Comparative genetic and epigenetic diversity in pairs of sympatric, closely related plants with contrasting distribution ranges in south-eastern Iberian mountains

Abstract Genetic diversity defines the evolutionary potential of a species, yet mounting evidence suggests that epigenetic diversity could also contribute to adaptation. Elucidating the complex interplay between genetic and epigenetic variation in wild populations remains a challenge for evolutionary biologists, and the intriguing possibility that epigenetic diversity could compensate for the loss of genetic diversity is one aspect that remains basically unexplored in wild plants. This hypothesis is addressed in this paper by comparing the extent and patterns of genetic and epigenetic diversity of phylogenetically closely related but ecologically disparate species. Seven pairs of congeneric species from Cazorla mountains in south-eastern Spain were studied, each pair consisting of one endemic, restricted-range species associated to stressful environments, and one widespread species occupying more favourable habitats. The prediction was tested that endemic species should have lower genetic diversity due to population fragmentation, and higher epigenetic diversity induced by environmental stress, than their widespread congeners. Genetic (DNA sequence variants) and epigenetic (DNA cytosine methylation variants) diversities and their possible co-variation were assessed in three populations of each focal species using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MSAP). All species and populations exhibited moderate to high levels of genetic polymorphism irrespective of their ecological characteristics. Epigenetic diversity was greater than genetic diversity in all cases. Only in endemic species were the two variables positively related, but the difference between epigenetic and genetic diversity was greater at populations with low genetic polymorphism. Results revealed that the relationship between genetic and epigenetic diversity can be more complex than envisaged by the simple hypothesis addressed in this study, and highlight the need of additional research on the actual role of epigenetic variation as a source of phenotypic diversity before a realistic understanding of the evolutionary relevance of epigenetic phenomena in plant adaptation can be achieved.

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Genetic and Epigenetic Changes during the Upward Expansion of Deyeuxia angustifolia Kom. in the Alpine Tundra of the Changbai Mountains, China

Plants ◽

10.3390/plants10020291 ◽

2021 ◽

Vol 10 (2) ◽

pp. 291

Author(s):

Biao Ni ◽

Jian You ◽

Jiangnan Li ◽

Yingda Du ◽

Wei Zhao ◽

...

Keyword(s):

Genetic Diversity ◽

Dna Methylation ◽

Genetic Variation ◽

Soil Properties ◽

Changbai Mountains ◽

Epigenetic Variation ◽

Geographical Distance ◽

Mantel Tests ◽

Epigenetic Diversity ◽

Different Populations

Ecological adaptation plays an important role in the process of plant expansion, and genetics and epigenetics are important in the process of plant adaptation. In this study, genetic and epigenetic analyses and soil properties were performed on D. angustifolia of 17 populations, which were selected in the tundra zone on the western slope of the Changbai Mountains. Our results showed that the levels of genetic and epigenetic diversity of D. angustifolia were relatively low, and the main variation occurred among different populations (amplified fragment length polymorphism (AFLP): 95%, methylation sensitive amplification polymorphism (MSAP): 87%). In addition, DNA methylation levels varied from 23.36% to 35.70%. Principal component analysis (PCA) results showed that soil properties of different populations were heterogeneous. Correlation analyses showed that soil moisture, pH and total nitrogen were significantly correlated with genetic diversity of D. angustifolia, and soil temperature and pH were closely related to epigenetic diversity. Simple Mantel tests and partial Mantel tests showed that genetic variation significantly correlated with habitat or geographical distance. However, the correlation between epigenetic variation and habitat or geographical distance was not significant. Our results showed that, in the case of low genetic variation and genetic diversity, epigenetic variation and DNA methylation may provide a basis for the adaptation of D. angustifolia.

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Genetic polymorphism among natural populations of Anacardium humile A. ST-HIL

Revista Brasileira de Fruticultura ◽

10.1590/0100-29452020476 ◽

2020 ◽

Vol 42 (1) ◽

Cited By ~ 1

Author(s):

Silvia Correa Santos ◽

Raquel dos Santos Carvalho ◽

Livia Maria Chamma Davide

Keyword(s):

