scholarly journals Extending the Genotype in Brachypodium by Including DNA Methylation Reveals a Joint Contribution with Genetics on Adaptive Traits

2020 ◽  
Vol 10 (5) ◽  
pp. 1629-1637 ◽  
Author(s):  
Steven R. Eichten ◽  
Akanksha Srivastava ◽  
Adam J. Reddiex ◽  
Diep R. Ganguly ◽  
Alison Heussler ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Methylation ◽  
Phenotypic Variation ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Epigenetic Inheritance ◽  
Genetic Differences ◽  
Linear Modeling ◽  
Climate Conditions ◽  
Joint Contribution

Epigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, with reduced genetic diversity there was diminished variation in DNA methylation within families. Mixed-effects linear modeling revealed large genetic differences between families and a minor contribution of DNA methylation variation on phenotypic variation in select traits. Taken together, this analysis suggests a limited but significant contribution of DNA methylation toward heritable phenotypic variation relative to genetic differences.

scholarly journals Extending the genotype in Brachypodium by including DNA methylation reveals a joint contribution with genetics on adaptive traits

2019 ◽  
Author(s):  
SR Eichten ◽  
A Srivastava ◽  
A Reddiex ◽  
DR Ganguly ◽  
A Heussler ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Methylation ◽  
Phenotypic Variation ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Epigenetic Inheritance ◽  
Genetic Differences ◽  
Climate Conditions ◽  
Joint Contribution ◽  
A Minor

AbstractEpigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, with reduced genetic diversity there was diminished variation in DNA methylation within families. Mixed-effects linear modelling revealed large genetic differences between families and a minor contribution of epigenomic variation on phenotypic variation in select traits. Taken together, this analysis suggests a limited but significant contribution of DNA methylation towards heritable phenotypic variation relative to genetic differences.

Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

1996 ◽  
Vol 26 (8) ◽  
pp. 1454-1462 ◽  
Author(s):  
Naoki Tani ◽  
Nobuhiro Tomaru ◽  
Masayuki Araki ◽  
Kihachiro Ohba
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Phylogenetic Trees ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Group Method ◽  
Stone Pine ◽  
Arithmetic Means ◽  
Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

Morphological and isozyme variation in Cerastium arvense (Caryophyllaceae) in the southern Andes

2002 ◽  
Vol 80 (7) ◽  
pp. 786-795 ◽  
Author(s):  
María Paula Quiroga ◽  
Andrea C Premoli ◽  
Cecilia Ezcurra
Keyword(s):  
Genetic Diversity ◽  
Natural Populations ◽  
Common Garden ◽  
High Elevation ◽  
Genetic Differences ◽  
Restricted Gene Flow ◽  
Common Garden Experiment ◽  
Southern Andes ◽  
Isozyme Electrophoresis ◽  
Ecotypic Variation

We tested the hypothesis that South Andean populations of the highly polymorphic and mostly Northern Hemisphere perennial forb Cerastium arvense L. show ecotypic variation along distinct habitats. We compared differences in morphology and flowering phenology among six natural populations occurring in different environments. Genetic differences were analyzed by a common-garden experiment and isozyme electrophoresis. Several of the morphological differences observed in the field were maintained after more than a year of cultivation in the common garden (e.g., plant height and leaf width). Mean tests and multivariate analyses on morphological traits generally distinguished high-elevation populations from the rest, and a similar grouping of populations was obtained from isozyme data at 10 loci. Cerastium arvense had genetic polymorphism levels of >50% in all populations and an average genetic diversity (HT = 0.254) of which approximately 20% was distributed among populations. These marked genetic differences are probably maintained by restricted gene flow due to variation in flowering time. Morphological and genetic differences suggest ecotypic variation in C. arvense in the southern Andes, which seems to have originated by disruptive selective pressures in different environments and the effect of genetic drift in response to the extreme climatic changes occurring during the Pleistocene.Key words: common-garden experiment, ecotypic variation, elevation and precipitation, genetic diversity, Patagonian Andes, phenology.

