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Chen B, Wang M, Guo Y, Zhang Z, Zhou W, Cao L, Zhang T, Ali S, Xie L, Li Y, Zinta G, Sun S, Zhang Q. Climate-related naturally occurring epimutation and their roles in plant adaptation in A. thaliana. Mol Ecol 2024:e17356. [PMID: 38634782 DOI: 10.1111/mec.17356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/27/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
DNA methylation has been proposed to be an important mechanism that allows plants to respond to their environments sometimes entirely uncoupled from genetic variation. To understand the genetic basis, biological functions and climatic relationships of DNA methylation at a population scale in Arabidopsis thaliana, we performed a genome-wide association analysis with high-quality single nucleotide polymorphisms (SNPs), and found that ~56% on average, especially in the CHH sequence context (71%), of the differentially methylated regions (DMRs) are not tagged by SNPs. Among them, a total of 3235 DMRs are significantly associated with gene expressions and potentially heritable. 655 of the 3235 DMRs are associated with climatic variables, and we experimentally verified one of them, HEI10 (HUMAN ENHANCER OF CELL INVASION NO.10). Such epigenetic loci could be subjected to natural selection thereby affecting plant adaptation, and would be expected to be an indicator of accessions at risk. We therefore incorporated these climate-related DMRs into a gradient forest model, and found that the natural A. thaliana accessions in Southern Europe that may be most at risk under future climate change. Our findings highlight the importance of integrating DNA methylation that is independent of genetic variations, and climatic data to predict plants' vulnerability to future climate change.
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Affiliation(s)
- Bowei Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- College of Biology Resources and Environmental Sciences, Jishou University, Jishou, China
| | - Min Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yile Guo
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zihui Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Wei Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Lesheng Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Shahid Ali
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Linan Xie
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Yuhua Li
- College of Life Science, Northeast Forestry University, Harbin, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, China
| | - Gaurav Zinta
- Integrative Plant AdaptOmics Lab (iPAL), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur (CSIR-IHBT), Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shanwen Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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Population structure and adaptive variation of Helichrysum italicum (Roth) G. Don along eastern Adriatic temperature and precipitation gradient. Sci Rep 2021; 11:24333. [PMID: 34934087 PMCID: PMC8692458 DOI: 10.1038/s41598-021-03548-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023] Open
Abstract
Immortelle (Helichrysum italicum (Roth) G. Don; Asteraceae) is a perennial plant species native to the Mediterranean region, known for many properties with wide application mainly in perfume and cosmetic industry. A total of 18 wild H. italicum populations systematically sampled along the eastern Adriatic environmental gradient were studied using AFLP markers to determine genetic diversity and structure and to identify loci potentially responsible for adaptive divergence. Results showed higher levels of intrapopulation diversity than interpopulation diversity. Genetic differentiation among populations was significant but low, indicating extensive gene flow between populations. Bayesian analysis of population structure revealed the existence of two genetic clusters. Combining the results of FST - outlier analysis (Mcheza and BayeScan) and genome-environment association analysis (Samβada, LFMM) four AFLP loci strongly associated with the bioclimatic variables Bio03 Isothermality, Bio08 Mean temperature of the wettest quarter, Bio15 Precipitation seasonality, and Bio17 Precipitation of driest quarter were found to be the main variables driving potential adaptive genetic variation in H. italicum along the eastern Adriatic environmental gradient. Redundancy analysis revealed that the partitioning of genetic variation was mainly associated with the adaptation to temperature oscillations. The results of the research may contribute to a clearer understanding of the importance of local adaptations for the genetic differentiation of Mediterranean plants and allow the planning of appropriate conservation strategies. However, considering that the identified outlier loci may be linked to genes under selection rather than being the target of natural selection, future studies must aim at their additional analysis.
