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Details of geographic locations of four sites representing four populations of Arabidopsis thaliana Coordinates
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Morphological trait variations in four populations of Arabidopsis thaliana that grow along altitudinal gradi-ents (~700 to ~3500 m amsl) are described. A total of 38 traits were analysed from each of the four popula-tions. Most of the quantitative traits were significantly correlated with each other among the four popula-tions, but biomass-related...
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Context 1
... (second week of February), Munsyari (first week of April), Sangla and Chitkul (third week of May). Details of geographical locations of the population are given in Table 1. These four populations are hereafter referred to as Deh, Mun, Sang and Chit respectively. ...
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... leaf traits were measured from three recently fully expanded leaves per individual and their averages were considered. Details of other trait measurements are given in Table S1 (see Supplementary material online). All the data were record- ed in the field, except the microscopic data, viz. ...
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... correlation matrix constructed using all the quantita- tive characters showed that most of the traits were signif- icantly correlated with each other. At population level, the Deh population was characterized by higher leaf count, more profuse branching, more number of inflo- rescence and larger siliques compared to the Mun, Sang and Chit populations (Table S1, see Supplementary mate- rial online). The leaves of Chit population were more fleshy and thick compared to Deh population (data not shown). ...
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Citations
... In our previous study, we observed negligible expression of miR158 in a particular A. thaliana population of the Indian west Himalayas under different growing conditions (Tripathi et al., 2019). These populations, which originate from an elevation range of 700 to 3400 m above mean sea level (amsl), having varied climatic conditions, were reported to be genetically and morphologically distinct from each other (Singh et al., 2015;Singh & Roy, 2017;Tyagi, Singh, et al., 2016). Here, we show that negligible or moderate expression of miR158 is due to deletion and insertion events, respectively, in the MIR158 gene, affecting its processing to mature miRNA. ...
Small RNAs such as microRNAs (miRNAs) and small interfering (si)RNAs are short 20-24-nucleotide non-coding RNAs. They are key regulators of gene expression in plants and other organisms. Several 22-nucleotide long miRNAs trigger biogenesis of cascades of trans-acting secondary small interfering RNAs, involved in various developmental and stress responses. Here we show that in Himalayan Arabidopsis thaliana accessions having natural mutations in miR158 locus exhibit robust cascade silencing in pentatricopeptide (PPR)-like locus. Furthermore, we show that these cascade sRNAs trigger tertiary silencing of a gene involved in transpiration and stomatal opening. The natural variants of MIR158 having deletions or insertions led to improper processing of miR158 precursors thereby blocking synthesis of mature miR158. Reduced miR158 led to increased level of its target, a pseudo-pentatricopeptide gene that is otherwise targeted by ta-siRNAs generated by miR173 cascade in other accessions. Using small RNA datasets derived from Indian Himalayan accessions, as well as overexpression and knockout lines of miR158, we show that absence of miR158 led to build up of pseudo-PPR derived tertiary small RNAs. These tertiary sRNAs mediated robust silencing of a gene involved in stomatal closure in Himalayan accessions lacking miR158 expression. We functionally validated the tertiary phasiRNA that targets NHX2 a Na+ -K+ /H+ antiporter protein thereby regulating transpiration and stomatal conductance. Overall, we deciphered a new module of sRNA network, miRNA-TAS-siRNA-pseudogene-tertiary phasiRNA-NHX2 in plant adaptation.
... The two populations were reported to be phenotypically and genetically distinct (Singh et al., 2015;Tyagi et al., 2016a). Overall, though there was significant effect of e[CO 2 ] on growth and development of both the populations however, population specific effect was insignificant (Fig. 1). ...
Unravelling the plants responses towards rising atmospheric [CO2] have largely been explored in genetical and morpho-physiological contexts. However, epigenetic factors including DNA methylation which play critical roles in adaptation are largely unexplored. Here we investigated the methylome, transcriptome and morpho-physiological responses of the two Arabidopsis thaliana populations evolved at high (3400 m amsl) and low elevation (700 m amsl) zones to elevated [CO2] (e[CO2]). We show that depending on the origin of the population, there were local level variations in DNA methylation when exposed to e[CO2], but global methyl cytosine (mC) content remained unchanged. Further, there was loss of methylation and more protein coding genes were differentially methylated than transposable elements and non-coding RNA genes, in both the populations but more so in the low elevation one. The differentially methylated genes of the two populations belonged to distinct functional categories. More genes related to methylation machinery were down-regulated in the high elevation population than the low elevation one. Although there was no correlation between methylation and gene expression at the global scale but a few genes exhibited methylation dependent expression level. Finally the hyper- and hypo-methylated status of a few genes due to e[CO2] treatment were validated. Overall, our data suggested the two populations responded differently towards e[CO2] with respect to methylome remodeling, phenotypic and molecular plasticity. However, methylome remodelling and molecular plasticity were more prominent in the low elevation population. Understanding the evolution of epigenetic response towards e[CO2] may help in future crop improvement strategies.