Genetic structure and proposed conservation strategy for natural populations of Calycanthus chinensis Cheng et S.Y. Chang (Calycanthaceae)

2008 ◽  
Vol 88 (1) ◽  
pp. 179-186 ◽  
Author(s):  
Chu-Chuan Fan ◽  
Nicola Pecchioni ◽  
Long-Qing Chen
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Population Level ◽  
Conservation Strategy ◽  
Information Index

Calycanthus chinensis Cheng et S.Y. Chang, a tertiary relic species in China, is a shade-loving and deciduous bush withan elegant shape and beautiful flower of high ornamental value. It was widely planted in gardens and miniature scapes in China.The objective of this study was to characterize the genetic variation and structure in the three extant populations of the species, in order to provide useful information for a future conservation strategy. Twenty-two of 120 RAPD primers were selected and a total of 257 stable and clear DNA fragments were scored. Calycanthus chinensis showed a lower level of genetic diversity. At the population level, the percentage of polymorphic loci, Nei's gene diversity and Shannon’s information index were 40.9%, 0.1641 and 0.2386, respectively; while at the species level, the corresponding values were 59.1%, 0.2097 and 0.3123, respectively. The estimates of genetic differentiation based on Shannon’s information index (0.2360), Nei’s gene diversity (0.2175) and AMOVA (24.94%) were very similar, and significantly higher than the average genetic differentiation reported in outcrossed spermatophyte. So it suggested high genetic differentiation emerged among populations of C. chinensis. Genetic relationships among populations were assessed by Nei’s standard genetic distance, which suggested that the Tiantai population was genetically distinct from the other two populations. Moreover, the genetic distance was significantly correlated with geographical distance among populations (r = 0.997, t > t0.05). The gene flow (Nm) was 0.8994, indicating that gene exchange among populations was restricted. A conservation strategy was proposed based on the low gene flow and habitat deterioration, which are contributing to the endangered status of this species. Key words: Genetic diversity, endangered plant, population genetics, RAPD

scholarly journals Genetic Diversity and Population Structure of Chinese Corylus heterophylla and Corylus kweichowensis Using Simple Sequence Repeat Markers

2020 ◽  
Vol 145 (5) ◽  
pp. 289-298
Author(s):  
Tiantian Zhao ◽  
Wenxu Ma ◽  
Qinghua Ma ◽  
Zhen Yang ◽  
Lisong Liang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Relationships ◽  
In Situ Conservation ◽  
Geographic Distance ◽  
Natural Populations ◽  
Distinct Species ◽  
Mantel Test ◽  
Conservation Of Genetic Resources ◽  
Genetic Clusters

Corylus heterophylla and Corylus kweichowensis are economically and ecologically important nut-producing woody shrubs that are distributed across northern and southern regions of China. However, few studies have examined the genetic diversity and genetic relationships between C. heterophylla and C. kweichowensis, and their taxonomic relationships have been questioned. In this study, 796 individuals collected from 34 natural populations (21 C. heterophylla and 13 C. kweichowensis populations) were investigated to assess the genetic diversity and population structure using 11 microsatellite loci. Analysis of molecular variance revealed that genetic differentiation of C. heterophylla and C. kweichowensis within populations accounted for 93.57% and 88.91% of total variation, respectively. The C. heterophylla and C. kweichowensis populations as a whole group were analyzed by multiple programs, which showed that the 34 populations were divided into two genetic clusters. One cluster included 21 C. heterophylla populations, and the second cluster contained 13 C. kweichowensis populations. We conclude from these results that C. heterophylla and C. kweichowensis are distinct species. The Mantel test showed that the genetic distance was significantly correlated with the geographic distance (r = 0.580, P < 0.001). The populations of C. heterophylla [e.g., populations WC (Weichang), MS (Mishan), and WA (Wu’an)] and C. kweichowensis [e.g., populations YX (Yuexi), ZP (Zhenping), LA (Lin’an), and TB (Taibai)] with high allelic richness are considered suitable for in situ conservation. Our study provides valuable information for breeding and conservation of genetic resources of C. heterophylla, C. kweichowensis, and related species.

scholarly journals Genetic diversity of Salvia tomentosa Miller (Lamiaceae) species using Touch-down Directed Amplification of Minisatellite DNA (Td-DAMD) molecular markers

2020 ◽  
Vol 63 (2) ◽  
pp. 135-141
Author(s):  
Basel Saleh
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Sea Level ◽  
Natural Population ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Mediterranean Species ◽  
Marker Index ◽  
Minisatellite Dna

