Genetic diversity of the natural populations of Arabidopsis thaliana in China

Molecular Fingerprinting and Phytochemical Investigation of Syzygium cumini L. from Different Agro-Ecological Zones of India

Syzygium cumini L. (ver Jamun; BlackBerry) is a native, evergreen multipurpose tree species of India. Besides being a fruit tree and for agroforestry in different regions, it is medicinally important too. This study aimed to determine genetic diversity using molecular and phytochemical markers in sixteen genotypes of Indian S. cumini from different agro-ecological zones. The present study used a combination of ISSR markers and the HPLC technique to explore these genotypes. The results showed a wide genetic diversity range based on the similarity coefficient values observed in S. cumini sixteen accessions from different sites. Four primary phenolic acids were discovered in all the accessions; caffeic acid (CA) was found in high concentrations. The intraspecific association between molecular and phytochemical characteristics was the primary goal of this investigation. By employing gene-specific markers for the route of secondary metabolites (polyphenols) production, it further investigated the progressive research of diversity analysis of polyphenol content in S. cumini accessions, which may also expand its nutraceutical and pharmaceutical utilization.

Polymorphisms in alternative oxidase genes from ecotypes of Arabidopsis and rice revealed an environment-induced linkage to altitude and rainfall

We investigated SNPs in alternative oxidase (AOX) genes and their connection to ecotype origins (climate, altitude, and rainfall) by using genomic data sets of Arabidopsis and rice populations from 1190 and 90 ecotypes, respectively. Parameters were defined to detect non-synonymous SNPs in the AOX ORF, which revealed amino acid (AA) changes in AOX1c, AOX1d, and AOX2 from Arabidopsis and AOX1c from rice in comparison to AOX references from Columbia-0 and Japonica ecotypes, respectively. Among these AA changes, Arabidopsis AOX1c_A161E&G165R and AOX1c_R242S revealed a link to high rainfall and high altitude, respectively, while all other changes in Arabidopsis and rice AOX was connected to high altitude and rainfall. Comparative 3D modeling showed that all mutant AOX presented structural differences in relation to the respective references. Molecular docking analysis uncovered lower binding affinity values between AOX and the substrate ubiquinol for most of the identified structures compared to their reference, indicating better enzyme-substrate binding affinities. Thus, our in silico data suggest that the majority of the AA changes found in the available ecotypes will confer better enzyme-subtract interactions and thus indicate environment-related, more efficient AOX activity.

Effect of light combination on the characteristics of dissolved organic matter and chemical forms of Cd in the rhizosphere of Arabidopsis thaliana involved in phytoremediation

Light, one of the most important natural resources for plant species, significantly influences the biomass yield and nutrient uptake capacity in plants. Light sources with different spectra combinations can impact the bioavailability, toxicity, and solubility of heavy metals in soils by altering the concentrations and fractionations of soil dissolved organic matter (DOM). A series of light irradiation treatments were performed to evaluate the influence of red, yellow, and blue lights on the characteristics of DOM in the rhizosphere soils of Arabidopsis thaliana. The results showed that monochromatic red light significantly raised the levels of DOM and proportions of hydrophilic fractionations in the rhizosphere of A. thaliana relative to the control, while monochromatic blue light had the opposite effect. Moreover, the proportions of hydrophobic acid, which can mobilize Cd effectively, also raised with increasing doses of red light, which stimulated Cd mobilization. The application of yellow light not only increased the levels of hydrophobic acid in monochromatic red light treatment but also decreased the proportion of hydrophobic fractions in monochromatic blue light treatment, partially weakening the negative impacts of pure blue light on soil Cd activation. Moreover, DOM from the combined red, yellow, and blue lights resulted in a significantly stronger Cd extraction efficiency than the other light irradiation treatments, consequently enhancing the Cd phytoextraction efficiency of A. thaliana. The findings of this study demonstrated that a suitable light combination could enhance the phytoremediation effect of A. thaliana by activating soil Cd, and this method can be extrapolated to the real field, where light irradiation can be easily applied and modulated.

