Phenotypic variation and covariation among natural populations ofArabidopsis thalianain North Xinjiang

2010 ◽  
Vol 18 (5) ◽  
pp. 497
Author(s):  
Li Lei ◽  
Liu Tong ◽  
Liu Bin ◽  
Liu Zhongquan ◽  
Si Langming ◽  
...  
Keyword(s):  
Phenotypic Variation ◽  
Natural Populations ◽  
North Xinjiang

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 Whole-genome modeling accurately predicts quantitative traits, as revealed in plants

2015 ◽  
Author(s):  
Laurent Gentzbittel ◽  
Cécile Ben ◽  
Mélanie Mazurier ◽  
Min-Gyoung Shin ◽  
Martin Triska ◽  
...  
Keyword(s):  
Phenotypic Variation ◽  
Symbiotic Nitrogen Fixation ◽  
Natural Populations ◽  
Whole Genome ◽  
Population Admixture ◽  
Admixture Proportion ◽  
Genome Wide ◽  
Polygenic Adaptation ◽  
In The Wild ◽  
Wild Legume

AbstractMany adaptive events in natural populations, as well as response to artificial selection, are caused by polygenic action. Under selective pressure, the adaptive traits can quickly respond via small allele frequency shifts spread across numerous loci. We hypothesize that a large proportion of current phenotypic variation between individuals may be best explained by population admixture.We thus consider the complete, genome-wide universe of genetic variability, spread across several ancestral populations originally separated. We experimentally confirmed this hypothesis by predicting the differences in quantitative disease resistance levels among accessions in the wild legume Medicago truncatula. We discovered also that variation in genome admixture proportion explains most of phenotypic variation for several quantitative functional traits, but not for symbiotic nitrogen fixation. We shown that positive selection at the species level might not explain current, rapid adaptation.These findings prove the infinitesimal model as a mechanism for adaptation of quantitative phenotypes. Our study produced the first evidence that the whole-genome modeling of DNA variants is the best approach to describe an inherited quantitative trait in a higher eukaryote organism and proved the high potential of admixture-based analyses. This insight contribute to the understanding of polygenic adaptation, and can accelerate plant and animal breeding, and biomedicine research programs.

scholarly journals FREQUENCIES OF NULL ALLELES AT ENZYME LOCI IN NATURAL POPULATIONS OF PONDEROSA AND RED PINE

Genetics ◽  
1982 ◽  
Vol 100 (3) ◽  
pp. 497-504
Author(s):  
Fred W Allendorf ◽  
Kathy L Knudsen ◽  
George M Blake
Keyword(s):  
Pinus Ponderosa ◽  
Ponderosa Pine ◽  
Phenotypic Variation ◽  
Natural Populations ◽  
Red Pine ◽  
Null Alleles ◽  
Enzyme Loci ◽  
Polygenic Variation

ABSTRACT Pinus ponderosa and P. resinosa population samples have mean frequencies of enzymatically inactive alleles of 0.0031 and 0.0028 at 29 and 27 enzyme loci, respectively. Such alleles are rare and are apparently maintained by selection-mutation balance. Ponderosa pine have much higher amounts of allozymic and polygenic phenotypic variation than red pine, yet both species have similar frequencies of null alleles. Thus, null alleles apparently do not contribute to polygenic variation, as has been suggested. The concordance between allozymic and polygenic variation adds support to the view that allozyme studies may be valuable in predicting the relative amount of polygenic variation in populations.

Erfassung der adaptiven genetischen Variation der Eiche im Hinblick auf den Klimawandel | Assessment of adaptive genetic variation in oaks with relation to climate change

2010 ◽  
Vol 161 (6) ◽  
pp. 216-222
Author(s):  
Oliver Gailing
Keyword(s):  
Climate Change ◽  
Genetic Variation ◽  
North America ◽  
Phenotypic Variation ◽  
Natural Populations ◽  
Genetic Adaptation ◽  
Adaptive Genetic Variation ◽  
Adaptation To Climate Change ◽  
Adaptive Traits ◽  
Wide Range

Climate change is projected to lead to a major reorganization of our forests. For example, higher annual mean temperatures, longer growth seasons and drier summers are predicted for many parts of central and southern Europe, and in North America. In order to understand the genetic adaptation to climate change we need a better understanding of the genetic regulation of key traits involved in tolerance of water and temperature stress. Oaks (Quercus spp.) are excellent model species to study the adaptation of forest trees to changing environments. They show a wide geographic distribution in Europe and in North America as dominant tree species in many forests growing under a wide range of climatic and edaphic conditions. With the availability of a growing amount of functional and expressional candidate genes we are now able to test the functional importance of genes by associating nucleotide variation in these genes with phenotypic variation in adaptive traits in segregating or natural populations. Studies trying to associate genetic variation with phenotypic variation in adaptive traits can be performed in full-sib families derived from controlled crosses (Quantitative Trait Loci [QTL] mapping) or in natural populations (association mapping). For several important adaptive traits QTL were mapped, the underlying genes have to be tested in natural populations. A future objective is to test whether genes that underlie phenotypic variation in adaptive traits are involved in local genetic adaptation and viability selection at the seedling stage, linked to reciprocal transplant experiments in order to assess the performance over climatic gradients.