Salvia tomentosa Miller (Lamiaceae) a Mediterranean species has an important role in various pharmacological applications. To reveal genetic relationships among S. tomentosa natural populations, 35 samples were collected from different regions of Syria. Touch-down Directed Amplification of Minisatellite DNA (Td-DAMD) markers have been investigated for this goal. Td-DAMD assay produced 158 total bands of which 131 (82.911%) were polymorphic with a mean polymorphic information content (PIC) value of 0.264 and a mean marker index (MI) value of 2.269. Clustering profile based on TdDAMD data showed that samples were grouped into two main clusters; the first cluster included Lattakia samples which split into two subclusters regardless their altitudes over the sea level. Whereas, the second cluster included Tartous and Hama samples. Td-DAMD assay successfully discriminate among the tested 35 samples belonged to the S. tomentosa natural population.

scholarly journals Local parasite pressures and host genotype may modulate epigenetic diversity in a mixed-mating fish

2019 ◽  
Author(s):  
Waldir M. Berbel-Filho ◽  
Carlos Garcia de Leaniz ◽  
Paloma Morán ◽  
Jo Cable ◽  
Sergio M. Q. Lima ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Methylation ◽  
Genetic Variation ◽  
Natural Populations ◽  
Mixed Mating ◽  
Host Genotype ◽  
Genetic Population ◽  
Low Genetic Diversity ◽  
Population Structuring ◽  
Epigenetic Diversity

AbstractParasite-mediated selection is one of the main drivers of genetic variation in natural populations. The persistence of asexual reproduction and self-fertilization, however, challenges the notion that low genetic variation and inbreeding compromise the host’s ability to respond to pathogens. DNA methylation represents a potential mechanism for generating additional adaptive variation under low genetic diversity. We compared genetic diversity (microsatellites and AFLPs), variation in DNA methylation (MSAFLPs), and parasite loads in three populations of Kryptolebias hermaphroditus, a unique mixed-mating (partially self-fertilising) fish, to analyse the potential adaptive value of DNA methylation in relation to genetic diversity and parasite loads. We found strong genetic population structuring, as well as differences in parasite loads and methylation levels among sampling sites and selfing lineages. Globally, the interaction between parasites and inbreeding with selfing lineages influenced DNA methylation, but parasites seemed more important in determining methylation levels at the local scale.

scholarly journals Studying of genetic polymorphism of olive varieties of Azerbaijan and Turkey

2020 ◽  
Vol 3 ◽  
pp. 91-95
Author(s):  
A. Mammadov ◽  
◽  
A. Ipek ◽  
S. H. Teoman-Duran ◽  
S. A. Aghayeva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Polymorphism ◽  
Ssr Markers ◽  
Genome Analysis ◽  
Genetic Relationships ◽  
Research Work ◽  
Natural Populations ◽  
Gene Pools ◽  
Olive Varieties

In the article, genetic diversity of olive samples from Azerbaijan and Turkey, genotyping of natural populations and gene pools with molecular markers, associative mapping, genome analysis, carried out jointly genetic relationships between genotypes of olives and genetics originating from Azerbaijan and Turkey are studied by molecular analysis through their SSR markers. When the research work is successful, the results of this study will be demonstrated the presence of SSR markers to distinguish olive genotypes and further studies on olive production in both countries will be undertaken.

scholarly journals Allozyme and RAPD Analysis of the Geographic Variation and Genetic Diversity in Natural Populations of the American Chestnut

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 591f-591 ◽  
Author(s):  
Hongwen Huang ◽  
Fenny Dane ◽  
Tom Kubisiak
Keyword(s):  
Genetic Diversity ◽  
New York ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Natural Populations ◽  
American Chestnut ◽  
The North ◽  
Natural Range ◽  
Carolina Population ◽  
Isozyme Loci

The population structure and genetic diversity of American chestnut trees collected in nine states along the natural range of the species was evaluated using 20 isozyme loci. Genetic heterozygosity (Ht:Nei, 1978) ranged from 0.089 in the Georgia and 0.094 in the North Carolina population to 0.172 in the northernmost (Connecticut) and 0.181 in the southernmost (Alabama) population. Four populations (Pennsylvania, New York, Virginia, and Alabama) were selected for RAPD analysis using 22 loci randomly distributed across the chestnut genome. The highest level of heterozygosity was in the Alabama population. UPGMA phenograms generated for the isozyme and RAPD markers using Nei's genetic identity showed similar genetic relationships among American chestnut populations.

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