Genetic Diversity ◽

Genetic Polymorphism ◽

Genetic Variability ◽

Genetic Divergence ◽

Genomic Dna ◽

Reproductive Strategies ◽

Rapd Markers ◽

Phenotypic Diversity ◽

Diversity Index ◽

Natural Populations

Abstract The genus Anacardium presents nine species, of these, three have sub-bush size, common in the Cerrado of the Center-West of Brazil. The objective of this work was to evaluate the genetic variability of the species, collected in eleven provenances, using RAPD markers. Genomic DNA from 122 accessions was extracted and amplified with 25 decamer primers. The results indicated polymorphism, ranging from 77.71% to 96.18%. The distribution of genetic diversity among and within populations shows that 27.14% of the variability is found between populations and 37.44% within the populations, suggesting the existence of genetic variability that may be related to the reproductive strategies adopted by the species throughout its evolution. The index of variation within the provenances (93.36%) was higher than the index found among populations (6.64%). Molecular analysis indicated that there is genetic divergence between and within the studied populations of Anacardium humile A. St. - Hill. The origin of Itajá-GO presented the highest genetic diversity, presenting the highest values of genetic diversity index, phenotypic diversity and higher percentage of polymorphic loci.

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Levels and patterns of genetic diversity differ between two closely related endemicArabidopsisspecies

10.1101/048785 ◽

2016 ◽

Author(s):

Julie Jacquemin ◽

Nora Hohmann ◽

Matteo Buti ◽

Alberto Selvaggi ◽

Thomas Müller ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Endemic Species ◽

Isolation By Distance ◽

Demographic History ◽

Adaptive Potential ◽

Effective Population ◽

Distribution Ranges ◽

Small Effective Population Size

AbstractTheory predicts that a small effective population size leads to slower accumulation of mutations, increased levels of genetic drift and reduction in the efficiency of natural selection. Therefore endemic species should harbor low levels of genetic diversity and exhibit a reduced ability of adaptation to environmental changes.Arabidopsis pedemontanaandArabidopsis cebennensis, two endemic species from Italy and France respectively, provide an excellent model to study the adaptive potential of species with small distribution ranges. To evaluate the genome-wide levels and patterns of genetic variation, effective population size and demographic history of both species, we genotyped 53A. pedemontanaand 28A. cebennensisindividuals across the entire species ranges with Genotyping-by-Sequencing. SNPs data confirmed a low genetic diversity forA. pedemontanaalthough its effective population size is relatively high. Only a weak population structure was observed over the small distribution range ofA. pedemontana, resulting from an isolation-by-distance pattern of gene flow. In contrary,A. cebennensisindividuals clustered in three populations according to their geographic distribution. Despite this and a larger distribution, the overall genetic diversity was even lower forA. cebennensisthan forA. pedemontana.A demographic analysis demonstrated that both endemics have undergone a strong population size decline in the past, without recovery. The more drastic decline observed inA. cebennensispartially explains the very small effective population size observed in the present population. In light of these results, we discuss the adaptive potential of these endemic species in the context of rapid climate change.

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Genetic Diversity Among Saudi Peganum harmala and Rhazya stricta Populations Using Chemical and ISSR Markers

Current Pharmaceutical Biotechnology ◽

10.2174/1389201020666190619105249 ◽

2019 ◽

Vol 20 (13) ◽

pp. 1134-1146

Author(s):

Magda E. Abd-Elgawad ◽

Modhi O. Alotaibi

Keyword(s):

Genetic Diversity ◽

Folk Medicine ◽

Issr Markers ◽

Wild Plants ◽

Gas Chromatography Mass Spectrometry ◽

Group Method ◽

Peganum Harmala ◽

Molecular Polymorphism ◽

Arithmetic Average ◽

Rhazya Stricta

Background:The vernacular name 'Harmal' is used for two plant species in Saudi Arabia, i.e. Peganum harmala L. and Rhazya stricta Decne. Both are important medicinal plants which offer interesting pharmacological properties.Objective:This study aimed to evaluate the genetic diversity among different populations of harmal based on chemical variations of alkaloids and molecular polymorphism.Methods:Total alkaloids were extracted from plants of three populations of each species and estimated by using spectrophotometer and the chemical compounds were analyzed by Gas chromatography mass spectrometry (GC-MS). Molecular polymorphism was estimated by using the Inter Simple Sequence Repeat (ISSR) fingerprints.Results:The results showed that the alkaloids content of R. stricta was higher than P. harmala populations. The GC-MS analysis revealed the presence of (65-53) compounds in R. stricta and P. harmala, and the percentage of polymorphism was found to be 93.2%. Sixteen ISSR primers produced 170 scorable bands with an average of 9.6 bands per primer and 75%-100% polymorphism. The cluster analysis using the unweighted pair-group method of the arithmetic average (UPGMA) method based on combined data of GC-MS and ISSR markers divided the six harmal genotypes into two major groups.Conclusion:The existence of variations in chemical and genetic markers is useful for the selection of potential genotypes for medicinal use, and for breeding lines for medicinal substances production to spare wild plants from uncontrolled harvesting for folk medicine.

