Capítulo 3. Aplicación del procedimiento para contribuir a mejorar el desempeño de la cadena de
3.1. Caracterización general de la cadena y establecimiento del equipo de trabajo
ECOLOGICAL CONTEXT
1.6.1 ARABIDOPSIS THALIANA: AN IDEAL MODEL
Though work on our own species has generally led the field – indeed, many of the concepts and methods to be discussed in this report will continue to cite work on human populations that has, in one way or another, blazed the trail – most of the knowledge gained and techniques pioneered in human genetic research are equally applicable to research in other species. First amongst these other species in plant genetics has been the model plant Arabidopsis thaliana, or Thale cress. This species is favoured by plant scientists for its ease of growth, extensive wild range and short generation time (Meyerowitz & Pruitt 1985), as a model for molecular genetic investigation of plant development, host-‐ pathogen interactions, and increasingly as an organism for ecological investigation of natural populations . Along with its extensive record of pre-‐ existing genetic experimentation, its small genome – one of the smallest of any flowering plant – made it an attractive proposition to the scientists involved in the first sequencing projects; and so it was one of the first eukaryotes ever sequenced, before even our own species.
Arabidopsis thaliana is a member of the family Brassicaceae, a large and
extremely diverse group that has radiated to a staggering range of habitats and ecological niches. Some wild relatives like Capsella bursa-pastoris (Shepherds Purse) are invasive weeds, whereas others have been domesticated as vegetable of oilseed crops such as Brassica oleracea (cabbage, broccoli, Brussels sprouts and cauliflower), B. napus (oilseed rape), Raphanus sativus (radish),
Brassica rapa (turnip), and Lepidium sativum (cress). A better understanding of
the biology of A. thaliana inevitably translates to a better understanding of these close relatives (Bancroft 2000).
A. thaliana is ideally suited for molecular genetic research. Its outcrossing
into small near-‐isogenic, relatively rarely intermingling groups known as ‘accessions’ (Mitchell-‐Olds 2001; Bergelson et al. 1998). Its wide native range, spanning much of the Northern hemisphere and a considerable range of latitudes, also makes it an excellent source of knowledge regarding adaptation to different climate types and habitats. Despite its propensity for self-‐ fertilisation, the wild population retains a large amount of genetic variation, including variation at loci associated with traits of significant agronomic importance to crop species within the Brassicaceae.
Additionally, A. thaliana has proved a great source of knowledge in terms of genomics. The genes controlling the plant’s development have been extensively mapped and studied. Much is known regarding the exact molecular mechanisms A. thaliana uses to detect and respond to changes in abiotic conditions such as temperature, day length and water availability in its environment. For example, GWAS experiments have revealed multiple genes associated with control of flowering time in response to day length (Ehrenreich et al. 2009).
A good deal is also known about the molecular mechanisms by which A.
thaliana detects and reacts to challenges from biotic factors, including
parasites; A. thaliana is known to possess both broad-‐spectrum defensive measures effective against a wide array of microbial species, such as those controlled by the jasmonic and salicylic acid defence pathways (Kniskern et al. 2007), and specific defenses that evolved as counters to the action of proteins secreted by pathogens in order to suppress or evade those defences. Parts of this project involving an attempt to identify instances of adaptation in A.
thaliana will take particular note of genes of the latter type, since they are likely
to be in a constant evolutionary arms race against their opposite numbers in species which parasitise A. thaliana. See Chapter 1.7 for an overview of our current understanding of interactions between plants and pathogens as described by the “zigzag model” (Dangl & Jones 2001; Jones & Dangl 2006),
Given this rare combination of existing knowledge and continued relevance to ongoing research, it was only a matter of time before the very latest genetic research methodology was applied to A. thaliana.
1.6.2 FROM MAN TO PLANT: ONE MODEL INFORMING ANOTHER
The International HapMap project provided an impetus for the plant research community to initiate its own A. thaliana HapMap project in 2005. This global project, comparable in scope to its human-‐based equivalent, utilised a high-‐
throughput technique based on RNA microarrays (Borevitz et al. 2003) to genotype A. thaliana samples. The European and UK-‐wide distribution of sites at which these accessions were sampled is shown in Figure 4. These accessions were initially genotyped using a low density set of 149 SNPs; these genotypes were then used to select a smaller subset of 916 accessions, covering as much of the population’s genetic diversity as possible, which were then genotyped at a higher density of 350,000 SNPs. Many of these SNPs were rejected due to duplication or uncertainty, leaving a final dataset of genotypic variation across 216000 SNP loci, known as the 250K dataset (Kim et al. 2007).
One of the first analyses completed from this dataset was a map of linkage disequilibrium across the Arabidopsis genome. Despite the low outcrossing rate of the species, Kim et al. (2007) found that linkage disequilibrium between loci breaks down when loci are separated by, on average, 10kb.
1.6.3 A. THALIANA AS A MEANS OF REVEALING ECOLOGICALLY IMPORTANT VARIATION
As with human genomics, genome-‐wide association studies have been performed for many ecologically and agronomically significant traits in A.
thaliana. A prominent example is that of flowering time. Since A. thaliana
inhabits such a surprisingly vast range of latitudes – from Scandinavia to the sub-‐tropics – it must be able to adapt to a wide variety of climatic temperature ranges and day lengths. In fact, A. thaliana is known to have developed different strategies for the combinations of these and other climatic variables it faces across its latitude range, and control of flowering time is known to play a key role in this adaptation (Michaels et al. 2003). Across most of its range, A.
thaliana typically lives as a winter annual, producing a single generation each
year. Growth begins with autumnal germination and continues the winter, terminating with flowering and seeding in the spring and seed dormancy over the summer. Towards the more northerly and colder extremes of its range, however, A. thaliana possesses alleles associated with a summer annual lifecycle (Michaels et al. 2003; Alonso-‐Blanco & Koornneef 2000). The genetic
basis of this alternative life cycle is known to involve variation in genes that control vernalisation and flowering time, as described by Michaels et al. (2003) Consequently, genes associated with this trait, and other genes associated with flowering time, are likely candidates for local adaptation. Analyses described in this project therefore sought signatures of selection acting upon these genes (see Chapter 4.3.3).