... The Köppen-Geiger climate classification [24,25] has been used to associate the mapping of mean climate with the ecosystem conditions in certain geographic areas and more recently in identifying potential changes in vegetation over time and climate variability on various temporal scales [26]. Other studies concentrated on the variation in the phenotypic characteristics based on environmental factors [27,28], altitude [29][30][31][32][33], and longtitude [34]. ...
The rapid developments in high-throughput sequencing technologies have allowed researchers to analyze the full genomic sequence of organisms faster and cheaper than ever before. An important application of such advancements is to identify the impact of single nucleotide polymorphisms (SNPs) on the phenotypes and genotypes of the same species by discovering the factors that affect the occurrence of SNPs. The focus of this study is to determine whether climate factors such as the main climate, the precipitation, and the temperature affecting a certain geographical area might be associated with specific variations in certain ecotypes of the plant Arabidopsisthaliana. To test our hypothesis we analyzed 18 genes that encode Forkhead-Associated domain-containing proteins. They were extracted from 80 genomic sequences gathered from within 8 Eurasian regions. We used k-means clustering to separate the plants into distinct groups and evaluated the clusters using an innovative scoring system based upon the Köppen-Geiger climate classification system. The methods we used allow the selection of candidate clusters most likely to contain samples with similar polymorphisms. These clusters show that there is a correlation between genomic variations and the geographic distribution of those ecotypes.
... These populations follow a summer-annual life history. Previous studies showed that these populations are distinct from each other at least at altitudinal level 51,52 . Tyagi et al. (2016) reported that the high light intensity prevalent in the high altitude area might play a critical role in the emergence of population-level variations in these populations 53 . ...
... The populations of A. thaliana growing along the altitudinal range of the West Himalaya inhabit a wide climatic condition ranging from sub-tropical to temperate 51,52 . Among these populations, Chit represents one of the highest elevation habitat reported so far for A. thaliana. ...
... The targets of these miRNAs were also found to be down-regulated in the high altitude populations. The overall growth, particularly leaf width and leaf number of this high altitude population was reported to be less as compared to the low altitude population 51 . This may be one of the strategies to minimize the UV and /or high light intensity absorption by the plant. ...
Plant populations growing along an altitudinal gradient are exposed to different environmental conditions. They are excellent resources to study regulatory mechanisms adopted by plants to respond to different environmental stresses. Regulation by miRNA is one of such strategies. Here, we report how different miRNAs are preferentially expressed in the three natural populations of A. thaliana originating from a wide altitudinal range. The expression level of miRNAs was mostly governed by temperature and radiation. Majority of the identified miRNAs expressed commonly in the three populations. However, 30 miRNAs expressed significantly at different level between the low and the high altitude populations. Most of these miRNAs regulate the genes associated with different developmental processes, abiotic stresses including UV, cold, secondary metabolites, etc. Further, the expression of miR397 and miR858 involved in lignin biosynthesis and regulation of secondary metabolites respectively, may be regulated by light intensity. A few miRNAs expressed at increasing level with the increase in the altitude of the site indicating environment driven tight regulation of these miRNAs. Further, several novel miRNAs and isomiR diversity specific to the Himalayas are reported which might have an adaptive advantage. To the best of our knowledge, this is the first report on miRNA expression from natural plant populations.
... The values in brackets represent the 95% confidence interval and longer siliques [27]. This indicates that these traits are fixed. ...
... On the other hand, leaf and rosette shape were variable (varying non-significantly in CG and significantly in GH) when compared between CG and GH. Again, these two traits were not variable in their native sites [27]. Differences in the level of significance among the populations and the environmental conditions indicate that these characters are merely random in response and lack any adaptive differentiation. ...
... This association of native altitude with the traits that were measured in the uncorrelated environmental conditions (CG and GH) predicts for an altitudinal divergence commonly found by other studies [17,35,37,54,55]. The similar association of altitude and climate with phenotypic and genetic data were observed earlier using same set of populations [23,24,27]. However, our analysis is limited due to use of low number of populations and thus caution may be taken to interpret this particular result. ...
Background:
Population differentiation and their adaptation to a particular environment depend on their ability to respond to a new environment. This, in turn is governed to an extent, by the degree of phenotypic plasticity exhibited by the populations. The populations of same species inhabiting different climatic conditions may differ in their phenotypic plasticity. Himalayan populations of Arabidopsis thaliana originating from a steep altitude are exposed to different climatic conditions ranging from sub-tropical to temperate. Thus they might have experienced different selection pressures during evolution and may respond differently under common environmental condition.