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Karunarathne P, Hojsgaard D. Single Independent Autopolyploidization Events From Distinct Diploid Gene Pools and Residual Sexuality Support Range Expansion of Locally Adapted Tetraploid Genotypes in a South American Grass. Front Genet 2021; 12:736088. [PMID: 34671384 PMCID: PMC8520906 DOI: 10.3389/fgene.2021.736088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 09/07/2021] [Indexed: 12/02/2022] Open
Abstract
Polyploidy plays a major role in plant evolution. The establishment of new polyploids is often a consequence of a single or few successful polyploidization events occurring within a species’ evolutionary trajectory. New polyploid lineages can play different roles in plant diversification and go through several evolutionary stages influenced by biotic and abiotic constraints and characterized by extensive genetic changes. The study of such changes has been crucial for understanding polyploid evolution. Here, we use the multiploid-species Paspalum intermedium to study population-level genetic and morphological variation and ecological differentiation in polyploids. Using flow cytometry, amplified fragment length polymorphism (AFLP) genetic markers, environmental variables, and morphological data, we assessed variations in ploidy, reproductive modes, and the genetic composition in 35 natural populations of P. intermedium along a latitudinal gradient in South America. Our analyses show that apomictic auto-tetraploids are of multiple independent origin. While overall genetic variation was higher in diploids, both diploids and tetraploids showed significant variation within and among populations. The spatial distribution of genetic variation provides evidence for a primary origin of the contact zone between diploids and tetraploids and further supports the hypothesis of geographic displacement between cytotypes. In addition, a strong link between the ecological differentiation of cytotypes and spatial distribution of genetic variation was observed. Overall, the results indicate that polyploidization in P. intermedium is a recurrent phenomenon associated to a shift in reproductive mode and that multiple polyploid lineages from genetically divergent diploids contributed to the successful establishment of local polyploid populations and dispersal into new environments.
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Affiliation(s)
- Piyal Karunarathne
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany.,Georg-August University School of Science, University of Goettingen, Goettingen, Germany.,Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
| | - Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany.,Taxonomy & Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Qiu T, Liu Z, Yang Y, Liu B. Epigenetic variation associated with responses to different habitats in the context of genetic divergence in Phragmites australis. Ecol Evol 2021; 11:11874-11889. [PMID: 34522347 PMCID: PMC8427615 DOI: 10.1002/ece3.7954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/03/2021] [Accepted: 07/06/2021] [Indexed: 01/13/2023] Open
Abstract
The mechanisms underlying heritable phenotypic divergence associated with adaptation in response to environmental stresses may involve both genetic and epigenetic variations. Several prior studies have revealed even higher levels of epigenetic variation than genetic variation. However, few population-level studies have explored the effects of epigenetic variation on species with high levels of genetic diversity distributed across different habitats. Using AFLP and methylation-sensitive AFLP markers, we tested the hypothesis that epigenetic variation may contribute to differences in plants occupying different habitats when genetic variation alone cannot fully explain adaptation. As a cosmopolitan invasive species, Phragmites australis (common reed) together with high genetic diversity and remarkable adaptability has been suggested as a model for responses to global change and indicators of environmental fluctuations. We found high levels of genetic and epigenetic diversity and significant genetic/epigenetic structure within each of 12 studied populations sampled from four natural habitats of P. australis. Possible adaptive epigenetic variation was suggested by significant correlations between DNA methylation-based epigenetic differentiation and adaptive genetic divergence in populations across the habitats. Meanwhile, various AMOVAs indicated that some epigenetic differences may respond to various local habitats. A partial Mantel test was used to tease out the correlations between genetic/epigenetic variation and habitat after controlling for the correlation between genetic and epigenetic variations. We found that epigenetic diversity was affected mostly by soil nutrient availability, suggesting that at least some epigenetic differentiation occurred independently of genetic variation. We also found stronger correlations between epigenetic variation and phenotypic traits than between genetic variation and such traits. Overall, our findings indicate that genetically based differentiation correlates with heterogeneous habitats, while epigenetic variation plays an important role in ecological differentiation in natural populations of P. australis. In addition, our results suggest that when assessing global change responses of plant species, intraspecific variation needs to be considered.
