. This will enable estimations of phenotypic
repeatability, genotype by environment interactions, and temporal variation of fitness and natural selection.
30. Aligned gene sequences available at the 1001 Arabidopsis genomes database are extracted from pseudogenomes that were
generated by alignment with Col reference strain. They include
SNPs and small indels identified in 1135 genome sequences
[22]. The complete gene sequence, or only the set of segregating SNPs within the gene, can be downloaded. Sequences can
be extracted for all worldwide accessions available, or for specific geographic regions. Complete gene sequences allow estimates of overall gene diversity including monomorphic sites.
Filtered files with only non-singleton (informative) polymorphic sites might be easier to handle for some nucleotide diversity analyses.
31. Gene sequences can be downloaded without alignment, and
they can be subsequently aligned with Clustal Omega. In this
case, alignments should be carefully inspected and corrected by
hand using free software packages such as GeneDoc or other
commercial packages (see Table 1).
32. It is necessary to inspect the file with the aligned nucleotide
sequences or polymorphisms to remove the accessions with
bad quality sequences (an excess of Ns—missing data—)
because they will strongly limit the gene regions to be included
Analyses of Natural Variation
105