Results:
Phenotypic plasticity and differentiation of natural populations of A. thaliana grown under common garden and controlled conditions were determined. A total of seventeen morphological traits, their plasticity, association between traits and environment were performed using 45 accessions from three populations. Plants from different altitudes differed in phenotypes, their selection and fitness under two conditions. Under both the conditions lower altitude population was characterized by higher leaf count and larger silique than higher and middle altitude population. Flowering time of high altitude population increased while that of low and medium altitude decreased under controlled condition compared to open field. An increase in seed weight and germination was observed for all the population under open field than controlled. Rosette area was under divergent selection in both the condition. The heritability of lower altitude population was the highest under both the conditions, where as it was the least for higher altitude population further indicating that the high altitude populations are more responsive towards phenotypic changes under new environmental conditions. Ninety-nine percent of variability in traits and their plasticity co-varied with the altitude of their origin. The population of high altitude was more plastic and differentiated as compared to the lower altitude one.
Conclusions:
Arabidopsis thaliana population native to different altitudes of the west Himalaya responds differently when grown under common environments. The success of high altitude population is more in common garden than the controlled conditions. The significant variability in phenotype and its association with altitude of origin predicts for non-random genetic differentiation among the populations.
... However, some insight is offered by model systems such as Arabidopsis thaliana (hereafter simply Arabidopsis). Arabidopsis has a fast generation time, and possesses a vastly underappreciated natural genetic and phenotypic variation (Koornneef et al., 2004;Singh et al., 2015). However, the microscopic size of Arabidopsis seeds poses methodological difficulties in characterizing seed phenotype, which prevented it from being a model to investigate evolutionary ecology of plant reproductive strategies. ...
The tradeoff between offspring size and number is ubiquitous and manifestly similar in plants and animals despite fundamental differences between the evolutionary histories of these two major life forms. Fecundity (offspring number) primarily affects parental fitness, while offspring size underpins the fitness of parents and offspring. We provide an overview of theoretical models dealing with offspring size and fitness relationships. We follow that with a detailed examination of life-history constraints and environmental effects on offspring size and number, separately in plants and animals. The emphasis is on seed plants, but we endeavor to also summarize information from distinct animal groups—insects, fishes, reptiles, birds, and mammals. Furthermore, we analyse genetic controls on offspring size and number in two model organisms—Arabidopsis and Drosophila. Despite the deep evolutionary divergence between plants and animals, we find four trends in reproductive strategy that are common to both lineages: (i) offspring size is generally less variable than offspring number, (ii) offspring size increases with increasing parent body size, (iii) maternal genes restrict offspring size and increase offspring numbers, while zygotic genes act to increase offspring size; such parent-offspring conflicts are enhanced when there is sibling rivalry, and (iv) variation in offspring size increases under sub-optimal (harsh) environmental conditions. The most salient difference between plants and animals is that the latter tend to produce larger (fewer) offspring under sub-optimal conditions while seed plants invest in smaller (many) seeds, suggesting that maternal genetic control over offspring size increases in plants but decreases in animals with parental care. The time is ripe for greater experimental exploration of genetic controls on reproductive allocation and parent-offspring conflicts in plants and animals under sub-optimal (harsh) environments.
... Clinal variation in the genome, growth parameters, multiple life history traits, and responses to, and tolerance of, low (freezing and chilling) and high temperature, drought, and irradiance (ultraviolet, visible, and far-red) in this species has been documented in numerous studies and typically presented in the context of a geographic gradient in one or more environmental factors (e.g., temperature, photoperiod, precipitation). Altitude has been the primary geographic variable in some studies (Ward and Strain, 1997;Montesinos-Navarro et al., 2011, 2012Picó, 2012;Wolfe and Tonsor, 2014;Botto, 2015;Luo et al., 2015;Singh et al., 2015;Vidigal et al., 2016), whereas a combination of altitude and distance from the ocean was examined in a few others (Montesinos et al., 2009;Lewandowska-Sabat et al., 2012;Kang et al., 2013). Variation (especially genetic) along longitudinal gradients has also been considered in a number of studies (Schmuths et al., 2004;Beck et al., 2008;Reininga et al., 2009;Panthee et al., 2011;Samis et al., 2012;Zuther et al., 2012;Brachi et al., 2015), and edaphic, biotic, and/or environmental factors were shown to correlate with genomic variation and life history traits in several studies (Lasky et al., 2012;Brachi et al., 2013;Manzano-Piedras et al., 2014). ...