Linking genes with ecological strategies in Arabidopsis thaliana

Arabidopsis thaliana is the most prominent model system in plant molecular biology and genetics. Although its ecology was initially neglected, collections of various genotypes revealed a complex population structure, with high levels of genetic diversity and substantial levels of phenotypic variation. This helped identify the genes and gene pathways mediating phenotypic change. Population genetics studies further demonstrated that this variation generally contributes to local adaptation. Here, we review evidence showing that traits affecting plant life history, growth rate, and stress reactions are not only locally adapted, they also often co-vary. Co-variation between these traits indicates that they evolve as trait syndromes, and reveals the ecological diversification that took place within A. thaliana. We argue that examining traits and the gene that control them within the context of global summary schemes that describe major ecological strategies will contribute to resolve important questions in both molecular biology and ecology.

Adaptation of Arabidopsis thaliana to the Yangtze River basin

Background

Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms adapt to climate changes is a crucial biological question that is still largely unanswered. The plant Arabidopsis thaliana is an excellent system to study this fundamental question. Its origin is in the Iberian Peninsula and North Africa, but it has spread to the Far East, including the most south-eastern edge of its native habitats, the Yangtze River basin, where the climate is very different.

Results

We sequenced 118 A. thaliana strains from the region surrounding the Yangtze River basin. We found that the Yangtze River basin population is a unique population and diverged about 61,409 years ago, with gene flows occurring at two different time points, followed by a population dispersion into the Yangtze River basin in the last few thousands of years. Positive selection analyses revealed that biological regulation processes, such as flowering time, immune and defense response processes could be correlated with the adaptation event. In particular, we found that the flowering time gene SVP has contributed to A. thaliana adaptation to the Yangtze River basin based on genetic mapping.

Conclusions

A. thaliana adapted to the Yangtze River basin habitat by promoting the onset of flowering, a finding that sheds light on how a species can adapt to locales with very different climates.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1378-9) contains supplementary material, which is available to authorized users.

Genetic diversity and population structure of Arabidopsis thaliana along an altitudinal gradient

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 the genetic diversity and population structure of A. thaliana from an altitudinal range of 700-3400 m above mean sea level 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 analysed using 19 microsatellites and 11 chloroplast markers. Genetic diversity analysis indicated populations to be highly diverse and comparable with worldwide populations. STRUCTURE, principal coordinate and isolation by distance (IBD) analyses showed that genetic variation in different populations is structured at geographical and altitudinal level. Further analyses indicate that these populations are genetically distinct from the rest of the world populations. Different parameters of the 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 populations may be the source of the west-east expansion model.

Phylogeography of Thlaspi arvense (Brassicaceae) in China Inferred from Chloroplast and Nuclear DNA Sequences and Ecological Niche Modeling

Thlaspi arvense is a well-known annual farmland weed with worldwide distribution, which can be found from sea level to above 4000 m high on the Qinghai-Tibetan Plateau (QTP). In this paper, a phylogeographic history of T. arvense including 19 populations from China was inferred by using three chloroplast (cp) DNA segments (trnL-trnF, rpl32-trnL and rps16) and one nuclear (n) DNA segment (Fe-regulated transporter-like protein, ZIP). A total of 11 chloroplast haplotypes and six nuclear alleles were identified, and haplotypes unique to the QTP were recognized (C4, C5, C7 and N4). On the basis of molecular dating, haplotypes C4, C5 and C7 have separated from others around 1.58 Ma for cpDNA, which corresponds to the QTP uplift. In addition, this article suggests that the T. arvense populations in China are a mixture of diverged subpopulations as inferred by hT/vT test (hT ≤ vT, cpDNA) and positive Tajima's D values (1.87, 0.05 < p < 0.10 for cpDNA and 3.37, p < 0.01 for nDNA). Multimodality mismatch distribution curves and a relatively large shared area of suitable environmental conditions between the Last Glacial Maximum (LGM) as well as the present time recognized by MaxEnt software reject the sudden expansion population model.