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Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.

BioTech ◽

10.3390/biotech10040023 ◽

2021 ◽

Vol 10 (4) ◽

pp. 23

Author(s):

Oxana Khapilina ◽

Ainur Turzhanova ◽

Alevtina Danilova ◽

Asem Tumenbayeva ◽

Vladislav Shevtsov ◽

...

Keyword(s):

Genetic Diversity ◽

Endemic Species ◽

Biological Diversity ◽

Natural Populations ◽

Subsequent Development ◽

Dna Profiling ◽

Primer Binding Site ◽

Anthropogenic Factors ◽

Habitat Specificity ◽

Interspersed Repeats

Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology.

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Phenotypic diversity of bread wheat lines with introgressions from the diploid cereal Aegilops speltoides for technological properties of grain and f lour

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj20.668 ◽

2020 ◽

Vol 24 (7) ◽

pp. 738-746

Author(s):

L. V. Shchukina ◽

I. F. Lapochkina ◽

T. A. Pshenichnikova

Keyword(s):

Genetic Diversity ◽

Bread Wheat ◽

Phenotypic Diversity ◽

Chromosomal Rearrangements ◽

Diploid Species ◽

Aegilops Speltoides ◽

Technological Properties ◽

Gluten Content ◽

Spring Variety ◽

Growing Conditions

The creation of varieties adapted to changing environmental conditions, resistant to various pathogens, and satisfying various grain purposes is impossible without using the genetic diversity of wheat. One of the ways to expand the genetic diversity of wheat is to introduce new variants of genes from the genetic pool of congeners and wild relatives into the genotypes of existing varieties. In this study, we used 10 lines from the Arsenal collection created on the genetic basis of the spring variety ‘Rodina’ and the diploid species Aegilops speltoides in the Federal Research Center “Nemchinovka” in 1994. The lines were previously characterized for the presence of translocations and chromosomal rearrangements cytologically and using molecular markers. Technological analyses were performed on grain obtained in Western Siberia and Moscow region. The aim of this study was to establish the possibilities of expanding the phenotypic diversity for technological properties of grain and flour as a result of such hybridization of bread wheat and the diploid cereal Aegilops speltoides. The variety ‘Rodina’ forms a vitreous grain with a high gluten content in Siberia, but has low physical properties of flour and dough. Five derived lines were found to have significantly higher protein and gluten content in grain. The highest values under both growing conditions were found in lines 73/00i, 82/00i, and 84/00i. Two lines (69/00i and 76/00i) showed a high flour strength and dough elasticity, characterizing the lines as strong and valuable in quality. These lines can be used for baking bread. Line 82/00i inherited from Ae. speltoides a soft-grain endosperm, which indicates the introgression of the Ha-Sp gene, homoeoallelic to the Ha gene of bread wheat, into ‘Rodina’. Flour of this line is suitable for the manufacture of confectionery without the use of technological additives. The lines generally retained their characteristics in different growing conditions. They can be attracted as donors of new alleles of genes that determine the technological properties of grain and resistance to biotic stresses.

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Effects of genomic and functional diversity on stand-level productivity and performance of non-native Arabidopsis

10.1101/2020.04.20.049593 ◽

2020 ◽

Author(s):

Kathryn G. Turner ◽

Claire M. Lorts ◽

Asnake T. Haile ◽

Jesse R. Lasky

Keyword(s):

Genetic Diversity ◽

Flowering Time ◽

Phenotypic Diversity ◽

A Priori ◽

Interference Competition ◽

Genomic Data ◽

Total Biomass ◽

High Resource ◽

And Performance ◽

Resource Conditions

AbstractBiodiversity can affect the properties of groups of organisms, such as ecosystem function and the persistence of colonizing populations. Genomic data offer a newly available window to diversity, complementary to other measures like taxonomic or phenotypic diversity. We tested whether native genetic diversity in field experimental stands of Arabidopsis thaliana affected their aboveground biomass and fecundity in their colonized range. We constructed some stands of genotypes that we a priori predicted would differ in performance or show overyielding. We found no relationship between genetic diversity and stand total biomass. However, increasing stand genetic diversity increased fecundity in high resource conditions. Polyculture (multiple genotype) stands consistently yielded less biomass than expected based on the yields of component genotypes in monoculture. This under-yielding was strongest in stands with late-flowering and high biomass genotypes, potentially due to interference competition by these genotypes. Using a new implementation of association mapping, we identified genetic loci whose diversity was associated with stand-level yield, revealing a major flowering time locus associated with under-yielding of polycultures. Our field experiment supports community ecology studies that find a range of diversity-function relationships. Nevertheless, our results suggest diversity in colonizing propagule pools can enhance population fitness. Furthermore, interference competition among genotypes differing in flowering time might limit the advantages of polyculture.

