論文の公開元へGenetic background of ecophysiological trait divergence along altitudinal gradient in a perennial herb Arabidopsis halleri
概要
Unraveling the mechanisms of phenotypic divergence and local adaptation is an important goal of the ecological research. Species having broad distributions would face different environments in each habitat and often acquire population-specific phenotypes based on genetic polymorphisms as a result of local adaptation to distinct environments (Pruisscher et al. 2018, Campbell-Staton et al. 2018). Such adaptive divergence is more likely to occur between the geographically isolated populations because increasing geographical distance can limit a gene flow between the populations and shape large environmental differences (Galloway and Fenster 2000, Kubota et al. 2015, Kesselring et al. 2019). At a small geographic scale, gene flow between populations may counteract the process of local adaptation by homogenizing allele differences (Conner and Hartl 2004). However, even with a short geographical distance, such adaptive divergence often occurs if there is a steep environmental gradient that causes strong selection (Skelly et al. 2004, Antonovics et al. 2006, Hämälä and Savolainen 2019). Investigating short-scale adaptive divergence would enable us to identify the traits under selection because neutral difference may be eliminated by the gene flow (Gonzalo-Turpin and Hazard 2009).
Along altitudes, there are steep environmental changes that serve different selective pressure to species. There are common or regional features of climate changes along altitudes (Körner 2003). The common features of climate changes along altitudes are in atmospheric pressure and temperature. Both of atmospheric pressure and temperature decrease with altitude. Though not necessarily common, other climate condition such as solar radiation, precipitation, wind and length of growing season also often change along altitude regionally. Such environmental changes along altitudes provide strong selection to species and lead to local adaptation. Species may require changing a set of traits to adapt to highland habitat where certain climatic factors differ from lowland. Comparing the trait diverged between the populations that inhabit different altitudes enables us to understand the mechanisms of altitudinal adaptation.
The variations in plant functional traits along altitudinal gradient have been studied by many researchers (reviewed by Körner 2003). In the highland, plants growth forms are generally characterized as low stature or prostrate shrubs, graminoids, cushion plants and perennial herbs forming rosettes. There are not generally but regionally important patterns; for example, annual plants are rare at high altitude, and in tropical mountains, plants tend to have giant rosettes. As a result of local adaptation, many plants inhabiting highland show higher tolerance to low temperature stresses than plants at low altitude.
Altitudinal divergence also occurs between highland and lowland populations even within a species. One of the most well-known altitudinal ecotype divergences is occurred in Metrosideros polymorpha in Hawaii. M. polymorpha shows great differences in leaf traits between highland and lowland ecotypes; highland ecotypes have smaller leaf area, greater leaf thickness, higher trichome density, and lower photosynthetic capacity (Kitayama et al. 1997, Cordell et al. 1998). Phenotypic divergences in physiologial and morphological traits have also been reported for other species; for example, tolerance to freezing temperature (Argyroxiphium sandwicense and Sophora chrysophylla; Lipp et al. 1994), photoinhibition (Lycopersicon hirsutum; Jung et al. 1998) and UV-B stress (Arabidopsis halleri; Wang Q et al. 2016) are higher in highland ecotypes. Previous studies also reported that many traits show a certain level of phenotypic plasticity, for instance, freezing tolerance is increased by cold acclimation (reviewed by Smallwood and Bowles 2002). Wang Q et al. (2016) also reported that Arabidopsis halleri showed differences in the phenotypic plasticity of UV-B tolerance between altitudes; the highland individuals have constantly high tolerance whereas the lowland individuals have more inducible tolerance increasing after UV-B exposure. To investigate such phenotypic differences between population, growth experiment under common condition is need (Savolainen et al. 2013).
Arabidopsis halleri Subsp. gemmifera, a perennial evergreen herb, has also been studied as a model plant for altitudinal divergence. This plant occurs in eastern Asia and the Russian Far East, and has a wide distribution in both latitude and altitude (Kudo et al. 2018). This is a closely related species of A. thaliana, one of the most popular model plants for molecular biology. The genome assembly of A. halleri has been published in Akama et al. (2014) and updated in Briskine et al. (2017). At Mt. Ibuki (Japan, altitude 1,377m, 35°25′04′′ N, 136°24′22′′ E at the highest peak), A. halleri has two contrasting habitats: the lowland habitat is the understory of forests near the base of mountain whereas the highland habitat is the semi-alpine open habitat near the summit (Honjo and Kudo 2019). A. halleri plants have visible differentiations between the two habitats; plants in the lowland habitat have glabrous leaves (hereafter lowland ecotype), whereas those in the highland habitat are characterized by dense trichomes on the leaves (hereafter highland ecotype), though the level of genome-wide genetic differentiation between the lowland and highland plants on Mt. Ibuki was low (FST = 0.017, Ikeda et al. 2010). Other phenotypic differences between ecotypes have been reported on resistance to UV-B stress (Wang Q et al. 2016), leaf wettability (Aryal et al. 2018) and response to soil nitrogen availability (Wang Q et al. 2019). In the intermediate altitude, there are many plants with scarce trichomes on the leaves, suggesting that genetic admixture occurs between highland and lowland ecotypes. Kubota et al. (2015) conducted genome scan at whole- genome level and identified candidate genes for altitudinal differentiation. However, the genetic and the phenotypic polymorphisms between A. halleri ecotypes have not been associated with each other.
In the present study, I focused on the genetic and ecophysiological mechanisms of altitudinal adaptation of A. halleri. This thesis comprises of three chapters.
In chapter Ⅰ, I investigated genetic differentiations in A. halleri plants along altitudinal gradient on Mt. Ibuki at a very fine spatial scale. One of the study aims was to identify the distribution of highland and lowland ecotypes along altitude. I was also interested in the gene flow between highland and lowland ecotypes. As mentioned above, existence of plants with low trichome density (intermediate trait between highland and lowland ecotypes) in the intermediate altitude suggests admixture of the ecotypes occurs in this area. I harvested plants at a very high spatial resolution (every 20 m on average from 359 m to 1,317 m above the sea level) and analyzed the whole genome of the harvested plants. I identified areas where highland, lowland and their admixed plants are distributed by the population genetic structure analysis and investigated genes selected in the admixed area, which may have a role in the genetic structure along altitude.
In chapter Ⅱ, I investigated key leaf functional traits of lowland and highland ecotypes of A. halleri grown under the common condition in the laboratory. I evaluated tolerance to photoinhibition at cold temperatures, freezing temperatures and leaf mass per area (LMA). Tolerance to photoinhibition at cold temperature and lower freezing temperature may be needed to adapt to high altitude environment (reviewed by Lütz 2010). Greater LMA has been observed in species or ecotypes inhabiting higher altitudes (Körner and Diemer 1987, Zhang et al. 2020), which may also contribute to adaptation to higher altitude. I also investigated these traits after plants were acclimated to low growth temperature. I addressed two questions; (1) are these traits different between ecotypes? and (2) is plasticity of these traits (cold acclimation) different between ecotypes?
In chapter Ⅲ, I investigated genes that are related to the trait variation between
highland and lowland ecotypes. I constructed an F2 population of highland and lowland ecotypes. Trait evaluation as in chapter Ⅱ and the whole-genome sequence were conducted, and GWAS (genome-wide association study) analysis was performed. I sought the genetic variants associated with each trait. Then, I identified genes that are associated to the trait variants and included in the altitude-dependent genome regions identified in chapter Ⅰ. I discuss the role of genes related to trait divergence along altitude.
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