alleles and polymorphisms affecting the function of these genes
(functional polymorphisms) is showing a pattern of repeated evolution for some traits, such as early flowering or dwarfism, which is
determined by multiple independent mutations in a few genes
[15–17].
Despite the expanding number of genes demonstrated as contributing to natural variation, the relevance of these genes and their
functional nucleotide polymorphisms in plant adaptation remain
mostly unknown. However, several recent developments are helping to elucidate the evolutionary mechanisms that maintain Arabidopsis natural variation. First, the number of genotypes collected in
natural populations (referred here to as wild accessions), with
precise geographic, climatic, and ecological information from
their original local populations, has substantially increased to incorporate native areas previously excluded, such as Africa and Asia
[7, 18–21]. Second, the genome sequence of more than 1200
wild accessions has been obtained [18, 20, 22], enabling genomic
comparisons for multiple purposes. In particular, genome-wide
association (GWA) studies have become a standard methodology
in Arabidopsis (see chapter on GWA analysis in this book) for the
identification of candidate genes underlying the phenotypic natural
variation for all kind of traits. Furthermore, genome-wide analyses
of nucleotide diversity are revealing the demographic history of
Arabidopsis before and after the last glaciations [18, 19, 21, 23],
which is also required for understanding Arabidopsis adaptive evolution. Third, phenotypic analyses under field (natural) conditions
are revealing strong significant genotype by environment interactions for numerous traits [24–27]. Thus, new loci and genes have
been found, which cannot be detected under laboratory conditions
[28–32]. In addition, these studies are also addressing the precise
environmental cues perceived by plants to regulate their development [33]; the relevance of local adaptation [34–36]; the fluctuating effects of natural selection, which depend on multiple
environmental factors [32, 36–39]; and the rapid genetic changes
related with the recent climate change, as measured through resurrection approaches [40, 41]. Overall, the availability of precise
phenotypes, genotypes, and environments for numerous Arabidopsis accessions is enabling the genetic, molecular, and ecological
dissection of plant adaptation at intraspecific (microevolutionary)
level. In this chapter, we describe two methodologies that are
becoming essential to understand the natural variation for any
trait and gene of interest: (1) growth of Arabidopsis in field experiments for phenotypic analyses (also called garden trials); (2) analysis
of nucleotide diversity and environmental associations for specific
genes.
94
Carlos Alonso-Blanco et al.
(functional polymorphisms) is showing a pattern of repeated evolution for some traits, such as early flowering or dwarfism, which is
determined by multiple independent mutations in a few genes
[15–17].
Despite the expanding number of genes demonstrated as contributing to natural variation, the relevance of these genes and their
functional nucleotide polymorphisms in plant adaptation remain
mostly unknown. However, several recent developments are helping to elucidate the evolutionary mechanisms that maintain Arabidopsis natural variation. First, the number of genotypes collected in
natural populations (referred here to as wild accessions), with
precise geographic, climatic, and ecological information from
their original local populations, has substantially increased to incorporate native areas previously excluded, such as Africa and Asia
[7, 18–21]. Second, the genome sequence of more than 1200
wild accessions has been obtained [18, 20, 22], enabling genomic
comparisons for multiple purposes. In particular, genome-wide
association (GWA) studies have become a standard methodology
in Arabidopsis (see chapter on GWA analysis in this book) for the
identification of candidate genes underlying the phenotypic natural
variation for all kind of traits. Furthermore, genome-wide analyses
of nucleotide diversity are revealing the demographic history of
Arabidopsis before and after the last glaciations [18, 19, 21, 23],
which is also required for understanding Arabidopsis adaptive evolution. Third, phenotypic analyses under field (natural) conditions
are revealing strong significant genotype by environment interactions for numerous traits [24–27]. Thus, new loci and genes have
been found, which cannot be detected under laboratory conditions
[28–32]. In addition, these studies are also addressing the precise
environmental cues perceived by plants to regulate their development [33]; the relevance of local adaptation [34–36]; the fluctuating effects of natural selection, which depend on multiple
environmental factors [32, 36–39]; and the rapid genetic changes
related with the recent climate change, as measured through resurrection approaches [40, 41]. Overall, the availability of precise
phenotypes, genotypes, and environments for numerous Arabidopsis accessions is enabling the genetic, molecular, and ecological
dissection of plant adaptation at intraspecific (microevolutionary)
level. In this chapter, we describe two methodologies that are
becoming essential to understand the natural variation for any
trait and gene of interest: (1) growth of Arabidopsis in field experiments for phenotypic analyses (also called garden trials); (2) analysis
of nucleotide diversity and environmental associations for specific
genes.
94
Carlos Alonso-Blanco et al.