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Comparative Population Genetics of Two Korean Aedes Mosquito Species with Vector Potential based on Mitochondrial DNA

10.21203/rs.3.rs-261518/v1 ◽

2021 ◽

Author(s):

Jiyeong Shin ◽

Jongwoo Jung

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Vector Control ◽

Endemic Species ◽

Korean Peninsula ◽

Mismatch Distribution ◽

Mosquito Species ◽

Mitochondrial Genes ◽

Rapid Expansion ◽

Number Of Individuals

Abstract Background: Mosquitoes of the genus Aedes are important invasive species contributing to the spread of chikungunya, dengue fever, yellow fever, Zika virus, and other dangerous vector-borne diseases. Aedes albopictus is native to southeast Asia with rapid expansion due to human activity, showing a wide distribution in the Korean peninsula. Aedes flavopictus is considered to be native to East Asia with a broad distribution in the region, including in the Korean peninsula. Gaining a better understanding of the genetic diversity of these species is critical for establishing strategies for disease prevention and vector control. Methods: We obtained DNA from 148 specimens of Ae. albopictus and 166 specimens of Ae. flavopictus in Korea, and amplified two mitochondrial genes (COI and ND5) to compare the genetic diversity and structure of the two species.Results: We obtained a 658-bp sequence of COI and a 423-bp sequence of ND5 from the two mosquito species. We found low diversity and an insignificant population genetic structure in Ae. albopictus, and high diversity and an insignificant structure in Ae. flavopictus for these two mitochondrial genes. Ae. albopictus had less haplotypes with respect to the number of individuals, and a slight mismatch distribution was confirmed. By contrast, Ae. flavopictus had a large number of haplotypes compared with the number of individuals, and a large unimodal-type mismatch distribution was confirmed. Although the genetic structure of both species was insignificant, Ae. flavopictus exhibited higher genetic diversity than Ae. albopictus.Conclusions: Ae. albopictus appears to be an introduced species, whereas Ae. flavopictus is an endemic species to the Korean peninsula, and the difference in genetic diversity between the two species is related to their adaptability and introduction history. As an endemic species, Ae. flavopictus is likely to have a larger population size than expected. Further studies on the genetic structure and diversity of these two mosquito species will provide useful data for vector control.

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RAPD-ANALYSIS OF CYCLAMEN SPP. GENOME POLYMORPHISM

CBU International Conference Proceedings ◽

10.12955/cbup.v7.1483 ◽

2019 ◽

Vol 7 ◽

pp. 949-953

Author(s):

Elza Makaradze ◽

Galina Meparishvili ◽

Natela Varshanidze ◽

Inga Diasamidze ◽

Ketevan Dolidze ◽

...

Keyword(s):

Genetic Polymorphism ◽

Species Diversity ◽

Rapd Markers ◽

Biological Diversity ◽

Molecular Genetic ◽

Wild Plants ◽

Large Species ◽

Genetic Studies ◽

Rapd Pcr ◽

Rare Endemic

Wild plants form the basis of biological resources both for Georgia and the whole world. A strategic task of any country is to preserve the biological diversity of plants. In the territory of Ajara, a large species diversity of plants grows, among which there are rare, endemic and relict plants. In particular, Cyclamen adzharicum. Modern systematics of wild plants in Georgia is based on classical methods of botany. In this regard, it is relevant to conduct genetic studies of species diversity and genetic polymorphism of species and populations using molecular genetic markers, in particular RAPD-PCR methods. The purpose of this study was to identify genetic polymorphism in Cyclamen L species using RAPD methods. As a result of the conducted research the 65 RAPD-markers in length from 150 to 1500 BP have been revealed. The number of the amplified fragments DNA varied depending on the primer from 6 (OPA-2) to 11 (OPB-4). The results of grouping Cyclamen adzharicum and C. coum samples allowed two clusters to be identified. In the first cluster were samples of three populations Cyclamen adzharicum and showed a low stubble in the intra-species variability. Cyclamen coum was attributed to the second cluster. The used primers gave the opportunity to identify polymorphism between the tested types of cyclamen.

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