Geographical variation in the male intromittent organ of the Trinidadian guppy (Poecilia reticulata)

2000 ◽  
Vol 78 (9) ◽  
pp. 1674-1680 ◽  
Author(s):  
Clint D Kelly ◽  
Jean-Guy J Godin ◽  
Ghada Abdallah
Keyword(s):  
Phenotypic Variation ◽  
Poecilia Reticulata ◽  
Natural Populations ◽  
Fish Predation ◽  
Species Variation ◽  
Body Coloration ◽  
Sexually Selected Traits ◽  
Predation Intensity ◽  
Trinidadian Guppy ◽  
Selected Traits

Sexual selection may favour the evolution of elaborated genital traits in males, particularly when phenotypic variation in such traits results in corresponding variation in reproductive success among males in the population. Compared with insects, very little is known about the natural variation in any male genital trait, and its causes, in vertebrates. Here we report on variation in a male intromittent organ both within and between natural populations of a vertebrate, the Trinidadian guppy (Poecilia reticulata). Male guppies inseminate females using an intromittent organ called the gonopodium. We demonstrate that males from populations that have evolved under high fish-predation intensity have, on average, a relatively longer gonopodium than males originating from populations under low fish-predation intensity. Compared with body coloration, the gonopodium exhibited relatively low phenotypic variation, but nonetheless was within the range of known variation for sexually selected traits. The male gonopodium was positively allometric in general. To our knowledge, this is the first report of within-species variation in an intromittent organ and of a positive allometric relationship between male genitalia and body size in a vertebrate species. Our results suggest that the length of the male intromittent organ in the guppy is under selection, which varies geographically.

scholarly journals Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast

2019 ◽  
Vol 36 (9) ◽  
pp. 1975-1989 ◽  
Author(s):  
Sergio Tusso ◽  
Bart P S Nieuwenhuis ◽  
Fritz J Sedlazeck ◽  
John W Davey ◽  
Daniel C Jeffares ◽  
...  
Keyword(s):  
Single Molecule ◽  
Phenotypic Variation ◽  
Natural Populations ◽  
Strand Break ◽  
Transgressive Segregation ◽  
Genomic Variation ◽  
Population History ◽  
Structural Genomic ◽  
History Of ◽  
Reproductive Compatibility

Abstract Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20–60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.

scholarly journals Genetic variation in senescence marker protein-30 is associated with natural variation in cold tolerance in Drosophila

2010 ◽  
Vol 92 (2) ◽  
pp. 103-113 ◽  
Author(s):  
KATIE J. CLOWERS ◽  
RICHARD F. LYMAN ◽  
TRUDY F. C. MACKAY ◽  
THEODORE J. MORGAN
Keyword(s):  
Cold Tolerance ◽  
Phenotypic Variation ◽  
Allelic Variation ◽  
Balancing Selection ◽  
Ion Homeostasis ◽  
Natural Populations ◽  
Molecular Variation ◽  
Marker Protein ◽  
Coding Regions ◽  
Close Proximity

SummaryA comprehensive understanding of the genetic basis of phenotypic adaptation in nature requires the identification of the functional allelic variation underlying adaptive phenotypes. The manner in which organisms respond to temperature extremes is an adaptation in many species. In the current study, we investigate the role of molecular variation in senescence marker protein-30 (Smp-30) on natural phenotypic variation in cold tolerance in Drosophila melanogaster. Smp-30 encodes a product that is thought to be involved in the regulation of Ca2+ ion homeostasis and has been shown previously to be differentially expressed in response to cold stress. Thus, we sought to assess whether molecular variation in Smp-30 was associated with natural phenotypic variation in cold tolerance in a panel of naturally derived inbred lines from a population in Raleigh, North Carolina. We identified four non-coding polymorphisms that were strongly associated with natural phenotypic variation in cold tolerance. Interestingly, two polymorphisms that were in close proximity to one another (2 bp apart) exhibited opposite phenotypic effects. Consistent with the maintenance of a pair of antagonistically acting polymorphisms, tests of molecular evolution identified a significant excess of maintained variation in this region, suggesting balancing selection is acting to maintain this variation. These results suggest that multiple mutations in non-coding regions can have significant effects on phenotypic variation in adaptive traits within natural populations, and that balancing selection can maintain polymorphisms with opposite effects on phenotypic variation.

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