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Affiliation(s)
- Tian Qiu
- School of Life SciencesChangchun Normal UniversityChangchunChina
- Institute of Grassland ScienceKey Laboratory of Vegetation EcologyMinistry of EducationNortheast Normal UniversityChangchunChina
- Key Laboratory of Molecular EpigeneticsMinistry of EducationNortheast Normal UniversityChangchunChina
| | - Zhiyuan Liu
- College of Computer Science and TechnologyChangchun UniversityChangchunChina
| | - Yunfei Yang
- Institute of Grassland ScienceKey Laboratory of Vegetation EcologyMinistry of EducationNortheast Normal UniversityChangchunChina
| | - Bao Liu
- Key Laboratory of Molecular EpigeneticsMinistry of EducationNortheast Normal UniversityChangchunChina
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5
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Bublyk O, Parnikoza I, Kunakh V. Assessing the Levels of Polymorphism and Differentiation in Iris pumila L. Populations Using Three Types of PCR Markers. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sheeja TE, Kumar IPV, Giridhari A, Minoo D, Rajesh MK, Babu KN. Amplified Fragment Length Polymorphism: Applications and Recent Developments. Methods Mol Biol 2021; 2222:187-218. [PMID: 33301096 DOI: 10.1007/978-1-0716-0997-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AFLP or amplified fragment length polymorphism is a PCR-based molecular technique that uses selective amplification of a subset of digested DNA fragments from any source to generate and compare unique fingerprints of genomes. It is more efficient in terms of time, economy, reproducibility, informativeness, resolution, and sensitivity, compared to other popular DNA markers. Besides, it requires very small quantities of DNA and no prior genome information. This technique is widely used in plants for taxonomy, genetic diversity, phylogenetic analysis, construction of high-resolution genetic maps, and positional cloning of genes, to determine relatedness among cultivars and varietal identity, etc. The review encompasses in detail the various applications of AFLP in plants and the major advantages and disadvantages. The review also considers various modifications of this technique and novel developments in detection of polymorphism. A wet-lab protocol is also provided.
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Affiliation(s)
- Thotten Elampilay Sheeja
- Indian Institute of Spices Research, Kozhikode, Kerala, India.
- Division of Crop Improvement and Biotechnology, ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, India.
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Grdiša M, Radosavljević I, Liber Z, Stefkov G, Ralli P, Chatzopoulou PS, Carović-Stanko K, Šatović Z. Divergent selection and genetic structure of Sideritis scardica populations from southern Balkan Peninsula as revealed by AFLP fingerprinting. Sci Rep 2019; 9:12767. [PMID: 31484938 PMCID: PMC6726656 DOI: 10.1038/s41598-019-49097-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/19/2019] [Indexed: 01/04/2023] Open
Abstract
Sideritis scardica Giseb. is a subalpine/alpine plant species endemic to the central part of the Balkan Peninsula. In this study, we combined Amplified Fragment Length Polymorphism (AFLP) and environmental data to examine the adaptive genetic variations in S. scardica natural populations sampled in contrasting environments. A total of 226 AFLP loci were genotyped in 166 individuals from nine populations. The results demonstrated low gene diversity, ranging from 0.095 to 0.133 and significant genetic differentiation ranging from 0.115 to 0.408. Seven genetic clusters were revealed by Bayesian clustering methods as well as by Discriminant Analysis of Principal Components and each population formed its respective cluster. The exception were populations P02 Mt. Shara and P07 Mt. Vermio, that were admixed between two clusters. Both landscape genetic methods Mcheza and BayeScan identified a total of seven (3.10%) markers exhibiting higher levels of genetic differentiation among populations. The spatial analysis method Samβada detected 50 individual markers (22.12%) associated with bioclimatic variables, among them seven were identified by both Mcheza and BayeScan as being under directional selection. Four bioclimatic variables associated with five out of seven outliers were related to precipitation, suggesting that this variable is the key factor affecting the adaptive variation of S. scardica.
