Chapter 3
Analyses of Natural Variation: Field Experiments
and Nucleotide Diversity for Your Favorite Gene
Carlos Alonso-Blanco, Bele ´ n Me ´ ndez-Vigo, and F. Xavier Pico ´
Abstract
Arabidopsis has become a model plant for ecological and population genomics, owing to the substantial
phenotypic and genotypic variation that exists among and within natural populations. Specially, the recent
availability of large worldwide collections of accessions, together with their full genome sequences, has
triggered the study of Arabidopsis natural variation. In this chapter, we describe two protocols that exploit
these new resources to understand the natural variation for any trait and gene: (1) the phenotypic analysis of
Arabidopsis plants grown in field experiments; (2) the analysis of nucleotide diversity and environmental
associations for specific genes.
Key words Arabidopsis, Genetics, Quantitative trait locus (QTL), Natural variation, Field experiment, Garden experiment, Nucleotide diversity, Environmental variation, Genome-wide association
(GWA)
1 Introduction
In the past decade, Arabidopsis thaliana (onward referred to as
Arabidopsis) has become a model plant not only for molecular
and developmental genetics [1], but also for ecological and population genomics [2–5]. As a wild cosmopolitan species, Arabidopsis
is native to Eurasia and Africa [6, 7], although it has recently been
introduced in North and South America, Australia, and Iceland [8–
10]. This broad geographic distribution covers substantial climatic
variation and it is presumed that the enormous genetic variation
found among natural populations of Arabidopsis reflects adaptations to the underlying ecological diversity. The genetic and molecular bases of this natural variation has been classically addressed by
standard quantitative trait locus (QTL) mapping and cloning strategies using permanent experimental populations [11–13]. The
QTL approach has led to the identification of dozens of genes
accounting for this variation, which might be useful for breeding
in crop species [14, 15]. In addition, the identification of natural
Jose J. Sanchez-Serrano and Julio Salinas (eds.), Arabidopsis Protocols, Methods in Molecular Biology, vol. 2200,
https://doi.org/10.1007/978-1-0716-0880-7_3, © Springer Science+Business Media, LLC, part of Springer Nature 2021
93
Analyses of Natural Variation: Field Experiments
and Nucleotide Diversity for Your Favorite Gene
Carlos Alonso-Blanco, Bele ´ n Me ´ ndez-Vigo, and F. Xavier Pico ´
Abstract
Arabidopsis has become a model plant for ecological and population genomics, owing to the substantial
phenotypic and genotypic variation that exists among and within natural populations. Specially, the recent
availability of large worldwide collections of accessions, together with their full genome sequences, has
triggered the study of Arabidopsis natural variation. In this chapter, we describe two protocols that exploit
these new resources to understand the natural variation for any trait and gene: (1) the phenotypic analysis of
Arabidopsis plants grown in field experiments; (2) the analysis of nucleotide diversity and environmental
associations for specific genes.
Key words Arabidopsis, Genetics, Quantitative trait locus (QTL), Natural variation, Field experiment, Garden experiment, Nucleotide diversity, Environmental variation, Genome-wide association
(GWA)
1 Introduction
In the past decade, Arabidopsis thaliana (onward referred to as
Arabidopsis) has become a model plant not only for molecular
and developmental genetics [1], but also for ecological and population genomics [2–5]. As a wild cosmopolitan species, Arabidopsis
is native to Eurasia and Africa [6, 7], although it has recently been
introduced in North and South America, Australia, and Iceland [8–
10]. This broad geographic distribution covers substantial climatic
variation and it is presumed that the enormous genetic variation
found among natural populations of Arabidopsis reflects adaptations to the underlying ecological diversity. The genetic and molecular bases of this natural variation has been classically addressed by
standard quantitative trait locus (QTL) mapping and cloning strategies using permanent experimental populations [11–13]. The
QTL approach has led to the identification of dozens of genes
accounting for this variation, which might be useful for breeding
in crop species [14, 15]. In addition, the identification of natural
Jose J. Sanchez-Serrano and Julio Salinas (eds.), Arabidopsis Protocols, Methods in Molecular Biology, vol. 2200,
https://doi.org/10.1007/978-1-0716-0880-7_3, © Springer Science+Business Media, LLC, part of Springer Nature 2021
93