Acclimatory adjustments of foliar vascular architecture, photosynthetic capacity, and transpiration rate in Arabidopsis thaliana ecotypes (Italian, Polish [Col-0], Swedish) were characterized in the context of habitat of origin. Temperatures of the habitat of origin decreased linearly with increasing habitat latitude, but habitat precipitation was greatest in Italy, lowest in Poland, and intermediate in Sweden. Plants of the three ecotypes raised under three different growth temperature regimes (low, moderate, and high) exhibited highest photosynthetic capacities, greatest leaf thickness, highest chlorophyll a/b ratio and levels of β-carotene, and greatest levels of wall ingrowths in phloem transfer cells, and, in the Col-0 and Swedish ecotypes, of phloem per minor vein in plants grown at the low temperature. In contrast, vein density and minor vein tracheary to sieve element ratio increased with increasing growth temperature – most strongly in Col-0 and least strongly in the Italian ecotype – and transpirational water loss correlated with vein density and number of tracheary elements per minor vein. Plotting of these vascular features as functions of climatic conditions in the habitat of origin suggested that temperatures during the evolutionary history of the ecotypes determined acclimatory responses of the foliar phloem and photosynthesis to temperature in this winter annual that upregulates photosynthesis in response to lower temperature, whereas the precipitation experienced during the evolutionary history of the ecotypes determined adjustment of foliar vein density, xylem, and transpiration to temperature. In particular, whereas photosynthetic capacity, leaf thickness, and foliar minor vein phloem features increased linearly with increasing latitude and decreasing temperature of the habitats of origin in response to experimental growth at low temperature, transpiration rate, foliar vein density, and minor vein tracheary element numbers and cross-sectional areas increased linearly with decreasing precipitation level in the habitats of origin in response to experimental growth at high temperature. This represents a situation where temperature acclimation of the apparent capacity for water flux through the xylem and transpiration rate in a winter annual responded differently from that of photosynthetic capacity, in contrast to previous reports of strong relationships between hydraulic conductance and photosynthesis in other studies.
... Changes in altitude cause variations in atmospheric temperature, pressure and solar light intensity 7,19 . These natural abiotic stresses are also known to cause several phenotypic changes in the highland populations 18,20 . ...
Environmental conditions play an important role in the emergence of genetic variations in natural populations. We identified genome-wide patterns of nucleotide variations in the coding regions of natural Arabidopsis thaliana populations. These populations originated from 700 m to 3400 m a.m.s.l. in the Western Himalaya. Using a pooled RNA-Seq approach, we identified the local and global level population-specific SNPs. The biological functions of the SNP-containing genes were primarily related to the high light intensity prevalent at high-altitude regions. The novel SNPs identified in these genes might have arisen de novo in these populations. In another approach, the FSTs of SNP-containing genes were correlated with the corresponding climatic factors. ‘Radiation in the growing season’ was the only environmental factor found to be strongly correlated with the gene-level FSTs. In both the approaches, the high light intensity was identified as the primary abiotic stress associated with the variations in these populations. The differential gene expression analysis between field and controlled condition grown plants also showed high light intensity as the primary abiotic stress, particularly for the high altitude populations. Our results provide a genome-wide perspective of nucleotide variations in populations along altitudinal gradient and their putative role in emergence of these variations.
... These populations were further compared with worldwide accessions reported by Yin et al. (2010). Recently, our group has characterized four of these populations using morphological traits and has shown that some of the morphological traits were highly correlated with their corresponding altitudes (Singh et al. 2015). Inclusion of Indian populations of A. thaliana will greatly enhance our understanding of global population structure and evolution of this model species. ...
The natural genetic variation within a plant species is primarily a consequence of its phylogeography and evolutionary history. This variation largely determines its present-day population structure. Arabidopsis thaliana as a model plant has been studied in great detail including its probable origin, local as well as global genetic diversity pattern, population structure, adaptation etc. However, no such studies have so far been reported from the Indian Himalayan region. Here, we describe a comprehensive study on genetic diversity and population structure of A. thaliana from altitudinal range of 700 m to 3400 m amsl, the highest altitudinal range reported so far. We also compare these populations with previously reported worldwide populations. A total of 48 accessions representing six populations were analyzed using 19 microsatellites and 11 chloroplast markers. Genetic diversity analysis indicated populations to be highly diverse and comparable with worldwide populations. STRUCTURE, PCoA and IBD analyses showed that genetic variation in different populations is structured at geographical and altitudinal level. Further analyses indicate these populations are genetically distinct from the rest of the world populations. Different parameters of demographic expansion model support a rapid expansion. Based on mismatch distribution, the initial time of expansion of west Himalayan populations was found to be about 130,000 years. Bayesian analysis of divergence time indicated that these populations have a long evolutionary history in this region. Based on the results of genetic diversity parameters, demographic expansion and divergence time estimation it appears that west Himalayan population may be the source of the west-east expansion model.