Seed dispersal in time can counteract the effect of gene flow between natural populations of Arabidopsis thaliana

Plants may escape unfavorable environments by dispersing to new sites, or by remaining in an ungerminated state at a given site until environmental conditions become favorable. There is limited evidence regarding the occurrence, interplay and relative importance of dispersal processes in time and space in plant populations. Thirty-six natural populations of the annual ruderal species Arabidopsis thaliana were monitored over five consecutive years, sampling both seed bank and above-ground cohorts. We show that immigration rates are considerably higher than previously inferred, averaging 1.7% per population yr(-1). On the other hand, almost one-third of the individuals in a given above-ground cohort result from seeds shed 2 or 3 yr back in time in 10 of the studied populations. Populations that disappeared one year were recolonized by regeneration from the seed bank the subsequent year. Thus, dispersal in both time and space is an important contributor to the structuring of genetic variability in natural populations of A. thaliana, where a high dispersal rate in time may partly counteract the homogenizing effects of spatial seed and pollen dispersal.

The genetic structure of Arabidopsis thaliana in the south-western Mediterranean range reveals a shared history between North Africa and southern Europe

BACKGROUND

Deciphering the genetic structure of Arabidopsis thaliana diversity across its geographic range provides the bases for elucidating the demographic history of this model plant. Despite the unique A. thaliana genomic resources currently available, its history in North Africa, the extreme southern limit in the biodiversity hotspot of the Mediterranean Basin, remains virtually unknown.

RESULTS

To approach A. thaliana evolutionary history in North Africa, we have analysed the genetic diversity and structure of 151 individuals collected from 20 populations distributed across Morocco. Genotyping of 249 genome-wide SNPs indicated that Morocco contains substantially lower diversity than most analyzed world regions. However, IBD, STRUCTURE and PCA clustering analyses showed that genetic variation is strongly geographically structured. We also determined the genetic relationships between Morocco and the closest European region, the Iberian Peninsula, by analyses of 201 populations from both regions genotyped with the same SNPs. These analyses detected four genetic groups, but all Moroccan accessions belonged to a common Iberian/Moroccan cluster that appeared highly differentiated from the remaining groups. Thus, we identified a genetic lineage with an isolated demographic history in the south-western Mediterranean region. The existence of this lineage was further supported by the study of several flowering genes and traits, which also found Moroccan accessions similar to the same Iberian group. Nevertheless, genetic diversity for neutral SNPs and flowering genes was higher in Moroccan than in Iberian populations of this lineage. Furthermore, we analyzed the genetic relationships between Morocco and other world regions by joint analyses of a worldwide collection of 337 accessions, which detected an additional weak relationship between North Africa and Asia.

CONCLUSIONS

The patterns of genetic diversity and structure of A. thaliana in Morocco show that North Africa is part of the species native range and support the occurrence of a glacial refugium in the Atlas Mountains. In addition, the identification of a genetic lineage specific of Morocco and the Iberian Peninsula indicates that the Strait of Gibraltar has been an A. thaliana migration route between Europe and Africa. Finally, the genetic relationship between Morocco and Asia suggests another migration route connecting north-western Africa and Asia.

Natural variation of C-repeat-binding factor (CBFs) genes is a major cause of divergence in freezing tolerance among a group of Arabidopsis thaliana populations along the Yangtze River in China

We used a monophyletic group of four natural populations of Arabidopsis thaliana expanded from a single ancestor along the Yangtze River c. 90,000 yr ago to study the molecular mechanism of the divergence in their freezing tolerance, in order to gain an insight into the genetic basis of their local adaption to low temperatures. Freezing tolerance assays, measurements of metabolites in the raffinose biosynthesis pathway and transactivation-activity assays of variation in forms of cold-responsive transcription factors were conducted on the four populations. Quantitative trait locus mapping was adopted with F₂ populations of the most- and least freezing-tolerant populations. The degree of freezing tolerance among the four populations was negatively correlated with the lowest monthly average temperature of January in their native habitats, and positively correlated to the expression level of some cold-regulated genes. We identified a major locus harboring three cold-responsive transcription factor genes CBF1-3, and found a nucleotide insertion in CBF2 in all populations except SXcgx, which generated a dysfunctional CBF2 protein. The CBF2 in SXcgx experienced a stronger natural selection in the cooler environment after CBF3 lost its response to low temperature, which possibly reflects a local adaptation of these populations during the expansion from a common ancestor.

