Data from: Correlations among genetic, epigenetic, and phenotypic variation of Phragmites australis along latitudes
Abstract
Aim: Estuarine vegetation routinely experiences natural tidal fluctuations and is highly vulnerable to extreme events such as heavy rainfall, leading to changes in plant population structure and adaptability. Genetic and epigenetic modifications are widely considered to be mechanisms of phenotypic variation, triggered in plants responding to extreme changing environments. However, understanding on correlations among genetic, epigenetic, and phenotypic variation of wild plant populations is still limited.
Location: China.
Methods: In this study, populations of the typical wetland clonal species Phragmites australis were selected from four estuaries along various latitudes in China. Genetic and epigenetic diversity, and phenotypic variation of these populations were analyzed.
Results: Phenotypic variation of P. australis populations was the highest at Yellow River Estuary and the lowest at Min River Estuary. Across all estuaries, Genetic and epigenetic diversity was strongly linear-correlated. Genetic diversity had significant correlations with variation in reproductive traits, while epigenetic diversity had significant correlations with variation in growth traits. Climatic factors of mean annual temperature and precipitation, as well as soil nitrogen and phosphorus, were negatively correlated with variation in genetic diversity, epigenetic diversity, and variation in reproductive traits of P. australis populations along latitudes. Variation in growth traits was negatively correlated with soil salinity, reflecting the limiting effect of salinity on plant growth.
Main Conclusion: Our findings found that genetic and epigenetic variation may play different roles in phenotypic variation of P. australis populations along latitudes, the variation becomes greater when the climatic and edaphic conditions deteriorate. The findings shed new light on the adaptation and evolution of wetland plant populations along a large latitudinal scale, and may contribute to the revegetation of estuary wetlands.
README: Description of the data and file structure
All raw data for the manuscript.
Descriptions
SSR data
- Sample: Individual ID of the 380 plants
- L: Liaohe Estuary
- YR: Yellow River Estuary
- Y: Yangtze Estuary
- M: Min River Estuary
- Pop: 38 population of the 380 plants
- 270-290: Different loci
- 0: No amplification product at this locus
- 1: Amplification product present at this locus
MSAP data
- Sample: Individual ID of the 380 plants
- L: Liaohe Estuary
- YR: Yellow River Estuary
- Y: Yangtze Estuary
- M: Min River Estuary
- Pop: 38 population of the 380 plants
- EX3Allele1——eX4Allele562: Different loci
- 0: No amplification product at this locus
- 1: Amplification product present at this locus
Phenotype raw data
- Plant: Individual ID of the 380 plants
- Base diameter, Functional leaf length, Plant height, Longest internode length, Leaf biomass, Stem biomass, Spike length, Average internode rhizome biomass, Spike biomass: Phenotype data we measured and calculated directly. The third to the fifth mature leaves from the top of plants were defined as functional leaves. Average internode rhizome biomass was fresh mass of spacers (rhizomes between two adjacent nodes) divided by nodes number
Z-score normalization transformation of GEN diversity data
ID: ID of the 38 populations with Estuary
- L: Liaohe Estuary
- YR: Yellow River Estuary
- Y: Yangtze Estuary
- M: Min River Estuary
Pop: 38 population
Z-trans-P-gen: Z-score normalization transformation of genetic percentage of polymorphic loci
Z-trans-I-gen: Z-score normalization transformation of genetic shannon's information index
Z-trans-He-gen: Z-score normalization transformation of genetic expected heterozygosity index
Z-score normalization transformation of EPI diversity data
ID: ID of the 38 populations with Estuary
- L: Liaohe Estuary
- YR: Yellow River Estuary
- Y: Yangtze Estuary
- M: Min River Estuary
Pop: 38 population
Z-trans-P-epi: Z-score normalization transformation of epigenetic percentage of polymorphic epiloci
Z-trans-I-epi: Z-score normalization transformation of epigenetic shannon's information index
Z-trans-He-epi: Z-score normalization transformation of epigenetic expected heterozygosity index
RDA indexes
Labels: ID of the 38 populations with Estuary
- L: Liaohe Estuary
- YR: Yellow River Estuary
- Y: Yangtze Estuary
- M: Min River Estuary
Genetic.diversity: Mean levels of genetic diversity, and it was evaluated by averaging the Z-score normalization transformation of genetic percentage of polymorphic loci, genetic shannon's information index, and genetic expected heterozygosity index in each population
Epigenetic.diversity: Mean levels of epigenetic diversity, and it was evaluated by averaging the Z-score normalization transformation of epigenetic percentage of polymorphic loci, epigenetic shannon's information index, and epigenetic expected heterozygosity index in each population
Growth.CV: Mean CVs (CV = 100 × standard deviation/mean) of growth traits, it was obtained by averaging the CVs of functional leaf length, plant height, longest internode length, stem basal diameter, leaf biomass, and stem biomass
Reproductive.CV: Mean CVs of reproductive traits, it was obtained by averaging the CVs of average internode rhizome biomass, spike length, and biomass
# Other environmental data used in RDA analysis were in the supplementary table (ddi13907-sup-0001-TablesS1-S6.docx)
Methods
Details of the methods are provided in the associated publication.