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Affiliation(s)
- Martina Grdiša
- University of Zagreb, Faculty of Agriculture, Department of Seed Science and Technology Svetošimunska 25, 10000, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska 25, 10000, Zagreb, Croatia
| | - Ivan Radosavljević
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska 25, 10000, Zagreb, Croatia.
- University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Marulićev trg 9A, 10000, Zagreb, Croatia.
| | - Zlatko Liber
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska 25, 10000, Zagreb, Croatia
- University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Marulićev trg 9A, 10000, Zagreb, Croatia
| | - Gjoshe Stefkov
- University Ss. Cyril and Methodius Skopje, Faculty of Pharmacy, Vodnjanska 17, 1000, Skopje, Republic of North Macedonia
| | - Parthenopi Ralli
- Hellenic Agricultural Organization DEMETER, Institute of Breeding and Plant Genetic Resources, Thermi - Thessalonikis, PO Box 60411, 57001, Thessaloniki, Greece
| | - Paschalina S Chatzopoulou
- Hellenic Agricultural Organization DEMETER, Institute of Breeding and Plant Genetic Resources, Thermi - Thessalonikis, PO Box 60411, 57001, Thessaloniki, Greece
| | - Klaudija Carović-Stanko
- University of Zagreb, Faculty of Agriculture, Department of Seed Science and Technology Svetošimunska 25, 10000, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska 25, 10000, Zagreb, Croatia
| | - Zlatko Šatović
- University of Zagreb, Faculty of Agriculture, Department of Seed Science and Technology Svetošimunska 25, 10000, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska 25, 10000, Zagreb, Croatia
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RAD-Seq Data Point to a Distinct Split in Liriodendron (Magnoliaceae) and Obvious East–West Genetic Divergence in L. chinense. FORESTS 2018. [DOI: 10.3390/f10010013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Liriodendron is a Tertiary period relic tree genus with a typical East Asian and North American disjunction distribution pattern. As an angiosperm base group of trees, Liriodendron provides a valuable resource for the study of evolution processes. Here, we reconstruct the phylogeny and population genetic structure of Liriodendron based on the restriction site-associated DNA sequencing (RAD-Seq) of a wide collection of individuals from 16 populations. Our results reveal a clear phylogenetic break between L. chinense and L. tulipifera and obvious genetic divergence between the eastern and western populations of L. chinense, which are consistent with the patterns of geographical distributions. The phylogeographic history and long-term geographical isolation of the genus may be responsible for this pattern. Furthermore, a closer relationship was found between L. tulipifera and the eastern populations of L. chinense, indicating the ancient phylogeny of L. chinense in this area. The results of this study will aid in the development of scientific strategies for the conservation and utilization of the Liriodendron germplasm.
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Li YS, Chang CT, Wang CN, Thomas P, Chung JD, Hwang SY. The Contribution of Neutral and Environmentally Dependent Processes in Driving Population and Lineage Divergence in Taiwania ( Taiwania cryptomerioides). FRONTIERS IN PLANT SCIENCE 2018; 9:1148. [PMID: 30135693 PMCID: PMC6092574 DOI: 10.3389/fpls.2018.01148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
The question of what determines divergence both between and within species has been the central topic in evolutionary biology. Neutral drift and environmentally dependent divergence are predicted to play roles in driving population and lineage divergence. However, neutral drift may preclude adaptation if the rate of gene flow between populations is high. Here, we sampled populations of three Taiwania (Taiwania cryptomerioides) lineages occurring in Taiwan, the mainland of China (Yunnan-Myanmar border), and northern Vietnam, and tested the relative strength of neutral drift and divergent selection in shaping divergence of those populations and lineages. We quantified genetic and epigenetic variation, respectively, using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP). Analysis of 1413 AFLP and 462 MSAP loci using frequency-based genome scan methods and generalized linear models (GLMs) found no potential selective outliers when only Taiwanese populations were examined, suggesting that neutral drift was the predominant evolutionary process driving differentiation between those populations. However, environmentally associated divergence was found when lineages were compared. Thirty-two potential selective outliers were identified based on genome scans and their associations with environmental variables were tested with GLMs, generalized linear mixed effect models (GLMMs), and model selection with a model averaging approach. Ten loci (six AFLP and four MSAP) were found to be strongly associated with environmental variables, particularly monthly temperature variation and normalized difference vegetation index (NDVI) using model selection and a model averaging approach. Because only a small portion of genetic and epigenetic loci were found to be potential selective outliers, neutral evolutionary process might also have played crucial roles in driving lineage divergence, particularly between geographically and genetically isolated island and mainland Asia lineages. Nevertheless, the vast amount of neutral drift causing genetic and epigenetic variations might have the potential for adaptation to future climate changes. These could be important for the survival of Taiwania in different geographic areas.