Application of resistance gene analog markers to analyses of genetic structure and diversity in rice

Plant disease resistance gene analog (RGA) markers were designed according to the conserved sequence of known RGAs and used to map resistance genes. We used genome-wide RGA markers for genetic analyses of structure and diversity in a global rice germplasm collection. Of the 472 RGA markers, 138 were polymorphic and these were applied to 178 entries selected from the USDA rice core collection. Results from the RGA markers were similar between two methods, UPGMA and STRUCTURE. Additionally, the results from RGA markers in our study were agreeable with those previously reported from SSR markers, including cluster of ancestral classification, genetic diversity estimates, genetic relatedness, and cluster of geographic origins. These results suggest that RGA markers are applicable for analyses of genetic structure and diversity in rice. However, unlike SSR markers, the RGA markers failed to differentiate temperate japonica, tropical japonica, and aromatic subgroups. The restricted way for developing RGA markers from the cDNA sequence might limit the polymorphism of RGA markers in the genome, thus limiting the discriminatory power in comparison with SSR markers. Genetic differentiation obtained using RGA markers may be useful for defining genetic diversity of a suite of random R genes in plants, as many studies show a differentiation of resistance to a wide array of pathogens. They could also help to characterize the genetic structure and geographic distribution in crops, including rice, wheat, barley, and banana.

Influence of mutation rate on estimators of genetic differentiation--lessons from Arabidopsis thaliana

BACKGROUND

The analysis of molecular variation within and between populations is crucial to establish strategies for conservation as well as to detect the footprint of spatially heterogeneous selection. The traditional estimator of genetic differentiation (F(ST)) has been shown to be misleading if genetic diversity is high. Alternative estimators of F(ST) have been proposed, but their robustness to variation in mutation rate is not clearly established. We first investigated the effect of mutation and migration rate using computer simulations and examined their joint influence on Q(ST), a measure of genetic differentiation for quantitative traits. We further used experimental data in natural populations of Arabidopsis thaliana to characterize the effect of mutation rate on various estimates of population differentiation. Since natural species exhibit various degrees of self-fertilisation, we also investigated the effect of mating system on the different estimators.

RESULTS

If mutation rate is high and migration rate low, classical measures of genetic differentiation are misleading. Only Phi(ST), an estimator that takes the mutational distances between alleles into account, is independent of mutation rate, for all migration rates. However, the performance of Phi(ST) depends on the underlying mutation model and departures from this model cause its performance to degrade. We further show that Q(ST) has the same bias. We provide evidence that, in A. thaliana, microsatellite variation correlates with mutation rate. We thereby demonstrate that our results on estimators of genetic differentiation have important implications, even for species that are well established models in population genetics and molecular biology.

CONCLUSIONS

We find that alternative measures of differentiation like F'(ST) and D are not suitable for estimating effective migration rate and should not be used in studies of local adaptation. Genetic differentiation should instead be measured using an estimator that takes mutation rate into account, such as Phi(ST). Furthermore, in systems where migration between populations is low, such as A. thaliana, Q(ST) < F(ST) cannot be taken as evidence for homogenising selection as has been traditionally thought.

Relationship between heavy metals pollution and genetic diversity in Mediterranean populations of the sandhopper Talitrus saltator (Montagu) (Crustacea, Amphipoda)

Trace metals are one of the groups of pollutants that reduce genetic variability in natural populations, causing the phenomenon known as "genetic erosion". In this study we evaluate the relationship between trace metals contamination (Hg, Cd and Cu) and genetic variability, assessed using fluorescent Inter-Simple Sequence Repeats (fISSRs). We used eight populations of a well-established biomonitor of trace metals on sandy beaches: the amphipod Talitrus saltator. The trace metals analysis confirmed the ability of sandhoppers to accumulate Hg, Cd and Cu. Moreover, populations from sites with high Hg availability had the lowest values of genetic diversity. Our results validate the use of fISSR markers in genetic studies in sandhoppers and support the "genetic erosion" hypothesis by showing the negative influence of Hg contamination on sandhopper genetic diversity. Therefore, genetic variability assessed with fISSR markers could be successfully employed as a biomarker of Hg exposure.

Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana

As Arabidopsis thaliana is increasingly employed in evolutionary and ecological studies, it is essential to understand patterns of natural genetic variation and the forces that shape them. Previous work focusing mostly on global and regional scales has demonstrated the importance of historical events such as long-distance migration and colonization. Far less is known about the role of contemporary factors or environmental heterogeneity in generating diversity patterns at local scales. We sampled 1,005 individuals from 77 closely spaced stands in diverse settings around Tübingen, Germany. A set of 436 SNP markers was used to characterize genome-wide patterns of relatedness and recombination. Neighboring genotypes often shared mosaic blocks of alternating marker identity and divergence. We detected recent outcrossing as well as stretches of residual heterozygosity in largely homozygous recombinants. As has been observed for several other selfing species, there was considerable heterogeneity among sites in diversity and outcrossing, with rural stands exhibiting greater diversity and heterozygosity than urban stands. Fine-scale spatial structure was evident as well. Within stands, spatial structure correlated negatively with observed heterozygosity, suggesting that the high homozygosity of natural A. thaliana may be partially attributable to nearest-neighbor mating of related individuals. The large number of markers and extensive local sampling employed here afforded unusual power to characterize local genetic patterns. Contemporary processes such as ongoing outcrossing play an important role in determining distribution of genetic diversity at this scale. Local "outcrossing hotspots" appear to reshuffle genetic information at surprising rates, while other stands contribute comparatively little. Our findings have important implications for sampling and interpreting diversity among A. thaliana accessions.

The origin of populations of Arabidopsis thaliana in China, based on the chloroplast DNA sequences

BACKGROUND

In the studies incorporating worldwide sampling of A. thaliana populations, the samples from East Asia, especially from China, were very scattered; and the studies focused on global patterns of cpDNA genetic variation among accessions of A. thaliana are very few. In this study, chloroplast DNA sequence variability was used to infer phylogenetic relationships among Arabidopsis thaliana accessions from around the world, with the emphasis on samples from China.

RESULTS

A data set comprising 77 accessions of A. thaliana, including 19 field-collected Chinese accessions together with three related species (A. arenosa, A. suecica, and Olimarabidopsis cabulica) as the out-group, was compiled. The analysis of the nucleotide sequences showed that the 77 accessions of A. thaliana were partitioned into two major differentiated haplotype classes (MDHCs). The estimated divergence time of the two MDHCs was about 0.39 mya. Forty-nine haplotypes were detected among the 77 accessions, which exhibited nucleotide diversity (pi) of 0.00169. The Chinese populations along the Yangtze River were characterized by five haplotypes, and the two accessions collected from the middle range of the Altai Mountains in China shared six specific variable sites.

CONCLUSIONS

The dimorphism in the chloroplast DNA could be due to founder effects during late Pleistocene glaciations and interglacial periods, although introgression cannot be ruled out. The Chinese populations along the Yangtze River may have dispersed eastwards to their present-day locations from the Himalayas. These populations originated from a common ancestor, and a rapid demographic expansion began approximately 90,000 years ago. Two accessions collected from the middle range of the Altai Mountains in China may have survived in a local refugium during late Pleistocene glaciations. The natural populations from China with specific genetic characteristics enriched the gene pools of global A. thaliana collections.

Natural genetic variation of Arabidopsis thaliana is geographically structured in the Iberian peninsula

To understand the demographic history of Arabidopsis thaliana within its native geographical range, we have studied its genetic structure in the Iberian Peninsula region. We have analyzed the amount and spatial distribution of A. thaliana genetic variation by genotyping 268 individuals sampled in 100 natural populations from the Iberian Peninsula. Analyses of 175 individuals from 7 of these populations, with 20 chloroplast and nuclear microsatellite loci and 109 common single nucleotide polymorphisms, show significant population differentiation and isolation by distance. In addition, analyses of one genotype from 100 populations detected significant isolation by distance over the entire Iberian Peninsula, as well as among six Iberian subregions. Analyses of these 100 genotypes with different model-based clustering algorithms inferred four genetic clusters, which show a clear-cut geographical differentiation pattern. On the other hand, clustering analysis of a worldwide sample showed a west-east Eurasian longitudinal spatial gradient of the commonest Iberian genetic cluster. These results indicate that A. thaliana genetic variation displays significant regional structure and consistently support the hypothesis that Iberia has been a glacial refugium for A. thaliana. Furthermore, the Iberian geographical structure indicates a complex regional population dynamics, suggesting that this region contained multiple Pleistocene refugia with a different contribution to the postglacial colonization of Europe.