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Affiliation(s)
- Yi-Shao Li
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chung-Te Chang
- Department of Geography, National Taiwan University, Taipei, Taiwan
| | - Chun-Neng Wang
- Institute of Ecology and Evolution, National Taiwan University, Taipei, Taiwan
| | - Philip Thomas
- International Conifer Conservation Programme of the Royal Botanic Garden, Edinburgh, United Kingdom
| | - Jeng-Der Chung
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Shih-Ying Hwang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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Qiu T, Jiang L, Li S, Yang Y. Small-Scale Habitat-Specific Variation and Adaptive Divergence of Photosynthetic Pigments in Different Alkali Soils in Reed Identified by Common Garden and Genetic Tests. FRONTIERS IN PLANT SCIENCE 2016; 7:2016. [PMID: 28111586 PMCID: PMC5216671 DOI: 10.3389/fpls.2016.02016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/19/2016] [Indexed: 05/14/2023]
Abstract
Flexibility of photosynthetic pigment traits is an important adaptive mechanism through which plants can increase mean fitness in a variable environment. Unlike morphological traits in plants, photosythesis has been shown to exhibit phenotypic plasticity, responding rapidly to environmental conditions. Meanwhile, local adaptation at small scales is considered to be rare. Thus, detecting the small-scale adaptive divergence of photosynthetic pigments presents a challenge. Leaf concentrations of photosynthetic pigments under stressful conditions may be reduced or maintained. Concentrations of some pigments and/or ratio of Chlorophyll a (Chla) to Chlorophyll b (Chlb) do not change markedly in some species, such as the common reed, Phragmites australis, a cosmopolitan grass and common invader. Little is known about photosynthetic responses of this plant to varying levels of alkali salt. Few studies have attempted to account for the relationship between pigment accumulation and leaf position in wild plant populations in grasslands. In this study, photosynthetic pigment concentrations and the total Chl(a+b)/Car ratio decreased as the growing season progressed and were shown to be significantly lower in the habitat with a higher soil pH value and less moisture when compared between habitats. The Chla/Chlb ratio did not differ significantly between habitats, although it increased significantly over time. Leaves in the middle position may be functionally important in the response to soil conditions because only pigment concentrations and the Chl(a+b)/Car ratio of those leaves varied between habitats significantly. The outlier loci, used to evaluate molecular signatures of selection, were detected by Arlequin, Bayescan, and Bayenv analyses. In the simulated habitats of common garden, the local genotypes had higher values of Chla, Chlb, Chl(a+b), Car in their home habitat than did genotypes originating from the other habitat. QST-FST comparisons provided evidence of divergent selection. It appears likely that soil moisture, pH and electric conductivity drove local adaptation. Combined approaches that utilize information on phenotypes from field and common garden experiments, genome-wide markers, and environmental data will be the most informative for understanding the adaptive nature of the intraspecific divergence.
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Affiliation(s)
- Tian Qiu
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal UniversityChangchun, China
- School of Life Sciences, Changchun Normal UniversityChangchun, China
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Northeast Normal UniversityChangchun, China
| | - LiLi Jiang
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Northeast Normal UniversityChangchun, China
| | - ShanZhi Li
- School of Life Sciences, Changchun Normal UniversityChangchun, China
| | - YunFei Yang
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal UniversityChangchun, China
- *Correspondence: YunFei Yang
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